diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index be246921..4aa6d9ff 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -96,48 +96,44 @@ jobs: - uses: r-lib/actions/setup-pandoc@master - name: Query dependencies - if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' + # if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' run: | install.packages('remotes') saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) shell: Rscript {0} - name: Cache R packages - if: runner.os != 'Windows' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' + if: runner.os != 'Windows' + # && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' uses: actions/cache@v1 with: path: ${{ env.R_LIBS_USER }} key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }} restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3- - - name: Install Linux dependencies - if: runner.os == 'Linux' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' - env: - RHUB_PLATFORM: linux-x86_64-ubuntu-gcc - run: | - Rscript -e "remotes::install_github('r-hub/sysreqs')" - sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") - sudo -s eval "$sysreqs" + # - name: Install Linux dependencies + # if: runner.os == 'Linux' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' + # env: + # RHUB_PLATFORM: linux-x86_64-ubuntu-gcc + # run: | + # Rscript -e "remotes::install_github('r-hub/sysreqs')" + # sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") + # sudo -s eval "$sysreqs" - - name: Install Linux dependencies on old R versions - if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' - env: - RHUB_PLATFORM: linux-x86_64-ubuntu-gcc + - name: Install Linux dependencies + if: runner.os == 'Linux' + # if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' + # env: + # RHUB_PLATFORM: linux-x86_64-ubuntu-gcc # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu). # we don't want to depend on the sysreqs pkg here, as it requires a quite new R version run: | sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev - - name: Install macOS dependencies - if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'devel' - run: | - brew install mariadb-connector-c - - name: Install package dependencies - if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' + # if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' run: | remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") shell: Rscript {0} - name: Session info @@ -147,17 +143,28 @@ jobs: as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] shell: Rscript {0} - - name: Run R CMD check - if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' - env: - _R_CHECK_CRAN_INCOMING_: false - _R_CHECK_LENGTH_1_CONDITION_: verbose - _R_CHECK_LENGTH_1_LOGIC2_: verbose - run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") - shell: Rscript {0} + # - name: Run R CMD check + # if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' + # env: + # _R_CHECK_CRAN_INCOMING_: false + # _R_CHECK_LENGTH_1_CONDITION_: verbose + # _R_CHECK_LENGTH_1_LOGIC2_: verbose + # run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") + # shell: Rscript {0} + + - name: Unpack AMR package on Linux and macOS + if: runner.os != 'Windows' + run: | + ls -lh + tar -xvf data-raw/AMR_latest.tar.gz + + - name: Unpack AMR package on Windows + if: runner.os == 'Windows' + run: | + tar -xvf data-raw/AMR_latest.tar.gz - - name: Run R CMD check on older R versions - if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' + - name: Run R CMD check + # if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' env: _R_CHECK_CRAN_INCOMING_: false _R_CHECK_FORCE_SUGGESTS_: false @@ -165,7 +172,6 @@ jobs: _R_CHECK_LENGTH_1_CONDITION_: verbose _R_CHECK_LENGTH_1_LOGIC2_: verbose run: | - tar -xvf data-raw/AMR_latest.tar.gz R CMD check AMR --no-manual --no-build-vignettes - name: Show testthat output diff --git a/DESCRIPTION b/DESCRIPTION index 82ed124a..5d91b419 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.6.0.9022 +Version: 1.6.0.9023 Date: 2021-05-13 Title: Antimicrobial Resistance Data Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 7407e568..d07d00e6 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.6.0.9022 +# `AMR` 1.6.0.9023 ## Last updated: 13 May 2021 ### New @@ -11,6 +11,7 @@ * The `first_isolate()` function can now take a vector of values for `col_keyantibiotics` and can have an episode length of `Inf` * Since the phenotype-based method is the new default, `filter_first_isolate()` renders the `filter_first_weighted_isolate()` function redundant. For this reason, `filter_first_weighted_isolate()` is now deprecated. * The documentation of the `first_isolate()` and `key_antimicrobials()` functions has been completely rewritten. +* Added `ggplot()` method for `resistance_predict()` ### Changed * Custom MDRO guidelines (`mdro()`, `custom_mdro_guideline()`): diff --git a/R/resistance_predict.R b/R/resistance_predict.R index 2addf09b..a2d9d1ad 100755 --- a/R/resistance_predict.R +++ b/R/resistance_predict.R @@ -347,6 +347,20 @@ plot.resistance_predict <- function(x, main = paste("Resistance Prediction of", col = "grey40") } + +#' @method ggplot resistance_predict +#' @rdname resistance_predict +# will be exported using s3_register() in R/zzz.R +ggplot.resistance_predict <- function(x, + main = paste("Resistance Prediction of", x_name), + ribbon = TRUE, + ...) { + x_name <- paste0(ab_name(attributes(x)$ab), " (", attributes(x)$ab, ")") + meet_criteria(main, allow_class = "character", has_length = 1) + meet_criteria(ribbon, allow_class = "logical", has_length = 1) + ggplot_rsi_predict(x = x, main = main, ribbon = ribbon, ...) +} + #' @rdname resistance_predict #' @export ggplot_rsi_predict <- function(x, @@ -360,14 +374,14 @@ ggplot_rsi_predict <- function(x, stop_ifnot_installed("ggplot2") stop_ifnot(inherits(x, "resistance_predict"), "`x` must be a resistance prediction model created with resistance_predict()") - if (attributes(x)$I_as_S == TRUE) { ylab <- "%R" } else { ylab <- "%IR" } - p <- ggplot2::ggplot(x, ggplot2::aes(x = year, y = value)) + + p <- ggplot2::ggplot(as.data.frame(x, stringsAsFactors = FALSE), + ggplot2::aes(x = year, y = value)) + ggplot2::geom_point(data = subset(x, !is.na(observations)), size = 2) + scale_y_percent(limits = c(0, 1)) + diff --git a/R/zzz.R b/R/zzz.R index bb4b999a..1d4ad5b0 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -64,6 +64,7 @@ if (utf8_supported && !is_latex) { s3_register("ggplot2::ggplot", "rsi") s3_register("ggplot2::ggplot", "mic") s3_register("ggplot2::ggplot", "disk") + s3_register("ggplot2::ggplot", "resistance_predict") # if mo source exists, fire it up (see mo_source()) try({ diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index 493341ea..7ae67f82 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/404.html b/docs/404.html index 3ff24366..72f99453 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9022 + 1.6.0.9023 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 24dbfdc7..b75c1157 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9022 + 1.6.0.9023 diff --git a/docs/articles/index.html b/docs/articles/index.html index 6c6aba65..b9a4299e 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9022 + 1.6.0.9023 diff --git a/docs/authors.html b/docs/authors.html index 7afcb0de..ec71a7ed 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9022 + 1.6.0.9023 diff --git a/docs/index.html b/docs/index.html index 97af1c2f..b9f99bb3 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.6.0.9022 + 1.6.0.9023 diff --git a/docs/news/index.html b/docs/news/index.html index c1be87cf..964bb198 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9022 + 1.6.0.9023 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

