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(v1.1.0.9010) lose dependencies

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dr. M.S. (Matthijs) Berends 2020-05-18 11:09:02 +02:00
parent bf0402a653
commit d659c9baef
14 changed files with 37 additions and 46 deletions
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4
.gitlab-ci.yml
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@ -101,8 +101,6 @@ R-release:
# build package # build package
- R CMD build . --no-build-vignettes --no-manual - R CMD build . --no-build-vignettes --no-manual
- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1) - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
- Rscript -e 'devtools::install_local("${PKG_FILE_NAME}")'
- Rscript -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)'
- Rscript -e 'Sys.setenv(NOT_CRAN = "true")' - Rscript -e 'Sys.setenv(NOT_CRAN = "true")'
- R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
artifacts: artifacts:
@ -130,8 +128,6 @@ R-devel:
# build package # build package
- Rdevel CMD build . --no-build-vignettes --no-manual - Rdevel CMD build . --no-build-vignettes --no-manual
- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1) - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
- Rscript -e 'devtools::install_local("${PKG_FILE_NAME}")'
- Rscript -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)'
- Rscript -e 'Sys.setenv(NOT_CRAN = "true")' - Rscript -e 'Sys.setenv(NOT_CRAN = "true")'
- Rdevel CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran - Rdevel CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
artifacts: artifacts:

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.1.0.9009 Version: 1.1.0.9010
Date: 2020-05-18 Date: 2020-05-18
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.1.0.9009 # AMR 1.1.0.9010
## <small>Last updated: 18-May-2020</small> ## <small>Last updated: 18-May-2020</small>
### Breaking ### Breaking

35
R/eucast_rules.R
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@ -520,7 +520,7 @@ eucast_rules <- function(x,
x[, col_mo] <- as.mo(x[, col_mo, drop = TRUE]) x[, col_mo] <- as.mo(x[, col_mo, drop = TRUE])
x <- x %>% x <- x %>%
left_join_microorganisms(by = col_mo, suffix = c("_oldcols", "")) left_join_microorganisms(by = col_mo, suffix = c("_oldcols", ""))
x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE]) x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL)
x$genus_species <- paste(x$genus, x$species) x$genus_species <- paste(x$genus, x$species)
if (ab_missing(AMP) & !ab_missing(AMX)) { if (ab_missing(AMP) & !ab_missing(AMX)) {
@ -658,7 +658,7 @@ eucast_rules <- function(x,
rule_group_current %like% "expert", rule_group_current %like% "expert",
paste0("\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (", paste0("\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (",
font_red(paste0("v", EUCAST_VERSION_EXPERT_RULES)), ")\n"), font_red(paste0("v", EUCAST_VERSION_EXPERT_RULES)), ")\n"),
"\nOther rules by this AMR package\n")))) "\nOther rules by this AMR package (turn on/off with 'rules' parameter)\n"))))
} }
# Print rule ------------------------------------------------------------- # Print rule -------------------------------------------------------------
if (rule_current != rule_previous) { if (rule_current != rule_previous) {
@ -678,32 +678,27 @@ eucast_rules <- function(x,
like_is_one_of <- eucast_rules_df[i, 2] like_is_one_of <- eucast_rules_df[i, 2]
# be sure to comprise all coagulase-negative/-positive Staphylococci when they are mentioned # be sure to comprise all coagulase-negative/-positive Staphylococci when they are mentioned
if (eucast_rules_df[i, 3] %like% "coagulase-") { if (eucast_rules_df[i, 3] %like% "coagulase") {
suppressWarnings( all_staph <- microorganisms[which(microorganisms$genus == "Staphylococcus"), ]
all_staph <- microorganisms %>% all_staph$CNS_CPS <- suppressWarnings(mo_name(all_staph$mo, Becker = "all", language = NULL))
filter(genus == "Staphylococcus") %>% if (eucast_rules_df[i, 3] %like% "coagulase") {
mutate(CNS_CPS = mo_name(mo, Becker = "all")) eucast_rules_df[i, 3] <- paste0("^(", paste0(all_staph[which(all_staph$CNS_CPS %like% "negative"),
) "fullname",
if (eucast_rules_df[i, 3] %like% "coagulase-") { drop = TRUE],
eucast_rules_df[i, 3] <- paste0("^(", collapse = "|"),
paste0(all_staph %>%
filter(CNS_CPS %like% "coagulase-negative") %>%
pull(fullname),
collapse = "|"),
")$") ")$")
} else { } else {
eucast_rules_df[i, 3] <- paste0("^(", eucast_rules_df[i, 3] <- paste0("^(", paste0(all_staph[which(all_staph$CNS_CPS %like% "positive"),
paste0(all_staph %>% "fullname",
filter(CNS_CPS %like% "coagulase-positive") %>% drop = TRUE],
pull(fullname), collapse = "|"),
collapse = "|"),
")$") ")$")
} }
like_is_one_of <- "like" like_is_one_of <- "like"
} }
if (like_is_one_of == "is") { if (like_is_one_of == "is") {
# so 'Enterococcus' will turn into '^Enterococcus$' # so e.g. 'Enterococcus' will turn into '^Enterococcus$'
mo_value <- paste0("^", eucast_rules_df[i, 3], "$") mo_value <- paste0("^", eucast_rules_df[i, 3], "$")
} else if (like_is_one_of == "one_of") { } else if (like_is_one_of == "one_of") {
# so 'Clostridium, Actinomyces, ...' will turn into '^(Clostridium|Actinomyces|...)$' # so 'Clostridium, Actinomyces, ...' will turn into '^(Clostridium|Actinomyces|...)$'

