Browse Source

(v1.7.1.9049) unit tests

development
parent
commit
2bcf28281d
  1. 4
      .github/workflows/check.yaml
  2. 6
      .github/workflows/codecovr.yaml
  3. 4
      DESCRIPTION
  4. 4
      NEWS.md
  5. 5
      R/aa_helper_functions.R
  6. 12
      R/mo.R
  7. 2
      codecov.yml
  8. BIN
      data-raw/AMR_latest.tar.gz
  9. 4
      docs/articles/datasets.html
  10. 12
      docs/news/index.html
  11. 4
      inst/tinytest/test-_misc.R
  12. 9
      inst/tinytest/test-ab_class_selectors.R
  13. 2
      inst/tinytest/test-ab_property.R
  14. 2
      inst/tinytest/test-bug_drug_combinations.R
  15. 2
      inst/tinytest/test-count.R
  16. 2
      inst/tinytest/test-disk.R
  17. 2
      inst/tinytest/test-episode.R
  18. 4
      inst/tinytest/test-eucast_rules.R
  19. 2
      inst/tinytest/test-first_isolate.R
  20. 2
      inst/tinytest/test-ggplot_rsi.R
  21. 2
      inst/tinytest/test-mdro.R
  22. 2
      inst/tinytest/test-mic.R
  23. 4
      inst/tinytest/test-mo.R
  24. 2
      inst/tinytest/test-mo_property.R
  25. 2
      inst/tinytest/test-pca.R
  26. 2
      inst/tinytest/test-proportion.R
  27. 2
      inst/tinytest/test-resistance_predict.R
  28. 8
      inst/tinytest/test-rsi.R

4
.github/workflows/check.yaml

@ -88,6 +88,8 @@ jobs:
- uses: r-lib/actions/setup-r@v1
with:
r-version: ${{ matrix.config.r }}
- uses: r-lib/actions/setup-pandoc@v1
- name: Install Linux dependencies
if: runner.os == 'Linux'
@ -95,7 +97,7 @@ jobs:
# we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
# as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
run: |
sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
sudo apt install -y libssl-dev libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
- name: Restore cached R packages
# this step will add the step 'Post Restore cached R packages' on a succesful run
if: runner.os != 'Windows'

6
.github/workflows/codecovr.yaml

@ -45,8 +45,10 @@ jobs:
- uses: r-lib/actions/setup-r@v1
with:
r-version: release
- uses: r-lib/actions/setup-pandoc@master
- uses: r-lib/actions/setup-pandoc@v1
# 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

4
DESCRIPTION

@ -1,6 +1,6 @@
Package: AMR
Version: 1.7.1.9048
Date: 2021-10-04
Version: 1.7.1.9049
Date: 2021-10-05
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

4
NEWS.md

@ -1,5 +1,5 @@
# `AMR` 1.7.1.9048
## <small>Last updated: 4 October 2021</small>
# `AMR` 1.7.1.9049
## <small>Last updated: 5 October 2021</small>
### Breaking changes
* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version

5
R/aa_helper_functions.R

@ -296,12 +296,15 @@ stop_ifnot_installed <- function(package) {
return(invisible())
}
pkg_is_available <- function(pkg, also_load = TRUE) {
pkg_is_available <- function(pkg, also_load = TRUE, min_version = NULL) {
if (also_load == TRUE) {
out <- suppressWarnings(require(pkg, character.only = TRUE, warn.conflicts = FALSE))
} else {
out <- requireNamespace(pkg, quietly = TRUE)
}
if (!is.null(min_version)) {
out <- out && packageVersion(pkg) >= min_version
}
isTRUE(out)
}

12
R/mo.R

@ -372,7 +372,7 @@ exec_as.mo <- function(x,
# Laboratory systems: remove (translated) entries like "no growth", etc.
x[trimws2(x) %like% translate_AMR("no .*growth", language = language)] <- NA_character_
x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
if (initial_search == TRUE) {
# keep track of time - give some hints to improve speed if it takes a long time
start_time <- Sys.time()
@ -495,9 +495,13 @@ exec_as.mo <- function(x,
# Fill in fullnames and MO codes directly
known_names <- tolower(x_backup) %in% MO_lookup$fullname_lower
x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname_lower), property, drop = TRUE]
known_codes <- toupper(x_backup) %in% MO_lookup$mo
x[known_codes] <- MO_lookup[match(toupper(x_backup)[known_codes], MO_lookup$mo), property, drop = TRUE]
already_known <- known_names | known_codes
known_codes_mo <- toupper(x_backup) %in% MO_lookup$mo
x[known_codes_mo] <- MO_lookup[match(toupper(x_backup)[known_codes_mo], MO_lookup$mo), property, drop = TRUE]
known_codes_lis <- toupper(x_backup) %in% microorganisms.codes$code
x[known_codes_lis] <- MO_lookup[match(microorganisms.codes[match(toupper(x_backup)[known_codes_lis],
microorganisms.codes$code), "mo", drop = TRUE],
MO_lookup$mo), property, drop = TRUE]
already_known <- known_names | known_codes_mo | known_codes_lis
# now only continue where the right taxonomic output is not already known
if (any(!already_known)) {

