diff --git a/DESCRIPTION b/DESCRIPTION index 96f120b..bf2a6c8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,10 +1,9 @@ -Package: ji.rpkg.template +Package: vimc.rpkg.template Title: Your Package Title in Title Case Version: 0.0.0.9000 Authors@R: c( - person("Pratik", "Gupte", , "pratik.gupte@lshtm.ac.uk", role = c("aut", "cre"), + person("Pratik", "Gupte", , "p.gupte24@imperial.ac.uk", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5294-7819")), - person("Abdul Latif Jameel Institute for Disease and Emergency Analytics", role = "fnd"), person("Imperial College of Science, Technology and Medicine", role = c("cph", "fnd")) ) Description: Your package description. It must end with a period (".") and @@ -18,7 +17,6 @@ Suggests: testthat (>= 3.0.0) VignetteBuilder: knitr -Config/Needs/website: jameel-institute/jameelinst.rpkg.theme Config/testthat/edition: 3 Encoding: UTF-8 Language: en-GB diff --git a/LICENSE b/LICENSE index 6b42746..0c4d079 100644 --- a/LICENSE +++ b/LICENSE @@ -1,2 +1,2 @@ -YEAR: 2024 -COPYRIGHT HOLDER: ji.rpkg.template authors +YEAR: 2025 +COPYRIGHT HOLDER: Imperial College of Science, Technology and Medicine diff --git a/LICENSE.md b/LICENSE.md index 8c8f560..41e260a 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,6 +1,6 @@ # MIT License -Copyright (c) 2024 ji.rpkg.template authors +Copyright (c) 2025 Imperial College of Science, Technology and Medicine Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/NEWS.md b/NEWS.md index 4db0b83..349c9d4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# ji.rpkg.template 0.0.1 +# vimc.rpkg.template 0.0.1 * This project now includes a [`NEWS.md`](https://r-pkgs.org/other-markdown.html#sec-news) file to inform diff --git a/R/ji.rpkg.template-package.R b/R/vimc.rpkg.template-package.R similarity index 100% rename from R/ji.rpkg.template-package.R rename to R/vimc.rpkg.template-package.R diff --git a/README.Rmd b/README.Rmd index 686c442..e00c56a 100644 --- a/README.Rmd +++ b/README.Rmd @@ -15,25 +15,25 @@ knitr::opts_chunk$set( ) ``` -# ji.rpkg.template: TAGLINE +# vimc.rpkg.template: TAGLINE [![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept) -[![R build status](https://github.com/jameel-institute/ji.rpkg.template/workflows/R-CMD-check/badge.svg)](https://github.com/jameel-institute/ji.rpkg.template/actions/workflows/R-CMD-check.yaml) -[![Codecov test coverage](https://codecov.io/gh/jameel-institute/ji.rpkg.template/branch/main/graph/badge.svg)](https://app.codecov.io/gh/jameel-institute/ji.rpkg.template?branch=main) -[![CRAN status](https://www.r-pkg.org/badges/version/ji.rpkg.template)](https://CRAN.R-project.org/package=ji.rpkg.template) +[![R build status](https://github.com/vimc/vimc.rpkg.template/workflows/R-CMD-check/badge.svg)](https://github.com/vimc/vimc.rpkg.template/actions/workflows/R-CMD-check.yaml) +[![Codecov test coverage](https://codecov.io/gh/vimc/vimc.rpkg.template/branch/main/graph/badge.svg)](https://app.codecov.io/gh/vimc/vimc.rpkg.template?branch=main) +[![CRAN status](https://www.r-pkg.org/badges/version/vimc.rpkg.template)](https://CRAN.R-project.org/package=vimc.rpkg.template) -_ji.rpkg.template_ is a template package and repository on which future Jameel Institute packages are based. +_vimc.rpkg.template_ is a template package and repository on which future VIMC R packages are based. -To use this template, select _ji.rpkg.template_ from the drop-down menu under **Repository template** when creating a new repository in the Jameel Institute organisation. -Replace all instances of "ji.rpkg.template" with your package name. Make sure to also: +To use this template, select _vimc.rpkg.template_ from the drop-down menu under **Repository template** when creating a new repository in the VIMC GitHub organisation. +Replace all instances of `"vimc.rpkg.template"` with your package name. Make sure to also: -1. Edit the `DESCRIPTION` as appropriate with the correct package information; +1. Edit the `DESCRIPTION` as appropriate with the correct package information, including authors; 2. Edit the files in `R/`, `tests/`, and `vignettes/` to suit your package; -3. Add spell check by running usethis::use_spell_check(lang = "en-GB") +3. Add spell check by running `usethis::use_spell_check(lang = "en-GB")`; 4. Remove these instructions from `README.Rmd`, and re-render the `.md` file using `devtools::render_readme()`. @@ -41,23 +41,25 @@ Replace all instances