Fix dependency

.github/workflows/R-CMD-check.yaml

@@ -49,7 +49,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Restore R package cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: IOHanalyzer
 Type: Package
 Title: Data Analysis Part of 'IOHprofiler'
-Version: 0.1.8.11
+Version: 0.1.8.12
 Maintainer: Diederick Vermetten <d.l.vermetten@liacs.leidenuniv.nl>
 Authors@R: c(
     person("Hao", "Wang", email = "h.wang@liacs.leidenuniv.nl", role = "aut", comment = c(ORCID = "0000-0002-4933-5181")),

R/DataSet.R

@@ -135,6 +135,10 @@ DataSet <-
       PAR <- list('by_FV' = RT[names(RT) != 'RT'],
                   'by_RT' = FV[names(FV) != 'FV'])
 
+      if (all(paste0('x', seq(0,info$DIM - 1)) %in% names(PAR$by_RT))) {
+        info$contains_position <- T
+      }
+
       RT <- RT$RT
       mode(RT) <- 'integer'
       FV <- FV$FV
@@ -335,11 +339,16 @@ c.DataSet <- function(...) {
         }), recursive = F)
   }
 
-  do.call(function(...)
+  res <- do.call(function(...)
     structure(list(
       RT = RT, FV = FV, PAR = PAR
     ), class = c('DataSet', 'list'), ...),
     c(info))
+
+  if (!is.null(attr(dsl[[1]], 'contains_full_FV')) && attr(dsl[[1]], 'contains_full_FV')) {
+    res$FV_raw_mat <- do.call(cbind, lapply(dsl, function(ds) unlist(ds$FV_raw_mat)))
+  }
+
 }
 
 #' S3 subset function for DataSet
@@ -666,7 +675,7 @@ get_PAR_name <- function(ds, which)
 #' @examples
 #' get_FV_overview(dsl)
 #' get_FV_overview(dsl[[1]])
-#' get_FV_overview(dsl, algorithm = '(1+1)_greedy_hill_climber_1')
+#' get_FV_overview(subset(dsl, algId == "(1+1)_greedy_hill_climber_1"))
 #' @export
 get_FV_overview <-
   function(ds, ...)

R/plotDataSetList.R

@@ -1357,6 +1357,7 @@ Plot.Stats.Significance_Graph.DataSetList <-
     }
     p_matrix <-
       pairwise.test(dsList, ftarget, bootstrap.size, which)
+    p_matrix[is.na(p_matrix)] <- 1
     g <-
       igraph::graph_from_adjacency_matrix(p_matrix <= alpha, mode = 'directed', diag = F)
     lab.locs <-

R/readFiles.R

@@ -1438,7 +1438,7 @@ read_pure_csv <- function(path,
       data$neval <-  ave(data$fval, data$run, FUN = seq_along)
     }
 
-    dt_for_allign <- dcast(data, neval ~ run, value.var = 'fval')
+    dt_for_allign <- dcast(data, neval ~ run, value.var = 'fval', fun.aggregate = ifelse(maximization, max, min))
 
     FV_mat <- as.matrix(dt_for_allign[, 2:ncol(dt_for_allign)])
     runtimes <- dt_for_allign$neval
@@ -1602,7 +1602,11 @@ read_IOH_v1plus <- function(info, full_sampling = FALSE) {
 
 
   paramnames <-
-    info$attributes[!info$attributes %in% c("evaluations", "raw_y")]
+    colnames(data)[!colnames(data) %in% c("evaluations", "raw_y", 'runnr')]
+
+  if (all(paste0('x', seq(0,info$DIM - 1)) %in% paramnames)) {
+    info$contains_position <- T
+  }
 
   PAR <- list(
     'by_RT' = lapply(paramnames, function(parname) {

README.md

@@ -37,7 +37,7 @@ It is _available through_:
 
 ## <a name="server"></a>Online Service
 
-A free server [https://iohanalyzer.liacs.nl](http://iohprofiler.liacs.nl) running the stable version of __IOHanalyzer__ is hosted in [Leiden Institute of Advanced Computer Science](https://liacs.leidenuniv.nl/). You're welcome to check it out!
+A free server [https://iohanalyzer.liacs.nl](https://iohanalyzer.liacs.nl) running the stable version of __IOHanalyzer__ is hosted in [Leiden Institute of Advanced Computer Science](https://liacs.leidenuniv.nl/). You're welcome to check it out!
 
