diff --git a/.github/workflows/run_cellchat.yml b/.github/workflows/run_cellchat.yml new file mode 100644 index 0000000..cb49bbb --- /dev/null +++ b/.github/workflows/run_cellchat.yml @@ -0,0 +1,120 @@ +name: CellChat Signaling Workflow + +on: + push: + branches: [main] + paths: + - '05_signaling/cellchat.qmd' + pull_request: + branches: [main] + paths: + - '05_signaling/cellchat.qmd' + workflow_dispatch: + +jobs: + r-cellchat: + runs-on: ubuntu-22.04 + + env: + RENV_PATHS_ROOT: ~/.local/share/renv + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Install pandoc + run: sudo apt-get update && sudo apt-get install -y pandoc + + - name: Set up R + uses: r-lib/actions/setup-r@v2 + + - name: Install system dependencies for R packages + run: | + sudo apt-get update + sudo apt-get install -y build-essential cmake libcurl4-openssl-dev libssl-dev libxml2-dev libgit2-dev libmagick++-dev libharfbuzz-dev libfribidi-dev libglpk-dev + shell: bash + + - name: Set up Python with conda + uses: conda-incubator/setup-miniconda@v3 + with: + python-version: 3.9 + auto-update-conda: true + + - name: Create and activate conda environment and install UMAP + run: | + conda env remove -n cellchat_env -y 2>/dev/null || true + conda create -n cellchat_env python=3.9 -y + source "$(conda info --base)/etc/profile.d/conda.sh" + conda activate cellchat_env + pip install --no-cache-dir umap-learn + shell: bash + + - name: Cache R packages (renv) + uses: actions/cache@v4 + with: + path: ${{ env.RENV_PATHS_ROOT }} + key: ${{ runner.os }}-renv-${{ hashFiles('05_signaling/renv.lock') }} + restore-keys: | + ${{ runner.os }}-renv- + + - name: Set repositories + run: Rscript ubuntu.R + + - name: Restore environment from renv.lock + run: | + install.packages("renv", repos = "https://cloud.r-project.org") + renv::restore(prompt = FALSE, lockfile = "05_signaling/renv.lock") + shell: Rscript {0} + + - name: Install presto (fast Wilcoxon for CellChat) + run: | + Rscript -e 'install.packages("https://github.com/immunogenomics/presto/archive/refs/heads/master.tar.gz", repos=NULL, type="source")' + shell: bash + + + - name: Install Quarto via conda (conda-forge) + run: | + # Use the existing conda installation to install quarto so we don't rely on the GitHub release URL + source "$(conda info --base)/etc/profile.d/conda.sh" + conda activate cellchat_env + conda install -y -c conda-forge quarto + quarto --version || true + shell: bash + + - name: Render CellChat QMD + id: render_qmd + run: | + source "$(conda info --base)/etc/profile.d/conda.sh" + conda activate cellchat_env + # Ensure reticulate uses the conda env Python (set explicit env var so R->reticulate picks it up) + export RETICULATE_PYTHON=$(which python) + echo "RETICULATE_PYTHON=$RETICULATE_PYTHON" + cd 05_signaling + quarto render cellchat.qmd -o cellchat.html + shell: bash + + - name: Deploy HTML to gh-pages + if: success() + run: | + git config --global user.name "github-actions[bot]" + git config --global user.email "github-actions[bot]@users.noreply.github.com" + OUTPUT_FILE="05_signaling/cellchat.html" + + # Fetch gh-pages (if exists) and create worktree + git fetch origin gh-pages || true + git worktree add /tmp/gh-pages gh-pages 2>/dev/null || git worktree add /tmp/gh-pages -b gh-pages + + # Copy the file into the worktree + mkdir -p "/tmp/gh-pages/$(dirname "$OUTPUT_FILE")" + cp "$OUTPUT_FILE" "/tmp/gh-pages/$(dirname "$OUTPUT_FILE")/" + + cd /tmp/gh-pages + + # Commit and push if there are changes + git add "$(dirname "$OUTPUT_FILE")/$(basename "$OUTPUT_FILE")" + git commit -m "Deploy $(basename "$OUTPUT_FILE") [skip ci]" + git push --force origin gh-pages + shell: bash + + + diff --git a/05_signaling/cellchat.Rmd b/05_signaling/cellchat.Rmd deleted file mode 100644 index 73203ca..0000000 --- a/05_signaling/cellchat.Rmd +++ /dev/null @@ -1,454 +0,0 @@ ---- -title: "CellChat" -author: "Harvard Chan Bioinformatics Core" -date: "`r Sys.Date()`" -output: - html_document: - code_folding: hide - df_print: paged - highlights: pygments - number_sections: false - self_contained: true - theme: default - toc: true - toc_float: - collapsed: true - smooth_scroll: true -params: - project_file: information.R - seurat_fn: ../data/fDat_sn_RC.rds - cellchat_fn: ../data/snrna_cellchat.qs - cellchat_grade2_fn: ../data/snrna_cellchat_grade2.qs - cellchat_grade0_fn: ../data/snrna_cellchat_grade0.qs ---- - -```{r, cache = FALSE, message = FALSE, warning=FALSE} -# This set up the working directory to this file so all files can be found -library(rstudioapi) -setwd(fs::path_dir(getSourceEditorContext()$path)) -# NOTE: This code will check version, this is our recommendation, it may work -#. other versions -stopifnot(R.version$major>= 4) # requires R4 -stopifnot(compareVersion(R.version$minor,"3.3")>=0) # requires >=4.3.3 -stopifnot(compareVersion(as.character(BiocManager::version()), "3.18")>=0) -stopifnot(compareVersion(as.character(packageVersion("Seurat")), "5.0.0")>=0) -``` - -This code is in this ![](https://img.shields.io/badge/status-draft-grey) revision. - -```{r load_libraries, cache = FALSE, message = FALSE, warning=FALSE, echo=FALSE} -# NOTE change or remove according your environment -reticulate::use_virtualenv("/n/app/bcbio/R4.3.1_python_cellchat") -reticulate::py_config() # should show v3.9.14 -Sys.getenv("PYTHONPATH") # should be empty - -current_libs <- .libPaths() -.libPaths(c('/n/app/bcbio/R4.3.1_cellchat/', current_libs)) -``` - -```{r} -library(CellChat) - -library(tidyverse) -library(Seurat) -library(bcbioR) -library(ggprism) -library(knitr) -library(tools) -library(qs) -library(patchwork) -library(ComplexHeatmap) - -options(stringsAsFactors = FALSE) - -colors=cb_friendly_cols(1:15) -ggplot2::theme_set(theme_prism(base_size = 14)) -opts_chunk[["set"]]( - cache = F, - cache.lazy = FALSE, - dev = c("png", "pdf"), - error = TRUE, - highlight = TRUE, - message = FALSE, - prompt = FALSE, - tidy = FALSE, - warning = FALSE, - echo = T, - fig.height = 4) - -# set seed for reproducibility -set.seed(1234567890L) - -cellchat_ran <- file.exists(params$cellchat_fn) -cellchat_rejection_ran <- file.exists(params$cellchat_grade2_fn) & file.exists(params$cellchat_grade0_fn) -``` - -# Clustering - -```{r load_data } - -snrna <- readRDS(params$seurat_fn) - -# in this case, Chris_annot = cell_type -DimPlot(snrna, reduction = 'umap', group.by = 'Chris_annot') - -``` - -```{r prep cellchat inputs, eval = !cellchat_ran } - -# need to use normalized counts as input -data.input <- snrna[["SCT"]]@data -labels <- snrna$Chris_annot -meta <- data.frame(labels = labels, row.names = names(labels), samples = snrna$orig.ident) - -``` - -```{r create cellchat object, eval = !cellchat_ran } -cellchat <- createCellChat(object = data.input, meta = meta, group.by = "labels") - -``` - -```{r set cellchat db, eval = !cellchat_ran} -CellChatDB <- CellChatDB.human -CellChatDB.use <- subsetDB(CellChatDB) -cellchat@DB <- CellChatDB.use - -``` - -```{r subset and preprocess data, eval = !cellchat_ran } - -cellchat <- subsetData(cellchat) -cellchat <- updateCellChat(cellchat) -future::plan("multisession", workers = 8) # recommend running with at 8-16 cores -cellchat <- identifyOverExpressedGenes(cellchat) # may take a couple minutes -cellchat <- identifyOverExpressedInteractions(cellchat) # may take a couple minutes - -``` - -```{r compute communication prob, eval = !cellchat_ran} - -# Not recommended: project gene expression data onto protein-protein interaction network. -# Useful with shallow sequencing depth but introduces many weak communications. -# If used, must set raw.use = FALSE when running computeCommunProb -# cellchat <- projectData(cellchat, PPI.human) - - -# this next command takes 0.5-2+ hours -# can choose various methods for caculating average gene exp per group, -# 'triMean' allegedly produces fewer but stronger interactions -cellchat <- computeCommunProb(cellchat, type = "triMean") - -# filter out the cell-cell communication if < 50 cells per group -cellchat <- filterCommunication(cellchat, min.cells = 50) - -qsave(cellchat, '../data/snrna_cellchat.qs', preset = 'fast') - -``` - -# Overall Results - -```{r load cellchat, eval = cellchat_ran} -cellchat <- qread(params$cellchat_fn) - -df.net <- subsetCommunication(cellchat) %>% dplyr::arrange(pval) -df.net %>% sanitize_datatable() - -``` - -## Top interactions {.tabset} -```{r check pairs, results = 'asis', fig.width = 8, fig.height = 12} - -top_ints <- (df.net %>% pull(interaction_name) %>% unique)[1:10] -for (interaction in top_ints){ - cat('\n') - cat('### ', as.character(interaction), '\n') - interactors <- unlist(strsplit(as.character(interaction), '_')) - p1 <- VlnPlot(snrna, features = interactors, group.by = 'Chris_annot', - pt.size = 0.1, log = T, ncol = 1) - print(p1) - cat('\n') -} - -``` - -```{r compute pathway communication probs, eval = cellchat_ran} -cellchat <- computeCommunProbPathway(cellchat) -cellchat <- aggregateNet(cellchat) - -``` - -## Visualize Cell-Cell Communication Networks - -```{r chord plots, fig.width = 10, fig.height = 8, eval = cellchat_ran} - -groupSize <- as.numeric(table(cellchat@idents)) -par(mfrow = c(1,2), xpd=TRUE) -netVisual_circle(cellchat@net$count, vertex.weight = rowSums(cellchat@net$count), - weight.scale = T, label.edge= F, title.name = "Number of interactions") -netVisual_circle(cellchat@net$weight, vertex.weight = rowSums(cellchat@net$weight), - weight.scale = T, label.edge= F, title.name = "Interaction weights/strength") - -``` - -```{r heatmaps, eval = cellchat_ran} - -netVisual_heatmap(cellchat, measure = "count", color.heatmap = "Blues") -netVisual_heatmap(cellchat, measure = "weight", color.heatmap = "Blues") - -``` - -# Comparison Results - -Here we run the CellChat analysis twice, once on the Grade 2 rejection samples and once on the Grade 0 rejection samples. We compare the significant signaling interactions and investigate changes in them between rejection grades. - -```{r prep inputs rejection, eval=!cellchat_rejection_ran} - -grade2 <- subset(snrna, orig.ident %in% c('BRI-2396', 'BRI-2402')) -grade0 <- subset(snrna, orig.ident %in% c('BRI-2395', 'BRI-2411')) - -data.input_grade2 <- grade2[["SCT"]]@data -labels_grade2 <- grade2$Chris_annot -meta_grade2 <- data.frame(labels = labels_grade2, row.names = names(labels_grade2), samples = grade2$orig.ident) - -data.input_grade0 <- grade0[["SCT"]]@data -labels_grade0 <- grade0$Chris_annot -meta_grade0 <- data.frame(labels = labels_grade0, row.names = names(labels_grade0), samples = grade0$orig.ident) - -``` - -```{r create cellchat object rejection, eval=!cellchat_rejection_ran} -cellchat_grade2 <- createCellChat(object = data.input_grade2, meta = meta_grade2, group.by = "labels") -cellchat_grade0 <- createCellChat(object = data.input_grade0, meta = meta_grade0, group.by = "labels") - -``` - -```{r subset and preprocess data rejection, eval=!cellchat_rejection_ran} - -future::plan("multisession", workers = 8) # recommend running with at 8-16 cores - -cellchat_grade2@DB <- CellChatDB.use -cellchat_grade0@DB <- CellChatDB.use - -cellchat_grade2 <- subsetData(cellchat_grade2) -cellchat_grade2 <- updateCellChat(cellchat_grade2) -cellchat_grade2 <- identifyOverExpressedGenes(cellchat_grade2) # may take a couple minutes -cellchat_grade2 <- identifyOverExpressedInteractions(cellchat_grade2) # may take a couple minutes - -cellchat_grade0 <- subsetData(cellchat_grade0) -cellchat_grade0 <- updateCellChat(cellchat_grade0) -cellchat_grade0 <- identifyOverExpressedGenes(cellchat_grade0) # may take a couple minutes -cellchat_grade0 <- identifyOverExpressedInteractions(cellchat_grade0) # may take a couple minutes - -``` - -```{r compute communication prob rejection, eval=!cellchat_rejection_ran} -cellchat_grade2 <- computeCommunProb(cellchat_grade2, type = "triMean") # command takes 0.5-2+ hours -cellchat_grade2 <- filterCommunication(cellchat_grade2, min.cells = 50) -qsave(cellchat_grade2, params$cellchat_grade2_fn, preset = 'fast') - -cellchat_grade0 <- computeCommunProb(cellchat_grade0, type = "triMean") # command takes 0.5-2+ hours -cellchat_grade0 <- filterCommunication(cellchat_grade0, min.cells = 50) -qsave(cellchat_grade0, params$cellchat_grade0_fn, preset = 'fast') - -``` - -```{r load cellchat rejection, eval = cellchat_rejection_ran} - -cellchat_grade2 <- qread(params$cellchat_grade2_fn) -cellchat_grade0 <- qread(params$cellchat_grade0_fn) - -cellchat_grade2 <- filterCommunication(cellchat_grade2, min.cells = 50) -cellchat_grade0 <- filterCommunication(cellchat_grade0, min.cells = 50) - -df.net_grade2 <- subsetCommunication(cellchat_grade2)%>% dplyr::arrange(pval) -df.net_grade0 <- subsetCommunication(cellchat_grade0)%>% dplyr::arrange(pval) - -``` - -## Grade 2 - -```{r datatable grade 2, eval = cellchat_rejection_ran} -df.net_grade2 %>% sanitize_datatable() - -``` - -### Top interactions {.tabset} -```{r check pairs grade 2, results = 'asis', fig.width = 8, fig.height = 12} - -top_ints <- (df.net_grade2 %>% pull(interaction_name) %>% unique)[1:10] -for (interaction in top_ints){ - cat('\n') - cat('#### ', as.character(interaction), '\n') - interactors <- unlist(strsplit(as.character(interaction), '_')) - p1 <- VlnPlot(snrna, features = interactors, group.by = 'Chris_annot', pt.size = 0.1, log = T, ncol = 1) - print(p1) - cat('\n') -} - -``` - - -## Grade 0 - -```{r datatable grade 0, eval = cellchat_rejection_ran} -df.net_grade0 %>% sanitize_datatable() - -``` - -### Top interactions {.tabset} -```{r check pairs grade 0, results = 'asis', fig.width = 8, fig.height = 12} - -top_ints <- (df.net_grade0 %>% pull(interaction_name) %>% unique)[1:10] -for (interaction in top_ints){ - cat('\n') - cat('#### ', as.character(interaction), '\n') - interactors <- unlist(strsplit(as.character(interaction), '_')) - p1 <- VlnPlot(snrna, features = interactors, group.by = 'Chris_annot', pt.size = 0.1, log = T, ncol = 1) - print(p1) - cat('\n') -} - -``` - -```{r merge rejection objects, eval = cellchat_rejection_ran} - -cellchat_grade2 <- computeCommunProbPathway(cellchat_grade2) -cellchat_grade2 <- aggregateNet(cellchat_grade2) -cellchat_grade2 <- netAnalysis_computeCentrality(cellchat_grade2) -cellchat_grade0 <- computeCommunProbPathway(cellchat_grade0) -cellchat_grade0 <- aggregateNet(cellchat_grade0) -cellchat_grade0 <- netAnalysis_computeCentrality(cellchat_grade0) - -object.list <- list(grade0 = cellchat_grade0, grade2 = cellchat_grade2) -cellchat_merged <- mergeCellChat(object.list, add.names = names(object.list)) - -df.net_merged <- subsetCommunication(cellchat_merged) - -``` - -## Compare Interactions/Interaction Strength - -```{r compare interactions, eval = cellchat_rejection_ran} - -gg1 <- compareInteractions(cellchat_merged, show.legend = F, group = c(1,2)) -gg2 <- compareInteractions(cellchat_merged, show.legend = F, group = c(1,2), measure = "weight") -gg1 + gg2 - -``` - -```{r chord plots merged, eval = cellchat_rejection_ran, fig.width = 10, fig.height = 8} -par(mfrow = c(1,2), xpd=TRUE) -netVisual_diffInteraction(cellchat_merged, weight.scale = T) -netVisual_diffInteraction(cellchat_merged, weight.scale = T, measure = "weight") - -``` - -```{r heatmaps merged, eval = cellchat_rejection_ran, fig.width = 10, fig.height = 8} - -gg1 <- netVisual_heatmap(cellchat_merged) -gg2 <- netVisual_heatmap(cellchat_merged, measure = "weight") -gg1 + gg2 - -``` - -## Compare Major Pathway Sources and Targets - -From the CellChat documentation: "Comparing the outgoing and incoming interaction strength in a 2D space allows ready identification of the cell populations with significant changes in sending or receiving signals between different datasets." - -```{r compare send/receive changes, eval = cellchat_rejection_ran, fig.width = 10, fig.height = 6} - -num.link <- sapply(object.list, function(x) {rowSums(x@net$count) + colSums(x@net$count)-diag(x@net$count)}) -weight.MinMax <- c(min(num.link), max(num.link)) # control the dot size in the different datasets -gg <- list() -for (i in 1:length(object.list)) { - gg[[i]] <- netAnalysis_signalingRole_scatter(object.list[[i]], title = names(object.list)[i], weight.MinMax = weight.MinMax) -} -patchwork::wrap_plots(plots = gg) -``` - - -```{r identify signaling changes, eval = cellchat_rejection_ran, fig.width = 12, fig.height = 12} -gg1 <- netAnalysis_signalingChanges_scatter(cellchat_merged, idents.use = "Vascular_EC") -gg2 <- netAnalysis_signalingChanges_scatter(cellchat_merged, idents.use = "Lymphatic_EC") -gg3 <- netAnalysis_signalingChanges_scatter(cellchat_merged, idents.use = "Pericyte") -patchwork::wrap_plots(plots = list(gg1,gg2,gg3), nrow = 3, ncol = 1) - -``` - -## Cluster Altered Signaling Interactions - -From the CellChat documentation: "CellChat performs joint manifold learning and classification of the inferred communication networks based on their functional and topological similarity across different conditions. - -By quantifying the similarity between the cellular communication networks of signaling pathways across conditions, this analysis highlights the potentially altered signaling pathways. CellChat adopts the concept of network rewiring from network biology and hypothesized that the difference between different communication networks may affect biological processes across conditions. UMAP is used for visualizing signaling relationship and interpreting our signaling outputs in an intuitive way without involving the classification of conditions. - -Functional similarity: High degree of functional similarity indicates major senders and receivers are similar, and it can be interpreted as the two signaling pathways or two ligand-receptor pairs exhibit similar and/or redundant roles. - -Structural similarity: A structural similarity was used to compare their signaling network structure, without considering the similarity of senders and receivers." - - -### Based on Functional Similarity - -```{r identify signaling groups functional, eval = cellchat_rejection_ran} - -cellchat_merged <- computeNetSimilarityPairwise(cellchat_merged, type = "functional") -cellchat_merged <- netEmbedding(cellchat_merged, type = "functional") -cellchat_merged <- netClustering(cellchat_merged, type = "functional") -netVisual_embeddingPairwise(cellchat_merged, type = "functional", label.size = 3.5) - -``` - -### Based on Structural Similarity - -```{r identify signaling groups structural, eval = cellchat_rejection_ran} -cellchat_merged <- computeNetSimilarityPairwise(cellchat_merged, type = "structural") -cellchat_merged <- netEmbedding(cellchat_merged, type = "structural") -cellchat_merged <- netClustering(cellchat_merged, type = "structural") -netVisual_embeddingPairwise(cellchat_merged, type = "structural", label.size = 3.5) -``` - -## Compare Overall Signaling Information Flow - -"CellChat can identify the conserved and context-specific signaling pathways by simply comparing the information flow for each signaling pathway, which is defined by the sum of communication probability among all pairs of cell groups in the inferred network (i.e., the total weights in the