.github/workflows/check-pr.yaml

@@ -32,9 +32,6 @@ name: R-code-check-PR
 
 jobs:
   R-code-check-PR:
-    # do not run if we are the authors - the other checks will already run
-    if: ${{ github.event.comment.author_association != 'MEMBER' && github.event.comment.author_association != 'OWNER' }}
-    
     runs-on: ${{ matrix.config.os }}
 
     continue-on-error: ${{ matrix.config.allowfail }}

.github/workflows/check.yaml

@@ -131,11 +131,9 @@ jobs:
           _R_CHECK_LENGTH_1_LOGIC2_: verbose
           # during 'R CMD check', R_LIBS_USER will be overwritten, so:
           R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
-          # this is a required value to run the unit tests:
           R_RUN_TINYTEST: true
         run: |
           cd ..
-          ls -lh
           R CMD build AMR
           R CMD check --no-manual --run-donttest --run-dontrun AMR_*.tar.gz
         shell: bash
@@ -143,8 +141,6 @@ jobs:
       - name: Show unit tests output
         if: always()
         run: |
-          ls -lh
-          cd AMR
           find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
         shell: bash
 

.github/workflows/codecovr.yaml

@@ -33,30 +33,54 @@ name: code-coverage
 
 jobs:
   code-coverage:
-    runs-on: ubuntu-latest
+    runs-on: macOS-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}
     steps:
       - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: release
-          # use RStudio Package Manager to quickly install packages
-          use-public-rspm: true
       
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: r-lib/actions/setup-pandoc@v2
+        # with:
+        #   pandoc-version: '2.7.3' # The pandoc version to download (if necessary) and use.
+
+      - name: Query dependencies
+        # this will change once a week, so it will cache dependency updates
+        run: |
+          writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
+        shell: Rscript {0}
+        
+      - name: Restore cached R packages
+        # this step will add the step 'Post Restore cached R packages' on a succesful run
+        uses: actions/cache@v2
         with:
-          extra-packages: any::covr
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
+
+      - name: Unpack AMR and install R dependencies
+        run: |
+          tar -xf data-raw/AMR_latest.tar.gz
+          Rscript -e "source('data-raw/_install_deps.R')"
+        shell: bash
+        
+      - name: Show session info
+        run: |
+          options(width = 100)
+          utils::sessionInfo()
+          as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
+        shell: Rscript {0}
 
       - name: Test coverage
         env:
-          R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
           R_RUN_TINYTEST: true
         run: |
+          install.packages("covr", repos = "https://cran.rstudio.com/")
+          library(AMR)
+          library(tinytest)
           x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
           print(x)
         shell: Rscript {0}

.github/workflows/lintr.yaml

@@ -33,23 +33,34 @@ name: lintr
 
 jobs:
   lintr:
-    runs-on: ubuntu-latest
+    runs-on: macOS-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
       - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: release
-          # use RStudio Package Manager to quickly install packages
-          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - 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}
+
+      - name: Cache R packages
+        uses: actions/cache@v2
         with:
-          extra-packages: any::lintr
+          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-
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("lintr")
+        shell: Rscript {0}
 
       - name: Lint
         run: lintr::lint_package(linters = lintr::with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_length_linter = lintr::object_length_linter(length = 50L)), exclusions = list("R/aa_helper_pm_functions.R"))

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.1.9040
+Version: 1.8.1.9034
 Date: 2022-08-28
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
@@ -42,7 +42,7 @@ Suggests:
   rvest,
   tinytest,
   xml2
-VignetteBuilder: knitr,rmarkdown
+VignetteBuilder: knitr
 URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
 BugReports: https://github.com/msberends/AMR/issues
 License: GPL-2 | file LICENSE

