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(v1.4.0.9036) more unit tests
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.4.0.9035
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Version: 1.4.0.9036
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Date: 2020-12-11
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.4.0.9035
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# AMR 1.4.0.9036
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## <small>Last updated: 11 December 2020</small>
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### New
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@ -619,9 +619,11 @@ eucast_rules <- function(x,
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# Other rules: enzyme inhibitors ------------------------------------------
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if (any(c("all", "other") %in% rules)) {
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if (info == TRUE) {
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cat(font_bold(paste0("\nRules by this AMR package (",
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cat("\n")
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cat(word_wrap(
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font_bold(paste0("Rules by this AMR package (",
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font_red(paste0("v", utils::packageDescription("AMR")$Version, ", ",
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format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"))), "), see ?eucast_rules\n")))
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format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"))), "), see ?eucast_rules\n"))))
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}
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ab_enzyme <- subset(antibiotics, name %like% "/")[, c("ab", "name")]
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@ -635,7 +637,7 @@ eucast_rules <- function(x,
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# Set base to R where base + enzyme inhibitor is R
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rule_current <- paste0("Set ", ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = R where ",
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ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = R")
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cat(rule_current)
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cat(word_wrap(rule_current))
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run_changes <- edit_rsi(x = x,
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col_mo = col_mo,
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to = "R",
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@ -664,7 +666,7 @@ eucast_rules <- function(x,
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rule_current <- paste0("Set ", ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = S where ",
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ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = S")
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if (info == TRUE) {
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cat(rule_current)
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cat(word_wrap(rule_current))
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}
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run_changes <- edit_rsi(x = x,
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col_mo = col_mo,
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@ -763,9 +765,10 @@ eucast_rules <- function(x,
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if (info == TRUE) {
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# Print EUCAST intro ------------------------------------------------------
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if (!rule_group_current %like% "other" & eucast_notification_shown == FALSE) {
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cat(paste0("\n", font_grey(strrep("-", 0.95 * options()$width)),
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"\nRules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)"),
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"\n", font_blue("https://eucast.org/"), "\n"))
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cat(
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paste0("\n", font_grey(strrep("-", 0.95 * options()$width)), "\n",
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word_wrap("Rules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)")), "\n",
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font_blue("https://eucast.org/"), "\n"))
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eucast_notification_shown <- TRUE
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}
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@ -775,12 +778,16 @@ eucast_rules <- function(x,
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cat(font_bold(
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ifelse(
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rule_group_current %like% "breakpoint",
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paste0("\n", breakpoints_info$title, " (",
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font_red(paste0(breakpoints_info$version_txt, ", ", breakpoints_info$year)), ")\n"),
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paste0("\n",
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word_wrap(
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breakpoints_info$title, " (",
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font_red(paste0(breakpoints_info$version_txt, ", ", breakpoints_info$year)), ")\n")),
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ifelse(
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rule_group_current %like% "expert",
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paste0("\n", expertrules_info$title, " (",
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font_red(paste0(expertrules_info$version_txt, ", ", expertrules_info$year)), ")\n"),
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paste0("\n",
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word_wrap(
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expertrules_info$title, " (",
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font_red(paste0(expertrules_info$version_txt, ", ", expertrules_info$year)), ")\n")),
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""))))
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}
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# Print rule -------------------------------------------------------------
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35
R/mo.R
35
R/mo.R
@ -748,7 +748,7 @@ exec_as.mo <- function(x,
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x_backup_without_spp[i])), uncertainty = -1)
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next
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}
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if (x_backup_without_spp[i] %like_case% "haemoly.*strept") {
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if (x_backup_without_spp[i] %like_case% "haemoly.*strep") {
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# Haemolytic streptococci in different languages
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x[i] <- lookup(mo == "B_STRPT_HAEM", uncertainty = -1)
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next
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@ -1011,8 +1011,8 @@ exec_as.mo <- function(x,
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if (!all(is.na(found)) & nchar(g.x_backup_without_spp) >= 6) {
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if (property == "ref") {
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# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
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# mo_ref("Chlamydia psittaci) = "Page, 1968" (with warning)
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# mo_ref("Chlamydophila psittaci) = "Everett et al., 1999"
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# mo_ref("Chlamydia psittaci") = "Page, 1968" (with warning)
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# mo_ref("Chlamydophila psittaci") = "Everett et al., 1999"
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x <- found["ref"]
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} else {
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x <- lookup(fullname == found["fullname_new"], haystack = MO_lookup)
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@ -1437,17 +1437,19 @@ exec_as.mo <- function(x,
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# - Becker et al. 2014, PMID 25278577
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# - Becker et al. 2019, PMID 30872103
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# - Becker et al. 2020, PMID 32056452
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post_Becker <- character(0) # 2020-10-20 currently all are mentioned in above papers
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if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
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post_Becker <- character(0) # 2020-10-20 currently all are mentioned in above papers (otherwise uncomment below)
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warning_("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ",
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font_italic(paste("S.",
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sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),
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collapse = ", ")),
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".",
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call = FALSE,
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immediate = TRUE)
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}
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# nolint start
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# if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
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# warning_("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ",
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# font_italic(paste("S.",
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# sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),
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# collapse = ", ")),
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# ".",
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# call = FALSE,
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# immediate = TRUE)
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# }
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# nolint end
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# 'MO_CONS' and 'MO_COPS' are <mo> vectors created in R/zzz.R
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CoNS <- MO_lookup[which(MO_lookup$mo %in% MO_CONS), property, drop = TRUE]
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@ -1976,10 +1978,3 @@ repair_reference_df <- function(reference_df) {
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reference_df[, "mo"] <- as.mo(reference_df[, "mo", drop = TRUE])
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reference_df
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}
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left_join_MO_lookup <- function(x, ...) {
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pm_left_join(x = x, y = MO_lookup, ...)