network)." - -```{r info flow, fig.height = 9, eval = cellchat_rejection_ran} - -rankNet(cellchat_merged, mode = "comparison", measure = "weight", sources.use = NULL, targets.use = NULL, stacked = F, do.stat = TRUE) - -``` - -## Compare Signaling Patterns Across Cell Populations - -"In this heatmap, colobar represents the relative signaling strength of a signaling pathway across cell groups (Note that values are row-scaled). The top colored bar plot shows the total signaling strength of a cell group by summarizing all signaling pathways displayed in the heatmap. The right grey bar plot shows the total signaling strength of a signaling pathway by summarizing all cell groups displayed in the heatmap." - - -```{r outgoing signaling, fig.height = 9, eval = cellchat_rejection_ran} - -i = 1 -pathway.union <- union(object.list[[i]]@netP$pathways, object.list[[i+1]]@netP$pathways) -ht1 = netAnalysis_signalingRole_heatmap(object.list[[i]], pattern = "outgoing", signaling = pathway.union, title = names(object.list)[i], width = 5, height = 16, cluster.cols = T) -ht2 = netAnalysis_signalingRole_heatmap(object.list[[i+1]], pattern = "outgoing", signaling = pathway.union, title = names(object.list)[i+1], width = 5, height = 16, cluster.cols = T) -draw(ht1 + ht2, ht_gap = unit(0.5, "cm")) -``` - -```{r incoming signaling, fig.height = 9, eval = cellchat_rejection_ran} -ht1 = netAnalysis_signalingRole_heatmap(object.list[[i]], pattern = "incoming", signaling = pathway.union, title = names(object.list)[i], width = 5, height = 16, cluster.cols = T) -ht2 = netAnalysis_signalingRole_heatmap(object.list[[i+1]], pattern = "incoming", signaling = pathway.union, title = names(object.list)[i+1], width = 5, height = 16, cluster.cols = T) -draw(ht1 + ht2, ht_gap = unit(0.5, "cm")) -``` - -## Identify Dysfunctional Interaction Signaling Using Communication Probabilities - -"CellChat can identify the up-regulated (increased) and down-regulated (decreased) signaling ligand-receptor pairs in one dataset compared to the other dataset by comparing the communication probability between two datasets for each L-R pair and each pair of cell groups" - -```{r compare signaling, fig.height = 12, fig.width = 8, eval = cellchat_rejection_ran} - -gg1 <- netVisual_bubble(cellchat_merged, - # sources.use = c('Vascular_EC', 'Lymphatic_EC', 'Pericyte'), - # targets.use = c('Vascular_EC', 'Lymphatic_EC', 'Pericyte'), - comparison = c(1, 2), - max.dataset = 2, - title.name = "Increased signaling in Grade 2", - angle.x = 45, - remove.isolate = T) -gg1 -signaling.grade2_increased = gg1$data diff --git a/05_signaling/cellchat.qmd b/05_signaling/cellchat.qmd new file mode 100644 index 0000000..cdae683 --- /dev/null +++ b/05_signaling/cellchat.qmd @@ -0,0 +1,269 @@ +--- +title: "CellChat" +author: "Harvard Chan Bioinformatics Core" +date: "`r Sys.Date()`" +format: + html: + number-sections: false + default-image-extension: svg + lightbox: true + callout-icon: false + format-links: true + toc: true + theme: sandstone + echo: true + eval: true + message: false + warning: false + code-copy: true + code-overflow: wrap + code-fold: true + code-line-numbers: true + embed-resources: true + standalone: true + html-math-method: katex + grid: + sidebar-width: 250px + body-width: 900px + margin-width: 300px + comments: + hypothesis: true +params: + seurat_obj: "https://github.com/bcbio/bcbioR-test-data/raw/refs/heads/main/singlecell/tiny.rds" + cellchat_fn: snrna_cellchat.qs + cellchat_group1_fn: snrna_cellchat_group1.qs + cellchat_group2_fn: snrna_cellchat_group2.qs + path_outs: cellchat_out +knitr: + opts_chunk: + audodep: true + cache: false + cache.lazy: false + error: true + echo: false + fig-height: 5 + fig.retina: 2 + fig-width: 11 + message: false + tidy: true + warning: false +--- + +```{r} +#| cache: false +#| message: false +#| warning: false + +stopifnot(R.version$major >= 4) # requires R4 +stopifnot(compareVersion(R.version$minor, "3.3") >= 0) # requires >=4.3.3 +stopifnot(compareVersion(as.character(BiocManager::version()), "3.18") >= 0) +stopifnot(compareVersion(as.character(packageVersion("Seurat")), "5.0.0") >= 0) +``` + +This code is in this ![](https://img.shields.io/badge/status-status-green) revision. + + +```{r} +library(CellChat) +library(presto) +library(tidyverse) +library(Seurat) +library(ggprism) +library(knitr) +library(tools) +library(qs) +library(patchwork) +library(ComplexHeatmap) +library(DT) + +options(stringsAsFactors = FALSE) + +invisible(list2env(params, environment())) + +if (!dir.exists(path_outs)) dir.create(path_outs, recursive = TRUE) +message("CellChat outputs will be written to: ", path_outs) + + +colors <- cb_friendly_cols(1:15) +ggplot2::theme_set(theme_prism(base_size = 14)) + +# set seed for reproducibility +set.seed(1234567890L) + +cellchat_ran <- file.exists(file.path(path_outs, cellchat_fn)) +## detect whether precomputed group CellChat results exist and set flag +cellchat_rejection_ran <- FALSE +grp1_basename <- tryCatch(basename(params$cellchat_group1_fn), error = function(e) NA_character_) +grp2_basename <- tryCatch(basename(params$cellchat_group2_fn), error = function(e) NA_character_) +if (!is.na(grp1_basename) && nzchar(grp1_basename) && !is.na(grp2_basename) && nzchar(grp2_basename)) { + grp1_path <- file.path(path_outs, grp1_basename) + grp2_path <- file.path(path_outs, grp2_basename) + cellchat_rejection_ran <- file.exists(grp1_path) && file.exists(grp2_path) + if (cellchat_rejection_ran) { + message("Found precomputed group CellChat results: ", grp1_basename, ", ", grp2_basename) + } else { + missing <- c(if (!file.exists(grp1_path)) grp1_path else NULL, if (!file.exists(grp2_path)) grp2_path else NULL) + message("Precomputed group CellChat results not found; missing: ", paste(missing, collapse = ", ")) + } +} else { + message("Params for group CellChat filenames not set; cellchat_rejection_ran = FALSE") + cellchat_rejection_ran <- FALSE +} +``` + +```{r sanitize-datatable} +# Create a function to clean up data frames +sanitize_datatable <- function(df, ...) { + # Remove dashes from row names and column names which cause wrapping + DT::datatable(df, ..., + rownames = gsub("-", "_", rownames(df)), + colnames = gsub("-", "_", colnames(df)) + ) %>% + formatRound(columns = names(df)[sapply(df, is.numeric)], digits = 3) +} +``` + +# Clustering + +```{r load_data} +if (exists("seurat_obj") && !is.null(seurat_obj) && nzchar(seurat_obj)) { + if (R.utils::isUrl(seurat_obj)) snrna <- readRDS(url(seurat_obj)) else snrna <- readRDS(seurat_obj) +} else { + snrna <- readRDS(params$seurat_fn) +} + +# Detect a normalized assay to use (prefer SCT then RNA) +available_assays <- names(snrna@assays) +preferred <- c("SCT", "RNA") +selected_assay <- intersect(preferred, available_assays) +if (length(selected_assay) == 0) selected_assay <- DefaultAssay(snrna) else selected_assay <- selected_assay[1] +message("Using assay for CellChat input: ", selected_assay) + +# Detect a metadata column to use as labels +meta_cols <- colnames(snrna@meta.data) +label_candidates <- c("Chris_annot", "celltype.age", "age_cluster", "integrated_snn_res.0.4", "cell_type", "seurat_clusters", "orig.ident") +label_col <- intersect(label_candidates, meta_cols) +if (length(label_col) == 0) { + label_col <- meta_cols[1] + warning("No preferred label column found; using first metadata column: ", label_col) +} else { + label_col <- label_col[1] +} +message("Using metadata column for labels: ", label_col) + +# Ensure UMAP reduction exists; if not, run PCA/FindNeighbors/RunUMAP with defaults +if (!"umap" %in% names(snrna@reductions)) { + message("UMAP not found; running PCA -> FindNeighbors -> RunUMAP with default parameters") + # ensure we have variable features or features to run PCA on + if (length(VariableFeatures(snrna)) == 0) { + tryCatch( + { + VariableFeatures(snrna) <- rownames(snrna)[1:min(2000, nrow(snrna))] + }, + error = function(e) NULL + ) + } + tryCatch( + { + snrna <- ScaleData(snrna, features = VariableFeatures(snrna)) + snrna <- RunPCA(snrna, features = VariableFeatures(snrna)) + snrna <- FindNeighbors(snrna, reduction = "pca", dims = 1:20) + snrna <- RunUMAP(snrna, reduction = "pca", dims = 1:20) + }, + error = function(e) warning("Failed to compute UMAP automatically: ", conditionMessage(e)) + ) +} + +# in this case, Chris_annot = cell_type +DimPlot(snrna, reduction = "umap", group.by = label_col) +``` + +```{r prep cellchat inputs} +#|eval: !expr "!cellchat_ran" + +## need to use normalized counts as input (features x cells) +## use `layer` to avoid deprecation warning; fallback to counts layer if data not present +data.input <- tryCatch(as.matrix(GetAssayData(snrna[[selected_assay]], layer = "data")), + error = function(e) as.matrix(GetAssayData(snrna[[selected_assay]], layer = "counts")) +) +labels <- snrna@meta.data[[label_col]] +meta <- data.frame(labels = labels, row.names = names(labels), samples = snrna$orig.ident) +``` + +```{r create cellchat object} +#| eval: !expr "!cellchat_ran" +cellchat <- createCellChat(object = data.input, meta = meta, group.by = "labels") +``` + +```{r set cellchat db} +#| eval: !expr "!cellchat_ran" +CellChatDB <- CellChatDB.human +CellChatDB.use <- subsetDB(CellChatDB) +cellchat@DB <- CellChatDB.use +``` + +```{r subset and preprocess data} +#| eval: !expr "!cellchat_ran" +cellchat <- subsetData(cellchat) +cellchat <- updateCellChat(cellchat) +future::plan("multisession", workers = 8) # recommend running with at 8-16 cores +cellchat <- identifyOverExpressedGenes(cellchat) # may take a couple minutes +cellchat <- identifyOverExpressedInteractions(cellchat) # may take a couple minutes +``` + +```{r compute communication prob} +#| eval: !expr "!cellchat_ran" + +# Not recommended: project gene !expression data onto protein-protein interaction network. +# Useful with shallow sequencing depth but introduces many weak communications. +# If used, must set raw.use = FALSE when running computeCommunProb +# cellchat <- projectData(cellchat, PPI.human) + + +# this next command takes 0.5-2+ hours +# can choose various methods for caculating average gene exp per group, +# 'triMean' allegedly produces fewer but stronger interactions +cellchat <- computeCommunProb(cellchat, type = "triMean") + +# filter out the cell-cell communication if < 50 cells per group +cellchat <- filterCommunication(cellchat, min.cells = 50) + +qsave(cellchat, file.path(path_outs, "snrna_cellchat.qs"), preset = "fast") +``` + +# Overall Results + +```{r load cellchat} +#| eval: !expr "cellchat_ran" +# read main cellchat from path_outs +cellchat <- tryCatch(qread(file.path(path_outs, "snrna_cellchat.qs")), error = function(e) qread(params$cellchat_fn)) +``` + +```{r} +df.net <- subsetCommunication(cellchat) %>% dplyr::arrange(pval) +df.net %>% sanitize_datatable() +``` + +## Top interactions + +```{r check pairs} +#| results: 'asis' +#| fig-width: 8 +#| fig-height: 12 +#| panel: tabset + +top_ints <- (df.net %>% pull(interaction_name) %>% unique())[1:10] +for (interaction in top_ints) { + cat("\n") + cat("### ", as.character(interaction), "\n") + interactors <- unlist(strsplit(as.character(interaction), "_")) + p1 <- VlnPlot(snrna, + features = interactors, group.by = label_col, + pt.size = 0.1, log = T, ncol = 1 + ) + print(p1) + cat("\n") +} +``` + + diff --git a/05_signaling/cellchat_out/snrna_cellchat.qs b/05_signaling/cellchat_out/snrna_cellchat.qs new file mode 100644 index 0000000..acd9ef3 Binary files /dev/null and b/05_signaling/cellchat_out/snrna_cellchat.qs differ diff --git a/05_signaling/renv.lock b/05_signaling/renv.lock new file mode 100644 index 0000000..04fe171 --- /dev/null +++ b/05_signaling/renv.lock @@ -0,0 +1,9267 @@ +{ + "R": { + "Version": "4.5.1", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cran.rstudio.com" + } + ] + }, + "Bioconductor": { + "Version": "3.21" + }, + "Packages": { + "BH": { + "Package": "BH", + "Version": "1.87.0-1", + "Source": "Repository", + "Type": "Package", + "Title": "Boost C++ Header Files", + "Date": "2024-12-17", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"John W.\", \"Emerson\", role = \"aut\"), person(\"Michael J.\", \"Kane\", role = \"aut\", comment = c(ORCID = \"0000-0003-1899-6662\")))", + "Description": "Boost provides free peer-reviewed portable C++ source libraries. 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Davis [ctb] (, SuiteSparse libraries, collaborators listed in dir(system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"), pattern=\"License\", full.names=TRUE, recursive=TRUE)), George Karypis [ctb] (, METIS library, Copyright: Regents of the University of Minnesota), Jason Riedy [ctb] (, GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), Jens Oehlschlägel [ctb] (initial nearPD()), R Core Team [ctb] (02zz1nj61, base R's matrix implementation)", + "Maintainer": "Martin Maechler ", + "Repository": "CRAN" + }, + "MatrixModels": { + "Package": "MatrixModels", + "Version": "0.5-4", + "Source": "Repository", + "VersionNote": "Released 0.5-3 on 2023-11-06", + "Date": "2025-03-25", + "Title": "Modelling with Sparse and Dense Matrices", + "Contact": "Matrix-authors@R-project.org", + "Authors@R": "c( person(\"Douglas\", \"Bates\", role = \"aut\", email = \"bates@stat.wisc.edu\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = c(\"aut\", \"cre\"), email = \"mmaechler+Matrix@gmail.com\", comment = c(ORCID = \"0000-0002-8685-9910\")))", + "Description": "Generalized Linear Modelling with sparse and dense 'Matrix' matrices, using modular prediction and response module classes.", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "stats", + "methods", + "Matrix (>= 1.6-0)", + "Matrix(< 1.8-0)" + ], + "ImportsNote": "_not_yet_stats4", + "Encoding": "UTF-8", + "LazyLoad": "yes", + "License": "GPL (>= 2)", + "URL": "https://Matrix.R-forge.R-project.org/, https://r-forge.r-project.org/R/?group_id=61", + "BugReports": "https://R-forge.R-project.org/tracker/?func=add&atid=294&group_id=61", + "NeedsCompilation": "no", + "Author": "Douglas Bates [aut] (), Martin Maechler [aut, cre] ()", + "Maintainer": "Martin Maechler ", + "Repository": "RSPM" + }, + "NMF": { + "Package": "NMF", + "Version": "0.28", + "Source": "Repository", + "Type": "Package", + "Title": "Algorithms and Framework for Nonnegative Matrix Factorization (NMF)", + "Date": "2024-08-19", + "Authors@R": "c( person(\"Renaud\", \"Gaujoux\", role = c(\"aut\")), person(\"Cathal\", \"Seoighe\", role = c(\"aut\")), person(\"Nicolas\", \"Sauwen\", role = c(\"cre\"), email = \"nicolas.sauwen@openanalytics.eu\") )", + "Maintainer": "Nicolas Sauwen ", + "Description": "Provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.", + "License": "GPL (>= 2)", + "URL": "http://renozao.github.io/NMF/", + "LazyLoad": "yes", + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)", + "methods", + "utils", + "registry", + "rngtools (>= 1.2.3)", + "cluster" + ], + "Imports": [ + "graphics", + "stats", + "stringr (>= 1.0.0)", + "digest", + "grid", + "grDevices", + "gridBase", + "colorspace", + "RColorBrewer", + "foreach", + "doParallel", + "ggplot2", + "reshape2", + "Biobase", + "codetools", + "BiocManager" + ], + "Suggests": [ + "fastICA", + "doMPI", + "bigmemory (>= 4.2)", + "synchronicity(>= 1.3.2)", + "corpcor", + "xtable", + "devtools", + "knitr", + "RUnit" + ], + "Collate": "'colorcode.R' 'options.R' 'grid.R' 'atracks.R' 'aheatmap.R' 'algorithmic.R' 'nmf-package.R' 'rmatrix.R' 'utils.R' 'versions.R' 'NMF-class.R' 'transforms.R' 'Bioc-layer.R' 'NMFstd-class.R' 'NMFOffset-class.R' 'heatmaps.R' 'NMFns-class.R' 'nmfModel.R' 'fixed-terms.R' 'NMFfit-class.R' 'NMFSet-class.R' 'NMFStrategy-class.R' 'registry.R' 'NMFSeed-class.R' 'NMFStrategyFunction-class.R' 'NMFStrategyIterative-class.R' 'NMFplots.R' 'registry-algorithms.R' 'algorithms-base.R' 'algorithms-lnmf.R' 'algorithms-lsnmf.R' 'algorithms-pe-nmf.R' 'algorithms-siNMF.R' 'algorithms-snmf.R' 'data.R' 'extractFeatures.R' 'parallel.R' 'registry-seed.R' 'nmf.R' 'rnmf.R' 'run.R' 'seed-base.R' 'seed-ica.R' 'seed-nndsvd.R' 'setNMFClass.R' 'simulation.R' 'tests.R' 'vignetteFunctions.R'", + "NeedsCompilation": "yes", + "Repository": "CRAN", + "RoxygenNote": "7.3.1", + "Author": "Renaud Gaujoux [aut], Cathal Seoighe [aut], Nicolas Sauwen [cre]" + }, + "R.methodsS3": { + "Package": "R.methodsS3", + "Version": "1.8.2", + "Source": "Repository", + "Depends": [ + "R (>= 2.13.0)" + ], + "Imports": [ + "utils" + ], + "Suggests": [ + "codetools" + ], + "Title": "S3 Methods Simplified", + "Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role=c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\"))", + "Author": "Henrik Bengtsson [aut, cre, cph]", + "Maintainer": "Henrik Bengtsson ", + "Description": "Methods that simplify the setup of S3 generic functions and S3 methods. 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This is a cross-platform package implemented in pure R that generates standard S3 methods.", + "License": "LGPL (>= 2.1)", + "LazyLoad": "TRUE", + "URL": "https://github.com/HenrikBengtsson/R.methodsS3", + "BugReports": "https://github.com/HenrikBengtsson/R.methodsS3/issues", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "R.oo": { + "Package": "R.oo", + "Version": "1.27.1", + "Source": "Repository", + "Depends": [ + "R (>= 2.13.0)", + "R.methodsS3 (>= 1.8.2)" + ], + "Imports": [ + "methods", + "utils" + ], + "Suggests": [ + "tools" + ], + "Title": "R Object-Oriented Programming with or without References", + "Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role=c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\"))", + "Author": "Henrik Bengtsson [aut, cre, cph]", + "Maintainer": "Henrik Bengtsson ", + "Description": "Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. 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Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.", + "License": "MIT + file LICENSE", + "URL": "https://r6.r-lib.org, https://github.com/r-lib/R6", + "BugReports": "https://github.com/r-lib/R6/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Suggests": [ + "lobstr", + "testthat (>= 3.0.0)" + ], + "Config/Needs/website": "tidyverse/tidytemplate, ggplot2, microbenchmark, scales", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Winston Chang [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Winston Chang ", + "Repository": "CRAN" + }, + "RANN": { + "Package": "RANN", + "Version": "2.6.2", + "Source": "Repository", + "Title": "Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric", + "Authors@R": "c( person(\"Gregory\",\"Jefferis\", email=\"jefferis@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0587-9355\")), person(given = c(\"Samuel\", \"E.