Merge pull request #44 from RossanaTat/update_all

Updating some tests, adding vignettes and website

.github/workflows/R-CMD-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, website]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, website]
 
 name: R-CMD-check
 

.github/workflows/pkgdown.yaml

@@ -1,48 +1,48 @@
+# 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
+    branches: [master, DEV, update_all]
+  pull_request:
+    branches: [master, DEV]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    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@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Deploy package
-        run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - 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/test-coverage.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, website]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, website]
 
 name: test-coverage
 

.gitignore

@@ -6,3 +6,4 @@
 inst/doc
 doc
 Meta
+docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: joyn
 Type: Package
 Title: Tool for Diagnosis of Tables Joins and Complementary Join Features
-Version: 0.1.5
+Version: 0.1.6
 Authors@R: c(person(given = "R.Andres", 
                     family = "Castaneda", 
                     email = "[email protected]",
@@ -20,7 +20,7 @@ Description: Tool for diagnosing table joins. It combines the speed of `collapse
      of the `merge` command in `Stata`.
 License: MIT + file LICENSE
 Encoding: UTF-8
-URL: https://github.com/randrescastaneda/joyn
+URL: https://github.com/randrescastaneda/joyn, https://rossanatat.github.io/joyn/
 BugReports: https://github.com/randrescastaneda/joyn/issues
 Suggests: 
     badger,
@@ -29,15 +29,16 @@ Suggests:
     rmarkdown,
     testthat (>= 3.0.0),
     withr,
-    dplyr
+    dplyr,
+    tibble
 Config/testthat/edition: 3
 Imports: 
     rlang,
     data.table,
     glue,
     cli,
     utils,
-    collapse (>= 2.0.7),
+    collapse (>= 2.0.9),
     lifecycle
 Depends: 
     R (>= 2.10)

NAMESPACE

@@ -8,6 +8,7 @@ export(is_id)
 export(joyn)
 export(joyn_msg)
 export(left_join)
+export(merge)
 export(possible_ids)
 export(rename_to_valid)
 export(right_join)

NEWS.md

@@ -1,3 +1,5 @@
+# joyn 0.1.6
+
 # joyn 0.1.5
 
 # joyn 0.1.4

R/checks.R

@@ -18,7 +18,7 @@
 #'                 x  = 11:15)
 #' y1 = data.table(id = c(1,2, 4),
 #'                 y  = c(11L, 15L, 16))
-#' check_xy(x = x1, y=y1)
+#' joyn:::check_xy(x = x1, y=y1)
 #' }
 check_xy  <- function(x,y) {
 
@@ -70,20 +70,22 @@ check_xy  <- function(x,y) {
 #' @param dt data.frame to check
 #' @param name var name to check if has duplicates in dt
 #' @return logical either TRUE, if any duplicates are found, or FALSE otherwise
+#' @keywords internal
+#'
 #' @examples
 #' \dontrun{
 #' # When no duplicates
 #' x1 = data.table(id = c(1L, 1L, 2L, 3L, NA_integer_),
 #'                 t  = c(1L, 2L, 1L, 2L, NA_integer_),
 #'                 x  = 11:15)
-#' check_duplicate_names(x1, "x")
+#' joyn:::check_duplicate_names(x1, "x")
 #'
 #' # When duplicates
 #' x1_duplicates = data.frame(id = c(1L, 1L, 2L, 3L, NA_integer_),
 #'                            x  = c(1L, 2L, 1L, 2L, NA_integer_),
 #'                            x  = 11:15,
 #'                            check.names = FALSE)
-#' check_duplicate_names(x1_duplicates, "x")
+#' joyn:::check_duplicate_names(x1_duplicates, "x")
 #' }
 check_duplicate_names <- \(dt, name) {
   nm_x = names(dt)
@@ -93,8 +95,8 @@ check_duplicate_names <- \(dt, name) {
     store_msg("err",
           err     = paste(cli::symbol$cross, "Error:"),
           pale    = " Table {.field {name}} has the following
-                    {cli::qty(length(dups))} column{?s} duplicated:", 
-          timing  = "{.var {dups}}", 
+                    {cli::qty(length(dups))} column{?s} duplicated:",
+          timing  = "{.var {dups}}",
           pale    = "\nPlease rename or remove and try again.")
     return(TRUE)
   }
@@ -111,21 +113,21 @@ check_duplicate_names <- \(dt, name) {
 #' @examples
 #' \dontrun{
 #' # When null - reporting variable not returned in merged dt
-#' check_reportvar(reportvar = NULL)
+#' joyn:::check_reportvar(reportvar = NULL)
 #' # When FALSE - reporting variable not returned in merged dt
-#' check_reportvar(reportvar = FALSE)
+#' joyn:::check_reportvar(reportvar = FALSE)
 #' # When character
-#' check_reportvar(reportvar = ".joyn")
+#' joyn:::check_reportvar(reportvar = ".joyn")
 #' }
 
 check_reportvar <-
   function(reportvar, verbose = getOption("joyn.verbose")) {
     if (is.character(reportvar)) {
       reportvar <- rename_to_valid(reportvar, verbose)
       store_msg("info",
-           ok = cli::symbol$info, "  ", ok = cli::symbol$pointer, 
+           ok = cli::symbol$info, "  ", ok = cli::symbol$pointer,
            "  ",
-           pale = "Joyn's report available in variable", 
+           pale = "Joyn's report available in variable",
            bolded_pale = "  {reportvar}")
 
       return(reportvar)
@@ -134,8 +136,8 @@ check_reportvar <-
 
      store_msg("info",
            ok           = paste(cli::symbol$info, "  Note:"),
-           pale         = "  Reporting variable is", 
-           bolded_pale  = "\nnot", 
+           pale         = "  Reporting variable is",
+           bolded_pale  = "\nnot",
            pale         = "\nreturned")
 
       return(NULL)
@@ -164,7 +166,7 @@ check_reportvar <-
 #' y1 = data.frame(id = 1:2,
 #'                 y  = c(11L, 15L))
 #' # With var "id" shared in x and y
-#' check_by_vars(by = "id", x = x1, y = y1)
+#' joyn:::check_by_vars(by = "id", x = x1, y = y1)
 #'}
 check_by_vars <- function(by, x, y) {
 