2
codecov.yml

@ -25,7 +25,7 @@
codecov:
require_ci_to_pass: no # allow fail
branch: master
branch: main
comment: no

BIN
data-raw/AMR_latest.tar.gz

4
docs/articles/datasets.html

@ -44,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9048</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9049</span>
</span>
</div>
@ -190,7 +190,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">04 October 2021</h4>
<h4 data-toc-skip class="date">05 October 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>

12
docs/news/index.html

@ -92,7 +92,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9048</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9049</span>
</span>
</div>
@ -240,12 +240,12 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1719048" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9048">
<a href="#amr-1719048" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9048</h1>
<div id="last-updated-4-october-2021" class="section level2">
<div id="amr-1719049" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9049">
<a href="#amr-1719049" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9049</h1>
<div id="last-updated-5-october-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-4-october-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 4 October 2021</small>
<a href="#last-updated-5-october-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 5 October 2021</small>
</h2>
<div id="breaking-changes" class="section level3">
<h3 class="hasAnchor">

4
inst/tinytest/test-_misc.R

@ -42,12 +42,12 @@ expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
expect_warning(AMR:::get_column_abx(example_isolates, hard_dependencies = "FUS"))
expect_message(AMR:::get_column_abx(example_isolates, soft_dependencies = "FUS"))
if (AMR:::pkg_is_available("dplyr")) {
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 = TRUE))
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 implement a test that checks for this:
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id)))
}

9
inst/tinytest/test-ab_class_selectors.R

@ -65,6 +65,9 @@ expect_equal(nrow(subset(example_isolates, any(carbapenems() == "R"))), 55, tole
# filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
expect_equal(nrow(example_isolates[any(carbapenems()), ]), 962, tolerance = 0.5)
expect_equal(nrow(example_isolates[all(carbapenems()), ]), 756, tolerance = 0.5)
expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)
expect_equal(nrow(example_isolates[any(carbapenems() != "R"), ]), 910, tolerance = 0.5)
expect_equal(nrow(example_isolates[carbapenems() != "R", ]), 704, tolerance = 0.5)
# filter with multiple antibiotic selectors using c()
expect_equal(nrow(example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]), 26, tolerance = 0.5)
@ -73,3 +76,9 @@ expect_equal(nrow(example_isolates[all(c(carbapenems(), aminoglycosides()) == "R
expect_equal(nrow(example_isolates[any(carbapenems() == "R"), penicillins()]), 55, tolerance = 0.5)
expect_equal(ncol(example_isolates[any(carbapenems() == "R"), penicillins()]), 7, tolerance = 0.5)
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_equal(example_isolates %>% select(administrable_per_os() & penicillins()) %>% ncol(), 5, tolerance = 0.5)
expect_equal(example_isolates %>% select(administrable_iv() & penicillins()) %>% ncol(), 7, tolerance = 0.5)
expect_equal(example_isolates %>% select(administrable_iv() | penicillins()) %>% ncol(), 37, tolerance = 0.5)
expect_warning(example_isolates %>% select(GEH = GEN) %>% select(aminoglycosides(only_treatable = TRUE)))
}

2
inst/tinytest/test-ab_property.R

@ -69,7 +69,7 @@ expect_identical(colnames(set_ab_names(example_isolates[, 20:25], language = "nl
c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine"))
expect_identical(colnames(set_ab_names(example_isolates[, 20:25], "atc")),
c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01"))
if (AMR:::pkg_is_available("dplyr") && packageVersion("dplyr") >= "1.0.0") {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_identical(example_isolates %>% set_ab_names(),
example_isolates %>% rename_with(set_ab_names))
}

2
inst/tinytest/test-bug_drug_combinations.R

@ -28,7 +28,7 @@ expect_inherits(b, "bug_drug_combinations")
expect_stdout(suppressMessages(print(b)))
expect_true(is.data.frame(format(b)))
expect_true(is.data.frame(format(b, combine_IR = TRUE, add_ab_group = FALSE)))
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_true(example_isolates %>%
group_by(hospital_id) %>%
bug_drug_combinations(FUN = mo_gramstain) %>%

2
inst/tinytest/test-count.R

@ -51,7 +51,7 @@ expect_error(count_susceptible("test", as_percent = "test"))
expect_error(count_df(c("A", "B", "C")))
expect_error(count_df(example_isolates[, "date"]))
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
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)

2
inst/tinytest/test-disk.R

@ -50,6 +50,6 @@ if (AMR:::pkg_is_available("ggplot2")) {
}
expect_stdout(print(as.disk(12)))
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_stdout(print(tibble(d = as.disk(12))))
}