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}
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left_join_MO.old_lookup <- function(x, ...) {
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pm_left_join(x = x, y = MO.old_lookup, ...)
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}
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@ -4,6 +4,7 @@
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<img src="https://www.r-pkg.org/badges/version-ago/AMR" />
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<img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" />
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<img src="https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg" />
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<img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9036</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9036</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9036</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9036</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9036</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9036</span>
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</span>
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</div>
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@ -236,9 +236,9 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1409035" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9035">
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<a href="#amr-1409035" class="anchor"></a>AMR 1.4.0.9035<small> Unreleased </small>
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<div id="amr-1409036" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9036">
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<a href="#amr-1409036" class="anchor"></a>AMR 1.4.0.9036<small> Unreleased </small>
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</h1>
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<div id="last-updated-11-december-2020" class="section level2">
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<h2 class="hasAnchor">
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@ -12,7 +12,7 @@ articles:
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2020-12-11T08:04Z
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last_built: 2020-12-11T11:03Z
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urls:
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9036</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9036</span>
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</span>
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</div>
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@ -116,6 +116,6 @@ test_that("EUCAST rules work", {
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expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
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# check verbose output
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expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, info = TRUE)))
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expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, rules = "all", info = TRUE)))
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})
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@ -57,8 +57,10 @@ test_that("as.mo works", {
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expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
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expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
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expect_equal(as.character(suppressWarnings(as.mo("B_STRPT_PNE"))), "B_STRPT_PNMN") # old MO code (<=v0.8.0)
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expect_equal(as.character(as.mo(c("mycobacterie", "mycobakterium"))), c("B_MYCBC", "B_MYCBC"))
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expect_equal(as.character(as.mo(c("GAS", "GBS", "a MGS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_MILL", "B_STRPT_HAEM"))
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expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("B_STRPT_GRPA", "B_STRPT_GRPB"))
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expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes
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@ -110,7 +112,8 @@ test_that("as.mo works", {
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rep("B_PRBRK_NODS", 4))
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# empty values
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expect_identical(as.character(as.mo(c("", NA, NaN))), rep(NA_character_, 3))
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expect_identical(as.character(as.mo(c("", " ", NA, NaN))), rep(NA_character_, 4))
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expect_identical(as.character(as.mo(" ")), NA_character_)
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# too few characters
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expect_warning(as.mo("ab"))
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@ -203,6 +206,7 @@ test_that("as.mo works", {
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# check old names
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expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
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print(mo_renamed())
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expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT"))
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# check uncertain names
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expect_equal(suppressMessages(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS")
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@ -210,7 +214,7 @@ test_that("as.mo works", {
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expect_message(as.mo("e coli extra_text", allow_uncertain = TRUE))
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expect_equal(suppressMessages(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS")
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expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY_COPS")
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expect_equal(suppressMessages(as.character(as.mo("Staphylococcus aureus unexisting", allow_uncertain = 3))), "B_STPHY_AURS_ANRB")
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expect_equal(suppressMessages(as.character(as.mo(c("s aur THISISATEST", "Staphylococcus aureus unexisting"), allow_uncertain = 3))), c("B_STPHY_AURS_ANRB", "B_STPHY_AURS_ANRB"))
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# predefined reference_df
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expect_equal(as.character(as.mo("TestingOwnID",
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@ -238,6 +242,9 @@ test_that("as.mo works", {
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"Raoultella (here some text) terrigena")))),
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c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG"))
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expect_output(print(mo_uncertainties()))
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x <- as.mo("S. aur")
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# many hits
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expect_output(print(mo_uncertainties()))
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# Salmonella (City) are all actually Salmonella enterica spp (City)
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expect_equal(suppressMessages(mo_name(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
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@ -285,4 +292,11 @@ test_that("as.mo works", {
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expect_warning(x[[1]] <- "invalid code")
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expect_warning(c(x[1], "test"))
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# ignoring patterns
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# frequency tables
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if (require("cleaner")) {
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expect_s3_class(cleaner::freq(example_isolates$mo), "freq")
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}
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})
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@ -122,6 +122,10 @@ test_that("mo_property works", {
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"vanco"),
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c(TRUE, FALSE, FALSE))
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# with reference data
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expect_equal(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")),
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"Escherichia coli")
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library(dplyr)
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expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),
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730)
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