\"), family = \"Kemp\", role = \"aut\"), person(given = \"Kirill\", family = \"M\\u00fcller\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"Sunil\",\"Arya\", role=c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-0939-4192\")), person(\"David\",\"Mount\", role=c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-3290-8932\")), person(\"University of Maryland\", role=\"cph\", comment = \"ANN library is copyright University of Maryland and Sunil Arya and David Mount. See file COPYRIGHT for details\") )", + "Description": "Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and 'bd' as well as 'kd' trees. The distance is computed using the L2 (Euclidean) metric. Please see package 'RANN.L1' for the same functionality using the L1 (Manhattan, taxicab) metric.", + "License": "GPL (>= 3)", + "URL": "https://github.com/jefferislab/RANN, https://jefferislab.github.io/RANN/", + "BugReports": "https://github.com/jefferislab/RANN/issues", + "Suggests": [ + "testthat" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Gregory Jefferis [aut, cre] (), Samuel E. Kemp [aut], Kirill Müller [ctb] (), Sunil Arya [aut, cph] (), David Mount [aut, cph] (), University of Maryland [cph] (ANN library is copyright University of Maryland and Sunil Arya and David Mount. See file COPYRIGHT for details)", + "Maintainer": "Gregory Jefferis ", + "Repository": "CRAN" + }, + "RApiSerialize": { + "Package": "RApiSerialize", + "Version": "0.1.4", + "Source": "Repository", + "Type": "Package", + "Title": "R API Serialization", + "Date": "2024-09-28", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Ei-ji\", \"Nakama\", role = \"aut\", comment = \"Code in package Rhpc\"), person(\"Junji\", \"Nakano\", role = \"aut\", comment = \"Code in package Rhpc\"), person(\"R Core\", role = \"aut\", comment = \"Code in R file src/main/serialize.c\"))", + "Description": "Access to the internal R serialization code is provided for use by other packages at the C function level by using the registration of native function mechanism. Client packages simply include a single header file RApiSerializeAPI.h provided by this package. 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ROCR is a flexible tool for creating cutoff-parameterized 2D performance curves by freely combining two from over 25 performance measures (new performance measures can be added using a standard interface). Curves from different cross-validation or bootstrapping runs can be averaged by different methods, and standard deviations, standard errors or box plots can be used to visualize the variability across the runs. The parameterization can be visualized by printing cutoff values at the corresponding curve positions, or by coloring the curve according to cutoff. All components of a performance plot can be quickly adjusted using a flexible parameter dispatching mechanism. Despite its flexibility, ROCR is easy to use, with only three commands and reasonable default values for all optional parameters.", + "Encoding": "UTF-8", + "License": "GPL (>= 2)", + "NeedsCompilation": "no", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "methods", + "graphics", + "grDevices", + "gplots", + "stats" + ], + "Suggests": [ + "testthat", + "knitr", + "rmarkdown" + ], + "URL": "http://ipa-tys.github.io/ROCR/", + "BugReports": "https://github.com/ipa-tys/ROCR/issues", + "RoxygenNote": "7.1.0", + "VignetteBuilder": "knitr", + "Author": "Tobias Sing [aut], Oliver Sander [aut], Niko Beerenwinkel [aut], Thomas Lengauer [aut], Thomas Unterthiner [ctb], Felix G.M. Ernst [cre] ()", + "Maintainer": "Felix G.M. Ernst ", + "Repository": "CRAN" + }, + "RSpectra": { + "Package": "RSpectra", + "Version": "0.16-2", + "Source": "Repository", + "Type": "Package", + "Title": "Solvers for Large-Scale Eigenvalue and SVD Problems", + "Date": "2024-07-18", + "Authors@R": "c( person(\"Yixuan\", \"Qiu\", , \"yixuan.qiu@cos.name\", c(\"aut\", \"cre\")), person(\"Jiali\", \"Mei\", , \"vermouthmjl@gmail.com\", \"aut\", comment = \"Function interface of matrix operation\"), person(\"Gael\", \"Guennebaud\", , \"gael.guennebaud@inria.fr\", \"ctb\", comment = \"Eigenvalue solvers from the 'Eigen' library\"), person(\"Jitse\", \"Niesen\", , \"jitse@maths.leeds.ac.uk\", \"ctb\", comment = \"Eigenvalue solvers from the 'Eigen' library\") )", + "Description": "R interface to the 'Spectra' library for large-scale eigenvalue and SVD problems. It is typically used to compute a few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, which is usually more efficient than eigen() if k << n. 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The matrix to be computed on can be dense, sparse, or in the form of an operator defined by the user.", + "License": "MPL (>= 2)", + "URL": "https://github.com/yixuan/RSpectra", + "BugReports": "https://github.com/yixuan/RSpectra/issues", + "Depends": [ + "R (>= 3.0.2)" + ], + "Imports": [ + "Matrix (>= 1.1-0)", + "Rcpp (>= 0.11.5)" + ], + "Suggests": [ + "knitr", + "rmarkdown", + "prettydoc" + ], + "LinkingTo": [ + "Rcpp", + "RcppEigen (>= 0.3.3.3.0)" + ], + "VignetteBuilder": "knitr, rmarkdown", + "RoxygenNote": "7.1.2", + "NeedsCompilation": "yes", + "Author": "Yixuan Qiu [aut, cre], Jiali Mei [aut] (Function interface of matrix operation), Gael Guennebaud [ctb] (Eigenvalue solvers from the 'Eigen' library), Jitse Niesen [ctb] (Eigenvalue solvers from the 'Eigen' library)", + "Maintainer": "Yixuan Qiu ", + "Repository": "CRAN" + }, + "Rcpp": { + "Package": "Rcpp", + "Version": "1.1.0", + "Source": "Repository", + "Title": "Seamless R and C++ Integration", + "Date": "2025-07-01", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"JJ\", \"Allaire\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Kevin\", \"Ushey\", role = \"aut\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Qiang\", \"Kou\", role = \"aut\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Nathan\", \"Russell\", role = \"aut\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"John\", \"Chambers\", role = \"aut\"))", + "Description": "The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at , the paper by Eddelbuettel and Francois (2011, ), the book by Eddelbuettel (2013, ) and the paper by Eddelbuettel and Balamuta (2018, ); see 'citation(\"Rcpp\")' for details.", + "Imports": [ + "methods", + "utils" + ], + "Suggests": [ + "tinytest", + "inline", + "rbenchmark", + "pkgKitten (>= 0.1.2)" + ], + "URL": "https://www.rcpp.org, https://dirk.eddelbuettel.com/code/rcpp.html, https://github.com/RcppCore/Rcpp", + "License": "GPL (>= 2)", + "BugReports": "https://github.com/RcppCore/Rcpp/issues", + "MailingList": "rcpp-devel@lists.r-forge.r-project.org", + "RoxygenNote": "6.1.1", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Romain Francois [aut] (ORCID: ), JJ Allaire [aut] (ORCID: ), Kevin Ushey [aut] (ORCID: ), Qiang Kou [aut] (ORCID: ), Nathan Russell [aut], Iñaki Ucar [aut] (ORCID: ), Doug Bates [aut] (ORCID: ), John Chambers [aut]", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "RSPM" + }, + "RcppAnnoy": { + "Package": "RcppAnnoy", + "Version": "0.0.22", + "Source": "Repository", + "Type": "Package", + "Title": "'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest Neighbors", + "Date": "2024-01-23", + "Author": "Dirk Eddelbuettel", + "Maintainer": "Dirk Eddelbuettel ", + "Description": "'Annoy' is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. 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Brazzale ", + "Note": "Maintainers are not available to give advice on using a package they did not author.", + "Description": "Functions and datasets for bootstrapping from the book \"Bootstrap Methods and Their Application\" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.", + "Title": "Bootstrap Functions (Originally by Angelo Canty for S)", + "Depends": [ + "R (>= 3.0.0)", + "graphics", + "stats" + ], + "Suggests": [ + "MASS", + "survival" + ], + "LazyData": "yes", + "ByteCompile": "yes", + "License": "Unlimited", + "NeedsCompilation": "no", + "Author": "Angelo Canty [aut] (author of original code for S), Brian Ripley [aut, trl] (conversion to R, maintainer 1999--2022, author of parallel support), Alessandra R. 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family = \"Mannakee\", role = \"ctb\", email = \"bmannakee@gmail.com\"), person(given = \"Drew\", family = \"Tyre\", role = \"ctb\", email = \"atyre2@unl.edu\"), person(given = \"Shreyas\", family = \"Singh\", role = \"ctb\", email = \"shreyas.singh.298@gmail.com\"), person(given = \"Laurens\", family = \"Geffert\", role = \"ctb\", email = \"laurensgeffert@gmail.com\"), person(given = \"Hong\", family = \"Ooi\", role = \"ctb\", email = \"hongooi@microsoft.com\"), person(given = \"Henrik\", family = \"Bengtsson\", role = \"ctb\", email = \"henrikb@braju.com\"), person(given = \"Eduard\", family = \"Szocs\", role = \"ctb\", email = \"eduardszoecs@gmail.com\"), person(given = \"David\", family = \"Hugh-Jones\", role = \"ctb\", email = \"davidhughjones@gmail.com\"), person(given = \"Matthieu\", family = \"Stigler\", role = \"ctb\", email = \"Matthieu.Stigler@gmail.com\"), person(given = \"Hugo\", family = \"Tavares\", role = \"ctb\", email = \"hm533@cam.ac.uk\", comment = c(ORCID = \"0000-0001-9373-2726\")), person(given = \"R. Willem\", family = \"Vervoort\", role = \"ctb\", email = \"Willemvervoort@gmail.com\"), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"ctb\", email = \"brenton@wiernik.org\"), person(given = \"Josh\", family = \"Yamamoto\", role = \"ctb\", email = \"joshuayamamoto5@gmail.com\"), person(given = \"Jasme\", family = \"Lee\", role = \"ctb\"), person(given = \"Taren\", family = \"Sanders\", role = \"ctb\", email = \"taren.sanders@acu.edu.au\", comment = c(ORCID = \"0000-0002-4504-6008\")), person(given = \"Ilaria\", family = \"Prosdocimi\", role = \"ctb\", email = \"prosdocimi.ilaria@gmail.com\", comment = c(ORCID = \"0000-0001-8565-094X\")), person(given = \"Daniel D.\", family = \"Sjoberg\", role = \"ctb\", email = \"danield.sjoberg@gmail.com\", comment = c(ORCID = \"0000-0003-0862-2018\")), person(given = \"Alex\", family = \"Reinhart\", role = \"ctb\", email = \"areinhar@stat.cmu.edu\", comment = c(ORCID = \"0000-0002-6658-514X\")))", + "Description": "Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", + "License": "MIT + file LICENSE", + "URL": "https://broom.tidymodels.org/, https://github.com/tidymodels/broom", + "BugReports": "https://github.com/tidymodels/broom/issues", + "Depends": [ + "R (>= 3.5)" + ], + "Imports": [ + "backports", + "cli", + "dplyr (>= 1.0.0)", + "generics (>= 0.0.2)", + "glue", + "lifecycle", + "purrr", + "rlang (>= 1.1.0)", + "stringr", + "tibble (>= 3.0.0)", + "tidyr (>= 1.0.0)" + ], + "Suggests": [ + "AER", + "AUC", + "bbmle", + "betareg (>= 3.2-1)", + "biglm", + "binGroup", + "boot", + "btergm (>= 1.10.6)", + "car (>= 3.1-2)", + "carData", + "caret", + "cluster", + "cmprsk", + "coda", + "covr", + "drc", + "e1071", + "emmeans", + "epiR", + "ergm (>= 3.10.4)", + "fixest (>= 0.9.0)", + "gam (>= 1.15)", + "gee", + "geepack", + "ggplot2", + "glmnet", + "glmnetUtils", + "gmm", + "Hmisc", + "irlba", + "interp", + "joineRML", + "Kendall", + "knitr", + "ks", + "Lahman", + "lavaan (>= 0.6.18)", + "leaps", + "lfe", + "lm.beta", + "lme4", + "lmodel2", + "lmtest (>= 0.9.38)", + "lsmeans", + "maps", + "margins", + "MASS", + "mclust", + "mediation", + "metafor", + "mfx", + "mgcv", + "mlogit", + "modeldata", + "modeltests (>= 0.1.6)", + "muhaz", + "multcomp", + "network", + "nnet", + "ordinal", + "plm", + "poLCA", + "psych", + "quantreg", + "rmarkdown", + "robust", + "robustbase", + "rsample", + "sandwich", + "spdep (>= 1.1)", + "spatialreg", + "speedglm", + "spelling", + "survey", + "survival (>= 3.6-4)", + "systemfit", + "testthat (>= 3.0.0)", + "tseries", + "vars", + "zoo" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Language": "en-US", + "Collate": "'aaa-documentation-helper.R' 'null-and-default.R' 'aer.R' 'auc.R' 'base.R' 'bbmle.R' 'betareg.R' 'biglm.R' 'bingroup.R' 'boot.R' 'broom-package.R' 'broom.R' 'btergm.R' 'car.R' 'caret.R' 'cluster.R' 'cmprsk.R' 'data-frame.R' 'deprecated-0-7-0.R' 'drc.R' 'emmeans.R' 'epiR.R' 'ergm.R' 'fixest.R' 'gam.R' 'geepack.R' 'glmnet-cv-glmnet.R' 'glmnet-glmnet.R' 'gmm.R' 'hmisc.R' 'import-standalone-obj-type.R' 'import-standalone-types-check.R' 'joinerml.R' 'kendall.R' 'ks.R' 'lavaan.R' 'leaps.R' 'lfe.R' 'list-irlba.R' 'list-optim.R' 'list-svd.R' 'list-xyz.R' 'list.R' 'lm-beta.R' 'lmodel2.R' 'lmtest.R' 'maps.R' 'margins.R' 'mass-fitdistr.R' 'mass-negbin.R' 'mass-polr.R' 'mass-ridgelm.R' 'stats-lm.R' 'mass-rlm.R' 'mclust.R' 'mediation.R' 'metafor.R' 'mfx.R' 'mgcv.R' 'mlogit.R' 'muhaz.R' 'multcomp.R' 'nnet.R' 'nobs.R' 'ordinal-clm.R' 'ordinal-clmm.R' 'plm.R' 'polca.R' 'psych.R' 'stats-nls.R' 'quantreg-nlrq.R' 'quantreg-rq.R' 'quantreg-rqs.R' 'robust-glmrob.R' 'robust-lmrob.R' 'robustbase-glmrob.R' 'robustbase-lmrob.R' 'sp.R' 'spdep.R' 'speedglm-speedglm.R' 'speedglm-speedlm.R' 'stats-anova.R' 'stats-arima.R' 'stats-decompose.R' 'stats-factanal.R' 'stats-glm.R' 'stats-htest.R' 'stats-kmeans.R' 'stats-loess.R' 'stats-mlm.R' 'stats-prcomp.R' 'stats-smooth.spline.R' 'stats-summary-lm.R' 'stats-time-series.R' 'survey.R' 'survival-aareg.R' 'survival-cch.R' 'survival-coxph.R' 'survival-pyears.R' 'survival-survdiff.R' 'survival-survexp.R' 'survival-survfit.R' 'survival-survreg.R' 'systemfit.R' 'tseries.R' 'utilities.R' 'vars.R' 'zoo.R' 'zzz.R'", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "David Robinson [aut], Alex Hayes [aut] (), Simon Couch [aut, cre] (), Posit Software, PBC [cph, fnd], Indrajeet Patil [ctb] (), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (), Jasper Cooper [ctb] (), E Auden Krauska [ctb] (), Alex Wang [ctb], Malcolm Barrett [ctb] (), Charles Gray [ctb] (), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (), Eduard Szoecs [ctb], Frederik Aust [ctb] (), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (), Bruna Wundervald [ctb] (), Joyce Cahoon [ctb] (), Grant McDermott [ctb] (), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (), Lukas Wallrich [ctb] (), James Martherus [ctb] (), Chuliang Xiao [ctb] (), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (), Ilaria Prosdocimi [ctb] (), Daniel D. 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Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".", + "Maintainer": "Martin Maechler ", + "Authors@R": "c(person(\"Martin\",\"Maechler\", role = c(\"aut\",\"cre\"), email=\"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) ,person(\"Peter\", \"Rousseeuw\", role=\"aut\", email=\"peter.rousseeuw@kuleuven.be\", comment = c(\"Fortran original\", ORCID = \"0000-0002-3807-5353\")) ,person(\"Anja\", \"Struyf\", role=\"aut\", comment= \"S original\") ,person(\"Mia\", \"Hubert\", role=\"aut\", email= \"Mia.Hubert@uia.ua.ac.be\", comment = c(\"S original\", ORCID = \"0000-0001-6398-4850\")) ,person(\"Kurt\", \"Hornik\", role=c(\"trl\", \"ctb\"), email=\"Kurt.Hornik@R-project.org\", comment=c(\"port to R; maintenance(1999-2000)\", ORCID=\"0000-0003-4198-9911\")) ,person(\"Matthias\", \"Studer\", role=\"ctb\") ,person(\"Pierre\", \"Roudier\", role=\"ctb\") ,person(\"Juan\", \"Gonzalez\", role=\"ctb\") ,person(\"Kamil\", \"Kozlowski\", role=\"ctb\") ,person(\"Erich\", \"Schubert\", role=\"ctb\", comment = c(\"fastpam options for pam()\", ORCID = \"0000-0001-9143-4880\")) ,person(\"Keefe\", \"Murphy\", role=\"ctb\", comment = \"volume.ellipsoid({d >= 3})\") #not yet ,person(\"Fischer-Rasmussen\", \"Kasper\", role = \"ctb\", comment = \"Gower distance for CLARA\") )", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "graphics", + "grDevices", + "stats", + "utils" + ], + "Suggests": [ + "MASS", + "Matrix" + ], + "SuggestsNote": "MASS: two examples using cov.rob() and mvrnorm(); Matrix tools for testing", + "Enhances": [ + "mvoutlier", + "fpc", + "ellipse", + "sfsmisc" + ], + "EnhancesNote": "xref-ed in man/*.Rd", + "LazyLoad": "yes", + "LazyData": "yes", + "ByteCompile": "yes", + "BuildResaveData": "no", + "License": "GPL (>= 2)", + "URL": "https://svn.r-project.org/R-packages/trunk/cluster/", + "NeedsCompilation": "yes", + "Author": "Martin Maechler [aut, cre] (), Peter Rousseeuw [aut] (Fortran original, ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", + "Repository": "CRAN" + }, + "coda": { + "Package": "coda", + "Version": "0.19-4.1", + "Source": "Repository", + "Date": "2020-09-30", + "Title": "Output Analysis and Diagnostics for MCMC", + "Authors@R": "c(person(\"Martyn\", \"Plummer\", role=c(\"aut\",\"cre\",\"trl\"), email=\"martyn.plummer@gmail.com\"), person(\"Nicky\", \"Best\", role=\"aut\"), person(\"Kate\", \"Cowles\", role=\"aut\"), person(\"Karen\", \"Vines\", role=\"aut\"), person(\"Deepayan\", \"Sarkar\", role=\"aut\"), person(\"Douglas\", \"Bates\", role=\"aut\"), person(\"Russell\", \"Almond\", role=\"aut\"), person(\"Arni\", \"Magnusson\", role=\"aut\"))", + "Depends": [ + "R (>= 2.14.0)" + ], + "Imports": [ + "lattice" + ], + "Description": "Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.", + "License": "GPL (>= 2)", + "NeedsCompilation": "no", + "Author": "Martyn Plummer [aut, cre, trl], Nicky Best [aut], Kate Cowles [aut], Karen Vines [aut], Deepayan Sarkar [aut], Douglas Bates [aut], Russell Almond [aut], Arni Magnusson [aut]", + "Maintainer": "Martyn Plummer ", + "Repository": "CRAN" + }, + "codetools": { + "Package": "codetools", + "Version": "0.2-20", + "Source": "Repository", + "Priority": "recommended", + "Author": "Luke Tierney ", + "Description": "Code analysis tools for R.", + "Title": "Code Analysis Tools for R", + "Depends": [ + "R (>= 2.1)" + ], + "Maintainer": "Luke Tierney ", + "URL": "https://gitlab.com/luke-tierney/codetools", + "License": "GPL", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "colorspace": { + "Package": "colorspace", + "Version": "2.1-1", + "Source": "Repository", + "Date": "2024-07-26", + "Title": "A Toolbox for Manipulating and Assessing Colors and Palettes", + "Authors@R": "c(person(given = \"Ross\", family = \"Ihaka\", role = \"aut\", email = \"ihaka@stat.auckland.ac.nz\"), person(given = \"Paul\", family = \"Murrell\", role = \"aut\", email = \"paul@stat.auckland.ac.nz\", comment = c(ORCID = \"0000-0002-3224-8858\")), person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(given = c(\"Jason\", \"C.\"), family = \"Fisher\", role = \"aut\", email = \"jfisher@usgs.gov\", comment = c(ORCID = \"0000-0001-9032-8912\")), person(given = \"Reto\", family = \"Stauffer\", role = \"aut\", email = \"Reto.Stauffer@uibk.ac.at\", comment = c(ORCID = \"0000-0002-3798-5507\")), person(given = c(\"Claus\", \"O.\"), family = \"Wilke\", role = \"aut\", email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(given = c(\"Claire\", \"D.