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(v2.1.1.9073) unit tests

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dr. M.S. (Matthijs) Berends 2024-09-19 13:57:36 +02:00
parent ef8ef28650
commit 4e96a56b6a
5 changed files with 16 additions and 26 deletions
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17
R/sir.R
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@ -623,7 +623,7 @@ as.sir.data.frame <- function(x,
} }
# -- host # -- host
if (missing(breakpoint_type) && any(host %in% AMR_env$host_preferred_order, na.rm = TRUE)) { if (missing(breakpoint_type) && any(host %in% clinical_breakpoints$host[!clinical_breakpoints$host %in% c("human", "ECOFF")], na.rm = TRUE)) {
message_("Assuming `breakpoint_type = \"animal\"` since `host` contains animal species.") message_("Assuming `breakpoint_type = \"animal\"` since `host` contains animal species.")
breakpoint_type <- "animal" breakpoint_type <- "animal"
} else if (any(!suppressMessages(convert_host(host)) %in% c("human", "ECOFF"), na.rm = TRUE)) { } else if (any(!suppressMessages(convert_host(host)) %in% c("human", "ECOFF"), na.rm = TRUE)) {
@ -865,16 +865,7 @@ convert_host <- function(x, lang = get_AMR_locale()) {
x_out[is.na(x_out) & (x %like% "sheep|ovine" | x %like% translate_AMR("sheep|sheeps|ovine", lang))] <- "sheep" x_out[is.na(x_out) & (x %like% "sheep|ovine" | x %like% translate_AMR("sheep|sheeps|ovine", lang))] <- "sheep"
x_out[is.na(x_out) & (x %like% "snake|serpentine" | x %like% translate_AMR("snake|snakes|serpentine", lang))] <- "snakes" x_out[is.na(x_out) & (x %like% "snake|serpentine" | x %like% translate_AMR("snake|snakes|serpentine", lang))] <- "snakes"
x_out[is.na(x_out) & (x %like% "turkey|meleagrine" | x %like% translate_AMR("turkey|turkeys|meleagrine", lang))] <- "turkey" x_out[is.na(x_out) & (x %like% "turkey|meleagrine" | x %like% translate_AMR("turkey|turkeys|meleagrine", lang))] <- "turkey"
if (any(x_out %in% c(NA_character_, "animal"))) {
x_out[is.na(x_out) & x == "animal"] <- AMR_env$host_preferred_order[1]
if (message_not_thrown_before("as.sir", "convert_host_missing")) {
message_(ifelse(any(is.na(x_out) & !is.na(x), na.rm = TRUE),
paste0("The following host(s) are invalid: ", vector_and(x[is.na(x_out) & !is.na(x)]), ". "),
""),
"For missing animal hosts, assuming \"", AMR_env$host_preferred_order[1], "\", since these have the highest breakpoint availability.")
x_out[is.na(x_out)] <- AMR_env$host_preferred_order[1]
}
}
x_out[x_out == "ecoff"] <- "ECOFF" x_out[x_out == "ecoff"] <- "ECOFF"
x_out x_out
} }
@ -929,9 +920,9 @@ as_sir_method <- function(method_short,
# get host # get host
if (breakpoint_type == "animal") { if (breakpoint_type == "animal") {
if (is.null(host)) { if (is.null(host)) {
host <- AMR_env$host_preferred_order[1] host <- "dogs"
if (message_not_thrown_before("as.sir", "host_missing")) { if (message_not_thrown_before("as.sir", "host_missing")) {
message_("Animal hosts not set in `host`, assuming `host = \"", host, "\"`, since these have the highest breakpoint availability.\n\n") message_("Animal hosts not set in `host`, assuming `host = \"dogs\"`, since these have the highest breakpoint availability.\n\n")
} }
} }
} else { } else {

2
R/zzz.R
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@ -205,8 +205,6 @@ AMR_env$cli_abort <- import_fn("cli_abort", "cli", error_on_fail = FALSE)
# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB) # they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
AMR_env$AB_lookup <- cbind(AMR::antibiotics, AB_LOOKUP) AMR_env$AB_lookup <- cbind(AMR::antibiotics, AB_LOOKUP)
AMR_env$AV_lookup <- cbind(AMR::antivirals, AV_LOOKUP) AMR_env$AV_lookup <- cbind(AMR::antivirals, AV_LOOKUP)
AMR_env$host_preferred_order <- names(sort(table(AMR::clinical_breakpoints$host[!AMR::clinical_breakpoints$host %in% AMR::clinical_breakpoints$type]), decreasing = TRUE))
} }
.onAttach <- function(lib, pkg) { .onAttach <- function(lib, pkg) {

2
inst/tinytest/test-mo_property.R
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@ -97,7 +97,7 @@ expect_equal(names(mo_info("Escherichia coli")), c(
"mo", "mo",
"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
"status", "synonyms", "gramstain", "oxygen_tolerance", "status", "synonyms", "gramstain", "oxygen_tolerance",
"url", "ref", "snomed", "lpsn", "gbif", "group_members" "url", "ref", "snomed", "lpsn", "mycobank", "gbif", "group_members"
)) ))
expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list") expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
expect_true(length(mo_group_members("B_HACEK")) > 1) expect_true(length(mo_group_members("B_HACEK")) > 1)

