diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..d262a6f --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,4 @@ +^trendsEnsemble\.Rproj$ +^\.Rproj\.user$ +^\.github$ +^README\.Rmd$ diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..0f2fe08 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,52 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + +name: R-CMD-check + +permissions: read-all + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..0b508ef --- /dev/null +++ b/.gitignore @@ -0,0 +1,5 @@ +.Rproj.user +.Rhistory +.RData +.Ruserdata +*.code-workspace diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..915f87d --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,31 @@ +Package: trendsEnsemble +Title: Functions to Create the UMass-trends_ensemble Model +Version: 0.0.0.9000 +Authors@R: c( + person(given = "Evan L", + family = "Ray", + email = "elray@umass.edu", + role = c("aut")), + person(given = "Li", + family = "Shandross", + role = c("aut", "cre"), + email = "lshandross@umass.edu", + comment = c(ORCID = "0009-0008-1348-1954")), + person(given = "Nutcha", + family = "Wattanachit", + role = c("aut")), + person(given = "Aaron", + family = "Gerding", + role = c("aut")), + person(given = "Nicholas G.", + family = "Reich", + role = c("aut"), + email = "nick@umass.edu", + comment = c(ORCID = "0000-0003-3503-9899"))) +Description: A collection of functions used to create the UMass-trends_ensemble, + an equally weighted ensemble of simple time series baseline models +License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a + license +Encoding: UTF-8 +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.3.1 diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..6ae9268 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,2 @@ +# Generated by roxygen2: do not edit by hand + diff --git a/README.Rmd b/README.Rmd new file mode 100644 index 0000000..07d795d --- /dev/null +++ b/README.Rmd @@ -0,0 +1,56 @@ +--- +output: github_document +--- + + + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>", + fig.path = "man/figures/README-", + out.width = "100%" +) +``` + +# trendsEnsemble + + +[![R-CMD-check](https://github.com/reichlab/trendsEnsemble/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/reichlab/trendsEnsemble/actions/workflows/R-CMD-check.yaml) + + +The goal of trendsEnsemble is to ... + +## Installation + +You can install the development version of trendsEnsemble from [GitHub](https://github.com/) with: + +``` r +# install.packages("devtools") +devtools::install_github("reichlab/trendsEnsemble") +``` + +## Example + +This is a basic example which shows you how to solve a common problem: + +```{r example, eval = FALSE} +library(trendsEnsemble) +## basic example code +``` + +What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so: + +```{r cars} +summary(cars) +``` + +You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. + +You can also embed plots, for example: + +```{r pressure, echo = FALSE} +plot(pressure) +``` + +In that case, don't forget to commit and push the resulting figure files, so they display on GitHub and CRAN. diff --git a/README.md b/README.md index bfb810d..eb8313f 100644 --- a/README.md +++ b/README.md @@ -1 +1,54 @@ -# trends-ensemble \ No newline at end of file + + + +# trendsEnsemble + + + +[![R-CMD-check](https://github.com/reichlab/trendsEnsemble/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/reichlab/trendsEnsemble/actions/workflows/R-CMD-check.yaml) + + +The goal of trendsEnsemble is to … + +## Installation + +You can install the development version of trendsEnsemble from +[GitHub](https://github.com/) with: + +``` r +# install.packages("devtools") +devtools::install_github("reichlab/trendsEnsemble") +``` + +## Example + +This is a basic example which shows you how to solve a common problem: + +``` r +library(trendsEnsemble) +## basic example code +``` + +What is special about using `README.Rmd` instead of just `README.md`? +You can include R chunks like so: + +``` r +summary(cars) +#> speed dist +#> Min. : 4.0 Min. : 2.00 +#> 1st Qu.:12.0 1st Qu.: 26.00 +#> Median :15.0 Median : 36.00 +#> Mean :15.4 Mean : 42.98 +#> 3rd Qu.:19.0 3rd Qu.: 56.00 +#> Max. :25.0 Max. :120.00 +``` + +You’ll still need to render `README.Rmd` regularly, to keep `README.md` +up-to-date. `devtools::build_readme()` is handy for this. + +You can also embed plots, for example: + + + +In that case, don’t forget to commit and push the resulting figure +files, so they display on GitHub and CRAN. diff --git a/man/figures/README-pressure-1.png b/man/figures/README-pressure-1.png new file mode 100644 index 0000000..c092055 Binary files /dev/null and b/man/figures/README-pressure-1.png differ diff --git a/trendsEnsemble.Rproj b/trendsEnsemble.Rproj new file mode 100644 index 0000000..766b3b2 --- /dev/null +++ b/trendsEnsemble.Rproj @@ -0,0 +1,22 @@ +Version: 1.0 + +RestoreWorkspace: No +SaveWorkspace: No +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: knitr +LaTeX: pdfLaTeX + +AutoAppendNewline: Yes +StripTrailingWhitespace: Yes +LineEndingConversion: Posix + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source +PackageRoxygenize: rd,collate,namespace