\"), family = \"McWhite\", role = \"aut\", email = \"claire.mcwhite@utmail.utexas.edu\", comment = c(ORCID = \"0000-0001-7346-3047\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")))", + "Description": "Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, ).", + "Depends": [ + "R (>= 3.0.0)", + "methods" + ], + "Imports": [ + "graphics", + "grDevices", + "stats" + ], + "Suggests": [ + "datasets", + "utils", + "KernSmooth", + "MASS", + "kernlab", + "mvtnorm", + "vcd", + "tcltk", + "shiny", + "shinyjs", + "ggplot2", + "dplyr", + "scales", + "grid", + "png", + "jpeg", + "knitr", + "rmarkdown", + "RColorBrewer", + "rcartocolor", + "scico", + "viridis", + "wesanderson" + ], + "VignetteBuilder": "knitr", + "License": "BSD_3_clause + file LICENSE", + "URL": "https://colorspace.R-Forge.R-project.org/, https://hclwizard.org/", + "BugReports": "https://colorspace.R-Forge.R-project.org/contact.html", + "LazyData": "yes", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Ross Ihaka [aut], Paul Murrell [aut] (), Kurt Hornik [aut] (), Jason C. Fisher [aut] (), Reto Stauffer [aut] (), Claus O. Wilke [aut] (), Claire D. McWhite [aut] (), Achim Zeileis [aut, cre] ()", + "Maintainer": "Achim Zeileis ", + "Repository": "RSPM" + }, + "commonmark": { + "Package": "commonmark", + "Version": "2.0.0", + "Source": "Repository", + "Type": "Package", + "Title": "High Performance CommonMark and Github Markdown Rendering in R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", ,\"jeroenooms@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"John MacFarlane\", role = \"cph\", comment = \"Author of cmark\"))", + "Description": "The CommonMark specification defines a rationalized version of markdown syntax. This package uses the 'cmark' reference implementation for converting markdown text into various formats including html, latex and groff man. In addition it exposes the markdown parse tree in xml format. Also includes opt-in support for GFM extensions including tables, autolinks, and strikethrough text.", + "License": "BSD_2_clause + file LICENSE", + "URL": "https://docs.ropensci.org/commonmark/ https://ropensci.r-universe.dev/commonmark", + "BugReports": "https://github.com/r-lib/commonmark/issues", + "Suggests": [ + "curl", + "testthat", + "xml2" + ], + "RoxygenNote": "7.3.2", + "Language": "en-US", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (ORCID: ), John MacFarlane [cph] (Author of cmark)", + "Maintainer": "Jeroen Ooms ", + "Repository": "RSPM" + }, + "conflicted": { + "Package": "conflicted", + "Version": "1.2.0", + "Source": "Repository", + "Title": "An Alternative Conflict Resolution Strategy", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = c(\"aut\", \"cre\")), person(\"RStudio\", role = c(\"cph\", \"fnd\")) )", + "Description": "R's default conflict management system gives the most recently loaded package precedence. This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that did not previously exist. 'conflicted' takes a different approach, making every conflict an error and forcing you to choose which function to use.", + "License": "MIT + file LICENSE", + "URL": "https://conflicted.r-lib.org/, https://github.com/r-lib/conflicted", + "BugReports": "https://github.com/r-lib/conflicted/issues", + "Depends": [ + "R (>= 3.2)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "memoise", + "rlang (>= 1.0.0)" + ], + "Suggests": [ + "callr", + "covr", + "dplyr", + "Matrix", + "methods", + "pkgload", + "testthat (>= 3.0.0)", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], RStudio [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "corrplot": { + "Package": "corrplot", + "Version": "0.95", + "Source": "Repository", + "Type": "Package", + "Title": "Visualization of a Correlation Matrix", + "Date": "2024-10-14", + "Authors@R": "c( person('Taiyun', 'Wei', email = 'weitaiyun@gmail.com', role = c('cre', 'aut')), person('Viliam', 'Simko', email = 'viliam.simko@gmail.com', role = 'aut'), person('Michael', 'Levy', email = 'michael.levy@healthcatalyst.com', role = 'ctb'), person('Yihui', 'Xie', email = 'xie@yihui.name', role = 'ctb'), person('Yan', 'Jin', email = 'jyfeather@gmail.com', role = 'ctb'), person('Jeff', 'Zemla', email = 'zemla@wisc.edu', role = 'ctb'), person('Moritz', 'Freidank', email = 'freidankm@googlemail.com', role = 'ctb'), person('Jun', 'Cai', email = 'cai-j12@mails.tsinghua.edu.cn', role = 'ctb'), person('Tomas', 'Protivinsky', email = 'tomas.protivinsky@gmail.com', role = 'ctb') )", + "Maintainer": "Taiyun Wei ", + "Suggests": [ + "seriation", + "knitr", + "RColorBrewer", + "rmarkdown", + "magrittr", + "prettydoc", + "testthat" + ], + "Description": "Provides a visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/taiyun/corrplot", + "BugReports": "https://github.com/taiyun/corrplot/issues", + "VignetteBuilder": "knitr", + "RoxygenNote": "7.2.1", + "NeedsCompilation": "no", + "Author": "Taiyun Wei [cre, aut], Viliam Simko [aut], Michael Levy [ctb], Yihui Xie [ctb], Yan Jin [ctb], Jeff Zemla [ctb], Moritz Freidank [ctb], Jun Cai [ctb], Tomas Protivinsky [ctb]", + "Repository": "CRAN" + }, + "cowplot": { + "Package": "cowplot", + "Version": "1.2.0", + "Source": "Repository", + "Title": "Streamlined Plot Theme and Plot Annotations for 'ggplot2'", + "Authors@R": "person( given = \"Claus O.\", family = \"Wilke\", role = c(\"aut\", \"cre\"), email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\") )", + "Description": "Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.", + "URL": "https://wilkelab.org/cowplot/", + "BugReports": "https://github.com/wilkelab/cowplot/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "ggplot2 (>= 3.5.2)", + "grid", + "gtable", + "grDevices", + "methods", + "rlang", + "scales" + ], + "License": "GPL-2", + "Suggests": [ + "Cairo", + "covr", + "dplyr", + "forcats", + "gridGraphics (>= 0.4-0)", + "knitr", + "lattice", + "magick", + "maps", + "PASWR", + "patchwork", + "rmarkdown", + "ragg", + "testthat (>= 1.0.0)", + "tidyr", + "vdiffr (>= 0.3.0)", + "VennDiagram" + ], + "VignetteBuilder": "knitr", + "Collate": "'add_sub.R' 'align_plots.R' 'as_grob.R' 'as_gtable.R' 'axis_canvas.R' 'cowplot.R' 'draw.R' 'get_plot_component.R' 'get_axes.R' 'get_titles.R' 'get_legend.R' 'get_panel.R' 'gtable.R' 'key_glyph.R' 'plot_grid.R' 'save.R' 'set_null_device.R' 'setup.R' 'stamp.R' 'themes.R' 'utils_ggplot2.R'", + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Claus O. Wilke [aut, cre] (ORCID: )", + "Maintainer": "Claus O. Wilke ", + "Repository": "RSPM" + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.5.2", + "Source": "Repository", + "Title": "A C++11 Interface for R's C Interface", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", email = \"davis@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Jim\",\"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Benjamin\", \"Kietzman\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (), Jim Hester [aut] (), Romain François [aut] (), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.3", + "Source": "Repository", + "Title": "Colored Terminal Output", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ + "grDevices", + "methods", + "utils" + ], + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "crosstalk": { + "Package": "crosstalk", + "Version": "1.2.1", + "Source": "Repository", + "Type": "Package", + "Title": "Inter-Widget Interactivity for HTML Widgets", + "Authors@R": "c( person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@posit.co\"), person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@posit.co\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(family = \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )", + "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). 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Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.73): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" + ], + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" + ], + "RoxygenNote": "7.3.2.9000", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (ORCID: ), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "data.table": { + "Package": "data.table", + "Version": "1.17.8", + "Source": "Repository", + "Title": "Extension of `data.frame`", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "bit64 (>= 4.0.0)", + "bit (>= 4.0.4)", + "R.utils", + "xts", + "zoo (>= 1.8-1)", + "yaml", + "knitr", + "markdown" + ], + "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.", + "License": "MPL-2.0 | file LICENSE", + "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table", + "BugReports": "https://github.com/Rdatatable/data.table/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "ByteCompile": "TRUE", + "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\"), person(\"Michael\",\"Chirico\", role=\"aut\", comment = c(ORCID=\"0000-0003-0787-087X\")), person(\"Toby\",\"Hocking\", role=\"aut\", comment = c(ORCID=\"0000-0002-3146-0865\")), person(\"Benjamin\",\"Schwendinger\",role=\"aut\", comment = c(ORCID=\"0000-0003-3315-8114\")), person(\"Ivan\", 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"Source": "Repository", + "Type": "Package", + "Title": "A 'dplyr' Back End for Databases", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Maximilian\", \"Girlich\", role = \"aut\"), person(\"Edgar\", \"Ruiz\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.", + "License": "MIT + file LICENSE", + "URL": "https://dbplyr.tidyverse.org/, https://github.com/tidyverse/dbplyr", + "BugReports": "https://github.com/tidyverse/dbplyr/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "blob (>= 1.2.0)", + "cli (>= 3.6.1)", + "DBI (>= 1.1.3)", + "dplyr (>= 1.1.2)", + "glue (>= 1.6.2)", + "lifecycle (>= 1.0.3)", + "magrittr", + "methods", + "pillar (>= 1.9.0)", + "purrr (>= 1.0.1)", + "R6 (>= 2.2.2)", + "rlang (>= 1.1.1)", + "tibble (>= 3.2.1)", + "tidyr (>= 1.3.0)", + "tidyselect (>= 1.2.1)", + "utils", + "vctrs (>= 0.6.3)", + "withr (>= 2.5.0)" + ], + "Suggests": [ + "bit64", + "covr", + "knitr", + "Lahman", + "nycflights13", + "odbc (>= 1.4.2)", + "RMariaDB (>= 1.2.2)", + "rmarkdown", + "RPostgres (>= 1.4.5)", + "RPostgreSQL", + "RSQLite (>= 2.3.1)", + "testthat (>= 3.1.10)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "TRUE", + "Encoding": "UTF-8", + "Language": "en-gb", + "RoxygenNote": "7.3.1", + "Collate": "'db-sql.R' 'utils-check.R' 'import-standalone-types-check.R' 'import-standalone-obj-type.R' 'utils.R' 'sql.R' 'escape.R' 'translate-sql-cut.R' 'translate-sql-quantile.R' 'translate-sql-string.R' 'translate-sql-paste.R' 'translate-sql-helpers.R' 'translate-sql-window.R' 'translate-sql-conditional.R' 'backend-.R' 'backend-access.R' 'backend-hana.R' 'backend-hive.R' 'backend-impala.R' 'verb-copy-to.R' 'backend-mssql.R' 'backend-mysql.R' 'backend-odbc.R' 'backend-oracle.R' 'backend-postgres.R' 'backend-postgres-old.R' 'backend-redshift.R' 'backend-snowflake.R' 'backend-spark-sql.R' 'backend-sqlite.R' 'backend-teradata.R' 'build-sql.R' 'data-cache.R' 'data-lahman.R' 'data-nycflights13.R' 'db-escape.R' 'db-io.R' 'db.R' 'dbplyr.R' 'explain.R' 'ident.R' 'import-standalone-s3-register.R' 'join-by-compat.R' 'join-cols-compat.R' 'lazy-join-query.R' 'lazy-ops.R' 'lazy-query.R' 'lazy-select-query.R' 'lazy-set-op-query.R' 'memdb.R' 'optimise-utils.R' 'pillar.R' 'progress.R' 'sql-build.R' 'query-join.R' 'query-select.R' 'query-semi-join.R' 'query-set-op.R' 'query.R' 'reexport.R' 'remote.R' 'rows.R' 'schema.R' 'simulate.R' 'sql-clause.R' 'sql-expr.R' 'src-sql.R' 'src_dbi.R' 'table-name.R' 'tbl-lazy.R' 'tbl-sql.R' 'test-frame.R' 'testthat.R' 'tidyeval-across.R' 'tidyeval.R' 'translate-sql.R' 'utils-format.R' 'verb-arrange.R' 'verb-compute.R' 'verb-count.R' 'verb-distinct.R' 'verb-do-query.R' 'verb-do.R' 'verb-expand.R' 'verb-fill.R' 'verb-filter.R' 'verb-group_by.R' 'verb-head.R' 'verb-joins.R' 'verb-mutate.R' 'verb-pivot-longer.R' 'verb-pivot-wider.R' 'verb-pull.R' 'verb-select.R' 'verb-set-ops.R' 'verb-slice.R' 'verb-summarise.R' 'verb-uncount.R' 'verb-window.R' 'zzz.R'", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Maximilian Girlich [aut], Edgar Ruiz [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "deldir": { + "Package": "deldir", + "Version": "2.0-4", + "Source": "Repository", + "Date": "2024-02-27", + "Title": "Delaunay Triangulation and Dirichlet (Voronoi) Tessellation", + "Author": "Rolf Turner", + "Maintainer": "Rolf Turner ", + "Depends": [ + "R (>= 3.5.0)" + ], + "Suggests": [ + "polyclip" + ], + "Imports": [ + "graphics", + "grDevices" + ], + "Description": "Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. Plots triangulations and tessellations in various ways. Clips tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation.\tCalculates the centroidal Voronoi (Dirichlet) tessellation using Lloyd's algorithm.", + "LazyData": "true", + "ByteCompile": "true", + "License": "GPL (>= 2)", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, + "digest": { + "Package": "digest", + "Version": "0.6.37", + "Source": "Repository", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\"), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\"), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", role=\"ctb\"), person(\"Wush\", \"Wu\", role=\"ctb\", comment = c(ORCID = \"0000-0001-5180-0567\")), person(\"Qiang\", \"Kou\", role=\"ctb\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Thierry\", \"Onkelinx\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8804-4216\")), person(\"Michel\", \"Lang\", role=\"ctb\", comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Viliam\", \"Simko\", role=\"ctb\"), person(\"Kurt\", \"Hornik\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Radford\", \"Neal\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2473-3407\")), person(\"Kendon\", \"Bell\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9093-8312\")), person(\"Matthew\", \"de Queljoe\", role=\"ctb\"), person(\"Dmitry\", \"Selivanov\", role=\"ctb\"), person(\"Ion\", \"Suruceanu\", role=\"ctb\"), person(\"Bill\", \"Denney\", role=\"ctb\"), person(\"Dirk\", \"Schumacher\", role=\"ctb\"), person(\"András\", \"Svraka\", role=\"ctb\"), person(\"Sergey\", \"Fedorov\", role=\"ctb\"), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\"), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\"))", + "Date": "2024-08-19", + "Title": "Create Compact Hash Digests of R Objects", + "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", + "URL": "https://github.com/eddelbuettel/digest, https://dirk.eddelbuettel.com/code/digest.html", + "BugReports": "https://github.com/eddelbuettel/digest/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "utils" + ], + "License": "GPL (>= 2)", + "Suggests": [ + "tinytest", + "simplermarkdown" + ], + "VignetteBuilder": "simplermarkdown", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (), Antoine Lucas [ctb], Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (), Simon Urbanek [ctb] (), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb], Duncan Murdoch [ctb], Jim Hester [ctb], Wush Wu [ctb] (), Qiang Kou [ctb] (), Thierry Onkelinx [ctb] (), Michel Lang [ctb] (), Viliam Simko [ctb], Kurt Hornik [ctb] (), Radford Neal [ctb] (), Kendon Bell [ctb] (), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb], Ion Suruceanu [ctb], Bill Denney [ctb], Dirk Schumacher [ctb], András Svraka [ctb], Sergey Fedorov [ctb], Will Landau [ctb] (), Floris Vanderhaeghe [ctb] (), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (), Mark van der Loo [ctb] (), Chris Muir [ctb] (), Moritz Beller [ctb] (), Sebastian Campbell [ctb], Winston Chang [ctb] (), Dean Attali [ctb] (), Michael Chirico [ctb] (), Kevin Ushey [ctb]", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "doBy": { + "Package": "doBy", + "Version": "4.7.0", + "Source": "Repository", + "Title": "Groupwise Statistics, LSmeans, Linear Estimates, Utilities", + "Authors@R": "c( person(given = \"Ulrich\", family = \"Halekoh\", email = \"uhalekoh@health.sdu.dk\", role = c(\"aut\", \"cph\")), person(given = \"Søren\", family = \"Højsgaard\", email = \"sorenh@math.aau.dk\", role = c(\"aut\", \"cre\", \"cph\")) )", + "Description": "Utility package containing: Main categories: Working with grouped data: 'do' something to data when stratified 'by' some variables. General linear estimates. Data handling utilities. Functional programming, in particular restrict functions to a smaller domain. Miscellaneous functions for data handling. Model stability in connection with model selection. 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This makes it a convenient and fast interface to C/C++ and Fortran code.", + "License": "GPL (>= 2)", + "URL": "https://git.math.uzh.ch/reinhard.furrer/dotCall64", + "BugReports": "https://git.math.uzh.ch/reinhard.furrer/dotCall64/-/issues", + "Depends": [ + "R (>= 4.0)" + ], + "Suggests": [ + "microbenchmark", + "RhpcBLASctl", + "RColorBrewer", + "roxygen2", + "spam", + "testthat" + ], + "Collate": "'vector_dc.R' 'dotCall64.R' 'zzz.R'", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Kaspar Moesinger [aut], Florian Gerber [aut] (), Reinhard Furrer [cre, ctb] ()", + "Maintainer": "Reinhard Furrer ", + "Repository": "CRAN" + }, + "dplyr": { + "Package": "dplyr", + "Version": "1.1.4", + "Source": "Repository", + "Type": "Package", + "Title": "A Grammar of Data Manipulation", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Lionel\", \"Henry\", role = \"aut\"), person(\"Kirill\", \"Müller\", role = \"aut\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A fast, consistent tool for working with data frame like objects, both in memory and out of memory.", + "License": "MIT + file LICENSE", + "URL": "https://dplyr.tidyverse.org, https://github.com/tidyverse/dplyr", + "BugReports": "https://github.com/tidyverse/dplyr/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "generics", + "glue (>= 1.3.2)", + "lifecycle (>= 1.0.3)", + "magrittr (>= 1.5)", + "methods", + "pillar (>= 1.9.0)", + "R6", + "rlang (>= 1.1.0)", + "tibble (>= 3.2.0)", + "tidyselect (>= 1.2.0)", + "utils", + "vctrs (>= 0.6.4)" + ], + "Suggests": [ + "bench", + "broom", + "callr", + "covr", + "DBI", + "dbplyr (>= 2.2.1)", + "ggplot2", + "knitr", + "Lahman", + "lobstr", + "microbenchmark", + "nycflights13", + "purrr", + "rmarkdown", + "RMySQL", + "RPostgreSQL", + "RSQLite", + "stringi (>= 1.7.6)", + "testthat (>= 3.1.5)", + "tidyr (>= 1.3.0)", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse, shiny, pkgdown, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre] (), Romain François [aut] (), Lionel Henry [aut], Kirill Müller [aut] (), Davis Vaughan [aut] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "dqrng": { + "Package": "dqrng", + "Version": "0.4.1", + "Source": "Repository", + "Type": "Package", + "Title": "Fast Pseudo Random Number Generators", + "Authors@R": "c( person(\"Ralf\", \"Stubner\", email = \"ralf.stubner@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0009-0009-1908-106X\")), person(\"daqana GmbH\", role = \"cph\"), person(\"David Blackman\", role = \"cph\", comment = \"Xoroshiro / Xoshiro family\"), person(\"Melissa O'Neill\", email = \"oneill@pcg-random.org\", role = \"cph\", comment = \"PCG family\"), person(\"Sebastiano Vigna\", email = \"vigna@acm.org\", role = \"cph\", comment = \"Xoroshiro / Xoshiro family\"), person(\"Aaron\", \"Lun\", role=\"ctb\"), person(\"Kyle\", \"Butts\", role = \"ctb\", email = \"kyle.butts@colorado.edu\"), person(\"Henrik\", \"Sloot\", role = \"ctb\"), person(\"Philippe\", \"Grosjean\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0002-2694-9471\")) )", + "Description": "Several fast random number generators are provided as C++ header only libraries: The PCG family by O'Neill (2014 ) as well as the Xoroshiro / Xoshiro family by Blackman and Vigna (2021 ). In addition fast functions for generating random numbers according to a uniform, normal and exponential distribution are included. The latter two use the Ziggurat algorithm originally proposed by Marsaglia and Tsang (2000, ). The fast sampling methods support unweighted sampling both with and without replacement. These functions are exported to R and as a C++ interface and are enabled for use with the default 64 bit generator from the PCG family, Xoroshiro128+/++/** and Xoshiro256+/++/** as well as the 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011, ) as provided by the package 'sitmo'.", + "License": "AGPL-3", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "Rcpp (>= 0.12.16)" + ], + "LinkingTo": [ + "Rcpp", + "BH (>= 1.64.0-1)", + "sitmo (>= 2.0.0)" + ], + "RoxygenNote": "7.3.1", + "Suggests": [ + "BH", + "testthat", + "knitr", + "rmarkdown", + "mvtnorm (>= 1.2-3)", + "bench", + "sitmo" + ], + "VignetteBuilder": "knitr", + "URL": "https://daqana.github.io/dqrng/, https://github.com/daqana/dqrng", + "BugReports": "https://github.com/daqana/dqrng/issues", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Ralf Stubner [aut, cre] (), daqana GmbH [cph], David Blackman [cph] (Xoroshiro / Xoshiro family), Melissa O'Neill [cph] (PCG family), Sebastiano Vigna [cph] (Xoroshiro / Xoshiro family), Aaron Lun [ctb], Kyle Butts [ctb], Henrik Sloot [ctb], Philippe Grosjean [ctb] ()", + "Maintainer": "Ralf Stubner ", + "Repository": "CRAN" + }, + "dtplyr": { + "Package": "dtplyr", + "Version": "1.3.1", + "Source": "Repository", + "Title": "Data Table Back-End for 'dplyr'", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"cre\", \"aut\")), person(\"Maximilian\", \"Girlich\", role = \"aut\"), person(\"Mark\", \"Fairbanks\", role = \"aut\"), person(\"Ryan\", \"Dickerson\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a data.table backend for 'dplyr'. The goal of 'dtplyr' is to allow you to write 'dplyr' code that is automatically translated to the equivalent, but usually much faster, data.table code.", + "License": "MIT + file LICENSE", + "URL": "https://dtplyr.tidyverse.org, https://github.com/tidyverse/dtplyr", + "BugReports": "https://github.com/tidyverse/dtplyr/issues", + "Depends": [ + "R (>= 3.3)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "data.table (>= 1.13.0)", + "dplyr (>= 1.1.0)", + "glue", + "lifecycle", + "rlang (>= 1.0.4)", + "tibble", + "tidyselect (>= 1.2.0)", + "vctrs (>= 0.4.1)" + ], + "Suggests": [ + "bench", + "covr", + "knitr", + "rmarkdown", + "testthat (>= 3.1.2)", + "tidyr (>= 1.1.0)", + "waldo (>= 0.3.