13
inst/tinytest/test-sir.R
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@ -312,14 +312,14 @@ vet <- data.frame(animal = c(rep("cat", 3), rep("dogs", 3), "canine", "equine",
FLR = mics, FLR = mics,
mo = mo_name(rep(c("B_ESCHR_COLI", "B_PSTRL_MLTC", "B_MNNHM_HMLY"), 4)[-1])) mo = mo_name(rep(c("B_ESCHR_COLI", "B_PSTRL_MLTC", "B_MNNHM_HMLY"), 4)[-1]))
out_vet <- as.sir(vet, host = vet$animal, guideline = "CLSI") out_vet <- as.sir(vet, host = vet$animal, guideline = "CLSI 2023")
# host column name instead of values # host column name instead of values
expect_identical(out_vet, expect_identical(out_vet,
as.sir(vet, host = "animal", guideline = "CLSI 2023")) as.sir(vet, host = "animal", guideline = "CLSI 2023"))
# check outcomes # check outcomes
expect_identical(out_vet$PRA, as.sir(c("S", NA, "S", "R", NA, "R", "R", NA, "R", "R", NA))) expect_identical(out_vet$PRA, as.sir(c("S", NA, "S", NA, NA, "R", NA, NA, NA, "I", NA)))
expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA, "R", "R"))) expect_identical(out_vet$FLR, as.sir(c(NA, NA, NA, NA, NA, NA, NA, NA, NA, "R", NA)))
out_vet <- as.sir(vet, host = "animal", guideline = "EUCAST 2023") out_vet <- as.sir(vet, host = "animal", guideline = "EUCAST 2023")
expect_identical(out_vet$PRA, rep(NA_sir_, 11)) expect_identical(out_vet$PRA, rep(NA_sir_, 11))
@ -327,9 +327,10 @@ expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA,
sir_history <- sir_interpretation_history() sir_history <- sir_interpretation_history()
expect_identical(sort(sir_history$host), expect_identical(sort(sir_history$host),
c("cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", c("cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats",
"cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs", "cats", "cats", "cats", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs",
"dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "horse", "horse", "horse", "horse", "horse", "poultry","poultry")) "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs",
"horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "poultry","poultry","poultry","poultry"))
# ECOFF ------------------------------------------------------------------- # ECOFF -------------------------------------------------------------------

8
vignettes/datasets.Rmd
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@ -131,10 +131,10 @@ The tab-separated text file and Microsoft Excel workbook both contain all SNOMED
This data set contains the full microbial taxonomy of `r AMR:::nr2char(length(unique(AMR::microorganisms$kingdom[!AMR::microorganisms$kingdom %like% "unknown"])))` kingdoms from the `r AMR:::TAXONOMY_VERSION$LPSN$name`, `r AMR:::TAXONOMY_VERSION$MycoBank$name`, and the `r AMR:::TAXONOMY_VERSION$GBIF$name`: This data set contains the full microbial taxonomy of `r AMR:::nr2char(length(unique(AMR::microorganisms$kingdom[!AMR::microorganisms$kingdom %like% "unknown"])))` kingdoms from the `r AMR:::TAXONOMY_VERSION$LPSN$name`, `r AMR:::TAXONOMY_VERSION$MycoBank$name`, and the `r AMR:::TAXONOMY_VERSION$GBIF$name`:
* `r AMR:::TAXONOMY_VERSION$LPSN$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$LPSN$url`> on `r documentation_date(AMR:::TAXONOMY_VERSION$LPSN$accessed_date)`. * `r AMR:::TAXONOMY_VERSION$LPSN$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$LPSN$url`> on `r AMR:::documentation_date(AMR:::TAXONOMY_VERSION$LPSN$accessed_date)`.
* `r AMR:::TAXONOMY_VERSION$MycoBank$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$MycoBank$url`> on `r documentation_date(AMR:::TAXONOMY_VERSION$MycoBank$accessed_date)`. * `r AMR:::TAXONOMY_VERSION$MycoBank$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$MycoBank$url`> on `r AMR:::documentation_date(AMR:::TAXONOMY_VERSION$MycoBank$accessed_date)`.
* `r AMR:::TAXONOMY_VERSION$GBIF$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$GBIF$url`> on `r documentation_date(AMR:::TAXONOMY_VERSION$GBIF$accessed_date)`. * `r AMR:::TAXONOMY_VERSION$GBIF$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$GBIF$url`> on `r AMR:::documentation_date(AMR:::TAXONOMY_VERSION$GBIF$accessed_date)`.
* `r AMR:::TAXONOMY_VERSION$BacDive$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$BacDive$url`> on `r documentation_date(AMR:::TAXONOMY_VERSION$BacDive$accessed_date)`. * `r AMR:::TAXONOMY_VERSION$BacDive$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$BacDive$url`> on `r AMR:::documentation_date(AMR:::TAXONOMY_VERSION$BacDive$accessed_date)`.
* `r AMR:::TAXONOMY_VERSION$SNOMED$citation` URL: <`r AMR:::TAXONOMY_VERSION$SNOMED$url`> * `r AMR:::TAXONOMY_VERSION$SNOMED$citation` URL: <`r AMR:::TAXONOMY_VERSION$SNOMED$url`>
### Example content ### Example content