vimc · pratikunterwegs · Apr 7, 2025 · Apr 7, 2025 · Apr 14, 2025
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -13,3 +13,4 @@
 ^docs$
 ^pkgdown$
 ^tools$
+^air.toml$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -54,4 +54,4 @@ jobs:
         with:
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
-          error-on: '"note"'
+          error-on: '"warning"'
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,24 +1,20 @@
-Package: ji.rpkg.template
-Title: Your Package Title in Title Case
+Package: vimclimate
+Title: Access Climate Data Time-series from the Vaccine Impact Modelling
+    Consortium
 Version: 0.0.0.9000
-Authors@R: c(
+Authors@R: 
     person("Pratik", "Gupte", , "[email protected]", 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
-    include relevant bibliographical references if applicable, using the
-    following format: Author et al. (2023) <doi:10.5281/zenodo.6619350>.
+           comment = c(ORCID = "0000-0001-5294-7819"))
+Description: Access pre-made climate data time-series.
 License: MIT + file LICENSE
+URL: https://github.com/vimc/vimclimate, https://vimc.github.io/vimclimate
 Suggests: 
     knitr,
     rmarkdown,
     spelling,
     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
@@ -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
@@ -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
@@ -1,5 +1,3 @@
-# ji.rpkg.template 0.0.1
+# vimclimate (development version)
 
-* This project now includes a
-   [`NEWS.md`](https://r-pkgs.org/other-markdown.html#sec-news) file to inform
-   users about changes and new features.
+- Initial package infrastructure from template.
diff --git a/R/ji.rpkg.template-package.R → R/vimclimate.R b/R/ji.rpkg.template-package.R → R/vimclimate.R
diff --git a/README.Rmd b/README.Rmd
@@ -15,58 +15,46 @@ knitr::opts_chunk$set(
 )
 ```
 
-# ji.rpkg.template: TAGLINE
+# vimclimate: Access climate data time-series from the Vaccine Impact Modelling Consortium
 
 <!-- badges: start -->
-[![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)
+[![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/vimc/vimclimate/workflows/R-CMD-check/badge.svg)](https://github.com/vimc/vimclimate/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/vimc/vimclimate/branch/main/graph/badge.svg)](https://app.codecov.io/gh/vimc/vimclimate?branch=main)
+[![CRAN status](https://www.r-pkg.org/badges/version/vimclimate)](https://CRAN.R-project.org/package=vimclimate)
 <!-- badges: end -->
 
-_ji.rpkg.template_ is a template package and repository on which future Jameel Institute 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:
-
-1. Edit the `DESCRIPTION` as appropriate with the correct package information;
-
-2. Edit the files in `R/`, `tests/`, and `vignettes/` to suit your package;
-
-3. Remove these instructions from `README.Rmd`, and re-render the `.md` file using `devtools::render_readme()`.
+_vimclimate_ is an R package that helps access pre-made climatic variable time-series data for use in modelling.
 
 ## Installation
 
-**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:
+You can install the development version of _vimclimate_ from GitHub [GitHub](https://github.com/) using the _pak_ package:
 
-```r
-# installation from R-universe
-# install.packages(
-#   "ji.rpkg.template", 
-#   repos = c(
-#     "https://jameel-institute.r-universe.dev", "https://cloud.r-project.org"
-#   )
-# )
+``` r
+install.packages("pak")
+pak::pak("vimc/vimclimate")
 ```
 
-or from GitHub [GitHub](https://github.com/) with:
+<!-- the [VIMC R-universe](https://vimc.r-universe.dev/) with:
 
-``` r
-# install.packages("pak")
-# pak::pak("jameel-institute/ji.rpkg.template")
+```r
+installation from R-universe
+install.packages(
+  "vimclimate", 
+  repos = c(
+    "https://vimc.r-universe.dev", "https://cloud.r-project.org"
+  )
+)
 ```
 
+or from -->
+
 ## Quick start
 
-Add a simple example of using the package's main feature(s) here, with a minimum amount of code.
-If preparatory or plotting steps are needed, prefer to hide them to keep focus on the package functionality.
+WIP.
 
 ## Related projects
 
-Add information and links to related projects, such as research papers or packages, here.
+- [_clim2parquet_](https://vimc.github.io/clim2parquet/): Used to prepare climate data in Parquet format; this is the data accessed by _vimclimate_.
 
 ## References
-
-Space for references: REMOVE this text.
diff --git a/README.md b/README.md
@@ -1,74 +1,55 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# ji.rpkg.template: TAGLINE
+# vimclimate: Access climate data time-series from the Vaccine Impact Modelling Consortium
 
 <!-- badges: start -->
 
-[![Project Status: Concept – Minimal or no implementation has been done
+[![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)
+status](https://github.com/vimc/vimclimate/workflows/R-CMD-check/badge.svg)](https://github.com/vimc/vimclimate/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/vimclimate/branch/main/graph/badge.svg)](https://app.codecov.io/gh/vimc/vimclimate?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/vimclimate)](https://CRAN.R-project.org/package=vimclimate)
 <!-- badges: end -->
 
-*ji.rpkg.template* is a template package and repository on which future
-Jameel Institute 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:
-
-1.  Edit the `DESCRIPTION` as appropriate with the correct package
-    information;
-
-2.  Edit the files in `R/`, `tests/`, and `vignettes/` to suit your
-    package;
-
-3.  Remove these instructions from `README.Rmd`, and re-render the `.md`
-    file using `devtools::render_readme()`.
+*vimclimate* is an R package that helps access pre-made climatic
+variable time-series data for use in modelling.
 
 ## Installation
 
-**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:
+You can install the development version of *vimclimate* from GitHub
+[GitHub](https://github.com/) using the *pak* package:
 