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [cre, aut], Maximilian Girlich [aut], Mark Fairbanks [aut], Ryan Dickerson [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "evaluate": { + "Package": "evaluate", + "Version": "1.0.4", + "Source": "Repository", + "Type": "Package", + "Title": "Parsing and Evaluation Tools that Provide More Details than the Default", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Yihui\", \"Xie\", role = \"aut\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Michael\", \"Lawrence\", role = \"ctb\"), person(\"Thomas\", \"Kluyver\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\"), person(\"Barret\", \"Schloerke\", role = \"ctb\"), person(\"Adam\", \"Ryczkowski\", role = \"ctb\"), person(\"Hiroaki\", \"Yutani\", role = \"ctb\"), person(\"Michel\", \"Lang\", role = \"ctb\"), person(\"Karolis\", \"Koncevičius\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.", + "License": "MIT + file LICENSE", + "URL": "https://evaluate.r-lib.org/, https://github.com/r-lib/evaluate", + "BugReports": "https://github.com/r-lib/evaluate/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Suggests": [ + "callr", + "covr", + "ggplot2 (>= 3.3.6)", + "lattice", + "methods", + "pkgload", + "ragg (>= 1.4.0)", + "rlang (>= 1.1.5)", + "knitr", + "testthat (>= 3.0.0)", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Yihui Xie [aut] (ORCID: ), Michael Lawrence [ctb], Thomas Kluyver [ctb], Jeroen Ooms [ctb], Barret Schloerke [ctb], Adam Ryczkowski [ctb], Hiroaki Yutani [ctb], Michel Lang [ctb], Karolis Koncevičius [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "RSPM" + }, + "expm": { + "Package": "expm", 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"Description": "Computation of the matrix exponential, logarithm, sqrt, and related quantities, using traditional and modern methods.", + "Depends": [ + "Matrix" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "RColorBrewer", + "sfsmisc", + "Rmpfr" + ], + "BuildResaveData": "no", + "License": "GPL (>= 2)", + "URL": "https://R-Forge.R-project.org/projects/expm/", + "BugReports": "https://R-forge.R-project.org/tracker/?atid=472&group_id=107", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Martin Maechler [aut, cre] (), Christophe Dutang [aut] (), Vincent Goulet [aut] (), Douglas Bates [ctb] (cosmetic clean up, in svn r42), David Firth [ctb] (expm(method= \"PadeO\" and \"TaylorO\")), Marina Shapira [ctb] (expm(method= \"PadeO\" and \"TaylorO\")), Michael Stadelmann [ctb] (\"Higham08*\" methods, see ?expm.Higham08...)", + "Maintainer": "Martin Maechler ", + "Repository": "CRAN" + }, + "farver": { + "Package": "farver", + "Version": "2.1.2", + "Source": "Repository", + "Type": "Package", + "Title": "High Performance Colour Space Manipulation", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Berendea\", \"Nicolae\", role = \"aut\", comment = \"Author of the ColorSpace C++ library\"), person(\"Romain\", \"François\", , \"romain@purrple.cat\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The encoding of colour can be handled in many different ways, using different colour spaces. As different colour spaces have different uses, efficient conversion between these representations are important. The 'farver' package provides a set of functions that gives access to very fast colour space conversion and comparisons implemented in C++, and offers speed improvements over the 'convertColor' function in the 'grDevices' package.", + "License": "MIT + file LICENSE", + "URL": "https://farver.data-imaginist.com, https://github.com/thomasp85/farver", + "BugReports": "https://github.com/thomasp85/farver/issues", + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (), Berendea Nicolae [aut] (Author of the ColorSpace C++ library), Romain François [aut] (), Posit, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" + }, + "fastDummies": { + "Package": "fastDummies", + "Version": "1.7.5", + "Source": "Repository", + "Type": "Package", + "Title": "Fast Creation of Dummy (Binary) Columns and Rows from Categorical Variables", + "Authors@R": "c( person(\"Jacob\", \"Kaplan\", email = \"jkkaplan6@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0601-0387\")), person(\"Benjamin\", \"Schlegel\", email = \"kontakt@benjaminschlegl.ch\", role = \"ctb\"))", + "Description": "Creates dummy columns from columns that have categorical variables (character or factor types). 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Fisher [ctb] (), Kipp Johnson [ctb] (), Tyler Rinker [ctb]", + "Repository": "RSPM" + }, + "ggplot2": { + "Package": "ggplot2", + "Version": "3.5.2", + "Source": "Repository", + "Title": "Create Elegant Data Visualisations Using the Grammar of Graphics", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Winston\", \"Chang\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Lionel\", \"Henry\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Kohske\", \"Takahashi\", role = \"aut\"), person(\"Claus\", \"Wilke\", role = \"aut\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(\"Kara\", \"Woo\", role = \"aut\", comment = c(ORCID = \"0000-0002-5125-4188\")), person(\"Hiroaki\", \"Yutani\", role = \"aut\", comment = c(ORCID = \"0000-0002-3385-7233\")), person(\"Dewey\", \"Dunnington\", role = \"aut\", comment = c(ORCID = \"0000-0002-9415-4582\")), person(\"Teun\", \"van den Brand\", role = \"aut\", comment = c(ORCID = \"0000-0002-9335-7468\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A system for 'declaratively' creating graphics, based on \"The Grammar of Graphics\". 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The 'Prism'-look is achieved with theme_prism() and scale_fill|colour_prism(), axes can be changed with custom guides like guide_prism_minor(), and significance indicators added with add_pvalue().", + "License": "GPL (>= 3.0)", + "URL": "https://csdaw.github.io/ggprism/, https://github.com/csdaw/ggprism", + "BugReports": "https://github.com/csdaw/ggprism/issues", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.3.2", + "Depends": [ + "R (>= 3.2)" + ], + "Imports": [ + "digest", + "ggplot2 (>= 3.2.0)", + "glue", + "grid", + "gtable (>= 0.1.1)", + "rlang (>= 0.3.0)", + "scales (>= 0.5.0)", + "stats", + "tibble", + "utils" + ], + "Suggests": [ + "covr", + "dplyr", + "ggbeeswarm", + "ggnewscale", + "knitr", + "magrittr", + "patchwork", + "rmarkdown", + "rstatix", + "tidyr", + "tinytest" + ], + "VignetteBuilder": "knitr", + "NeedsCompilation": "no", + "Author": "Charlotte Dawson [aut, cre] (ORCID: )", + "Maintainer": "Charlotte Dawson ", + "Repository": "CRAN" + }, + "ggpubr": { + "Package": "ggpubr", + "Version": "0.6.1", + "Source": "Repository", + "Type": "Package", + "Title": "'ggplot2' Based Publication Ready Plots", + "Date": "2025-06-27", + "Authors@R": "c( person(\"Alboukadel\", \"Kassambara\", role = c(\"aut\", \"cre\"), email = \"alboukadel.kassambara@gmail.com\"))", + "Description": "The 'ggplot2' package is excellent and flexible for elegant data visualization in R. 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The \"v4\" refers to the fact that the Sheets API is currently at version 4. This package can read and write both the metadata and the cell data in a Sheet.", + "License": "MIT + file LICENSE", + "URL": "https://googlesheets4.tidyverse.org, https://github.com/tidyverse/googlesheets4", + "BugReports": "https://github.com/tidyverse/googlesheets4/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cellranger", + "cli (>= 3.0.0)", + "curl", + "gargle (>= 1.5.0)", + "glue (>= 1.3.0)", + "googledrive (>= 2.1.0)", + "httr", + "ids", + "lifecycle", + "magrittr", + "methods", + "purrr", + "rematch2", + "rlang (>= 1.0.2)", + "tibble (>= 2.1.1)", + "utils", + "vctrs (>= 0.2.3)", + "withr" + ], + "Suggests": [ + "readr", + "rmarkdown", + "spelling", + "testthat (>= 3.1.7)" + ], + "ByteCompile": "true", + "Config/Needs/website": "tidyverse, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Jennifer Bryan [cre, aut] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "gplots": { + "Package": "gplots", + "Version": "3.2.0", + "Source": "Repository", + "Title": "Various R Programming Tools for Plotting Data", + "Description": "Various R programming tools for plotting data, including: - calculating and plotting locally smoothed summary function as ('bandplot', 'wapply'), - enhanced versions of standard plots ('barplot2', 'boxplot2', 'heatmap.2', 'smartlegend'), - manipulating colors ('col2hex', 'colorpanel', 'redgreen', 'greenred', 'bluered', 'redblue', 'rich.colors'), - calculating and plotting two-dimensional data summaries ('ci2d', 'hist2d'), - enhanced regression diagnostic plots ('lmplot2', 'residplot'), - formula-enabled interface to 'stats::lowess' function ('lowess'), - displaying textual data in plots ('textplot', 'sinkplot'), - plotting dots whose size reflects the relative magnitude of the elements ('balloonplot', 'bubbleplot'), - plotting \"Venn\" diagrams ('venn'), - displaying Open-Office style plots ('ooplot'), - plotting multiple data on same region, with separate axes ('overplot'), - plotting means and confidence intervals ('plotCI', 'plotmeans'), - spacing points in an x-y plot so they don't overlap ('space').", + "Depends": [ + "R (>= 3.0)" + ], + "Imports": [ + "gtools", + "stats", + "caTools", + "KernSmooth", + "methods" + ], + "Suggests": [ + "grid", + "MASS", + "knitr", + "rmarkdown", + "r2d2", + "nlme" + ], + "LazyData": "yes", + "VignetteBuilder": "knitr", + "Date": "2024-10-05", + "Authors@R": "c( person(\"Gregory R.\", \"Warnes\", , role = \"aut\"), person(\"Ben\", \"Bolker\", , role = \"aut\"), person(\"Lodewijk\", \"Bonebakker\", , role = \"aut\"), person(\"Robert\", \"Gentleman\", role = \"aut\"), person(\"Wolfgang\", \"Huber\", role = \"aut\"), person(\"Andy\", \"Liaw\", role = \"aut\"), person(\"Thomas\", \"Lumley\", role = \"aut\"), person(\"Martin\", \"Maechler\", role = \"aut\"), person(\"Arni\", \"Magnusson\", role = \"aut\"), person(\"Steffen\", \"Moeller\", role = \"aut\"), person(\"Marc\", \"Schwartz\", role = \"aut\"), person(\"Bill\", \"Venables\", role = \"aut\"), person(\"Tal\", \"Galili\", , \"tal.galili@gmail.com\", c(\"aut\", \"cre\")) )", + "License": "GPL-2", + "URL": "https://github.com/talgalili/gplots, https://talgalili.github.io/gplots/", + "BugReports": "https://github.com/talgalili/gplots/issues", + "NeedsCompilation": "no", + "Author": "Gregory R. 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The 'gtable' package defines a 'gtable' grob class that specifies a grid along with a list of grobs and their placement in the grid. Further the package makes it easy to manipulate and combine 'gtable' objects so that complex compositions can be built up sequentially.", + "License": "MIT + file LICENSE", + "URL": "https://gtable.r-lib.org, https://github.com/r-lib/gtable", + "BugReports": "https://github.com/r-lib/gtable/issues", + "Depends": [ + "R (>= 4.0)" + ], + "Imports": [ + "cli", + "glue", + "grid", + "lifecycle", + "rlang (>= 1.1.0)", + "stats" + ], + "Suggests": [ + "covr", + "ggplot2", + "knitr", + "profvis", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2024-10-25", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" + }, + "gtools": { + "Package": "gtools", + "Version": "3.9.5", + "Source": "Repository", + "Title": "Various R Programming Tools", + "Description": "Functions to assist in R programming, including: - assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse logit transformations ('logit', 'inv.logit'), - test if a value is missing, empty or contains only NA and NULL values ('invalid'), - manipulate R's .Last function ('addLast'), - define macros ('defmacro'), - detect odd and even integers ('odd', 'even'), - convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'), - perform a binary search ('binsearch'), - sort strings containing both numeric and character components ('mixedsort'), - create a factor variable from the quantiles of a continuous variable ('quantcut'), - enumerate permutations and combinations ('combinations', 'permutation'), - calculate and convert between fold-change and log-ratio ('foldchange', 'logratio2foldchange', 'foldchange2logratio'), - calculate probabilities and generate random numbers from Dirichlet distributions ('rdirichlet', 'ddirichlet'), - apply a function over adjacent subsets of a vector ('running'), - modify the TCP_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of data frames, even if the column names don't match ('smartbind'), - generate significance stars from p-values ('stars.pval'), - convert characters to/from ASCII codes ('asc', 'chr'), - convert character vector to ASCII representation ('ASCIIfy'), - apply title capitalization rules to a character vector ('capwords').", + "Authors@R": "c(person(\"Gregory R.\", \"Warnes\", role = \"aut\"), person(\"Ben\", \"Bolker\", role = c(\"aut\", \"cre\"), email = \"bolker@mcmaster.ca\", comment=c(ORCID=\"0000-0002-2127-0443\")), person(\"Thomas\", \"Lumley\", role = \"aut\"), person(\"Arni\", \"Magnusson\", role = \"aut\"), person(\"Bill\", \"Venables\", role = \"aut\"), person(\"Genei\", \"Ryodan\", role = \"aut\"), person(\"Steffen\", \"Moeller\", role = \"aut\"), person(\"Ian\", \"Wilson\", role = \"ctb\"), person(\"Mark\", \"Davis\", role = \"ctb\"), person(\"Nitin\", \"Jain\", role=\"ctb\"), person(\"Scott\", \"Chamberlain\", role = \"ctb\"))", + "License": "GPL-2", + "Depends": [ + "methods", + "stats", + "utils" + ], + "URL": "https://github.com/r-gregmisc/gtools", + "BugReports": "https://github.com/r-gregmisc/gtools/issues", + "Language": "en-US", + "Suggests": [ + "car", + "gplots", + "knitr", + "rstudioapi", + "SGP", + "taxize" + ], + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Gregory R. 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Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).", + "License": "MIT + file LICENSE", + "URL": "https://httr.r-lib.org/, https://github.com/r-lib/httr", + "BugReports": "https://github.com/r-lib/httr/issues", + "Depends": [ + "R (>= 3.5)" + ], + "Imports": [ + "curl (>= 5.0.2)", + "jsonlite", + "mime", + "openssl (>= 0.8)", + "R6" + ], + "Suggests": [ + "covr", + "httpuv", + "jpeg", + "knitr", + "png", + "readr", + "rmarkdown", + "testthat (>= 0.8.0)", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Posit, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "ica": { + "Package": "ica", + "Version": "1.0-3", + "Source": "Repository", + "Type": "Package", + "Title": "Independent Component Analysis", + "Date": "2022-07-08", + "Author": "Nathaniel E. 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W.\", \"Lewis\", role=c(\"aut\",\"cre\",\"cph\"), email=\"blewis@illposed.net\"))", + "Description": "Fast and memory efficient methods for truncated singular value decomposition and principal components analysis of large sparse and dense matrices.", + "Depends": [ + "R (>= 3.6.2)", + "Matrix" + ], + "LinkingTo": [ + "Matrix" + ], + "Imports": [ + "stats", + "methods" + ], + "License": "GPL-3", + "BugReports": "https://github.com/bwlewis/irlba/issues", + "RoxygenNote": "5.0.1", + "NeedsCompilation": "yes", + "Author": "Jim Baglama [aut, cph], Lothar Reichel [aut, cph], B. W. Lewis [aut, cre, cph]", + "Maintainer": "B. W. 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The function rst2pdf() requires rst2pdf (https://github.com/rst2pdf/rst2pdf).", + "Collate": "'block.R' 'cache.R' 'citation.R' 'hooks-html.R' 'plot.R' 'utils.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (, https://yihui.org), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. 