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.1.9040
+# AMR 1.8.1.9034
 
 ### New
 * EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.

R/aa_helper_functions.R

@@ -651,7 +651,7 @@ dataset_UTF8_to_ASCII <- function(df) {
       df[, i] <- col
     }
   }
-  import_fn("as_tibble", "tibble")(df)
+  tibble::as_tibble(df)
 }
 
 # for eucast_rules() and mdro(), creates markdown output with URLs and names

R/first_isolate.R

@@ -529,7 +529,7 @@ first_isolate <- function(x = NULL,
   }
   if (!is.null(col_icu)) {
     if (icu_exclude == TRUE) {
-      message_("Excluding ", format(sum(col_icu, na.rm = TRUE), big.mark = ","), " isolates from ICU.",
+      message_("Excluding ", format(sum(!col_icu, na.rm = TRUE), big.mark = ","), " isolates from ICU.",
         add_fn = font_black,
         as_note = FALSE
       )

R/mo.R

@@ -204,12 +204,12 @@ as.mo <- function(x,
     ))
   }
 
-  reference_df <- repair_reference_df(reference_df)
   if (!is.null(reference_df) &&
     check_validity_mo_source(reference_df) &&
     isFALSE(Becker) &&
     isFALSE(Lancefield) &&
-    all(x %in% reference_df[, 1, drop = TRUE], na.rm = TRUE)) {
+    all(x %in% unlist(reference_df), na.rm = TRUE)) {
+    reference_df <- repair_reference_df(reference_df)
     suppressWarnings(
       y <- data.frame(x = x, stringsAsFactors = FALSE) %pm>%
         pm_left_join(reference_df, by = "x") %pm>%
@@ -221,7 +221,6 @@ as.mo <- function(x,
     y <- x
   } else {
     # will be checked for mo class in validation and uses exec_as.mo internally if necessary
-
     y <- mo_validate(
       x = x, property = "mo",
       Becker = Becker, Lancefield = Lancefield,
@@ -421,7 +420,7 @@ exec_as.mo <- function(x,
   }
 
   # all empty
-  if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0, na.rm = TRUE)) {
+  if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0)) {
     if (property == "mo") {
       return(set_clean_class(rep(NA_character_, length(x_input)),
         new_class = c("mo", "character")
@@ -429,7 +428,7 @@ exec_as.mo <- function(x,
     } else {
       return(rep(NA_character_, length(x_input)))
     }
-  } else if (all(x %in% reference_df[, 1, drop = TRUE], na.rm = TRUE)) {
+  } else if (all(x %in% reference_df[, 1, drop = TRUE][[1]])) {
     # all in reference df
     colnames(reference_df)[1] <- "x"
     suppressWarnings(
@@ -2358,9 +2357,6 @@ replace_ignore_pattern <- function(x, ignore_pattern) {
 }
 
 repair_reference_df <- function(reference_df) {
-  if (is.null(reference_df)) {
-    return(NULL)
-  }
   # has valid own reference_df
   reference_df <- reference_df %pm>%
     pm_filter(!is.na(mo))

data-raw/_install_deps.R

@@ -26,6 +26,7 @@
 # some old R instances have trouble installing tinytest, so we ship it too
 install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "Imports", "LinkingTo"))
 install.packages(getwd(), repos = NULL, type = "source")
+# install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
 
 pkg_suggests <- gsub(
   "[^a-zA-Z0-9]+", "",

data-raw/_pre_commit_hook.R

@@ -475,11 +475,6 @@ rm(current_globalenv)
 devtools::load_all(quiet = TRUE)
 