@@ -215,10 +217,10 @@ check_by_vars <- function(by, x, y) {
 #'        x  = 11:15)
 #' y1 = data.frame(id = 1:2,
 #'                 y  = c(11L, 15L))
-#' check_match_type(x = x1, y=y1, by="id", match_type = "m:1")
+#' joyn:::check_match_type(x = x1, y=y1, by="id", match_type = "m:1")
 #'
 #' # Inconsistent match type
-#' check_match_type(x = x1, y=y1, by="id", match_type = "1:1")
+#' joyn:::check_match_type(x = x1, y=y1, by="id", match_type = "1:1")
 #' }
 check_match_type <- function(x, y, by, match_type, verbose) {
 
@@ -335,7 +337,7 @@ check_match_type <- function(x, y, by, match_type, verbose) {
 #' x1 = data.table(id = c(1L, 1L, 2L, 3L, NA_integer_),
 #'                 t  = c(1L, 2L, 1L, 2L, NA_integer_),
 #'                 x  = 11:15)
-#' is_match_type_error(x1, name = "x1", by = "id")
+#' joyn:::is_match_type_error(x1, name = "x1", by = "id")
 #' }
 
 is_match_type_error <- function(x, name, by, verbose, match_type_error) {
@@ -349,7 +351,7 @@ is_match_type_error <- function(x, name, by, verbose, match_type_error) {
     store_msg("err",
               err         = paste(cli::symbol$cross, "Error:"),
               pale        = "   table",
-              bolded_pale = "  {name}", 
+              bolded_pale = "  {name}",
               pale        = "  is not uniquely identified by",
               bolded_pale = "  {by2}")
 
@@ -375,11 +377,11 @@ is_match_type_error <- function(x, name, by, verbose, match_type_error) {
 #' y1 = data.table(id = 1:2,
 #'                y  = c(11L, 15L))
 #' # With y_vars_to_keep TRUE
-#' check_y_vars_to_keep(TRUE, y1, by = "id")
+#' joyn:::check_y_vars_to_keep(TRUE, y1, by = "id")
 #' # With y_vars_to_keep FALSE
-#' check_y_vars_to_keep(FALSE, y1, by = "id")
+#' joyn:::check_y_vars_to_keep(FALSE, y1, by = "id")
 #' # Specifying which y vars to keep
-#' check_y_vars_to_keep("y", y1, by = "id")
+#' joyn:::check_y_vars_to_keep("y", y1, by = "id")
 #' }
 
 check_y_vars_to_keep <- function(y_vars_to_keep, y, by) {
@@ -456,11 +458,11 @@ check_y_vars_to_keep <- function(y_vars_to_keep, y, by) {
 #'                 yd = c(1, 2, 5, 6, 3),
 #'                 y  = c(11L, 15L, 20L, 13L, 10L),
 #'                 x  = c(16:20))
-#' y_vars_to_keep <- check_y_vars_to_keep(TRUE, y2, by = "id")
+#' joyn:::y_vars_to_keep <- check_y_vars_to_keep(TRUE, y2, by = "id")
 #' x2 = data.frame(id = c(1, 1, 2, 3, NA),
 #'                 t  = c(1L, 2L, 1L, 2L, NA_integer_),
 #'                 x  = c(16, 12, NA, NA, 15))
-#' check_new_y_vars(x = x2, by="id", y_vars_to_keep)
+#' joyn:::check_new_y_vars(x = x2, by="id", y_vars_to_keep)
 #' }
 
 check_new_y_vars <- \(x, by, y_vars_to_keep) {
@@ -478,8 +480,8 @@ check_new_y_vars <- \(x, by, y_vars_to_keep) {
         "note",
         ok          = paste(cli::symbol$info, "  ", cli::symbol$pointer, "  "),
         pale        = "variable{?s} ",
-        bolded_pale = "{upvars}", 
-        pale        = "  in table", 
+        bolded_pale = "{upvars}",
+        pale        = "  in table",
         bolded_pale = "  {y}",
         pale        = "  {?is/are} ignored because arguments",
         bolded_pale = "  update_NAs and update_values",
@@ -510,13 +512,13 @@ check_new_y_vars <- \(x, by, y_vars_to_keep) {
 #'                  t  = c(1L, 2L, 1L, 2L, NA_integer_),
 #'                  x  = 11:15)
 #'
-#' is_valid_m_key(x1, by = c("id", "t"))
+#' joyn:::is_valid_m_key(x1, by = c("id", "t"))
 
 #' # example with valid specified "many" relationship
 #' x2 = data.frame(id  = c(1L, 1L, 1L, 3L, NA_integer_),
 #'                  t  = c(1L, 2L, 1L, 2L, NA_integer_),
 #'                  x  = 11:15)
-#' is_valid_m_key(x2, by = c("id", "t"))
+#' joyn:::is_valid_m_key(x2, by = c("id", "t"))
 #' }
 is_valid_m_key <- function(dt, by){
 
@@ -536,7 +538,6 @@ is_valid_m_key <- function(dt, by){
     FALSE
 }
 
-# Q: Do we document and test this function?
 
 check_suffixes <- function(suffixes) {