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Kamvar [ctb] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "labeling": { + "Package": "labeling", + "Version": "0.4.3", + "Source": "Repository", + "Type": "Package", + "Title": "Axis Labeling", + "Date": "2023-08-29", + "Author": "Justin Talbot,", + "Maintainer": "Nuno Sempere ", + "Description": "Functions which provide a range of axis labeling algorithms.", + "License": "MIT + file LICENSE | Unlimited", + "Collate": "'labeling.R'", + "NeedsCompilation": "no", + "Imports": [ + "stats", + "graphics" + ], + "Repository": "CRAN" + }, + "later": { + "Package": "later", + "Version": "1.4.2", + "Source": "Repository", + "Type": "Package", + "Title": "Utilities for Scheduling Functions to Execute Later with Event Loops", + "Authors@R": "c( person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@posit.co\"), person(\"Joe\", \"Cheng\", role = c(\"aut\"), email = \"joe@posit.co\"), person(\"Charlie\", \"Gao\", role = c(\"aut\"), email = \"charlie.gao@shikokuchuo.net\", comment = c(ORCID = \"0000-0002-0750-061X\")), person(family = \"Posit Software, PBC\", role = \"cph\"), person(\"Marcus\", \"Geelnard\", role = c(\"ctb\", \"cph\"), comment = \"TinyCThread library, https://tinycthread.github.io/\"), person(\"Evan\", \"Nemerson\", role = c(\"ctb\", \"cph\"), comment = \"TinyCThread library, https://tinycthread.github.io/\") )", + "Description": "Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied. The functions are scheduled in an event loop.", + "URL": "https://r-lib.github.io/later/, https://github.com/r-lib/later", + "BugReports": "https://github.com/r-lib/later/issues", + "License": "MIT + file LICENSE", + "Imports": [ + "Rcpp (>= 0.12.9)", + "rlang" + ], + "LinkingTo": [ + "Rcpp" + ], + "RoxygenNote": "7.3.2", + "Suggests": [ + "knitr", + "nanonext", + "R6", + "rmarkdown", + "testthat (>= 2.1.0)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Winston Chang [aut, cre], Joe Cheng [aut], Charlie Gao [aut] (), Posit Software, PBC [cph], Marcus Geelnard [ctb, cph] (TinyCThread library, https://tinycthread.github.io/), Evan Nemerson [ctb, cph] (TinyCThread library, https://tinycthread.github.io/)", + "Maintainer": "Winston Chang ", + "Repository": "CRAN" + }, + "lattice": { + "Package": "lattice", + "Version": "0.22-7", + "Source": "Repository", + "Date": "2025-03-31", + "Priority": "recommended", + "Title": "Trellis Graphics for R", + "Authors@R": "c(person(\"Deepayan\", \"Sarkar\", role = c(\"aut\", \"cre\"), email = \"deepayan.sarkar@r-project.org\", comment = c(ORCID = \"0000-0003-4107-1553\")), person(\"Felix\", \"Andrews\", role = \"ctb\"), person(\"Kevin\", \"Wright\", role = \"ctb\", comment = \"documentation\"), person(\"Neil\", \"Klepeis\", role = \"ctb\"), person(\"Johan\", \"Larsson\", role = \"ctb\", comment = \"miscellaneous improvements\"), person(\"Zhijian (Jason)\", \"Wen\", role = \"cph\", comment = \"filled contour code\"), person(\"Paul\", \"Murrell\", role = \"ctb\", email = \"paul@stat.auckland.ac.nz\"), person(\"Stefan\", \"Eng\", role = \"ctb\", comment = \"violin plot improvements\"), person(\"Achim\", \"Zeileis\", role = \"ctb\", comment = \"modern colors\"), person(\"Alexandre\", \"Courtiol\", role = \"ctb\", comment = \"generics for larrows, lpolygon, lrect and lsegments\") )", + "Description": "A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements. See ?Lattice for an introduction.", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "KernSmooth", + "MASS", + "latticeExtra", + "colorspace" + ], + "Imports": [ + "grid", + "grDevices", + "graphics", + "stats", + "utils" + ], + "Enhances": [ + "chron", + "zoo" + ], + "LazyLoad": "yes", + "LazyData": "yes", + "License": "GPL (>= 2)", + "URL": "https://lattice.r-forge.r-project.org/", + "BugReports": "https://github.com/deepayan/lattice/issues", + "NeedsCompilation": "yes", + "Author": "Deepayan Sarkar [aut, cre] (), Felix Andrews [ctb], Kevin Wright [ctb] (documentation), Neil Klepeis [ctb], Johan Larsson [ctb] (miscellaneous improvements), Zhijian (Jason) Wen [cph] (filled contour code), Paul Murrell [ctb], Stefan Eng [ctb] (violin plot improvements), Achim Zeileis [ctb] (modern colors), Alexandre Courtiol [ctb] (generics for larrows, lpolygon, lrect and lsegments)", + "Maintainer": "Deepayan Sarkar ", + "Repository": "CRAN" + }, + "lazyeval": { + "Package": "lazyeval", + "Version": "0.2.2", + "Source": "Repository", + "Title": "Lazy (Non-Standard) Evaluation", + "Description": "An alternative approach to non-standard evaluation using formulas. Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", ,\"hadley@rstudio.com\", c(\"aut\", \"cre\")), person(\"RStudio\", role = \"cph\") )", + "License": "GPL-3", + "LazyData": "true", + "Depends": [ + "R (>= 3.1.0)" + ], + "Suggests": [ + "knitr", + "rmarkdown (>= 0.2.65)", + "testthat", + "covr" + ], + "VignetteBuilder": "knitr", + "RoxygenNote": "6.1.1", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], RStudio [cph]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "leidenbase": { + "Package": "leidenbase", + "Version": "0.1.35", + "Source": "Repository", + "Type": "Package", + "Title": "R and C/C++ Wrappers to Run the Leiden find_partition() Function", + "Authors@R": "c( person('Brent', 'Ewing', email = 'bge@uw.edu', role = c('aut', 'cre')), person('Vincent', 'Traag', role = 'ctb'), person('Gábor', 'Csárdi', role = 'ctb'), person('Tamás', 'Nepusz', role = 'ctb'), person('Szabolcs', 'Horvat', role = 'ctb'), person('Fabio', 'Zanini', role = 'ctb'))", + "Description": "An R to C/C++ interface that runs the Leiden community detection algorithm to find a basic partition (). It runs the equivalent of the 'leidenalg' find_partition() function, which is given in the 'leidenalg' distribution file 'leiden/src/functions.py'. This package includes the required source code files from the official 'leidenalg' distribution and functions from the R 'igraph' package. The 'leidenalg' distribution is available from and the R 'igraph' package is available from . The Leiden algorithm is described in the article by Traag et al. (2019) . 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The models and their components are represented using S4 classes and methods. 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Krivitsky [ctb] (), Brendan Knapp [ctb] (), Michał Bojanowski [ctb] (), Chad Klumb [ctb]", + "Repository": "RSPM" + }, + "nlme": { + "Package": "nlme", + "Version": "3.1-168", + "Source": "Repository", + "Date": "2025-03-31", + "Priority": "recommended", + "Title": "Linear and Nonlinear Mixed Effects Models", + "Authors@R": "c(person(\"José\", \"Pinheiro\", role = \"aut\", comment = \"S version\"), person(\"Douglas\", \"Bates\", role = \"aut\", comment = \"up to 2007\"), person(\"Saikat\", \"DebRoy\", role = \"ctb\", comment = \"up to 2002\"), person(\"Deepayan\", \"Sarkar\", role = \"ctb\", comment = \"up to 2005\"), person(\"EISPACK authors\", role = \"ctb\", comment = \"src/rs.f\"), person(\"Siem\", \"Heisterkamp\", role = \"ctb\", comment = \"Author fixed sigma\"), person(\"Bert\", \"Van Willigen\",role = \"ctb\", comment = \"Programmer fixed sigma\"), person(\"Johannes\", \"Ranke\", role = \"ctb\", comment = \"varConstProp()\"), person(\"R Core Team\", email = \"R-core@R-project.org\", role = c(\"aut\", \"cre\"), comment = c(ROR = \"02zz1nj61\")))", + "Contact": "see 'MailingList'", + "Description": "Fit and compare Gaussian linear and nonlinear mixed-effects models.", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "graphics", + "stats", + "utils", + "lattice" + ], + "Suggests": [ + "MASS", + "SASmixed" + ], + "LazyData": "yes", + "Encoding": "UTF-8", + "License": "GPL (>= 2)", + "BugReports": "https://bugs.r-project.org", + "MailingList": "R-help@r-project.org", + "URL": "https://svn.r-project.org/R-packages/trunk/nlme/", + "NeedsCompilation": "yes", + "Author": "José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), Johannes Ranke [ctb] (varConstProp()), R Core Team [aut, cre] (02zz1nj61)", + "Maintainer": "R Core Team ", + "Repository": "CRAN" + }, + "nloptr": { + "Package": "nloptr", + "Version": "2.2.1", + "Source": "Repository", + "Type": "Package", + "Title": "R Interface to NLopt", + "Authors@R": "c(person(\"Jelmer\", \"Ypma\", role = \"aut\", email = \"uctpjyy@ucl.ac.uk\"), person(c(\"Steven\", \"G.\"), \"Johnson\", role = \"aut\", comment = \"author of the NLopt C library\"), person(\"Aymeric\", \"Stamm\", role = c(\"ctb\", \"cre\"), email = \"aymeric.stamm@cnrs.fr\", comment = c(ORCID = \"0000-0002-8725-3654\")), person(c(\"Hans\", \"W.\"), \"Borchers\", role = \"ctb\", email = \"hwborchers@googlemail.com\"), person(\"Dirk\", \"Eddelbuettel\", role = \"ctb\", email = \"edd@debian.org\"), person(\"Brian\", \"Ripley\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Kurt\", \"Hornik\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Julien\", \"Chiquet\", role = \"ctb\"), person(\"Avraham\", \"Adler\", role = \"ctb\", email = \"Avraham.Adler@gmail.com\", comment = c(ORCID = \"0000-0002-3039-0703\")), person(\"Xiongtao\", \"Dai\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\", email = \"jeroen@berkeley.edu\"), person(\"Tomas\", \"Kalibera\", role = \"ctb\"), person(\"Mikael\", \"Jagan\", role = \"ctb\"))", + "Description": "Solve optimization problems using an R interface to NLopt. 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Accurate calculations are done using 'Richardson''s' extrapolation or, when applicable, a complex step derivative is available. A simple difference method is also provided. Simple difference is (usually) less accurate but is much quicker than 'Richardson''s' extrapolation and provides a useful cross-check. 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Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.", + "License": "MIT + file LICENSE", + "URL": "https://jeroen.r-universe.dev/openssl", + "BugReports": "https://github.com/jeroen/openssl/issues", + "SystemRequirements": "OpenSSL >= 1.0.2", + "VignetteBuilder": "knitr", + "Imports": [ + "askpass" + ], + "Suggests": [ + "curl", + "testthat (>= 2.1.0)", + "digest", + "knitr", + "rmarkdown", + "jsonlite", + "jose", + "sodium" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (ORCID: ), Oliver Keyes [ctb]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "parallelly": { + "Package": "parallelly", + "Version": "1.45.0", + "Source": "Repository", + "Title": "Enhancing the 'parallel' Package", + "Imports": [ + "parallel", + "tools", + "utils" + ], + "Suggests": [ + "commonmark", + "base64enc" + ], + "VignetteBuilder": "parallelly", + "Authors@R": "c( person(\"Henrik\", \"Bengtsson\", role = c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Mike\", \"Cheng\", role = c(\"ctb\"), email = \"mikefc@coolbutuseless.com\") )", + "Description": "Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.", + "License": "LGPL (>= 2.1)", + "LazyLoad": "TRUE", + "ByteCompile": "TRUE", + "URL": "https://parallelly.futureverse.org, https://github.com/futureverse/parallelly", + "BugReports": "https://github.com/futureverse/parallelly/issues", + "Language": "en-US", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Henrik Bengtsson [aut, cre, cph] (ORCID: ), Mike Cheng [ctb]", + "Maintainer": "Henrik Bengtsson ", + "Repository": "CRAN" + }, + "patchwork": { + "Package": "patchwork", + "Version": "1.3.1", + "Source": "Repository", + "Type": "Package", + "Title": "The Composer of Plots", + "Authors@R": "person(given = \"Thomas Lin\", family = \"Pedersen\", role = c(\"cre\", \"aut\"), email = \"thomasp85@gmail.com\", comment = c(ORCID = \"0000-0002-5147-4711\"))", + "Maintainer": "Thomas Lin Pedersen ", + "Description": "The 'ggplot2' package provides a strong API for sequentially building up a plot, but does not concern itself with composition of multiple plots. 'patchwork' is a package that expands the API to allow for arbitrarily complex composition of plots by, among others, providing mathematical operators for combining multiple plots. Other packages that try to address this need (but with a different approach) are 'gridExtra' and 'cowplot'.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Imports": [ + "ggplot2 (>= 3.0.0)", + "gtable (>= 0.3.6)", + "grid", + "stats", + "grDevices", + "utils", + "graphics", + "rlang (>= 1.0.0)", + "cli", + "farver" + ], + "RoxygenNote": "7.3.2", + "URL": "https://patchwork.data-imaginist.com, https://github.com/thomasp85/patchwork", + "BugReports": "https://github.com/thomasp85/patchwork/issues", + "Suggests": [ + "knitr", + "rmarkdown", + "gridGraphics", + "gridExtra", + "ragg", + "testthat (>= 2.1.0)", + "vdiffr", + "covr", + "png", + "gt (>= 0.11.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "gifski", + "NeedsCompilation": "no", + "Author": "Thomas Lin Pedersen [cre, aut] (ORCID: )", + "Repository": "CRAN" + }, + "pbapply": { + "Package": "pbapply", + "Version": "1.7-2", + "Source": "Repository", + "Type": "Package", + "Title": "Adding Progress Bar to '*apply' Functions", + "Date": "2023-06-27", + "Authors@R": "c(person(given = \"Peter\", family = \"Solymos\", comment = c(ORCID = \"0000-0001-7337-1740\"), role = c(\"aut\", \"cre\"), email = \"psolymos@gmail.com\"), person(given = \"Zygmunt\", family = \"Zawadzki\", role = \"aut\", email = \"zygmunt@zstat.pl\"), person(given = \"Henrik\", family = \"Bengtsson\", role = \"ctb\", email = \"henrikb@braju.com\"), person(\"R Core Team\", role = c(\"cph\", \"ctb\")))", + "Maintainer": "Peter Solymos ", + "Description": "A lightweight package that adds progress bar to vectorized R functions ('*apply'). The implementation can easily be added to functions where showing the progress is useful (e.g. bootstrap). The type and style of the progress bar (with percentages or remaining time) can be set through options. Supports several parallel processing backends including future.", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ + "parallel" + ], + "Suggests": [ + "shiny", + "future", + "future.apply" + ], + "License": "GPL (>= 2)", + "URL": "https://github.com/psolymos/pbapply", + "BugReports": "https://github.com/psolymos/pbapply/issues", + "NeedsCompilation": "no", + "Author": "Peter Solymos [aut, cre] (), Zygmunt Zawadzki [aut], Henrik Bengtsson [ctb], R Core Team [cph, ctb]", + "Repository": "CRAN" + }, + "pbkrtest": { + "Package": "pbkrtest", + "Version": "0.5.4", + "Source": "Repository", + "Title": "Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models", + "Authors@R": "c( person(given = \"Ulrich\", family = \"Halekoh\", email = \"uhalekoh@health.sdu.dk\", role = c(\"aut\", \"cph\")), person(given = \"Søren\", family = \"Højsgaard\", email = \"sorenh@math.aau.dk\", role = c(\"aut\", \"cre\", \"cph\")) )", + "Maintainer": "Søren Højsgaard ", + "Description": "Computes p-values based on (a) Satterthwaite or Kenward-Rogers degree of freedom methods and (b) parametric bootstrap for mixed effects models as implemented in the 'lme4' package. Implements parametric bootstrap test for generalized linear mixed models as implemented in 'lme4' and generalized linear models. The package is documented in the paper by Halekoh and Højsgaard, (2012, ). 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and created by Yann Collet; the 'lz4' library created and owned by Yann Collet; xxHash library created and owned by Yann Collet; and code derived from the 'Blosc' library created and owned by Francesc Alted.", + "URL": "https://github.com/qsbase/qs", + "BugReports": "https://github.com/qsbase/qs/issues", + "NeedsCompilation": "yes", + "Author": "Travers Ching [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd, lz4 and xxHash code), Facebook, Inc. 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Portfolio selection methods based on expected shortfall risk are also now included. See Koenker, R. (2005) Quantile Regression, Cambridge U. Press, and Koenker, R. et al. (2017) Handbook of Quantile Regression, CRC Press, .", + "Authors@R": "c( person(\"Roger\", \"Koenker\", role = c(\"cre\",\"aut\"), email = \"rkoenker@illinois.edu\"), person(\"Stephen\", \"Portnoy\", role = c(\"ctb\"), comment = \"Contributions to Censored QR code\", email = \"sportnoy@illinois.edu\"), person(c(\"Pin\", \"Tian\"), \"Ng\", role = c(\"ctb\"), comment = \"Contributions to Sparse QR code\", email = \"pin.ng@nau.edu\"), person(\"Blaise\", \"Melly\", role = c(\"ctb\"), comment = \"Contributions to preprocessing code\", email = \"mellyblaise@gmail.com\"), person(\"Achim\", \"Zeileis\", role = c(\"ctb\"), comment = \"Contributions to dynrq code essentially identical to his dynlm code\", email = \"Achim.Zeileis@uibk.ac.at\"), person(\"Philip\", \"Grosjean\", role = c(\"ctb\"), comment = \"Contributions to nlrq code\", email = \"phgrosjean@sciviews.org\"), person(\"Cleve\", \"Moler\", role = c(\"ctb\"), comment = \"author of several linpack routines\"), person(\"Yousef\", \"Saad\", role = c(\"ctb\"), comment = \"author of sparskit2\"), person(\"Victor\", \"Chernozhukov\", role = c(\"ctb\"), comment = \"contributions to extreme value inference code\"), person(\"Ivan\", \"Fernandez-Val\", role = c(\"ctb\"), comment = \"contributions to extreme value inference code\"), person(\"Martin\", \"Maechler\", role = \"ctb\", comment = c(\"tweaks (src/chlfct.f, 'tiny','Large')\", ORCID = \"0000-0002-8685-9910\")), person(c(\"Brian\", \"D\"), \"Ripley\", role = c(\"trl\",\"ctb\"), comment = \"Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice\", email = \"ripley@stats.ox.ac.uk\"))", + "Maintainer": "Roger Koenker ", + "Repository": "CRAN", + "Depends": [ + "R (>= 3.5)", + "stats", + "SparseM" + ], + "Imports": [ + "methods", + "graphics", + "Matrix", + "MatrixModels", + "survival", + "MASS" + ], + "Suggests": [ + "interp", + "rgl", + "logspline", + "nor1mix", + "Formula", + "zoo", + "R.rsp", + "conquer" + ], + "License": "GPL (>= 2)", + "URL": "https://www.r-project.org", + "NeedsCompilation": "yes", + "VignetteBuilder": "R.rsp", + "Author": "Roger Koenker [cre, aut], Stephen Portnoy [ctb] (Contributions to Censored QR code), Pin Tian Ng [ctb] (Contributions to Sparse QR code), Blaise Melly [ctb] (Contributions to preprocessing code), Achim Zeileis [ctb] (Contributions to dynrq code essentially identical to his dynlm code), Philip Grosjean [ctb] (Contributions to nlrq code), Cleve Moler [ctb] (author of several linpack routines), Yousef Saad [ctb] (author of sparskit2), Victor Chernozhukov [ctb] (contributions to extreme value inference code), Ivan Fernandez-Val [ctb] (contributions to extreme value inference code), Martin Maechler [ctb] (tweaks (src/chlfct.f, 'tiny','Large'), ), Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice)" + }, + "ragg": { + "Package": "ragg", + "Version": "1.4.0", + "Source": "Repository", + "Type": "Package", + "Title": "Graphic Devices Based on AGG", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Maxim\", \"Shemanarev\", role = c(\"aut\", \"cph\"), comment = \"Author of AGG\"), person(\"Tony\", \"Juricic\", , \"tonygeek@yahoo.com\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Milan\", \"Marusinec\", , \"milan@marusinec.sk\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Spencer\", \"Garrett\", role = \"ctb\", comment = \"Contributor to AGG\"), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Maintainer": "Thomas Lin Pedersen ", + "Description": "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D drawing library. The 'ragg' package provides a set of graphic devices based on AGG to use as alternative to the raster devices provided through the 'grDevices' package.", + "License": "MIT + file LICENSE", + "URL": "https://ragg.r-lib.org, https://github.com/r-lib/ragg", + "BugReports": "https://github.com/r-lib/ragg/issues", + "Imports": [ + "systemfonts (>= 1.0.3)", + "textshaping (>= 0.3.0)" + ], + "Suggests": [ + "covr", + "graphics", + "grid", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "systemfonts", + "textshaping" + ], + "Config/Needs/website": "ggplot2, devoid, magick, bench, tidyr, ggridges, hexbin, sessioninfo, pkgdown, tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "freetype2, libpng, libtiff, libjpeg", + "Config/testthat/edition": "3", + "Config/build/compilation-database": "true", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (), Maxim Shemanarev [aut, cph] (Author of AGG), Tony Juricic [ctb, cph] (Contributor to AGG), Milan Marusinec [ctb, cph] (Contributor to AGG), Spencer Garrett [ctb] (Contributor to AGG), Posit, PBC [cph, fnd]", + "Repository": "CRAN" + }, + "rappdirs": { + "Package": "rappdirs", + "Version": "0.3.3", + "Source": "Repository", + "Type": "Package", + "Title": "Application Directories: Determine Where to Save Data, Caches, and Logs", + "Authors@R": "c(person(given = \"Hadley\", family = \"Wickham\", role = c(\"trl\", \"cre\", \"cph\"), email = \"hadley@rstudio.com\"), person(given = \"RStudio\", role = \"cph\"), person(given = \"Sridhar\", family = \"Ratnakumar\", role = \"aut\"), person(given = \"Trent\", family = \"Mick\", role = \"aut\"), person(given = \"ActiveState\", role = \"cph\", comment = \"R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs\"), person(given = \"Eddy\", family = \"Petrisor\", role = \"ctb\"), person(given = \"Trevor\", family = \"Davis\", role = c(\"trl\", \"aut\")), person(given = \"Gabor\", family = \"Csardi\", role = \"ctb\"), person(given = \"Gregory\", family = \"Jefferis\", role = \"ctb\"))", + "Description": "An easy way to determine which directories on the users computer you should use to save data, caches and logs. A port of Python's 'Appdirs' () to R.", + "License": "MIT + file LICENSE", + "URL": "https://rappdirs.r-lib.org, https://github.com/r-lib/rappdirs", + "BugReports": "https://github.com/r-lib/rappdirs/issues", + "Depends": [ + "R (>= 3.2)" + ], + "Suggests": [ + "roxygen2", + "testthat (>= 3.0.0)", + "covr", + "withr" + ], + "Copyright": "Original python appdirs module copyright (c) 2010 ActiveState Software Inc. R port copyright Hadley Wickham, RStudio. 