of "ji.rpkg.template" with your package name. Make sure to **NOTE:** Remove or comment out installation sources as appropriate. -You can install the development version of ji.rpkg.template from the Jameel Institute R-universe with: +**Remember** to add the package to the [VIMC R-universe](https://github.com/vimc/vimc.r-universe.dev). + +You can install the development version of _vimc.rpkg.template_ from the VIMC R-universe with: ```r -# installation from R-universe -# install.packages( -# "ji.rpkg.template", -# repos = c( -# "https://jameel-institute.r-universe.dev", "https://cloud.r-project.org" -# ) -# ) +installation from R-universe +install.packages( + "vimc.rpkg.template", + repos = c( + "https://vimc.r-universe.dev", "https://cloud.r-project.org" + ) +) ``` or from GitHub [GitHub](https://github.com/) with: ``` r -# install.packages("pak") -# pak::pak("jameel-institute/ji.rpkg.template") +install.packages("pak") +pak::pak("vimc/vimc.rpkg.template") ``` ## Quick start diff --git a/README.md b/README.md index a651400..896e83e 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ -# ji.rpkg.template: TAGLINE +# vimc.rpkg.template: TAGLINE @@ -10,28 +10,29 @@ yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept) [![R build -status](https://github.com/jameel-institute/ji.rpkg.template/workflows/R-CMD-check/badge.svg)](https://github.com/jameel-institute/ji.rpkg.template/actions/workflows/R-CMD-check.yaml) +status](https://github.com/vimc/vimc.rpkg.template/workflows/R-CMD-check/badge.svg)](https://github.com/vimc/vimc.rpkg.template/actions/workflows/R-CMD-check.yaml) [![Codecov test -coverage](https://codecov.io/gh/jameel-institute/ji.rpkg.template/branch/main/graph/badge.svg)](https://app.codecov.io/gh/jameel-institute/ji.rpkg.template?branch=main) +coverage](https://codecov.io/gh/vimc/vimc.rpkg.template/branch/main/graph/badge.svg)](https://app.codecov.io/gh/vimc/vimc.rpkg.template?branch=main) [![CRAN -status](https://www.r-pkg.org/badges/version/ji.rpkg.template)](https://CRAN.R-project.org/package=ji.rpkg.template) +status](https://www.r-pkg.org/badges/version/vimc.rpkg.template)](https://CRAN.R-project.org/package=vimc.rpkg.template) -*ji.rpkg.template* is a template package and repository on which future -Jameel Institute packages are based. +*vimc.rpkg.template* is a template package and repository on which +future VIMC R packages are based. -To use this template, select *ji.rpkg.template* from the drop-down menu -under **Repository template** when creating a new repository in the -Jameel Institute organisation. Replace all instances of -“ji.rpkg.template” with your package name. Make sure to also: +To use this template, select *vimc.rpkg.template* from the drop-down +menu under **Repository template** when creating a new repository in the +VIMC GitHub organisation. Replace all instances of +`"vimc.rpkg.template"` with your package name. Make sure to also: 1. Edit the `DESCRIPTION` as appropriate with the correct package - information; + information, including authors; 2. Edit the files in `R/`, `tests/`, and `vignettes/` to suit your package; -3. Add spell check by running usethis::use_spell_check(lang = “en-GB”) +3. Add spell check by running + `usethis::use_spell_check(lang = "en-GB")`; 4. Remove these instructions from `README.Rmd`, and re-render the `.md` file using `devtools::render_readme()`. @@ -40,24 +41,27 @@ Jameel Institute organisation. Replace all instances of **NOTE:** Remove or comment out installation sources as appropriate. -You can install the development version of ji.rpkg.template from the -Jameel Institute R-universe with: +**Remember** to add the package to the [VIMC +R-universe](https://github.com/vimc/vimc.r-universe.dev). + +You can install the development version of *vimc.rpkg.template* from the +VIMC R-universe with: ``` r -# installation from R-universe -# install.packages( -# "ji.rpkg.template", -# repos = c( -# "https://jameel-institute.r-universe.dev", "https://cloud.r-project.org" -# ) -# ) +installation from R-universe +install.packages( + "vimc.rpkg.template", + repos = c( + "https://vimc.r-universe.dev", "https://cloud.r-project.org" + ) +) ``` or from GitHub [GitHub](https://github.com/) with: ``` r -# install.packages("pak") -# pak::pak("jameel-institute/ji.rpkg.template") +install.packages("pak") +pak::pak("vimc/vimc.rpkg.template") ``` ## Quick start diff --git a/_pkgdown.yml b/_pkgdown.yml index 