14
R/guess_ab_col.R
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@ -79,8 +79,8 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE) {
if (search_string.ab %in% colnames(x)) { if (search_string.ab %in% colnames(x)) {
ab_result <- colnames(x)[colnames(x) == search_string.ab][1L] ab_result <- colnames(x)[colnames(x) == search_string.ab][1L]
} else if (any(tolower(colnames(x)) %in% tolower(unlist(ab_property(search_string.ab, "abbreviations"))))) { } else if (any(tolower(colnames(x)) %in% tolower(unlist(ab_property(search_string.ab, "abbreviations", language = NULL))))) {
ab_result <- colnames(x)[tolower(colnames(x)) %in% tolower(unlist(ab_property(search_string.ab, "abbreviations")))][1L] ab_result <- colnames(x)[tolower(colnames(x)) %in% tolower(unlist(ab_property(search_string.ab, "abbreviations", language = NULL)))][1L]
} else { } else {
# sort colnames on length - longest first # sort colnames on length - longest first
@ -96,13 +96,13 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE) {
if (length(ab_result) == 0) { if (length(ab_result) == 0) {
if (verbose == TRUE) { if (verbose == TRUE) {
message(paste0("No column found as input for `", search_string, message(paste0("No column found as input for `", search_string,
"` (", ab_name(search_string, language = "en", tolower = TRUE), ").")) "` (", ab_name(search_string, language = NULL, tolower = TRUE), ")."))
} }
return(NULL) return(NULL)
} else { } else {
if (verbose == TRUE) { if (verbose == TRUE) {
message(font_blue(paste0("NOTE: Using column `", font_bold(ab_result), "` as input for `", search_string, message(font_blue(paste0("NOTE: Using column `", font_bold(ab_result), "` as input for `", search_string,
"` (", ab_name(search_string, language = "en", tolower = TRUE), ")."))) "` (", ab_name(search_string, language = NULL, tolower = TRUE), ").")))
} }
return(ab_result) return(ab_result)
} }
@ -173,11 +173,11 @@ get_column_abx <- function(x,
for (i in seq_len(length(x))) { for (i in seq_len(length(x))) {
if (verbose == TRUE & !names(x[i]) %in% names(duplicates)) { if (verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
message(font_blue(paste0("NOTE: Using column `", font_bold(x[i]), "` as input for `", names(x)[i], message(font_blue(paste0("NOTE: Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE), ")."))) "` (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")))
} }
if (names(x[i]) %in% names(duplicates)) { if (names(x[i]) %in% names(duplicates)) {
warning(font_red(paste0("Using column `", font_bold(x[i]), "` as input for `", names(x)[i], warning(font_red(paste0("Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE), "` (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
"), although it was matched for multiple antibiotics or columns.")), "), although it was matched for multiple antibiotics or columns.")),
call. = FALSE, call. = FALSE,
immediate. = verbose) immediate. = verbose)
@ -210,7 +210,7 @@ get_column_abx <- function(x,
} }
generate_warning_abs_missing <- function(missing, any = FALSE) { generate_warning_abs_missing <- function(missing, any = FALSE) {
missing <- paste0(missing, " (", ab_name(missing, tolower = TRUE), ")") missing <- paste0(missing, " (", ab_name(missing, tolower = TRUE, language = NULL), ")")
if (any == TRUE) { if (any == TRUE) {
any_txt <- c(" any of", "is") any_txt <- c(" any of", "is")
} else { } else {

4
appveyor.yml
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@ -52,10 +52,10 @@ matrix:
build_script: build_script:
# - travis_tool.sh clean_library # turn off for caching, turn on for release of new R versions # - travis_tool.sh clean_library # turn off for caching, turn on for release of new R versions
- travis_tool.sh install_deps - travis-tool.sh install_deps
test_script: test_script:
- travis_tool.sh run_tests - travis-tool.sh run_tests
on_failure: on_failure:
- 7z a failure.zip *.Rcheck\* - 7z a failure.zip *.Rcheck\*

2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9009</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9010</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.1.0.9009</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9010</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.1.0.9009</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9010</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.1.0.9009</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9010</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.1.0.9009</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9010</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.1.0.9009</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9010</span>
</span> </span>
</div> </div>
@ -229,9 +229,9 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1-1-0-9009" class="section level1"> <div id="amr-1-1-0-9010" class="section level1">
<h1 class="page-header" data-toc-text="1.1.0.9009"> <h1 class="page-header" data-toc-text="1.1.0.9010">
<a href="#amr-1-1-0-9009" class="anchor"></a>AMR 1.1.0.9009<small> Unreleased </small> <a href="#amr-1-1-0-9010" class="anchor"></a>AMR 1.1.0.9010<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-18-may-2020" class="section level2"> <div id="last-updated-18-may-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

2
docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html WHONET: WHONET.html
benchmarks: benchmarks.html benchmarks: benchmarks.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
last_built: 2020-05-18T08:29Z last_built: 2020-05-18T09:07Z
urls: urls:
reference: https://msberends.gitlab.io/AMR/reference reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles article: https://msberends.gitlab.io/AMR/articles

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.1.0.9009</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9010</span>
</span> </span>
</div> </div>