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Convert between bibliography formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and 'Bibentry'. Includes a port of the 'bibutils' utilities by Chris Putnam . Supports all bibliography formats and character encodings implemented in 'bibutils'.", + "License": "GPL-2", + "URL": "https://geobosh.github.io/rbibutils/ (doc), https://github.com/GeoBosh/rbibutils (devel)", + "BugReports": "https://github.com/GeoBosh/rbibutils/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Imports": [ + "utils", + "tools" + ], + "Suggests": [ + "testthat" + ], + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Config/Needs/memcheck": "devtools, rcmdcheck", + "Author": "Georgi N. 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Boshnakov ", + "Repository": "RSPM" + }, + "readr": { + "Package": "readr", + "Version": "2.1.5", + "Source": "Repository", + "Title": "Read Rectangular Text Data", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Romain\", \"Francois\", role = \"ctb\"), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = c(\"ctb\", \"cph\"), comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = c(\"ctb\", \"cph\"), comment = \"grisu3 implementation\") )", + "Description": "The goal of 'readr' is to provide a fast and friendly way to read rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.", + "License": "MIT + file LICENSE", + "URL": "https://readr.tidyverse.org, https://github.com/tidyverse/readr", + "BugReports": "https://github.com/tidyverse/readr/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.2.0)", + "clipr", + "crayon", + "hms (>= 0.4.1)", + "lifecycle (>= 0.2.0)", + "methods", + "R6", + "rlang", + "tibble", + "utils", + "vroom (>= 1.6.0)" + ], + "Suggests": [ + "covr", + "curl", + "datasets", + "knitr", + "rmarkdown", + "spelling", + "stringi", + "testthat (>= 3.2.0)", + "tzdb (>= 0.1.1)", + "waldo", + "withr", + "xml2" + ], + "LinkingTo": [ + "cpp11", + "tzdb (>= 0.1.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "false", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Jim Hester [aut], Romain Francois [ctb], Jennifer Bryan [aut, cre] (), Shelby Bearrows [ctb], Posit Software, PBC [cph, fnd], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [ctb, cph] (grisu3 implementation), Mikkel Jørgensen [ctb, cph] (grisu3 implementation)", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "readxl": { + "Package": "readxl", + "Version": "1.4.5", + "Source": "Repository", + "Title": "Read Excel Files", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = \"Copyright holder of all R code and all C/C++ code without explicit copyright attribution\"), person(\"Marcin\", \"Kalicinski\", role = c(\"ctb\", \"cph\"), comment = \"Author of included RapidXML code\"), person(\"Komarov Valery\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Christophe Leitienne\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Bob Colbert\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"David Hoerl\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Evan Miller\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\") )", + "Description": "Import excel files into R. 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authors listed in inst/www/shared/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/www/shared/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Prem Nawaz Khan [ctb] (Bootstrap accessibility plugin), Victor Tsaran [ctb] (Bootstrap accessibility plugin), Dennis Lembree [ctb] (Bootstrap accessibility plugin), Srinivasu Chakravarthula [ctb] (Bootstrap accessibility plugin), Cathy O'Connor [ctb] (Bootstrap accessibility plugin), PayPal, Inc [cph] (Bootstrap accessibility plugin), Stefan Petre [ctb, cph] (Bootstrap-datepicker library), Andrew Rowls [ctb, cph] (Bootstrap-datepicker library), Brian Reavis [ctb, cph] (selectize.js library), Salmen Bejaoui [ctb, cph] (selectize-plugin-a11y library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library), SpryMedia Limited [ctb, cph] (DataTables library), John Fraser [ctb, cph] (showdown.js library), John Gruber [ctb, cph] (showdown.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), R Core Team [ctb, cph] (tar implementation from R)", + "Maintainer": "Winston Chang ", + "Repository": "RSPM" + }, + "sitmo": { + "Package": "sitmo", + "Version": "2.0.2", + "Source": "Repository", + "Title": "Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header Files", + "Authors@R": "c(person(\"James\", \"Balamuta\", email = \"balamut2@illinois.edu\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0003-2826-8458\")), person(\"Thijs\",\"van den Berg\", email = \"thijs@sitmo.com\", role = c(\"aut\", \"cph\")), person(\"Ralf\", \"Stubner\", email = \"ralf.stubner@daqana.com\", role = c(\"ctb\")))", + "Description": "Provided within are two high quality and fast PPRNGs that may be used in an 'OpenMP' parallel environment. 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person(\"Neba\", \"Funwi-Gabga\", role=\"ctb\"), person(\"DJ\", \"Gerrard\", role=\"ctb\"), person(\"Andy\", \"Green\", role=\"ctb\"), person(\"Tim\", \"Griffin\", role=\"ctb\"), person(\"Ute\", \"Hahn\", role=\"ctb\"), person(\"RD\", \"Harkness\", role=\"ctb\"), person(\"Arthur\", \"Hickman\", role=\"ctb\"), person(\"Stephen\", \"Hubbell\", role=\"ctb\"), person(\"Austin\", \"Hughes\", role=\"ctb\"), person(\"Jonathan\", \"Huntington\", role=\"ctb\"), person(\"MJ\", \"Hutchings\", role=\"ctb\"), person(\"Jackie\", \"Inwald\", role=\"ctb\"), person(\"Valerie\", \"Isham\", role=\"ctb\"), person(\"Aruna\", \"Jammalamadaka\", role=\"ctb\"), person(\"Carl\", \"Knox-Robinson\", role=\"ctb\"), person(\"Mahdieh\", \"Khanmohammadi\", role=\"ctb\"), person(\"Tero\", \"Kokkila\", role=\"ctb\"), person(\"Bas\", \"Kooijman\", role=\"ctb\"), person(\"Kenneth\", \"Kosik\", role=\"ctb\"), person(\"Peter\", \"Kovesi\", role=\"ctb\"), person(\"Lily\", \"Kozmian-Ledward\", role=\"ctb\"), person(\"Robert\", \"Lamb\", role=\"ctb\"), person(\"NA\", \"Laskurain\", role=\"ctb\"), person(\"George\", \"Leser\", role=\"ctb\"), person(\"Marie-Colette\", \"van Lieshout\", role=\"ctb\"), person(\"AF\", \"Mark\", role=\"ctb\"), person(\"Sebastian\", \"Meyer\", role=\"ctb\"), person(\"Jorge\", \"Mateu\", role=\"ctb\"), person(\"Annikki\", \"Makela\", role=\"ctb\"), person(\"Enrique\", \"Miranda\", role=\"ctb\"), person(\"Nicoletta\", \"Nava\", role=\"ctb\"), person(\"M\", \"Numata\", role=\"ctb\"), person(\"Matti\", \"Nummelin\", role=\"ctb\"), person(\"Jens Randel\", \"Nyengaard\", role=\"ctb\"), person(\"Yosihiko\", \"Ogata\", role=\"ctb\"), person(\"Si\", \"Palmer\", role=\"ctb\"), person(\"Antti\", \"Penttinen\", role=\"ctb\"), person(\"Sandra\", \"Pereira\", role=\"ctb\"), person(\"Nicolas\", \"Picard\", role=\"ctb\"), person(\"William\", \"Platt\", role=\"ctb\"), person(\"Stephen\", \"Rathbun\", role=\"ctb\"), person(\"Brian\", \"Ripley\", role=\"ctb\"), person(\"Roger\", \"Sainsbury\", role=\"ctb\"), person(\"Dietrich\", \"Stoyan\", role=\"ctb\"), person(\"David\", \"Strauss\", role=\"ctb\"), person(\"L\", \"Strand\", role=\"ctb\"), person(\"Masaharu\", \"Tanemura\", role=\"ctb\"), person(\"Graham\", \"Upton\", role=\"ctb\"), person(\"Bill\", \"Venables\", role=\"ctb\"), person(\"Ulrich\", \"Vogel\", role=\"ctb\"), person(\"Sasha\", \"Voss\", role=\"ctb\"), person(\"Rasmus\", \"Waagepetersen\", role=\"ctb\"), person(\"Keith\", \"Watkins\", role=\"ctb\"), person(\"H\", \"Wendrock\", role=\"ctb\") )", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "spatstat.utils (>= 3.1-2)", + "Matrix" + ], + "Suggests": [ + "spatstat.geom", + "spatstat.random", + "spatstat.explore", + "spatstat.model", + "spatstat.linnet" + ], + "Description": "Contains all the datasets for the 'spatstat' family of packages.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "LazyData": "true", + "NeedsCompilation": "no", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.data/issues", + "Author": "Adrian Baddeley [aut, cre] (), Rolf Turner [aut] (), Ege Rubak [aut] (), W Aherne [ctb], Freda Alexander [ctb], Qi Wei Ang [ctb], Sourav Banerjee [ctb], Mark Berman [ctb], R Bernhardt [ctb], Thomas Berndtsen [ctb], Andrew Bevan [ctb], Jeffrey Betts [ctb], Ray Cartwright [ctb], Lucia Cobo Sanchez [ctb], Richard Condit [ctb], Francis Crick [ctb], Marcelino de la Cruz Rot [ctb], Jack Cuzick [ctb], Tilman Davies [ctb], Peter Diggle [ctb], Michael Drinkwater [ctb], Stephen Eglen [ctb], Robert Edwards [ctb], Johannes Elias [ctb], AE Esler [ctb], Gregory Evans [ctb], Bernard Fingleton [ctb], Olivier Flores [ctb], David Ford [ctb], Robin Foster [ctb], Janet Franklin [ctb], Neba Funwi-Gabga [ctb], DJ Gerrard [ctb], Andy Green [ctb], Tim Griffin [ctb], Ute Hahn [ctb], RD Harkness [ctb], Arthur Hickman [ctb], Stephen Hubbell [ctb], Austin Hughes [ctb], Jonathan Huntington [ctb], MJ Hutchings [ctb], Jackie Inwald [ctb], Valerie Isham [ctb], Aruna Jammalamadaka [ctb], Carl Knox-Robinson [ctb], Mahdieh Khanmohammadi [ctb], Tero Kokkila [ctb], Bas Kooijman [ctb], Kenneth Kosik [ctb], Peter Kovesi [ctb], Lily Kozmian-Ledward [ctb], Robert Lamb [ctb], NA Laskurain [ctb], George Leser [ctb], Marie-Colette van Lieshout [ctb], AF Mark [ctb], Sebastian Meyer [ctb], Jorge Mateu [ctb], Annikki Makela [ctb], Enrique Miranda [ctb], Nicoletta Nava [ctb], M Numata [ctb], Matti Nummelin [ctb], Jens Randel Nyengaard [ctb], Yosihiko Ogata [ctb], Si Palmer [ctb], Antti Penttinen [ctb], Sandra Pereira [ctb], Nicolas Picard [ctb], William Platt [ctb], Stephen Rathbun [ctb], Brian Ripley [ctb], Roger Sainsbury [ctb], Dietrich Stoyan [ctb], David Strauss [ctb], L Strand [ctb], Masaharu Tanemura [ctb], Graham Upton [ctb], Bill Venables [ctb], Ulrich Vogel [ctb], Sasha Voss [ctb], Rasmus Waagepetersen [ctb], Keith Watkins [ctb], H Wendrock [ctb]", + "Repository": "CRAN" + }, + "spatstat.explore": { + "Package": "spatstat.explore", + "Version": "3.4-3", + "Source": "Repository", + "Date": "2025-05-21", + "Title": "Exploratory Data Analysis for the 'spatstat' Family", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Kasper\", \"Klitgaard Berthelsen\", role = \"ctb\"), person(\"Warick\", \"Brown\", role = \"cph\"), person(\"Achmad\", \"Choiruddin\", role = \"ctb\"), person(\"Ya-Mei\", \"Chang\", role = \"ctb\"), person(\"Jean-Francois\", \"Coeurjolly\", role = \"ctb\"), person(\"Ottmar\", \"Cronie\", role = \"ctb\"), person(\"Tilman\", \"Davies\", role = c(\"ctb\", \"cph\")), person(\"Julian\", \"Gilbey\", role = \"ctb\"), person(\"Jonatan\", \"Gonzalez\", role = \"ctb\"), person(\"Yongtao\", \"Guan\", role = \"ctb\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Martin\", \"Hazelton\", role = \"ctb\"), person(\"Kassel\", \"Hingee\", role = c(\"ctb\", \"cph\")), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Frederic\", \"Lavancier\", role = \"ctb\"), person(\"Marie-Colette\", \"van Lieshout\", role = c(\"ctb\", \"cph\")), person(\"Greg\", \"McSwiggan\", role = \"ctb\"), person(\"Robin K\", \"Milne\", role = \"cph\"), person(\"Tuomas\", \"Rajala\", role = \"ctb\"), person(\"Suman\", \"Rakshit\", role = c(\"ctb\", \"cph\")), person(\"Dominic\", \"Schuhmacher\", role = \"ctb\"), person(\"Rasmus\", \"Plenge Waagepetersen\", role = \"ctb\"), person(\"Hangsheng\", \"Wang\", role = \"ctb\"), person(\"Tingting\", \"Zhan\", role=\"ctb\"))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "spatstat.data (>= 3.1-2)", + "spatstat.univar (>= 3.1-2)", + "spatstat.geom (>= 3.3-6)", + "spatstat.random (>= 3.3-2)", + "stats", + "graphics", + "grDevices", + "utils", + "methods", + "nlme" + ], + "Imports": [ + "spatstat.utils (>= 3.1-0)", + "spatstat.sparse (>= 3.1-0)", + "goftest (>= 1.2-2)", + "Matrix", + "abind" + ], + "Suggests": [ + "sm", + "gsl", + "locfit", + "spatial", + "fftwtools (>= 0.9-8)", + "spatstat.linnet (>= 3.2-1)", + "spatstat.model (>= 3.3-1)", + "spatstat (>= 3.1-1)" + ], + "Description": "Functionality for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.explore/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Kasper Klitgaard Berthelsen [ctb], Warick Brown [cph], Achmad Choiruddin [ctb], Ya-Mei Chang [ctb], Jean-Francois Coeurjolly [ctb], Ottmar Cronie [ctb], Tilman Davies [ctb, cph], Julian Gilbey [ctb], Jonatan Gonzalez [ctb], Yongtao Guan [ctb], Ute Hahn [ctb], Martin Hazelton [ctb], Kassel Hingee [ctb, cph], Abdollah Jalilian [ctb], Frederic Lavancier [ctb], Marie-Colette van Lieshout [ctb, cph], Greg McSwiggan [ctb], Robin K Milne [cph], Tuomas Rajala [ctb], Suman Rakshit [ctb, cph], Dominic Schuhmacher [ctb], Rasmus Plenge Waagepetersen [ctb], Hangsheng Wang [ctb], Tingting Zhan [ctb]", + "Repository": "CRAN" + }, + "spatstat.geom": { + "Package": "spatstat.geom", + "Version": "3.4-1", + "Source": "Repository", + "Date": "2025-05-20", + "Title": "Geometrical Functionality of the 'spatstat' Family", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Warick\", \"Brown\" , role = \"ctb\"), person(\"Tilman\", \"Davies\", role = \"ctb\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Martin\", \"Hazelton\", role = \"ctb\"), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Greg\", \"McSwiggan\", role = c(\"ctb\", \"cph\")), person(\"Sebastian\", \"Meyer\", role = c(\"ctb\", \"cph\")), person(\"Jens\", \"Oehlschlaegel\", role = c(\"ctb\", \"cph\")), person(\"Suman\", \"Rakshit\", role = \"ctb\"), person(\"Dominic\", \"Schuhmacher\", role = \"ctb\"), person(\"Rasmus\", \"Waagepetersen\", role = \"ctb\"))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "spatstat.data (>= 3.1)", + "spatstat.univar (>= 3.1)", + "stats", + "graphics", + "grDevices", + "utils", + "methods" + ], + "Imports": [ + "spatstat.utils (>= 3.1-4)", + "deldir (>= 1.0-2)", + "polyclip (>= 1.10)" + ], + "Suggests": [ + "spatstat.random (>= 3.3)", + "spatstat.explore (>= 3.3)", + "spatstat.model (>= 3.3)", + "spatstat.linnet (>= 3.2)", + "spatial", + "fftwtools (>= 0.9-8)", + "spatstat (>= 3.3)" + ], + "Description": "Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.geom/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Warick Brown [ctb], Tilman Davies [ctb], Ute Hahn [ctb], Martin Hazelton [ctb], Abdollah Jalilian [ctb], Greg McSwiggan [ctb, cph], Sebastian Meyer [ctb, cph], Jens Oehlschlaegel [ctb, cph], Suman Rakshit [ctb], Dominic Schuhmacher [ctb], Rasmus Waagepetersen [ctb]", + "Repository": "CRAN" + }, + "spatstat.random": { + "Package": "spatstat.random", + "Version": "3.4-1", + "Source": "Repository", + "Date": "2025-05-20", + "Title": "Random Generation Functionality for the 'spatstat' Family", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Tilman\", \"Davies\", role = c(\"aut\", \"cph\"), comment=c(ORCID=\"0000-0003-0565-1825\")), person(\"Kasper\", \"Klitgaard Berthelsen\", role = c(\"ctb\", \"cph\")), person(\"David\", \"Bryant\", role = c(\"ctb\", \"cph\")), person(\"Ya-Mei\", \"Chang\", role = c(\"ctb\", \"cph\"), email = \"yamei628@gmail.com\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Dominic\", \"Schuhmacher\", role = c(\"ctb\", \"cph\")), person(\"Rasmus\", \"Plenge Waagepetersen\", role = c(\"ctb\", \"cph\")))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "spatstat.data (>= 3.1)", + "spatstat.univar (>= 3.1)", + "spatstat.geom (>= 3.3-6)", + "stats", + "utils", + "methods", + "grDevices" + ], + "Imports": [ + "spatstat.utils (>= 3.1-4)" + ], + "Suggests": [ + "spatial", + "spatstat.linnet (>= 3.2)", + "spatstat.explore", + "spatstat.model", + "spatstat (>= 3.3)", + "gsl" + ], + "Description": "Functionality for random generation of spatial data in the 'spatstat' family of packages. Generates random spatial patterns of points according to many simple rules (complete spatial randomness, Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns (thinning, random shift, jittering), simulated realisations of random point processes including simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes (using direct, Brix-Kendall, or hybrid algorithms), log-Gaussian Cox processes, product shot noise cluster processes and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs sampler, or coupling-from-the-past perfect simulation). Also generates random spatial patterns of line segments, random tessellations, and random images (random noise, random mosaics). Excludes random generation on a linear network, which is covered by the separate package 'spatstat.linnet'.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.random/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Tilman Davies [aut, cph] (ORCID: ), Kasper Klitgaard Berthelsen [ctb, cph], David Bryant [ctb, cph], Ya-Mei Chang [ctb, cph], Ute Hahn [ctb], Abdollah Jalilian [ctb], Dominic Schuhmacher [ctb, cph], Rasmus Plenge Waagepetersen [ctb, cph]", + "Repository": "CRAN" + }, + "spatstat.sparse": { + "Package": "spatstat.sparse", + "Version": "3.1-0", + "Source": "Repository", + "Date": "2024-06-21", + "Title": "Sparse Three-Dimensional Arrays and Linear Algebra Utilities", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "stats", + "utils", + "methods", + "Matrix", + "abind", + "tensor" + ], + "Imports": [ + "spatstat.utils (>= 3.0-5)" + ], + "Description": "Defines sparse three-dimensional arrays and supports standard operations on them. The package also includes utility functions for matrix calculations that are common in statistics, such as quadratic forms.