1d4fe01..ca4c87b 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,6 +1,5 @@ # NOTE: Update the `url` field as needed -# e.g. "https://jameel-institute.github.io/daedalus/" +# e.g. "https://vimc.github.io/vimpact/" url: ~ template: bootstrap: 5 - package: jameelinst.rpkg.theme diff --git a/inst/WORDLIST b/inst/WORDLIST index e91f4b5..5d6e36f 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,10 +1,9 @@ Codecov -Jameel ORCID TAGLINE -Un +VIMC doi -ji pkgdown rpkg +vimc zenodo diff --git a/man/ji.rpkg.template-package.Rd b/man/vimc.rpkg.template-package.Rd similarity index 57% rename from man/ji.rpkg.template-package.Rd rename to man/vimc.rpkg.template-package.Rd index 6711019..4fa3a28 100644 --- a/man/ji.rpkg.template-package.Rd +++ b/man/vimc.rpkg.template-package.Rd @@ -1,19 +1,18 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/ji.rpkg.template-package.R +% Please edit documentation in R/vimc.rpkg.template-package.R \docType{package} -\name{ji.rpkg.template-package} -\alias{ji.rpkg.template} -\alias{ji.rpkg.template-package} -\title{ji.rpkg.template: Your Package Title in Title Case} +\name{vimc.rpkg.template-package} +\alias{vimc.rpkg.template} +\alias{vimc.rpkg.template-package} +\title{vimc.rpkg.template: Your Package Title in Title Case} \description{ Your package description. It must end with a period (".") and include relevant bibliographical references if applicable, using the following format: Author et al. (2023) \doi{10.5281/zenodo.6619350}. } \author{ -\strong{Maintainer}: Pratik Gupte \email{pratik.gupte@lshtm.ac.uk} (\href{https://orcid.org/0000-0001-5294-7819}{ORCID}) +\strong{Maintainer}: Pratik Gupte \email{p.gupte24@imperial.ac.uk} (\href{https://orcid.org/0000-0001-5294-7819}{ORCID}) Other contributors: \itemize{ - \item Abdul Latif Jameel Institute for Disease and Emergency Analytics [funder] \item Imperial College of Science, Technology and Medicine [copyright holder, funder] } diff --git a/tests/spelling.R b/tests/spelling.R index 13f77d9..d60e024 100644 --- a/tests/spelling.R +++ b/tests/spelling.R @@ -1,6 +1,7 @@ if (requireNamespace("spelling", quietly = TRUE)) { spelling::spell_check_test( - vignettes = TRUE, error = FALSE, + vignettes = TRUE, + error = FALSE, skip_on_cran = TRUE ) } diff --git a/tests/testthat.R b/tests/testthat.R index 3320784..cc799fa 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -7,6 +7,6 @@ # * https://testthat.r-lib.org/articles/special-files.html library(testthat) -library(ji.rpkg.template) +library(vimc.rpkg.template) -test_check("ji.rpkg.template") +test_check("vimc.rpkg.template") diff --git a/tests/testthat/helper-state.R b/tests/testthat/helper-state.R index 513ecdb..afb0459 100644 --- a/tests/testthat/helper-state.R +++ b/tests/testthat/helper-state.R @@ -17,18 +17,17 @@ get_pars_toreset <- function() { if (getRversion() >= "4.0.0") { testthat::set_state_inspector(function() { list( - attached = search(), + attached = search(), connections = getAllConnections(), - cwd = getwd(), - envvars = Sys.getenv(), - handlers = globalCallingHandlers(), - libpaths = .libPaths(), - locale = Sys.getlocale(), - options = options(), - par = get_pars_toreset(), - packages = .packages(all.available = TRUE), - sink = sink.number(), - timezone = Sys.timezone(), + cwd = getwd(), + envvars = Sys.getenv(), + handlers = globalCallingHandlers(), + libpaths = .libPaths(), + locale = Sys.getlocale(), + options = options(), + packages = .packages(all.available = TRUE), + sink = sink.number(), + timezone = Sys.timezone(), NULL ) }) diff --git a/vignettes/ji-rpkg-template.Rmd b/vignettes/vimc-rpkg-template.Rmd similarity index 86% rename from vignettes/ji-rpkg-template.Rmd rename to vignettes/vimc-rpkg-template.Rmd index ad95a26..2d33504 100644 --- a/vignettes/ji-rpkg-template.Rmd +++ b/vignettes/vimc-rpkg-template.Rmd @@ -1,8 +1,8 @@ --- -title: "ji-rpkg-template" +title: "vimc-rpkg-template" output: rmarkdown::html_vignette vignette: > - %\VignetteIndexEntry{ji-rpkg-template} + %\VignetteIndexEntry{vimc-rpkg-template} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- @@ -15,7 +15,7 @@ knitr::opts_chunk$set( ``` ```{r setup} -library(ji.rpkg.template) +library(vimc.rpkg.template) ``` This is a special vignette, which shares the same name as the package. diff --git a/ji.rpkg.template.Rproj b/vimc.rpkg.template.Rproj similarity index 100% rename from ji.rpkg.template.Rproj rename to vimc.rpkg.template.Rproj