2
inst/tinytest/test-episode.R

@ -36,7 +36,7 @@ test_df <- rbind(
expect_equal(get_episode(test_df$date, 365),
c(1, 1, 2, 2, 2, 3, 3, 4, 1, 2, 2, 2, 3))
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
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))

4
inst/tinytest/test-eucast_rules.R

@ -72,7 +72,7 @@ b <- data.frame(mo = c("Staphylococcus aureus",
expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
# piperacillin must be R in Enterobacteriaceae when tica is R
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_equal(suppressWarnings(
example_isolates %>%
filter(mo_family(mo) == "Enterobacteriaceae") %>%
@ -110,7 +110,7 @@ expect_equal(
"S")
# also test norf
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_stdout(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
}

2
inst/tinytest/test-first_isolate.R

@ -110,7 +110,7 @@ expect_error(first_isolate(example_isolates,
col_date = "non-existing col",
col_mo = "mo"))
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
# if mo is not an mo class, result should be the same
expect_identical(example_isolates %>%
mutate(mo = as.character(mo)) %>%

2
inst/tinytest/test-ggplot_rsi.R

@ -23,7 +23,7 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
if (AMR:::pkg_is_available("dplyr") & AMR:::pkg_is_available("ggplot2")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0") & AMR:::pkg_is_available("ggplot2")) {
pdf(NULL) # prevent Rplots.pdf being created

2
inst/tinytest/test-mdro.R

@ -232,7 +232,7 @@ expect_warning(mdro(example_isolates,
info = FALSE))
# print groups
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_stdout(x <- mdro(example_isolates %>% group_by(hospital_id), info = TRUE))
expect_stdout(x <- mdro(example_isolates %>% group_by(hospital_id), guideline = custom, info = TRUE))
}

2
inst/tinytest/test-mic.R

@ -58,7 +58,7 @@ expect_stdout(print(as.mic(c(1, 2, 4, 8))))
expect_inherits(summary(as.mic(c(2, 8))), c("summaryDefault", "table"))
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_stdout(print(tibble(m = as.mic(2:4))))
}

4
inst/tinytest/test-mo.R

@ -143,7 +143,7 @@ expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_S
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
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
# select with one column
expect_identical(
example_isolates[1:10, ] %>%
@ -272,7 +272,7 @@ expect_equal(as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
expect_equal(suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))),
c("F_YEAST", "F_FUNGUS"))
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
# print tibble
expect_stdout(print(tibble(mo = as.mo("B_ESCHR_COLI"))))
}

2
inst/tinytest/test-mo_property.R

@ -119,7 +119,7 @@ expect_equal(mo_is_intrinsic_resistant(c("Escherichia coli", "Staphylococcus aur
# with reference data
expect_equal(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")),
"Escherichia coli")
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),
730, tolerance = 0.5)
expect_equal(example_isolates %>% filter(mo_is_gram_positive()) %>% nrow(),

2
inst/tinytest/test-pca.R

@ -47,7 +47,7 @@ if (AMR:::pkg_is_available("ggplot2")) {
ggplot_pca(pca_model, arrows_textangled = FALSE)
}
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
resistance_data <- example_isolates %>%
group_by(order = mo_order(mo),
genus = mo_genus(mo)) %>%

2
inst/tinytest/test-proportion.R

@ -35,7 +35,7 @@ expect_equal(proportion_R(example_isolates$AMX) + proportion_I(example_isolates$
expect_equal(proportion_S(example_isolates$AMX) + proportion_I(example_isolates$AMX),
proportion_SI(example_isolates$AMX))
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_equal(example_isolates %>% proportion_SI(AMC),
0.7626397,
tolerance = 0.0001)

2
inst/tinytest/test-resistance_predict.R

@ -23,7 +23,7 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_stdout(AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COLI") %>%
rsi_predict(col_ab = "AMX",

8
inst/tinytest/test-rsi.R

@ -51,7 +51,7 @@ expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)),
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"))
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
# 40 rsi columns
expect_equal(example_isolates %>%
mutate_at(vars(PEN:RIF), as.character) %>%
@ -66,7 +66,7 @@ if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("skimr")) {
expect_inherits(skim(example_isolates),
"data.frame")
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_inherits(example_isolates %>%
mutate(m = as.mic(2),
d = as.disk(20)) %>%
@ -96,7 +96,7 @@ expect_equal(as.rsi(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020
as.rsi("S"))
expect_equal(as.rsi(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
as.rsi("R"))
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_true(suppressWarnings(example_isolates %>%
mutate(amox_mic = as.mic(2)) %>%
select(mo, amox_mic) %>%
@ -123,7 +123,7 @@ expect_equal(as.character(
ab = "ERY",
guideline = "CLSI")),
"R")
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_true(example_isolates %>%
mutate(amox_disk = as.disk(15)) %>%
select(mo, amox_disk) %>%

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