chore: migrate to GitHub Actions, update dotfiles and readme

.Rbuildignore

@@ -1,5 +1,33 @@
 ^.*\.Rproj$
-^\.Rproj\.user$
+^CITATION\.cff$
+^CRAN-RELEASE$
+^CRAN-SUBMISSION$
+^Dockerfile$
+^LICENSE\.md$
+^Meta$
 ^README\.Rmd$
-^\.travis\.yml$
-^appveyor\.yml$
+^README\.html$
+^\.Renviron$
+^\.Rproj\.user$
+^\.ccache$
+^\.dockerignore$
+^\.editorconfig$
+^\.github$
+^\.gitignore$
+^\.httr-oauth$
+^\.ignore$
+^\.lintr$
+^\.pre-commit-config\.yaml$
+^\.vscode$
+^_pkgdown\.yml$
+^codecov\.yml$
+^compose\.ya?ml$
+^cran-comments\.md$
+^data-raw$
+^doc$
+^docs$
+^inst/extdata/.+\.R$
+^man-roxygen$
+^paper$
+^pkgdown$
+^revdep$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/pkgdown.yaml

@@ -0,0 +1,50 @@
+# 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]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/quick-check.yaml

@@ -0,0 +1,34 @@
+# 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: [dev]
+  pull_request:
+    branches: [dev]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          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")'

.gitignore

@@ -1,32 +1,58 @@
 # History files
 .Rhistory
 .Rapp.history
-*icloud*
 
 # Session Data files
 .RData
+.RDataTmp
+
+# User-specific files
+.Ruserdata
+
 # Example code in package build process
 *-Ex.R
+
 # Output files from R CMD build
 /*.tar.gz
+
 # Output files from R CMD check
 /*.Rcheck/
+
 # RStudio files
 .Rproj.user/
+
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf
-vignettes/*.R
+doc/
+Meta/
+
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
+
 # knitr and R markdown default cache directories
-/*_cache/
+*_cache/
 /cache/
+
 # Temporary files created by R markdown
 *.utf8.md
 *.knit.md
-.Rproj.user
-inst/doc
 
-# complete data files in /data-raw/
-/data-raw/*.csv
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/
+
+# CRAN
+CRAN-RELEASE
+CRAN-SUBMISSION
+
+# MacOS
+.DS_Store

DESCRIPTION

@@ -1,26 +1,38 @@
-Package: refundr
 Type: Package
+Package: refundr
 Title: Tidier regression with functional data
 Version: 0.1.0
 Date: 2019-08-30
-Authors@R: c(person("Julia", "Wrobel", email = "[email protected]", role = c("aut", "cre")),person("Fabian", "Scheipl", email = "[email protected]", role = c("aut")), person("Sara", "Kim", email = "[email protected]", role = c("aut")),person("Jeff", "Goldsmith", role = c("aut")))
-Description: Interfaces key functions from the refund package with framework from the tidyfun package to provide a tidier interface to FPCA and regression for functional data.
-Depends: R (>= 3.4)
+Authors@R: c(
+    person("Julia", "Wrobel", , "[email protected]", role = c("aut", "cre")),
+    person("Fabian", "Scheipl", , "[email protected]", role = "aut"),
+    person("Sara", "Kim", , "[email protected]", role = "aut"),
+    person("Jeff", "Goldsmith", role = "aut")
+  )
+Description: Interfaces key functions from the refund package with
+    framework from the tidyfun package to provide a tidier interface to
+    FPCA and regression for functional data.
+License: GPL-3
+Depends: 
+    R (>= 3.4)
 Imports:
-    dplyr, 
-    gamm4, 
-    MASS, 
-    Matrix, 
-    mgcv, 
-    stats, 
-    rlang, 
-    tidyfun, 
+    dplyr,
+    gamm4,
+    MASS,
+    Matrix,
+    mgcv,
+    rlang,
+    stats,
+    tidyfun,
     tidyr
-Remotes: github::tidyfun/tidyfun@dev
-License: GPL-3
+Suggests: 
+    modelr,
+    testthat,
+    tibble,
+    tidyverse
+Remotes: 
+    github::tidyfun/tidyfun@dev
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
-Suggests: 
-    testthat, tibble, tidyverse, modelr
 Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2