 ``` r
-# installation from R-universe
-# install.packages(
-#   "ji.rpkg.template", 
-#   repos = c(
-#     "https://jameel-institute.r-universe.dev", "https://cloud.r-project.org"
-#   )
-# )
+install.packages("pak")
+pak::pak("vimc/vimclimate")
 ```
 
-or from GitHub [GitHub](https://github.com/) with:
-
-``` r
-# install.packages("pak")
-# pak::pak("jameel-institute/ji.rpkg.template")
+<!-- the [VIMC R-universe](https://vimc.r-universe.dev/) with:
+&#10;```r
+installation from R-universe
+install.packages(
+  "vimclimate", 
+  repos = c(
+    "https://vimc.r-universe.dev", "https://cloud.r-project.org"
+  )
+)
 ```
+&#10;or from -->
 
 ## Quick start
 
-Add a simple example of using the package’s main feature(s) here, with a
-minimum amount of code. If preparatory or plotting steps are needed,
-prefer to hide them to keep focus on the package functionality.
+WIP.
 
 ## Related projects
 
-Add information and links to related projects, such as research papers
-or packages, here.
+- [*clim2parquet*](https://vimc.github.io/clim2parquet/): Used to
+  prepare climate data in Parquet format; this is the data accessed by
+  *vimclimate*.
 
 ## References
-
-Space for references: REMOVE this text.
diff --git 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/"
-url: ~
+# e.g. "https://vimc.github.io/vimclimate/"
+url: https://vimc.github.io/vimclimate/
 template:
   bootstrap: 5
-  package: jameelinst.rpkg.theme
diff --git a/air.toml b/air.toml
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1,10 +1,10 @@
 Codecov
-Jameel
 ORCID
 TAGLINE
-Un
+VIMC
+WIP
+clim
 doi
-ji
+pak
 pkgdown
-rpkg
 zenodo
diff --git a/man/ji.rpkg.template-package.Rd b/man/ji.rpkg.template-package.Rd
diff --git a/man/vimclimate-package.Rd b/man/vimclimate-package.Rd
diff --git 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
@@ -7,6 +7,6 @@
 # * https://testthat.r-lib.org/articles/special-files.html
 
 library(testthat)
-library(ji.rpkg.template)
+library(vimclimate)
 
-test_check("ji.rpkg.template")
+test_check("vimclimate")
diff --git a/tests/testthat/helper-state.R b/tests/testthat/helper-state.R
@@ -17,18 +17,18 @@ 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(),
+      par = get_pars_toreset(),
+      packages = .packages(all.available = TRUE),
+      sink = sink.number(),
+      timezone = Sys.timezone(),
       NULL
     )
   })

diff --git a/vignettes/ji-rpkg-template.Rmd → vignettes/vimclimate.Rmd b/vignettes/ji-rpkg-template.Rmd → vignettes/vimclimate.Rmd
@@ -1,8 +1,8 @@
 ---
-title: "ji-rpkg-template"
+title: "Getting started with vimclimate"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{ji-rpkg-template}
+  %\VignetteIndexEntry{Getting started with vimclimate}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -15,7 +15,7 @@ knitr::opts_chunk$set(
 ```
 
 ```{r setup}
-library(ji.rpkg.template)
+library(vimclimate)
 ```
 
 This is a special vignette, which shares the same name as the package.

diff --git a/ji.rpkg.template.Rproj → vimclimate.Rproj b/ji.rpkg.template.Rproj → vimclimate.Rproj
-Original file line number
+Diff line change
@@ Expand Up / @@ -13,3 +13,4 @@ @@
     ^docs$
     ^pkgdown$
     ^tools$
+    ^air.toml$