- Unreleased AMR 1.6.0.9022

+
+

+ Unreleased AMR 1.6.0.9023

Last updated: 13 May 2021 @@ -262,6 +262,8 @@
  • The documentation of the first_isolate() and key_antimicrobials() functions has been completely rewritten.
    • +
  • Added ggplot() method for resistance_predict() +

    • @@ -346,7 +348,7 @@ #> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"

  • Support for custom MDRO guidelines, using the new custom_mdro_guideline() function, please see mdro() for additional info

    • -

  • ggplot() generics for classes <mic> and <disk>

    • +

  • ggplot() generics for classes <mic> and <disk>

  • Function mo_is_yeast(), which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:

    @@ -403,7 +405,7 @@
 
  • Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent
    • 
 
  • All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)
    • 
 
  • Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see translate)
    • 
-
  • Plotting is now possible with base R using plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
    • 
+
  • Plotting is now possible with base R using plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
    •
  • Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the microorganisms data set
    • @@ -420,7 +422,7 @@ is.rsi.eligible() now detects if the column name resembles an antibiotic name or code and now returns TRUE immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.
  • Functions get_episode() and is_new_episode() now support less than a day as value for argument episode_days (e.g., to include one patient/test per hour)
  • Argument ampc_cephalosporin_resistance in eucast_rules() now also applies to value “I” (not only “S”)
    • -
  • Functions print() and summary() on a Principal Components Analysis object (pca()) now print additional group info if the original data was grouped using dplyr::group_by() +
  • Functions print() and summary() on a Principal Components Analysis object (pca()) now print additional group info if the original data was grouped using dplyr::group_by()
  • Improved speed and reliability of guess_ab_col(). As this also internally improves the reliability of first_isolate() and mdro(), this might have a slight impact on the results of those functions.
  • Fix for mo_name() when used in other languages than English
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 36ac5e84..5e8dc398 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -12,7 +12,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2021-05-13T13:55Z +last_built: 2021-05-13T17:31Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/index.html b/docs/reference/index.html index 292064ef..d2aeef5d 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9022 + 1.6.0.9023
    @@ -538,7 +538,7 @@ -

    resistance_predict() rsi_predict() plot(<resistance_predict>) ggplot_rsi_predict()

    +

    resistance_predict() rsi_predict() plot(<resistance_predict>) ggplot(<resistance_predict>) ggplot_rsi_predict()