R/refundr-package.R

@@ -1,14 +1,13 @@
 #' refundr
 #'
-#'
-#'@description  `refundr` makes functional data analyses
-#' in `R` more consistent and user friendly\cr\cr
+#'@description
+#' `refundr` makes functional data analyses in `R` more consistent and
+#' user friendly\cr\cr
 #' `refundr` provides:
 #' - tidy interface for common fpca methods and funcional regression
 #' - plays nice with the `tidyfun` package for wrangling functional data
 #'
 #' Also see `vignette("refundr")` for a brief introduction.
 #'
-#' @name refundr
-#' @docType package
-NULL
+#' @keywords internal
+"_PACKAGE"

README.Rmd

@@ -7,13 +7,11 @@ output: github_document
 ```{r, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
-  comment = "##",
-  fig.width = 8, 
-  fig.height = 5.5,
-  out.width = "90%"
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
 )
 
-
 library(tidyverse)
 library(tidyfun)
 library(refundr)
@@ -25,26 +23,22 @@ options(
   ggplot2.continuous.colour = "viridis",
   ggplot2.continuous.fill = "viridis"
 )
-scale_colour_discrete = scale_colour_viridis_d
-scale_fill_discrete = scale_fill_viridis_d
-
-library("refundr")
-
+scale_colour_discrete <- scale_colour_viridis_d
+scale_fill_discrete <- scale_fill_viridis_d
 ```
 
 # refundr
 
 <!-- badges: start -->
-[![Travis build status](https://travis-ci.org/tidyfun/refundr.svg?branch=master)](https://travis-ci.org/tidyfun/refundr)
-[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/tidyfun/refundr?branch=master&svg=true)](https://ci.appveyor.com/project/tidyfun/refundr)
 <!-- badges: end -->
 
 The goal of **`refundr`** is to interface **`refund`** and **`tidyfun`**.
 
 ## Installation
 
-``` r
-devtools::install_github("tidyfun/refundr")
+```{r, eval = FALSE}
+# install.packages("pak")
+pak::pak("tidyfun/refundr")
 ```
 
 ## `rfr_fpca()`
@@ -54,26 +48,25 @@ The `rfr_fpca()` function peforms `fpca` using functions from the `refund` packa
 Below are examples using the dti and chf datasets. 
 
 
-```{r}
-
+```{r, eval = FALSE}
 library(refundr)
 library(tidyfun)
 library(tidyverse)
 
-# irregular data 
+# irregular data
 data(dti_df)
-dti_fpca = rfr_fpca(Y = "cca", data = dti_df)
-
-dti_df %>% 
-  modelr::add_predictions(dti_fpca, var = "cca_fits") %>% 
-  filter(case == "control") %>% 
-  ggplot(aes(y = cca_fits)) + 
-  geom_spaghetti(alpha = .4) + 
-  geom_spaghetti(aes(y = cca), color = "blue", alpha = .3) + 
+dti_fpca <- rfr_fpca(Y = "cca", data = dti_df)
+
+dti_df %>%
+  modelr::add_predictions(dti_fpca, var = "cca_fits") %>%
+  filter(case == "control") %>%
+  ggplot(aes(y = cca_fits)) +
+  geom_spaghetti(alpha = 0.4) +
+  geom_spaghetti(aes(y = cca), color = "blue", alpha = 0.3) +
   facet_grid(~sex)
 
 # regular data
 data(chf_df)
-dti_fpca = rfr_fpca(Y = "activity", data = chf_df)
+dti_fpca <- rfr_fpca(Y = "activity", data = chf_df)
 ```