mirror of https://github.com/msberends/AMR.git
(v2.1.1.9073) unit tests
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17
R/sir.R
17
R/sir.R
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@ -623,7 +623,7 @@ as.sir.data.frame <- function(x,
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}
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# -- host
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if (missing(breakpoint_type) && any(host %in% AMR_env$host_preferred_order, na.rm = TRUE)) {
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if (missing(breakpoint_type) && any(host %in% clinical_breakpoints$host[!clinical_breakpoints$host %in% c("human", "ECOFF")], na.rm = TRUE)) {
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message_("Assuming `breakpoint_type = \"animal\"` since `host` contains animal species.")
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breakpoint_type <- "animal"
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} else if (any(!suppressMessages(convert_host(host)) %in% c("human", "ECOFF"), na.rm = TRUE)) {
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@ -865,16 +865,7 @@ convert_host <- function(x, lang = get_AMR_locale()) {
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x_out[is.na(x_out) & (x %like% "sheep|ovine" | x %like% translate_AMR("sheep|sheeps|ovine", lang))] <- "sheep"
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x_out[is.na(x_out) & (x %like% "snake|serpentine" | x %like% translate_AMR("snake|snakes|serpentine", lang))] <- "snakes"
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x_out[is.na(x_out) & (x %like% "turkey|meleagrine" | x %like% translate_AMR("turkey|turkeys|meleagrine", lang))] <- "turkey"
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if (any(x_out %in% c(NA_character_, "animal"))) {
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x_out[is.na(x_out) & x == "animal"] <- AMR_env$host_preferred_order[1]
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if (message_not_thrown_before("as.sir", "convert_host_missing")) {
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message_(ifelse(any(is.na(x_out) & !is.na(x), na.rm = TRUE),
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paste0("The following host(s) are invalid: ", vector_and(x[is.na(x_out) & !is.na(x)]), ". "),
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""),
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"For missing animal hosts, assuming \"", AMR_env$host_preferred_order[1], "\", since these have the highest breakpoint availability.")
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x_out[is.na(x_out)] <- AMR_env$host_preferred_order[1]
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}
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}
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x_out[x_out == "ecoff"] <- "ECOFF"
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x_out
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}
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@ -929,9 +920,9 @@ as_sir_method <- function(method_short,
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# get host
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if (breakpoint_type == "animal") {
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if (is.null(host)) {
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host <- AMR_env$host_preferred_order[1]
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host <- "dogs"
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if (message_not_thrown_before("as.sir", "host_missing")) {
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message_("Animal hosts not set in `host`, assuming `host = \"", host, "\"`, since these have the highest breakpoint availability.\n\n")
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message_("Animal hosts not set in `host`, assuming `host = \"dogs\"`, since these have the highest breakpoint availability.\n\n")
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}
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}
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} else {
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2
R/zzz.R
2
R/zzz.R
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@ -205,8 +205,6 @@ AMR_env$cli_abort <- import_fn("cli_abort", "cli", error_on_fail = FALSE)
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# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
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AMR_env$AB_lookup <- cbind(AMR::antibiotics, AB_LOOKUP)
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AMR_env$AV_lookup <- cbind(AMR::antivirals, AV_LOOKUP)
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AMR_env$host_preferred_order <- names(sort(table(AMR::clinical_breakpoints$host[!AMR::clinical_breakpoints$host %in% AMR::clinical_breakpoints$type]), decreasing = TRUE))
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}
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.onAttach <- function(lib, pkg) {
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@ -97,7 +97,7 @@ expect_equal(names(mo_info("Escherichia coli")), c(
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"mo",
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"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
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"status", "synonyms", "gramstain", "oxygen_tolerance",
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"url", "ref", "snomed", "lpsn", "gbif", "group_members"
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"url", "ref", "snomed", "lpsn", "mycobank", "gbif", "group_members"
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))