    Predict antimicrobial resistance

    diff --git a/docs/reference/plot.html b/docs/reference/plot.html index 5faa684f..6b0ab2ee 100644 --- a/docs/reference/plot.html +++ b/docs/reference/plot.html @@ -82,7 +82,7 @@ AMR (for R) - 1.6.0.9021 + 1.6.0.9023
    @@ -258,7 +258,7 @@ ) # S3 method for mic -ggplot( +ggplot( data, mapping = NULL, title = paste("MIC values of", deparse(substitute(data))), @@ -289,7 +289,7 @@ ) # S3 method for disk -ggplot( +ggplot( data, mapping = NULL, title = paste("Disk zones of", deparse(substitute(data))), @@ -314,7 +314,7 @@ ) # S3 method for rsi -ggplot( +ggplot( data, mapping = NULL, title = paste("Resistance Overview of", deparse(substitute(data))), diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html index f8f32b4d..5fd413e6 100644 --- a/docs/reference/resistance_predict.html +++ b/docs/reference/resistance_predict.html @@ -82,7 +82,7 @@ AMR (for R) - 1.6.0.9021 + 1.6.0.9023 @@ -275,6 +275,9 @@ # S3 method for resistance_predict plot(x, main = paste("Resistance Prediction of", x_name), ...) +# S3 method for resistance_predict +ggplot(x, main = paste("Resistance Prediction of", x_name), ribbon = TRUE, ...) + ggplot_rsi_predict( x, main = paste("Resistance Prediction of", x_name), diff --git a/docs/survey.html b/docs/survey.html index f15ab302..5e9b786b 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9022 + 1.6.0.9023 diff --git a/man/resistance_predict.Rd b/man/resistance_predict.Rd index b35914ba..e178ff79 100644 --- a/man/resistance_predict.Rd +++ b/man/resistance_predict.Rd @@ -4,6 +4,7 @@ \alias{resistance_predict} \alias{rsi_predict} \alias{plot.resistance_predict} +\alias{ggplot.resistance_predict} \alias{ggplot_rsi_predict} \title{Predict antimicrobial resistance} \usage{ @@ -39,6 +40,8 @@ rsi_predict( \method{plot}{resistance_predict}(x, main = paste("Resistance Prediction of", x_name), ...) +\method{ggplot}{resistance_predict}(x, main = paste("Resistance Prediction of", x_name), ribbon = TRUE, ...) + ggplot_rsi_predict( x, main = paste("Resistance Prediction of", x_name), diff --git a/tests/testthat.R b/tests/testthat.R index d9acb765..f818b976 100755 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -26,8 +26,7 @@ # the testthat package is in Suggests, but very old R versions will not be # able to install it. Yet, we want basic R CMD CHECK's in those R versions # as well, so only run unit tests in later R versions: -if (require("testthat")) { - library(testthat, warn.conflicts = FALSE) +if (require("testthat", warn.conflicts = FALSE)) { library(AMR) test_check("AMR") } diff --git a/tests/testthat/test-_misc.R b/tests/testthat/test-_misc.R index 8827ece3..b1b82ab0 100755 --- a/tests/testthat/test-_misc.R +++ b/tests/testthat/test-_misc.R @@ -57,9 +57,10 @@ test_that("looking up ab columns works", { test_that("looking up ab columns works", { skip_on_cran() - library(dplyr) - - # we rely on "grouped_tbl" being a class of grouped tibbles, so: - expect_true(is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id))) + + # we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this: + if (require("dplyr")) { + expect_true(is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id))) + } }) diff --git a/tests/testthat/test-count.R b/tests/testthat/test-count.R index 8a765a45..f60f62ae 100644 --- a/tests/testthat/test-count.R +++ b/tests/testthat/test-count.R @@ -41,42 +41,6 @@ test_that("counts work", { expect_equal(suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX), count_SI(example_isolates$AMX)) - library(dplyr, warn.conflicts = FALSE) - expect_equal(example_isolates %>% count_susceptible(AMC), 1433) - expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687) - expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764) - expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), 1798) - expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = FALSE), 1936) - expect_identical(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), - example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE) + - example_isolates %>% count_resistant(AMC, GEN, only_all_tested = TRUE)) - - # count of cases - expect_equal(example_isolates %>% - group_by(hospital_id) %>% - summarise(cipro = count_susceptible(CIP), - genta = count_susceptible(GEN), - combination = count_susceptible(CIP, GEN)) %>% - pull(combination), - c(253, 465, 192, 558)) - - # count_df - expect_equal( - example_isolates %>% select(AMX) %>% count_df() %>% pull(value), - c(example_isolates$AMX %>% count_susceptible(), - example_isolates$AMX %>% count_resistant()) - ) - expect_equal( - example_isolates %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value), - c(suppressWarnings(example_isolates$AMX %>% count_S()), - suppressWarnings(example_isolates$AMX %>% count_IR())) - ) - expect_equal( - example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value), - c(suppressWarnings(example_isolates$AMX %>% count_S()), - example_isolates$AMX %>% count_I(), - example_isolates$AMX %>% count_R()) - ) # warning for speed loss reset_all_thrown_messages() @@ -94,11 +58,49 @@ test_that("counts work", { expect_error(count_df(c("A", "B", "C"))) expect_error(count_df(example_isolates[, "date"])) - # grouping in rsi_calc_df() (= backbone of rsi_df()) - expect_true("hospital_id" %in% (example_isolates %>% - group_by(hospital_id) %>% - select(hospital_id, AMX, CIP, gender) %>% - rsi_df() %>% - colnames())) + if (require("dplyr")) { + expect_equal(example_isolates %>% count_susceptible(AMC), 1433) + expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687) + expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764) + expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), 1798) + expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = FALSE), 1936) + expect_identical(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), + example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE) + + example_isolates %>% count_resistant(AMC, GEN, only_all_tested = TRUE)) + + # count of cases + expect_equal(example_isolates %>% + group_by(hospital_id) %>% + summarise(cipro = count_susceptible(CIP), + genta = count_susceptible(GEN), + combination = count_susceptible(CIP, GEN)) %>% + pull(combination), + c(253, 465, 192, 558)) + + # count_df + expect_equal( + example_isolates %>% select(AMX) %>% count_df() %>% pull(value), + c(example_isolates$AMX %>% count_susceptible(), + example_isolates$AMX %>% count_resistant()) + ) + expect_equal( + example_isolates %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value), + c(suppressWarnings(example_isolates$AMX %>% count_S()), + suppressWarnings(example_isolates$AMX %>% count_IR())) + ) + expect_equal( + example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value), + c(suppressWarnings(example_isolates$AMX %>% count_S()), + example_isolates$AMX %>% count_I(), + example_isolates$AMX %>% count_R()) + ) + + # grouping in rsi_calc_df() (= backbone of rsi_df()) + expect_true("hospital_id" %in% (example_isolates %>% + group_by(hospital_id) %>% + select(hospital_id, AMX, CIP, gender) %>% + rsi_df() %>% + colnames())) + } }) diff --git a/tests/testthat/test-disk.R b/tests/testthat/test-disk.R index 9eef32b9..82a94e4d 100755 --- a/tests/testthat/test-disk.R +++ b/tests/testthat/test-disk.R @@ -54,7 +54,8 @@ test_that("disk works", { } expect_output(print(as.disk(12))) - library(dplyr, warn.conflicts = FALSE) - expect_output(print(tibble(d = as.disk(12)))) + if (require("dplyr")) { + expect_output(print(tibble(d = as.disk(12)))) + } }) diff --git a/tests/testthat/test-episode.R b/tests/testthat/test-episode.R index fc27b40c..e909cfc9 100644 --- a/tests/testthat/test-episode.R +++ b/tests/testthat/test-episode.R @@ -41,18 +41,18 @@ test_that("episodes work", { expect_equal(get_episode(test_df$date, 365), c(1, 1, 2, 2, 2, 3, 3, 4, 1, 2, 2, 2, 3)) - library(dplyr) - expect_identical(test_df %>% group_by(patient_id) %>% mutate(f = is_new_episode(date, 365)) %>% pull(f), - c(TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE)) - - suppressMessages( - x <- example_isolates %>% - mutate(out = first_isolate(., include_unknown = TRUE, method = "episode-based", info = FALSE)) - ) - - y <- example_isolates %>% - group_by(patient_id, mo) %>% - mutate(out = is_new_episode(date, 365)) - - expect_identical(which(x$out), which(y$out)) + if (require("dplyr")) { + expect_identical(test_df %>% group_by(patient_id) %>% mutate(f = is_new_episode(date, 365)) %>% pull(f), + c(TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE)) + + suppressMessages( + x <- example_isolates %>% + mutate(out = first_isolate(., include_unknown = TRUE, method = "episode-based", info = FALSE)) + ) + y <- example_isolates %>% + group_by(patient_id, mo) %>% + mutate(out = is_new_episode(date, 365)) + + expect_identical(which(x$out), which(y$out)) + } }) diff --git a/tests/testthat/test-filter_ab_class.R b/tests/testthat/test-filter_ab_class.R index 439551b0..4065bc6b 100644 --- a/tests/testthat/test-filter_ab_class.R +++ b/tests/testthat/test-filter_ab_class.R @@ -28,26 +28,27 @@ context("filter_ab_class.R") test_that("ATC-group filtering works", { skip_on_cran() - library(dplyr) - expect_gt(example_isolates %>% filter_ab_class("carbapenem") %>% nrow(), 0) - expect_gt(example_isolates %>% filter_aminoglycosides() %>% ncol(), 0) - expect_gt(example_isolates %>% filter_carbapenems() %>% ncol(), 0) - expect_gt(example_isolates %>% filter_cephalosporins() %>% ncol(), 0) - expect_gt(example_isolates %>% filter_1st_cephalosporins() %>% ncol(), 0) - expect_gt(example_isolates %>% filter_2nd_cephalosporins() %>% ncol(), 0) - expect_gt(example_isolates %>% filter_3rd_cephalosporins() %>% ncol(), 0) - expect_gt(example_isolates %>% filter_4th_cephalosporins() %>% ncol(), 0) - expect_gt(example_isolates %>% filter_5th_cephalosporins() %>% ncol(), 0) - expect_gt(example_isolates %>% filter_fluoroquinolones() %>% ncol(), 0) - expect_gt(example_isolates %>% filter_glycopeptides() %>% ncol(), 0) - expect_gt(example_isolates %>% filter_macrolides() %>% ncol(), 0) - expect_gt(example_isolates %>% filter_oxazolidinones() %>% ncol(), 0) - expect_gt(example_isolates %>% filter_penicillins() %>% ncol(), 0) - expect_gt(example_isolates %>% filter_tetracyclines() %>% ncol(), 0) - - expect_gt(example_isolates %>% filter_carbapenems("R", "all") %>% nrow(), 0) - - expect_error(example_isolates %>% filter_carbapenems(result = "test")) - expect_error(example_isolates %>% filter_carbapenems(scope = "test")) - expect_message(example_isolates %>% select(1:3) %>% filter_carbapenems()) + if (require("dplyr")) { + expect_gt(example_isolates %>% filter_ab_class("carbapenem") %>% nrow(), 0) + expect_gt(example_isolates %>% filter_aminoglycosides() %>% ncol(), 0) + expect_gt(example_isolates %>% filter_carbapenems() %>% ncol(), 0) + expect_gt(example_isolates %>% filter_cephalosporins() %>% ncol(), 0) + expect_gt(example_isolates %>% filter_1st_cephalosporins() %>% ncol(), 0) + expect_gt(example_isolates %>% filter_2nd_cephalosporins() %>% ncol(), 0) + expect_gt(example_isolates %>% filter_3rd_cephalosporins() %>% ncol(), 0) + expect_gt(example_isolates %>% filter_4th_cephalosporins() %>% ncol(), 0) + expect_gt(example_isolates %>% filter_5th_cephalosporins() %>% ncol(), 0) + expect_gt(example_isolates %>% filter_fluoroquinolones() %>% ncol(), 0) + expect_gt(example_isolates %>% filter_glycopeptides() %>% ncol(), 0) + expect_gt(example_isolates %>% filter_macrolides() %>% ncol(), 0) + expect_gt(example_isolates %>% filter_oxazolidinones() %>% ncol(), 0) + expect_gt(example_isolates %>% filter_penicillins() %>% ncol(), 0) + expect_gt(example_isolates %>% filter_tetracyclines() %>% ncol(), 0) + + expect_gt(example_isolates %>% filter_carbapenems("R", "all") %>% nrow(), 0) + + expect_error(example_isolates %>% filter_carbapenems(result = "test")) + expect_error(example_isolates %>% filter_carbapenems(scope = "test")) + expect_message(example_isolates %>% select(1:3) %>% filter_carbapenems()) + } }) diff --git a/tests/testthat/test-ggplot_rsi.R b/tests/testthat/test-ggplot_rsi.R index c8dad2b5..5ce82c08 100644 --- a/tests/testthat/test-ggplot_rsi.R +++ b/tests/testthat/test-ggplot_rsi.R @@ -26,64 +26,65 @@ context("ggplot_rsi.R") test_that("ggplot_rsi works", { - + skip_on_cran() skip_if_not_installed("ggplot2") - - library(dplyr, warn.conflicts = FALSE) - library(ggplot2) - - pdf(NULL) # prevent Rplots.pdf being created - - # data should be equal - expect_equal( - (example_isolates %>% select(AMC, CIP) %>% ggplot_rsi())$data %>% summarise_all(resistance) %>% as.double(), - example_isolates %>% select(AMC, CIP) %>% summarise_all(resistance) %>% as.double() - ) - - print(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic")) - print(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation")) - - expect_equal( - (example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))$data %>% summarise_all(resistance) %>% as.double(), - example_isolates %>% select(AMC, CIP) %>% summarise_all(resistance) %>% as.double() - ) - - expect_equal( - (example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>% summarise_all(resistance) %>% as.double(), - example_isolates %>% select(AMC, CIP) %>% summarise_all(resistance) %>% as.double() - ) - - expect_equal( - (example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>% summarise_all(count_resistant) %>% as.double(), - example_isolates %>% select(AMC, CIP) %>% summarise_all(count_resistant) %>% as.double() - ) - - # support for scale_type ab and mo - expect_equal(class((data.frame(mo = as.mo(c("e. coli", "s aureus")), - n = c(40, 100)) %>% - ggplot(aes(x = mo, y = n)) + - geom_col())$data), - "data.frame") - expect_equal(class((data.frame(ab = as.ab(c("amx", "amc")), - n = c(40, 100)) %>% - ggplot(aes(x = ab, y = n)) + - geom_col())$data), - "data.frame") - - expect_equal(class((data.frame(ab = as.ab(c("amx", "amc")), - n = c(40, 100)) %>% - ggplot(aes(x = ab, y = n)) + - geom_col())$data), - "data.frame") - - # support for manual colours - expect_equal(class((ggplot(data.frame(x = c("Value1", "Value2", "Value3"), - y = c(1, 2, 3), - z = c("Value4", "Value5", "Value6"))) + - geom_col(aes(x = x, y = y, fill = z)) + - scale_rsi_colours(Value4 = "S", Value5 = "I", Value6 = "R"))$data), - "data.frame") + skip_if_not_installed("dplyr") + if (require("dplyr") & require("ggplot2")) { + + pdf(NULL) # prevent Rplots.pdf being created + + # data should be equal + expect_equal( + (example_isolates %>% select(AMC, CIP) %>% ggplot_rsi())$data %>% summarise_all(resistance) %>% as.double(), + example_isolates %>% select(AMC, CIP) %>% summarise_all(resistance) %>% as.double() + ) + + print(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic")) + print(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation")) + + expect_equal( + (example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))$data %>% summarise_all(resistance) %>% as.double(), + example_isolates %>% select(AMC, CIP) %>% summarise_all(resistance) %>% as.double() + ) + + expect_equal( + (example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>% summarise_all(resistance) %>% as.double(), + example_isolates %>% select(AMC, CIP) %>% summarise_all(resistance) %>% as.double() + ) + + expect_equal( + (example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>% summarise_all(count_resistant) %>% as.double(), + example_isolates %>% select(AMC, CIP) %>% summarise_all(count_resistant) %>% as.double() + ) + + # support for scale_type ab and mo + expect_equal(class((data.frame(mo = as.mo(c("e. coli", "s aureus")), + n = c(40, 100)) %>% + ggplot(aes(x = mo, y = n)) + + geom_col())$data), + "data.frame") + expect_equal(class((data.frame(ab = as.ab(c("amx", "amc")), + n = c(40, 100)) %>% + ggplot(aes(x = ab, y = n)) + + geom_col())$data), + "data.frame") + + expect_equal(class((data.frame(ab = as.ab(c("amx", "amc")), + n = c(40, 100)) %>% + ggplot(aes(x = ab, y = n)) + + geom_col())$data), + "data.frame") + + # support for manual colours + expect_equal(class((ggplot(data.frame(x = c("Value1", "Value2", "Value3"), + y = c(1, 2, 3), + z = c("Value4", "Value5", "Value6"))) + + geom_col(aes(x = x, y = y, fill = z)) + + scale_rsi_colours(Value4 = "S", Value5 = "I", Value6 = "R"))$data), + "data.frame") + + } }) diff --git a/tests/testthat/test-key_antimicrobials.R b/tests/testthat/test-key_antimicrobials.R index ad00f676..2a5910e4 100644 --- a/tests/testthat/test-key_antimicrobials.R +++ b/tests/testthat/test-key_antimicrobials.R @@ -37,6 +37,5 @@ test_that("key_antimcrobials work", { expect_true(antimicrobials_equal(".SS", "SI.", ignore_I = TRUE, type = "keyantimicrobials")) expect_false(antimicrobials_equal(".SS", "SI.", ignore_I = FALSE, type = "keyantimicrobials")) - library(dplyr, warn.conflicts = FALSE) - expect_warning(key_antimicrobials(example_isolates %>% slice(rep(1, 10)))) + expect_warning(key_antimicrobials(example_isolates[rep(1, 10), ])) }) diff --git a/tests/testthat/test-mdro.R b/tests/testthat/test-mdro.R index b5423e73..838a9cd6 100755 --- a/tests/testthat/test-mdro.R +++ b/tests/testthat/test-mdro.R @@ -44,7 +44,6 @@ test_that("mdro works", { # check class expect_equal(class(outcome), c("ordered", "factor")) - library(dplyr) # example_isolates should have these finding using Dutch guidelines expect_equal(as.double(table(outcome)), c(1970, 24, 6)) # 1970 neg, 24 unconfirmed, 6 pos @@ -245,8 +244,8 @@ test_that("mdro works", { info = FALSE)) # print groups - library(dplyr) - expect_output(x <- mdro(example_isolates %>% group_by(hospital_id), info = TRUE)) - expect_output(x <- mdro(example_isolates %>% group_by(hospital_id), guideline = custom, info = TRUE)) - + if (require("dplyr")) { + expect_output(x <- mdro(example_isolates %>% group_by(hospital_id), info = TRUE)) + expect_output(x <- mdro(example_isolates %>% group_by(hospital_id), guideline = custom, info = TRUE)) + } }) diff --git a/tests/testthat/test-mic.R b/tests/testthat/test-mic.R index 0befef74..d4afad7b 100755 --- a/tests/testthat/test-mic.R +++ b/tests/testthat/test-mic.R @@ -62,8 +62,9 @@ test_that("mic works", { expect_s3_class(summary(as.mic(c(2, 8))), c("summaryDefault", "table")) - library(dplyr, warn.conflicts = FALSE) - expect_output(print(tibble(m = as.mic(2:4)))) + if (require("dplyr")) { + expect_output(print(tibble(m = as.mic(2:4)))) + } }) test_that("mathematical functions on mic work", { diff --git a/tests/testthat/test-mo.R b/tests/testthat/test-mo.R index e1f13688..7afb945d 100644 --- a/tests/testthat/test-mo.R +++ b/tests/testthat/test-mo.R @@ -28,10 +28,8 @@ context("mo.R") test_that("as.mo works", { skip_on_cran() - - library(dplyr, warn.conflicts = FALSE) - - MOs <- microorganisms %>% filter(!is.na(mo), nchar(mo) > 3) + + MOs <- subset(microorganisms, !is.na(mo) & nchar(mo) > 3) expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo))) expect_identical( @@ -152,37 +150,43 @@ test_that("as.mo works", { expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SLVR") expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRPK") # group K - # select with one column - expect_identical( - example_isolates[1:10, ] %>% - left_join_microorganisms() %>% - select(genus) %>% - as.mo() %>% - as.character(), - c("B_ESCHR", "B_ESCHR", "B_STPHY", "B_STPHY", "B_STPHY", - "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY")) - - # select with two columns - expect_identical( - example_isolates[1:10, ] %>% - pull(mo), - example_isolates[1:10, ] %>% - left_join_microorganisms() %>% - select(genus, species) %>% - as.mo()) + if (require("dplyr")) { + # select with one column + expect_identical( + example_isolates[1:10, ] %>% + left_join_microorganisms() %>% + select(genus) %>% + as.mo() %>% + as.character(), + c("B_ESCHR", "B_ESCHR", "B_STPHY", "B_STPHY", "B_STPHY", + "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY")) + + # select with two columns + expect_identical( + example_isolates[1:10, ] %>% + pull(mo), + example_isolates[1:10, ] %>% + left_join_microorganisms() %>% + select(genus, species) %>% + as.mo()) + + # too many columns + expect_error(example_isolates %>% select(1:3) %>% as.mo()) + + # test pull + expect_equal(nrow(example_isolates %>% mutate(mo = as.mo(mo))), + 2000) + expect_true(example_isolates %>% pull(mo) %>% is.mo()) + } # unknown results expect_warning(as.mo(c("INVALID", "Yeah, unknown"))) - # too many columns - expect_error(example_isolates %>% select(1:3) %>% as.mo()) - + # print expect_output(print(as.mo(c("B_ESCHR_COLI", NA)))) - # test pull - expect_equal(nrow(example_isolates %>% mutate(mo = as.mo(mo))), - 2000) + # test data.frame expect_equal(nrow(data.frame(test = as.mo("B_ESCHR_COLI"))), @@ -265,7 +269,6 @@ test_that("as.mo works", { rep("UNKNOWN", 3)) expect_null(mo_failures()) - expect_true(example_isolates %>% pull(mo) %>% is.mo()) expect_error(translate_allow_uncertain(5)) diff --git a/tests/testthat/test-mo_property.R b/tests/testthat/test-mo_property.R index 968797a2..c7b338c8 100644 --- a/tests/testthat/test-mo_property.R +++ b/tests/testthat/test-mo_property.R @@ -131,11 +131,12 @@ test_that("mo_property works", { expect_equal(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")), "Escherichia coli") - library(dplyr) - expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(), - 730) - expect_equal(example_isolates %>% filter(mo_is_gram_positive()) %>% nrow(), - 1238) - expect_equal(example_isolates %>% filter(mo_is_intrinsic_resistant(ab = "Vancomycin")) %>% nrow(), - 710) + if (require("dplyr")) { + expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(), + 