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.sparse/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (), Rolf Turner [aut, cph] (), Ege Rubak [aut, cph] ()", + "Repository": "CRAN" + }, + "spatstat.univar": { + "Package": "spatstat.univar", + "Version": "3.1-4", + "Source": "Repository", + "Date": "2025-07-13", + "Title": "One-Dimensional Probability Distribution Support for the 'spatstat' Family", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(c(\"Tilman\", \"M.\"), \"Davies\", role = c(\"aut\", \"ctb\", \"cph\"), email = \"Tilman.Davies@otago.ac.nz\", comment = c(ORCID=\"0000-0003-0565-1825\")), person(c(\"Martin\", \"L.\"), \"Hazelton\", role = c(\"aut\", \"ctb\", \"cph\"), email = \"Martin.Hazelton@otago.ac.nz\", comment = c(ORCID=\"0000-0001-7831-725X\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Greg\", \"McSwiggan\", role = c(\"ctb\", \"cph\")))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "stats" + ], + "Imports": [ + "spatstat.utils (>= 3.1-2)", + "graphics" + ], + "Description": "Estimation of one-dimensional probability distributions including kernel density estimation, weighted empirical cumulative distribution functions, Kaplan-Meier and reduced-sample estimators for right-censored data, heat kernels, kernel properties, quantiles and integration.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.univar/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Tilman M. Davies [aut, ctb, cph] (ORCID: ), Martin L. Hazelton [aut, ctb, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Greg McSwiggan [ctb, cph]", + "Repository": "CRAN" + }, + "spatstat.utils": { + "Package": "spatstat.utils", + "Version": "3.1-4", + "Source": "Repository", + "Date": "2025-05-15", + "Title": "Utility Functions for 'spatstat'", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = \"aut\", email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = \"aut\", email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "stats", + "graphics", + "grDevices", + "utils", + "methods" + ], + "Suggests": [ + "spatstat.model" + ], + "Description": "Contains utility functions for the 'spatstat' family of packages which may also be useful for other purposes.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.utils/issues", + "Author": "Adrian Baddeley [aut, cre] (ORCID: ), Rolf Turner [aut] (ORCID: ), Ege Rubak [aut] (ORCID: )", + "Repository": "CRAN" + }, + "statnet.common": { + "Package": "statnet.common", + "Version": "4.12.0", + "Source": "Repository", + "Date": "2025-05-30", + "Title": "Common R Scripts and Utilities Used by the Statnet Project Software", + "Authors@R": "c( person(c(\"Pavel\", \"N.\"), \"Krivitsky\", role=c(\"aut\",\"cre\"), email=\"pavel@statnet.org\", comment=c(ORCID=\"0000-0002-9101-3362\", affiliation=\"University of New South Wales\")), person(\"Skye\", \"Bender-deMoll\", role=c(\"ctb\"), email=\"skyebend@uw.edu\"), person(\"Chad\", \"Klumb\", role=c(\"ctb\"), email=\"cklumb@gmail.com\", comment=c(affiliation=\"University of Washington\")), person(\"Michał\", \"Bojanowski\", role=c(\"ctb\"), email=\"michal2992@gmail.com\", comment=c(ORCID=\"0000-0001-7503-852X\")))", + "Description": "Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "utils", + "methods", + "coda", + "parallel", + "tools", + "Matrix" + ], + "BugReports": "https://github.com/statnet/statnet.common/issues", + "License": "GPL-3 + file LICENSE", + "URL": "https://statnet.org", + "RoxygenNote": "7.3.2.9000", + "Encoding": "UTF-8", + "Suggests": [ + "covr", + "roxygen2", + "rlang (>= 1.1.1)", + "purrr", + "MASS" + ], + "NeedsCompilation": "yes", + "Author": "Pavel N. Krivitsky [aut, cre] (ORCID: , affiliation: University of New South Wales), Skye Bender-deMoll [ctb], Chad Klumb [ctb] (affiliation: University of Washington), Michał Bojanowski [ctb] (ORCID: )", + "Maintainer": "Pavel N. 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It makes it easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.", + "License": "MIT + file LICENSE", + "URL": "https://tidyselect.r-lib.org, https://github.com/r-lib/tidyselect", + "BugReports": "https://github.com/r-lib/tidyselect/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "cli (>= 3.3.0)", + "glue (>= 1.3.0)", + "lifecycle (>= 1.0.3)", + "rlang (>= 1.0.4)", + "vctrs (>= 0.5.2)", + "withr" + ], + "Suggests": [ + "covr", + "crayon", + "dplyr", + "knitr", + "magrittr", + "rmarkdown", + "stringr", + "testthat (>= 3.1.1)", + "tibble (>= 2.1.3)" + ], + "VignetteBuilder": "knitr", + "ByteCompile": "true", + "Config/testthat/edition": "3", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.0.9000", + "NeedsCompilation": "yes", + "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" + }, + "tidyverse": { + "Package": "tidyverse", + "Version": "2.0.0", + "Source": "Repository", + "Title": "Easily Install and Load the 'Tidyverse'", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = c(\"aut\", \"cre\")), person(\"RStudio\", role = c(\"cph\", \"fnd\")) )", + "Description": "The 'tidyverse' is a set of packages that work in harmony because they share common data representations and 'API' design. 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This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.", + "Imports": [ + "xfun (>= 0.48)" + ], + "Suggests": [ + "testit", + "rstudioapi" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/rstudio/tinytex", + "BugReports": "https://github.com/rstudio/tinytex/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre, cph] (), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (), Devon Ryan [ctb] (), Ethan Heinzen [ctb], Fernando Cagua [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "tzdb": { + "Package": "tzdb", + "Version": "0.5.0", + "Source": "Repository", + "Title": "Time Zone Database Information", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Howard\", \"Hinnant\", role = \"cph\", comment = \"Author of the included date library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the 'date' library. 'date' provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. Headers are provided for calendar specific calculations, along with a limited interface for time zone manipulations.", + "License": "MIT + file LICENSE", + "URL": "https://tzdb.r-lib.org, https://github.com/r-lib/tzdb", + "BugReports": "https://github.com/r-lib/tzdb/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.5.2)" + ], + "Biarch": "yes", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Davis Vaughan [aut, cre], Howard Hinnant [cph] (Author of the included date library), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.6", + "Source": "Repository", + "Title": "Unicode Text Processing", + "Authors@R": "c(person(given = c(\"Patrick\", \"O.\"), family = \"Perry\", role = c(\"aut\", \"cph\")), person(given = \"Kirill\", family = \"M\\u00fcller\", role = \"cre\", email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(given = \"Unicode, Inc.\", role = c(\"cph\", \"dtc\"), comment = \"Unicode Character Database\"))", + "Description": "Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.", + "License": "Apache License (== 2.0) | file LICENSE", + "URL": "https://krlmlr.github.io/utf8/, https://github.com/krlmlr/utf8", + "BugReports": "https://github.com/krlmlr/utf8/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "cli", + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr, rmarkdown", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2.9000", + "NeedsCompilation": "yes", + "Author": "Patrick O. Perry [aut, cph], Kirill Müller [cre] (ORCID: ), Unicode, Inc. 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(2018) . It also provides means to transform new data and to carry out supervised dimensionality reduction. An implementation of the related LargeVis method of Tang et al. (2016) is also provided. This is a complete re-implementation in R (and C++, via the 'Rcpp' package): no Python installation is required. See the uwot website () for more documentation and examples.", + "License": "GPL (>= 3)", + "URL": "https://github.com/jlmelville/uwot, https://jlmelville.github.io/uwot/", + "BugReports": "https://github.com/jlmelville/uwot/issues", + "Depends": [ + "Matrix" + ], + "Imports": [ + "FNN", + "irlba", + "methods", + "Rcpp", + "RcppAnnoy (>= 0.0.17)", + "RSpectra" + ], + "Suggests": [ + "bigstatsr", + "covr", + "knitr", + "RcppHNSW", + "rmarkdown", + "rnndescent", + "testthat" + ], + "LinkingTo": [ + "dqrng", + "Rcpp", + "RcppAnnoy", + "RcppProgress" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "rmarkdown", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "James Melville [aut, cre, cph], Aaron Lun [ctb], Mohamed Nadhir Djekidel [ctb], Yuhan Hao [ctb], Dirk Eddelbuettel [ctb], Wouter van der Bijl [ctb]", + "Maintainer": "James Melville ", + "Repository": "CRAN" + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.6.5", + "Source": "Repository", + "Title": "Vector Helpers", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"aut\"), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"data.table team\", role = \"cph\", comment = \"Radix sort based on data.table's forder() and their contribution to R's order()\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analysing function interfaces.", + "License": "MIT + file LICENSE", + "URL": "https://vctrs.r-lib.org/, https://github.com/r-lib/vctrs", + "BugReports": "https://github.com/r-lib/vctrs/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "glue", + "lifecycle (>= 1.0.3)", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "bit64", + "covr", + "crayon", + "dplyr (>= 0.8.5)", + "generics", + "knitr", + "pillar (>= 1.4.4)", + "pkgdown (>= 2.0.1)", + "rmarkdown", + "testthat (>= 3.0.0)", + "tibble (>= 3.1.3)", + "waldo (>= 0.2.0)", + "withr", + "xml2", + "zeallot" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-GB", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Lionel Henry [aut], Davis Vaughan [aut, cre], data.table team [cph] (Radix sort based on data.table's forder() and their contribution to R's order()), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.2", + "Source": "Repository", + "Type": "Package", + "Title": "Colorblind-Friendly Color Maps (Lite Version)", + "Date": "2023-05-02", + "Authors@R": "c( person(\"Simon\", \"Garnier\", email = \"garnier@njit.edu\", role = c(\"aut\", \"cre\")), person(\"Noam\", \"Ross\", email = \"noam.ross@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Bob\", \"Rudis\", email = \"bob@rud.is\", role = c(\"ctb\", \"cph\")), person(\"Marco\", \"Sciaini\", email = \"sciaini.marco@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Antônio Pedro\", \"Camargo\", role = c(\"ctb\", \"cph\")), person(\"Cédric\", \"Scherer\", email = \"scherer@izw-berlin.de\", role = c(\"ctb\", \"cph\")) )", + "Maintainer": "Simon Garnier ", + "Description": "Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "ggplot2 (>= 1.0.1)", + "testthat", + "covr" + ], + "URL": "https://sjmgarnier.github.io/viridisLite/, https://github.com/sjmgarnier/viridisLite/", + "BugReports": "https://github.com/sjmgarnier/viridisLite/issues/", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" + }, + "vroom": { + "Package": "vroom", + "Version": "1.6.5", + "Source": "Repository", + "Title": "Read and Write Rectangular Text Data Quickly", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial indexing step, then reads the values lazily , so only the data you actually use needs to be read. 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Also supports XML schema validation; for 'XSLT' transformations see the 'xslt' package.", + "License": "MIT + file LICENSE", + "URL": "https://xml2.r-lib.org, https://r-lib.r-universe.dev/xml2", + "BugReports": "https://github.com/r-lib/xml2/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "cli", + "methods", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "covr", + "curl", + "httr", + "knitr", + "magrittr", + "mockery", + "rmarkdown", + "testthat (>= 3.2.0)", + "xslt" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "libxml2: libxml2-dev (deb), libxml2-devel (rpm)", + "Collate": "'S4.R' 'as_list.R' 'xml_parse.R' 'as_xml_document.R' 'classes.R' 'format.R' 'import-standalone-obj-type.R' 'import-standalone-purrr.R' 'import-standalone-types-check.R' 'init.R' 'nodeset_apply.R' 'paths.R' 'utils.R' 'xml2-package.R' 'xml_attr.R' 'xml_children.R' 'xml_document.R' 'xml_find.R' 'xml_missing.R' 'xml_modify.R' 'xml_name.R' 'xml_namespaces.R' 'xml_node.R' 'xml_nodeset.R' 'xml_path.R' 'xml_schema.R' 'xml_serialize.R' 'xml_structure.R' 'xml_text.R' 'xml_type.R' 'xml_url.R' 'xml_write.R' 'zzz.R'", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Jim Hester [aut], Jeroen Ooms [aut, cre], Posit Software, PBC [cph, fnd], R Foundation [ctb] (Copy of R-project homepage cached as example)", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Date": "2019-04-08", + "Title": "Export Tables to LaTeX or HTML", + "Authors@R": "c(person(\"David B.\", \"Dahl\", role=\"aut\"), person(\"David\", \"Scott\", role=c(\"aut\",\"cre\"), email=\"d.scott@auckland.ac.nz\"), person(\"Charles\", \"Roosen\", role=\"aut\"), person(\"Arni\", \"Magnusson\", role=\"aut\"), person(\"Jonathan\", \"Swinton\", role=\"aut\"), person(\"Ajay\", \"Shah\", role=\"ctb\"), person(\"Arne\", \"Henningsen\", role=\"ctb\"), person(\"Benno\", \"Puetz\", role=\"ctb\"), person(\"Bernhard\", \"Pfaff\", role=\"ctb\"), person(\"Claudio\", \"Agostinelli\", role=\"ctb\"), person(\"Claudius\", \"Loehnert\", role=\"ctb\"), person(\"David\", \"Mitchell\", role=\"ctb\"), person(\"David\", \"Whiting\", role=\"ctb\"), person(\"Fernando da\", \"Rosa\", role=\"ctb\"), person(\"Guido\", \"Gay\", role=\"ctb\"), person(\"Guido\", \"Schulz\", role=\"ctb\"), person(\"Ian\", \"Fellows\", role=\"ctb\"), person(\"Jeff\", \"Laake\", role=\"ctb\"), person(\"John\", \"Walker\", role=\"ctb\"), person(\"Jun\", \"Yan\", role=\"ctb\"), person(\"Liviu\", \"Andronic\", role=\"ctb\"), person(\"Markus\", \"Loecher\", role=\"ctb\"), person(\"Martin\", \"Gubri\", role=\"ctb\"), person(\"Matthieu\", \"Stigler\", role=\"ctb\"), person(\"Robert\", \"Castelo\", role=\"ctb\"), person(\"Seth\", \"Falcon\", role=\"ctb\"), person(\"Stefan\", \"Edwards\", role=\"ctb\"), person(\"Sven\", \"Garbade\", role=\"ctb\"), person(\"Uwe\", \"Ligges\", role=\"ctb\"))", + "Maintainer": "David Scott ", + "Imports": [ + "stats", + "utils" + ], + "Suggests": [ + "knitr", + "plm", + "zoo", + "survival" + ], + "VignetteBuilder": "knitr", + "Description": "Coerce data to LaTeX and HTML tables.", + "URL": "http://xtable.r-forge.r-project.org/", + "Depends": [ + "R (>= 2.10.0)" + ], + "License": "GPL (>= 2)", + "Repository": "CRAN", + "NeedsCompilation": "no", + "Author": "David B. Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.10", + "Source": "Repository", + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Date": "2024-07-22", + "Suggests": [ + "RUnit" + ], + "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]", + "Maintainer": "Shawn Garbett ", + "License": "BSD_3_clause + file LICENSE", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "URL": "https://github.com/vubiostat/r-yaml/", + "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, + "zoo": { + "Package": "zoo", + "Version": "1.8-14", + "Source": "Repository", + "Date": "2025-04-09", + "Title": "S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)", + "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Gabor\", family = \"Grothendieck\", role = \"aut\", email = \"ggrothendieck@gmail.com\"), person(given = c(\"Jeffrey\", \"A.\"), family = \"Ryan\", role = \"aut\", email = \"jeff.a.ryan@gmail.com\"), person(given = c(\"Joshua\", \"M.\"), family = \"Ulrich\", role = \"ctb\", email = \"josh.m.ulrich@gmail.com\"), person(given = \"Felix\", family = \"Andrews\", role = \"ctb\", email = \"felix@nfrac.org\"))", + "Description": "An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.", + "Depends": [ + "R (>= 3.1.0)", + "stats" + ], + "Suggests": [ + "AER", + "coda", + "chron", + "ggplot2 (>= 3.5.0)", + "mondate", + "scales", + "stinepack", + "strucchange", + "timeDate", + "timeSeries", + "tinyplot", + "tis", + "tseries", + "xts" + ], + "Imports": [ + "utils", + "graphics", + "grDevices", + "lattice (>= 0.20-27)" + ], + "License": "GPL-2 | GPL-3", + "URL": "https://zoo.R-Forge.R-project.org/", + "NeedsCompilation": "yes", + "Author": "Achim Zeileis [aut, cre] (), Gabor Grothendieck [aut], Jeffrey A. Ryan [aut], Joshua M. Ulrich [ctb], Felix Andrews [ctb]", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" + } + } +} diff --git a/README.md b/README.md index 2bc2407..273b541 100644 --- a/README.md +++ b/README.md @@ -51,4 +51,8 @@ Read full documentation at [03_differential_expression/README.md](03_differentia # Gene Expression Imputation -![](https://img.shields.io/badge/status-stable-green) [`Imputation Analysis`](05_imputation/imputation.qmd) is a template to run gene expression imputation with two different methods, ALRA and MAGIC. 👀 [See an example](https://bcbio.github.io/singlecell-reports/05_imputation/imputation.html) \ No newline at end of file +![](https://img.shields.io/badge/status-stable-green) [`Imputation Analysis`](05_imputation/imputation.qmd) is a template to run gene expression imputation with two different methods, ALRA and MAGIC. 👀 [See an example](https://bcbio.github.io/singlecell-reports/05_imputation/imputation.html) + +# Cell-Cell Interaction + +![](https://img.shields.io/badge/status-stable-green) [`Cell-Cell Interaction`](05_signaling/cellchat.qmd) is a template to run cell-cell interaction analysis with CellChat. 👀 [See an example](https://bcbio.github.io/singlecell-reports/05_signaling/cellchat.html) \ No newline at end of file diff --git a/install-dependencies.R b/install-dependencies.R index de25ac6..5c5ddd5 100644 --- a/install-dependencies.R +++ b/install-dependencies.R @@ -1,3 +1,21 @@ install.packages("BiocManager") BiocManager::install("renv") +BiocManager::install("immunogenomics/presto") +BiocManager::install("sqjin/CellChat") BiocManager::install(renv::dependencies(path = ".")[["Package"]]) + +create_snapshot <- function(folder, extra_libs = NULL) { + pkgs <- renv::dependencies(path = folder)[["Package"]] + if (!is.null(extra_libs)) { + pkgs <- c(pkgs, renv::dependencies(path = extra_libs)[["Package"]]) + } + renv::snapshot(lockfile = file.path(folder, "renv.lock"), packages = pkgs) +} + +# Snapshots for each folder +create_snapshot("01_quality_assessment") +create_snapshot("02_integration") +create_snapshot("03_differential_expression") +create_snapshot("04_compositional") +create_snapshot("05_signaling") +create_snapshot("06_imputation")