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expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
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expect_true(length(mo_group_members("B_HACEK")) > 1)
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@ -312,14 +312,14 @@ vet <- data.frame(animal = c(rep("cat", 3), rep("dogs", 3), "canine", "equine",
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FLR = mics,
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mo = mo_name(rep(c("B_ESCHR_COLI", "B_PSTRL_MLTC", "B_MNNHM_HMLY"), 4)[-1]))
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out_vet <- as.sir(vet, host = vet$animal, guideline = "CLSI")
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out_vet <- as.sir(vet, host = vet$animal, guideline = "CLSI 2023")
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# host column name instead of values
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expect_identical(out_vet,
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as.sir(vet, host = "animal", guideline = "CLSI 2023"))
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# check outcomes
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expect_identical(out_vet$PRA, as.sir(c("S", NA, "S", "R", NA, "R", "R", NA, "R", "R", NA)))
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expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA, "R", "R")))
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expect_identical(out_vet$PRA, as.sir(c("S", NA, "S", NA, NA, "R", NA, NA, NA, "I", NA)))
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expect_identical(out_vet$FLR, as.sir(c(NA, NA, NA, NA, NA, NA, NA, NA, NA, "R", NA)))
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out_vet <- as.sir(vet, host = "animal", guideline = "EUCAST 2023")
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expect_identical(out_vet$PRA, rep(NA_sir_, 11))
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@ -327,9 +327,10 @@ expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA,
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sir_history <- sir_interpretation_history()
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expect_identical(sort(sir_history$host),
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c("cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle",
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"cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs",
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"dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "horse", "horse", "horse", "horse", "horse", "poultry","poultry"))
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c("cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats",
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"cats", "cats", "cats", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs",
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"dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs",
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"horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "poultry","poultry","poultry","poultry"))
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# ECOFF -------------------------------------------------------------------
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@ -131,10 +131,10 @@ The tab-separated text file and Microsoft Excel workbook both contain all SNOMED
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This data set contains the full microbial taxonomy of `r AMR:::nr2char(length(unique(AMR::microorganisms$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$name`:
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* `r AMR:::TAXONOMY_VERSION$LPSN$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$LPSN$url`> on `r documentation_date(AMR:::TAXONOMY_VERSION$LPSN$accessed_date)`.
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* `r AMR:::TAXONOMY_VERSION$MycoBank$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$MycoBank$url`> on `r documentation_date(AMR:::TAXONOMY_VERSION$MycoBank$accessed_date)`.
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* `r AMR:::TAXONOMY_VERSION$GBIF$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$GBIF$url`> on `r documentation_date(AMR:::TAXONOMY_VERSION$GBIF$accessed_date)`.
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* `r AMR:::TAXONOMY_VERSION$BacDive$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$BacDive$url`> on `r documentation_date(AMR:::TAXONOMY_VERSION$BacDive$accessed_date)`.
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* `r AMR:::TAXONOMY_VERSION$LPSN$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$LPSN$url`> on `r AMR:::documentation_date(AMR:::TAXONOMY_VERSION$LPSN$accessed_date)`.
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* `r AMR:::TAXONOMY_VERSION$MycoBank$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$MycoBank$url`> on `r AMR:::documentation_date(AMR:::TAXONOMY_VERSION$MycoBank$accessed_date)`.
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* `r AMR:::TAXONOMY_VERSION$GBIF$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$GBIF$url`> on `r AMR:::documentation_date(AMR:::TAXONOMY_VERSION$GBIF$accessed_date)`.
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* `r AMR:::TAXONOMY_VERSION$BacDive$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$BacDive$url`> on `r AMR:::documentation_date(AMR:::TAXONOMY_VERSION$BacDive$accessed_date)`.
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* `r AMR:::TAXONOMY_VERSION$SNOMED$citation` URL: <`r AMR:::TAXONOMY_VERSION$SNOMED$url`>
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### Example content
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