 ## <a name="install"></a>Installation
 
@@ -107,28 +107,27 @@ then you just need to compress the data folder obtained from the experiment into
 
 ## Our Team
 
-* [Hao Wang](https://www.lip6.fr/actualite/personnes-fiche.php?ident=D2381), Sorbonne Université, LIP6, France.
-* [Diederick Vermetten](https://www.universiteitleiden.nl/en/staffmembers/diederick-vermetten), Leiden Institute of Advanced Computer Science, The Netherlands.
+* [Hao Wang](https://www.universiteitleiden.nl/en/staffmembers/hao-wang), Leiden Institute of Advanced Computer Science, The Netherlands.
+* [Diederick Vermetten](https://www.lip6.fr/actualite/personnes-fiche.php?ident=D2799), Sorbonne Université, CNRS, LIP6, France.
 * [Furong Ye](https://www.universiteitleiden.nl/en/staffmembers/furong-ye), Leiden Institute of Advanced Computer Science, The Netherlands.
 * [Ofer M. Shir](https://ofersh.github.io/telhai/), Tel-Hai College, Israel.
-* [Carola Doerr](http://www-desir.lip6.fr/~doerr/), Sorbonne Université, CNRS, LIP6, France.
+* [Carola Doerr](https://doerr.perso.lip6.fr/), Sorbonne Université, CNRS, LIP6, France.
 * [Thomas Bäck](https://www.universiteitleiden.nl/en/staffmembers/thomas-back), Leiden Institute of Advanced Computer Science, The Netherlands.
 
 When using IOHprofiler and parts thereof, please kindly cite this work as
 
 Hao Wang, Diederick Vermettern, Furong Ye, Carola Doerr and Thomas Bäck: _IOHanalyzer: Performance Analysis for Iterative Optimization Heuristic_, arXiv e-prints:2007.03953, 2020.
 
 ```bibtex
-@ARTICLE{IOHprofiler,
-  author = {Hao Wang and Diederick Vermettern and Furong Ye and Carola Doerr and Thomas B{\"a}ck},
-  title = {{IOHanalyzer: Performance Analysis for Iterative Optimization Heuristic}},
-  journal = {arXiv e-prints:2007.03953},
-  archivePrefix = "arXiv",
-  eprint = {2007.03953},
-  year = 2020,
-  month = July,
-  keywords = {Computer Science - Neural and Evolutionary Computing},
-  url = {https://arxiv.org/abs/2007.03953}
+@article{IOHanalzyer,
+  title={IOHanalyzer: Detailed performance analyses for iterative optimization heuristics},
+  author={Wang, Hao and Vermetten, Diederick and Ye, Furong and Doerr, Carola and B{\"a}ck, Thomas},
+  journal={ACM Transactions on Evolutionary Learning and Optimization},
+  volume={2},
+  number={1},
+  pages={1--29},
+  year={2022},
+  publisher={ACM New York, NY}
 }
 ```
 

inst/shiny-server/server/upload.R

@@ -31,6 +31,10 @@ observe({
                    such as the ones provided on the IOHProfiler github-page.")
     updateSelectInput(session, 'repository.dataset', choices = NULL, selected = NULL)
   }
+  meta_file <- list.files(dir, pattern = 'meta.json', full.names = T)
+  if (length(meta_file) == 1) {
+    shinyjs::html("repository_meta", print(rjson::fromJSON(file=meta_file))[['description']])
+  }
 })
 
 # load repository that is selected

inst/shiny-server/ui/upload_box.R

@@ -240,7 +240,7 @@ overal_loading_box <- function(width = 12, collapsible = T,
 
                        selectInput('repository.type', label = "Select the dataset source",
                                    choices = NULL, selected = NULL, width = '80%'),
-
+                       verbatimTextOutput('repository_meta'),
                        selectInput('repository.dataset',
                                    label = "Select the dataset",
                                    choices = NULL, selected = NULL, width = '80%', multiple = T),