diff --git a/.Rbuildignore b/.Rbuildignore index bfe7068..e2ff48a 100644 --- 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 index e1c58b9..27b1a3f 100644 --- 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 index 96f120b..868b429 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,16 +1,13 @@ -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", , "pratik.gupte@lshtm.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 - include relevant bibliographical references if applicable, using the - following format: Author et al. (2023) . + 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, @@ -18,7 +15,6 @@ 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..a492ee0 100644 --- 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 b/R/vimclimate.R similarity index 100% rename from R/ji.rpkg.template-package.R rename to R/vimclimate.R diff --git a/README.Rmd b/README.Rmd index b4eac9a..b3783ae 100644 --- 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 -[![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) -_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: + + ## 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 index 8c4134e..de5cb38 100644 --- a/README.md +++ b/README.md @@ -1,74 +1,55 @@ -# ji.rpkg.template: TAGLINE +# vimclimate: Access climate data time-series from the Vaccine Impact Modelling Consortium -[![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) -*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") + ## 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 index 1d4fe01..29e6b2f 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/" -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 new file mode 100644 index 0000000..e69de29 diff --git a/inst/WORDLIST b/inst/WORDLIST index e91f4b5..41a0a85 100644 --- 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 deleted file mode 100644 index 6711019..0000000 --- a/man/ji.rpkg.template-package.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/ji.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} -\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}) - -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] -} - -} -\keyword{internal} diff --git a/man/vimclimate-package.Rd b/man/vimclimate-package.Rd new file mode 100644 index 0000000..8eaae00 --- /dev/null +++ b/man/vimclimate-package.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/vimclimate.R +\docType{package} +\name{vimclimate-package} +\alias{vimclimate} +\alias{vimclimate-package} +\title{vimclimate: Access Climate Data Time-series from the Vaccine Impact Modelling Consortium} +\description{ +Access pre-made climate data time-series. +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/vimc/vimclimate} + \item \url{https://vimc.github.io/vimclimate} +} + +} +\author{ +\strong{Maintainer}: Pratik Gupte \email{pratik.gupte@lshtm.ac.uk} (\href{https://orcid.org/0000-0001-5294-7819}{ORCID}) + +} +\keyword{internal} 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..2e3658d 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(vimclimate) -test_check("ji.rpkg.template") +test_check("vimclimate") diff --git a/tests/testthat/helper-state.R b/tests/testthat/helper-state.R index 513ecdb..a05ee48 100644 --- 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 b/vignettes/vimclimate.Rmd similarity index 83% rename from vignettes/ji-rpkg-template.Rmd rename to vignettes/vimclimate.Rmd index ad95a26..21b1f70 100644 --- a/vignettes/ji-rpkg-template.Rmd +++ b/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 b/vimclimate.Rproj similarity index 100% rename from ji.rpkg.template.Rproj rename to vimclimate.Rproj