730) + expect_equal(example_isolates %>% filter(mo_is_gram_positive()) %>% nrow(), + 1238) + expect_equal(example_isolates %>% filter(mo_is_intrinsic_resistant(ab = "Vancomycin")) %>% nrow(), + 710) + } }) diff --git a/tests/testthat/test-proportion.R b/tests/testthat/test-proportion.R index 009bb90e..987c1fa0 100755 --- a/tests/testthat/test-proportion.R +++ b/tests/testthat/test-proportion.R @@ -52,30 +52,49 @@ test_that("proportions works", { 0.9382647, tolerance = 0.0001) - library(dplyr) - # percentages - expect_equal(example_isolates %>% - group_by(hospital_id) %>% - summarise(R = proportion_R(CIP, as_percent = TRUE), - I = proportion_I(CIP, as_percent = TRUE), - S = proportion_S(CIP, as_percent = TRUE), - n = n_rsi(CIP), - total = n()) %>% - pull(n) %>% - sum(), - 1409) - - # count of cases - expect_equal(example_isolates %>% - group_by(hospital_id) %>% - summarise(cipro_p = proportion_SI(CIP, as_percent = TRUE), - cipro_n = n_rsi(CIP), - genta_p = proportion_SI(GEN, as_percent = TRUE), - genta_n = n_rsi(GEN), - combination_p = proportion_SI(CIP, GEN, as_percent = TRUE), - combination_n = n_rsi(CIP, GEN)) %>% - pull(combination_n), - c(305, 617, 241, 711)) + if (require("dplyr")) { + # percentages + expect_equal(example_isolates %>% + group_by(hospital_id) %>% + summarise(R = proportion_R(CIP, as_percent = TRUE), + I = proportion_I(CIP, as_percent = TRUE), + S = proportion_S(CIP, as_percent = TRUE), + n = n_rsi(CIP), + total = n()) %>% + pull(n) %>% + sum(), + 1409) + + # count of cases + expect_equal(example_isolates %>% + group_by(hospital_id) %>% + summarise(cipro_p = proportion_SI(CIP, as_percent = TRUE), + cipro_n = n_rsi(CIP), + genta_p = proportion_SI(GEN, as_percent = TRUE), + genta_n = n_rsi(GEN), + combination_p = proportion_SI(CIP, GEN, as_percent = TRUE), + combination_n = n_rsi(CIP, GEN)) %>% + pull(combination_n), + c(305, 617, 241, 711)) + + # proportion_df + expect_equal( + example_isolates %>% select(AMX) %>% proportion_df() %>% pull(value), + c(example_isolates$AMX %>% proportion_SI(), + example_isolates$AMX %>% proportion_R()) + ) + expect_equal( + example_isolates %>% select(AMX) %>% proportion_df(combine_IR = TRUE) %>% pull(value), + c(example_isolates$AMX %>% proportion_S(), + example_isolates$AMX %>% proportion_IR()) + ) + expect_equal( + example_isolates %>% select(AMX) %>% proportion_df(combine_SI = FALSE) %>% pull(value), + c(example_isolates$AMX %>% proportion_S(), + example_isolates$AMX %>% proportion_I(), + example_isolates$AMX %>% proportion_R()) + ) + } reset_all_thrown_messages() expect_warning(proportion_R(as.character(example_isolates$AMC))) @@ -115,24 +134,6 @@ test_that("proportions works", { expect_warning(proportion_I(as.character(example_isolates$GEN))) reset_all_thrown_messages() expect_warning(proportion_S(example_isolates$AMC, as.character(example_isolates$GEN))) - - # proportion_df - expect_equal( - example_isolates %>% select(AMX) %>% proportion_df() %>% pull(value), - c(example_isolates$AMX %>% proportion_SI(), - example_isolates$AMX %>% proportion_R()) - ) - expect_equal( - example_isolates %>% select(AMX) %>% proportion_df(combine_IR = TRUE) %>% pull(value), - c(example_isolates$AMX %>% proportion_S(), - example_isolates$AMX %>% proportion_IR()) - ) - expect_equal( - example_isolates %>% select(AMX) %>% proportion_df(combine_SI = FALSE) %>% pull(value), - c(example_isolates$AMX %>% proportion_S(), - example_isolates$AMX %>% proportion_I(), - example_isolates$AMX %>% proportion_R()) - ) expect_error(proportion_df(c("A", "B", "C"))) expect_error(proportion_df(example_isolates[, "date"])) diff --git a/tests/testthat/test-resistance_predict.R b/tests/testthat/test-resistance_predict.R index 4e9f1ff7..e66bdd6b 100644 --- a/tests/testthat/test-resistance_predict.R +++ b/tests/testthat/test-resistance_predict.R @@ -28,65 +28,71 @@ context("resistance_predict.R") test_that("prediction of rsi works", { skip_on_cran() - library(dplyr) - expect_output(AMX_R <- example_isolates %>% - filter(mo == "B_ESCHR_COLI") %>% - rsi_predict(col_ab = "AMX", - col_date = "date", - model = "binomial", - minimum = 10, - info = TRUE) %>% - pull("value")) - # AMX resistance will increase according to data set `example_isolates` - expect_true(AMX_R[3] < AMX_R[20]) - - expect_output(x <- suppressMessages(resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial", info = TRUE))) + if (require("dplyr")) { + expect_output(AMX_R <- example_isolates %>% + filter(mo == "B_ESCHR_COLI") %>% + rsi_predict(col_ab = "AMX", + col_date = "date", + model = "binomial", + minimum = 10, + info = TRUE) %>% + pull("value")) + # AMX resistance will increase according to data set `example_isolates` + expect_true(AMX_R[3] < AMX_R[20]) + } + + expect_output(x <- suppressMessages(resistance_predict(example_isolates, + col_ab = "AMX", + year_min = 2010, + model = "binomial", + info = TRUE))) pdf(NULL) # prevent Rplots.pdf being created expect_silent(plot(x)) expect_silent(ggplot_rsi_predict(x)) + expect_silent(ggplot(x)) expect_error(ggplot_rsi_predict(example_isolates)) - expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"), + expect_output(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"), model = "binomial", col_ab = "AMX", col_date = "date", info = TRUE)) - expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"), + expect_output(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"), model = "loglin", col_ab = "AMX", col_date = "date", info = TRUE)) - expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"), + expect_output(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"), model = "lin", col_ab = "AMX", col_date = "date", info = TRUE)) - expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"), + expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"), model = "INVALID MODEL", col_ab = "AMX", col_date = "date", info = TRUE)) - expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"), + expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"), model = "binomial", col_ab = "NOT EXISTING COLUMN", col_date = "date", info = TRUE)) - expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"), + expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"), model = "binomial", col_ab = "AMX", col_date = "NOT EXISTING COLUMN", info = TRUE)) - expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"), + expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"), col_ab = "AMX", col_date = "NOT EXISTING COLUMN", info = TRUE)) - expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"), + expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"), col_ab = "AMX", col_date = "date", info = TRUE)) # almost all E. coli are MEM S in the Netherlands :) - expect_error(resistance_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"), + expect_error(resistance_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"), model = "binomial", col_ab = "MEM", col_date = "date", diff --git a/tests/testthat/test-rsi.R b/tests/testthat/test-rsi.R index 2de92259..e70829ed 100644 --- a/tests/testthat/test-rsi.R +++ b/tests/testthat/test-rsi.R @@ -59,30 +59,36 @@ test_that("rsi works", { expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)), rep(FALSE, length(example_isolates))) - library(dplyr, warn.conflicts = FALSE) - # 40 rsi columns - expect_equal(example_isolates %>% - mutate_at(vars(PEN:RIF), as.character) %>% - lapply(is.rsi.eligible) %>% - as.logical() %>% - sum(), - 40) - - expect_output(print(tibble(ab = as.rsi("S")))) - expect_error(as.rsi.mic(as.mic(16))) expect_error(as.rsi.disk(as.disk(16))) expect_error(get_guideline("this one does not exist")) - expect_s3_class(example_isolates %>% - mutate(m = as.mic(2), - d = as.disk(20)) %>% - skimr::skim(), - "data.frame") - expect_s3_class(skimr::skim(example_isolates), - "data.frame") - + if (require("dplyr")) { + # 40 rsi columns + expect_equal(example_isolates %>% + mutate_at(vars(PEN:RIF), as.character) %>% + lapply(is.rsi.eligible) %>% + as.logical() %>% + sum(), + 40) + expect_equal(sum(is.rsi(example_isolates)), 40) + + expect_output(print(tibble(ab = as.rsi("S")))) + } + + if (require("skimr")) { + expect_s3_class(skim(example_isolates), + "data.frame") + if (require("dplyr")) { + expect_s3_class(example_isolates %>% + mutate(m = as.mic(2), + d = as.disk(20)) %>% + skim(), + "data.frame") + } + } + }) test_that("mic2rsi works", { @@ -110,12 +116,14 @@ test_that("mic2rsi works", { expect_equal(as.rsi(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020"), as.rsi("R")) - expect_true(suppressWarnings(example_isolates %>% - mutate(amox_mic = as.mic(2)) %>% - select(mo, amox_mic) %>% - as.rsi() %>% - pull(amox_mic) %>% - is.rsi())) + if (require("dplyr")) { + expect_true(suppressWarnings(example_isolates %>% + mutate(amox_mic = as.mic(2)) %>% + select(mo, amox_mic) %>% + as.rsi() %>% + pull(amox_mic) %>% + is.rsi())) + } }) test_that("disk2rsi works", { @@ -140,13 +148,15 @@ test_that("disk2rsi works", { ab = "ERY", guideline = "CLSI")), "R") - - expect_true(example_isolates %>% - mutate(amox_disk = as.disk(15)) %>% - select(mo, amox_disk) %>% - as.rsi(guideline = "CLSI") %>% - pull(amox_disk) %>% - is.rsi()) + + if (require("dplyr")) { + expect_true(example_isolates %>% + mutate(amox_disk = as.disk(15)) %>% + select(mo, amox_disk) %>% + as.rsi(guideline = "CLSI") %>% + pull(amox_disk) %>% + is.rsi()) + } # frequency tables if (require("cleaner")) { @@ -165,20 +175,18 @@ test_that("data.frame2rsi works", { TOB = as.disk(16), ERY = "R", # note about assigning class CLR = "V") # note about cleaning - expect_s3_class(suppressWarnings(as.rsi(df)), "data.frame") + expect_s3_class(suppressWarnings(as.rsi(df)), + "data.frame") expect_s3_class(suppressWarnings(as.rsi(data.frame(mo = "Escherichia coli", - amoxi = c("R", "S", "I", "invalid")))$amoxi), "rsi") - expect_warning(data.frame(mo = "E. coli", - NIT = c("<= 2", 32)) %>% - as.rsi()) - expect_message(data.frame(mo = "E. coli", - NIT = c("<= 2", 32), - uti = TRUE) %>% - as.rsi()) - expect_message( - data.frame(mo = "E. coli", - NIT = c("<= 2", 32), - specimen = c("urine", "blood")) %>% - as.rsi()) + amoxi = c("R", "S", "I", "invalid")))$amoxi), + "rsi") + expect_warning(as.rsi(data.frame(mo = "E. coli", + NIT = c("<= 2", 32)))) + expect_message(as.rsi(data.frame(mo = "E. coli", + NIT = c("<= 2", 32), + uti = TRUE))) + expect_message(as.rsi(data.frame(mo = "E. coli", + NIT = c("<= 2", 32), + specimen = c("urine", "blood")))) }) diff --git a/tests/testthat/test-zzz.R b/tests/testthat/test-zzz.R index c3dff30a..6e8dcc2c 100644 --- a/tests/testthat/test-zzz.R +++ b/tests/testthat/test-zzz.R @@ -56,7 +56,7 @@ test_that("imports work", { call_functions <- c( # cleaner "freq.default" = "cleaner", - # skmir + # skimr "inline_hist" = "skimr", "sfl" = "skimr", # set_mo_source