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(v1.4.0.9036) more unit tests

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dr. M.S. (Matthijs) Berends
2020-12-11 12:17:23 +01:00
parent 23ddc6004b
commit 2edd3339db
17 changed files with 72 additions and 51 deletions
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31
R/eucast_rules.R
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@ -619,9 +619,11 @@ eucast_rules <- function(x,
# Other rules: enzyme inhibitors ------------------------------------------
if (any(c("all", "other") %in% rules)) {
if (info == TRUE) {
cat(font_bold(paste0("\nRules by this AMR package (",
font_red(paste0("v", utils::packageDescription("AMR")$Version, ", ",
format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"))), "), see ?eucast_rules\n")))
cat("\n")
cat(word_wrap(
font_bold(paste0("Rules by this AMR package (",
font_red(paste0("v", utils::packageDescription("AMR")$Version, ", ",
format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"))), "), see ?eucast_rules\n"))))
}
ab_enzyme <- subset(antibiotics, name %like% "/")[, c("ab", "name")]
@ -635,7 +637,7 @@ eucast_rules <- function(x,
# Set base to R where base + enzyme inhibitor is R
rule_current <- paste0("Set ", ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = R where ",
ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = R")
cat(rule_current)
cat(word_wrap(rule_current))
run_changes <- edit_rsi(x = x,
col_mo = col_mo,
to = "R",
@ -664,7 +666,7 @@ eucast_rules <- function(x,
rule_current <- paste0("Set ", ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = S where ",
ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = S")
if (info == TRUE) {
cat(rule_current)
cat(word_wrap(rule_current))
}
run_changes <- edit_rsi(x = x,
col_mo = col_mo,
@ -763,9 +765,10 @@ eucast_rules <- function(x,
if (info == TRUE) {
# Print EUCAST intro ------------------------------------------------------
if (!rule_group_current %like% "other" & eucast_notification_shown == FALSE) {
cat(paste0("\n", font_grey(strrep("-", 0.95 * options()$width)),
"\nRules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)"),
"\n", font_blue("https://eucast.org/"), "\n"))
cat(
paste0("\n", font_grey(strrep("-", 0.95 * options()$width)), "\n",
word_wrap("Rules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)")), "\n",
font_blue("https://eucast.org/"), "\n"))
eucast_notification_shown <- TRUE
}
@ -775,12 +778,16 @@ eucast_rules <- function(x,
cat(font_bold(
ifelse(
rule_group_current %like% "breakpoint",
paste0("\n", breakpoints_info$title, " (",
font_red(paste0(breakpoints_info$version_txt, ", ", breakpoints_info$year)), ")\n"),
paste0("\n",
word_wrap(
breakpoints_info$title, " (",
font_red(paste0(breakpoints_info$version_txt, ", ", breakpoints_info$year)), ")\n")),
ifelse(
rule_group_current %like% "expert",
paste0("\n", expertrules_info$title, " (",
font_red(paste0(expertrules_info$version_txt, ", ", expertrules_info$year)), ")\n"),
paste0("\n",
word_wrap(
expertrules_info$title, " (",
font_red(paste0(expertrules_info$version_txt, ", ", expertrules_info$year)), ")\n")),
""))))
}
# Print rule -------------------------------------------------------------

37
R/mo.R
View File

@ -748,7 +748,7 @@ exec_as.mo <- function(x,
x_backup_without_spp[i])), uncertainty = -1)
next
}
if (x_backup_without_spp[i] %like_case% "haemoly.*strept") {
if (x_backup_without_spp[i] %like_case% "haemoly.*strep") {
# Haemolytic streptococci in different languages
x[i] <- lookup(mo == "B_STRPT_HAEM", uncertainty = -1)
next
@ -1011,8 +1011,8 @@ exec_as.mo <- function(x,
if (!all(is.na(found)) & nchar(g.x_backup_without_spp) >= 6) {
if (property == "ref") {
# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
# mo_ref("Chlamydia psittaci) = "Page, 1968" (with warning)
# mo_ref("Chlamydophila psittaci) = "Everett et al., 1999"
# mo_ref("Chlamydia psittaci") = "Page, 1968" (with warning)
# mo_ref("Chlamydophila psittaci") = "Everett et al., 1999"
x <- found["ref"]
} else {
x <- lookup(fullname == found["fullname_new"], haystack = MO_lookup)
@ -1437,17 +1437,19 @@ exec_as.mo <- function(x,
# - Becker et al. 2014, PMID 25278577
# - Becker et al. 2019, PMID 30872103
# - Becker et al. 2020, PMID 32056452
post_Becker <- character(0) # 2020-10-20 currently all are mentioned in above papers
if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
warning_("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ",
font_italic(paste("S.",
sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),
collapse = ", ")),
".",
call = FALSE,
immediate = TRUE)
}
post_Becker <- character(0) # 2020-10-20 currently all are mentioned in above papers (otherwise uncomment below)
# nolint start
# if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
# warning_("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ",
# font_italic(paste("S.",
# sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),
# collapse = ", ")),
# ".",
# call = FALSE,
# immediate = TRUE)
# }
# nolint end
# 'MO_CONS' and 'MO_COPS' are <mo> vectors created in R/zzz.R
CoNS <- MO_lookup[which(MO_lookup$mo %in% MO_CONS), property, drop = TRUE]
@ -1976,10 +1978,3 @@ repair_reference_df <- function(reference_df) {
reference_df[, "mo"] <- as.mo(reference_df[, "mo", drop = TRUE])
reference_df
}
left_join_MO_lookup <- function(x, ...) {
pm_left_join(x = x, y = MO_lookup, ...)
}
left_join_MO.old_lookup <- function(x, ...) {
pm_left_join(x = x, y = MO.old_lookup, ...)
}