 
-# Update URLs -------------------------------------------------------------
-usethis::ui_info("Checking URLs for redirects")
-invisible(capture.output(urlchecker::url_update()))
-
-
 # Document pkg ------------------------------------------------------------
 usethis::ui_info("Documenting package")
 suppressMessages(devtools::document(quiet = TRUE))

data-raw/microorganisms.old.md5

@@ -1 +1 @@
-b57c9cc7380a233a2616a80e8e904a81
+19af89838b60bc8549d4474609629e8d

inst/tinytest/test-_misc.R

@@ -47,7 +47,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
 }
 
-# we rely on "grouped_tbl" being a class of grouped tibbles, so run a test that checks for this:
+# we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this:
 if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(ward)))
 }

inst/tinytest/test-ab_property.R

@@ -68,15 +68,15 @@ expect_true(ab_url("AMX") %like% "whocc.no")
 expect_warning(ab_url("ASP"))
 
 expect_identical(
-  colnames(set_ab_names(example_isolates[, 17:22])),
+  colnames(set_ab_names(example_isolates[, 20:25])),
   c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin")
 )
 expect_identical(
-  colnames(set_ab_names(example_isolates[, 17:22], language = "nl", snake_case = FALSE)),
+  colnames(set_ab_names(example_isolates[, 20:25], language = "nl", snake_case = FALSE)),
   c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine")
 )
 expect_identical(
-  colnames(set_ab_names(example_isolates[, 17:22], property = "atc")),
+  colnames(set_ab_names(example_isolates[, 20:25], property = "atc")),
   c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01")
 )
 

inst/tinytest/test-count.R

@@ -79,7 +79,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
         combination = count_susceptible(CIP, GEN)
       ) %>%
       pull(combination),
-    c(946, 428, 94)
+    c(253, 465, 192, 558)
   )
 
   # count_df

inst/tinytest/test-data.R

@@ -53,13 +53,12 @@ expect_false(any(is.na(as.disk(rsi_translation[which(rsi_translation$method == "
 # antibiotic names must always be coercible to their original AB code
 expect_identical(as.ab(antibiotics$name), antibiotics$ab)
 
-if (AMR:::pkg_is_available("tibble", also_load = FALSE)) {
-  # there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
-  datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
-  for (i in seq_len(length(datasets))) {
-    dataset <- get(datasets[i], envir = asNamespace("AMR"))
-    expect_identical(AMR:::dataset_UTF8_to_ASCII(dataset), dataset, info = datasets[i])
-  }
+# there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
+datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
+for (i in seq_len(length(datasets))) {
+  dataset <- get(datasets[i], envir = asNamespace("AMR"))
+  expect_identical(class(dataset), "data.frame")
+  expect_identical(AMR:::dataset_UTF8_to_ASCII(dataset), dataset, info = datasets[i])
 }
 
 df <- AMR:::MO_lookup

inst/tinytest/test-first_isolate.R

@@ -75,7 +75,7 @@ expect_equal(
     ),
     na.rm = TRUE
   ),
-  942
+  941
 )
 
 # set 1500 random observations to be of specimen type 'Urine'
@@ -160,7 +160,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
 
   # support for WHONET
   expect_message(example_isolates %>%
-    select(-patient) %>%
+    select(-patient_id) %>%
     mutate(
       `First name` = "test",
       `Last name` = "test",

inst/tinytest/test-proportion.R

@@ -84,7 +84,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
         combination_n = n_rsi(CIP, GEN)
       ) %>%
       pull(combination_n),
-    c(1181, 577, 116)
+    c(305, 617, 241, 711)
   )
 
   # proportion_df

tests/tinytest.R

@@ -27,9 +27,8 @@
 if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
   # env var 'R_LIBS_USER' got overwritten during 'R CMD check' in GitHub Actions, so:
   .libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
-  if (AMR:::pkg_is_available("tinytest", also_load = TRUE)) {
+  if (AMR:::pkg_is_available("tinytest")) {
     library(AMR)
-    set_AMR_locale("English")
     out <- test_package("AMR",
       testdir = ifelse(AMR:::dir.exists("inst/tinytest"),
         "inst/tinytest",
@@ -38,7 +37,7 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
       verbose = 99,
       color = FALSE
     )
-    cat("\n\nSUMMARY:\n")
+    cat("SUMMARY:\n")
     print(summary(out))
   }
 }