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CI tests
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@ -140,6 +140,7 @@ export(mo_fullname)
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export(mo_genus)
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export(mo_gramstain)
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export(mo_kingdom)
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export(mo_name)
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export(mo_order)
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export(mo_phylum)
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export(mo_property)
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1
NEWS.md
1
NEWS.md
@ -3,6 +3,7 @@
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#### New
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* Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use `as.rsi()` on an MIC value (created with `as.mic()`), a disk diffusion value (created with the new `as.disk()`) or on a complete date set containing columns with MIC or disk diffusion values.
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* Function `mo_name()` as alias of `mo_fullname()`
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#### Changed
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* Completely reworked the `antibiotics` data set:
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72
R/mdro.R
72
R/mdro.R
@ -374,42 +374,42 @@ eucast_exceptional_phenotypes <- function(x, country = "EUCAST", ...) {
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mdro(x = x, country = "EUCAST", ...)
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}
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is_ESBL <- function(x, col_mo = NULL, ...) {
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col_mo <- get_column_mo(tbl = x, col_mo = col_mo)
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cols_ab <- get_column_abx(tbl = x,
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soft_dependencies = c("AMX", "AMP"),
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hard_dependencies = c("CAZ"),
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...)
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if (!any(c("AMX", "AMP") %in% names(cols_ab))) {
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# both ampicillin and amoxicillin are missing
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generate_warning_abs_missing(c("AMX", "AMP"), any = TRUE)
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return(rep(NA, nrow(x)))
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}
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ESBLs <- rep(NA, nrow(x))
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# first make all eligible cases FALSE
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ESBLs[which(mo_family(x[, col_mo]) == "Enterobacteriaceae"
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& x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
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& x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
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& x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
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)] <- FALSE
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# now make the positives cases TRUE
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ESBLs[which(!is.na(ESBLs)
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& x[, get_ab_col(cols_ab, "AMX")] == "R"
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& x[, get_ab_col(cols_ab, "CAZ")] == "R")] <- TRUE
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ESBLs
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}
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is_3MRGN <- function(x, ...) {
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}
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is_4MRGN <- function(x, ...) {
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}
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# is_ESBL <- function(x, col_mo = NULL, ...) {
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# col_mo <- get_column_mo(tbl = x, col_mo = col_mo)
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# cols_ab <- get_column_abx(tbl = x,
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# soft_dependencies = c("AMX", "AMP"),
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# hard_dependencies = c("CAZ"),
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# ...)
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#
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# if (!any(c("AMX", "AMP") %in% names(cols_ab))) {
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# # both ampicillin and amoxicillin are missing
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# generate_warning_abs_missing(c("AMX", "AMP"), any = TRUE)
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# return(rep(NA, nrow(x)))
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# }
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#
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# ESBLs <- rep(NA, nrow(x))
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#
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# # first make all eligible cases FALSE
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# ESBLs[which(mo_family(x[, col_mo]) == "Enterobacteriaceae"
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# & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
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# & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
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# & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
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# )] <- FALSE
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# # now make the positives cases TRUE
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# ESBLs[which(!is.na(ESBLs)
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# & x[, get_ab_col(cols_ab, "AMX")] == "R"
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# & x[, get_ab_col(cols_ab, "CAZ")] == "R")] <- TRUE
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# ESBLs
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#
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# }
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#
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# is_3MRGN <- function(x, ...) {
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#
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# }
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#
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# is_4MRGN <- function(x, ...) {
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#
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# }
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get_column_mo <- function(tbl, col_mo = NULL) {
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# throws a blue note about which column will be used if guessed
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8
R/misc.R
8
R/misc.R
@ -306,17 +306,17 @@ get_column_abx <- function(tbl,
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TOB = TOB, TMP = TMP, SXT = SXT, VAN = VAN)
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if (!is.null(hard_dependencies)) {
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if (!all(hard_dependencies %in% names(columns_available))) {
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if (!all(hard_dependencies %in% names(columns_available[!is.na(columns_available)]))) {
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# missing a hard dependency will return NA and consequently the data will not be analysed
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missing <- hard_dependencies[!hard_dependencies %in% names(columns_available)]
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missing <- hard_dependencies[!hard_dependencies %in% names(columns_available[!is.na(columns_available)])]
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generate_warning_abs_missing(missing, any = FALSE)
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return(NA)
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}
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}
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if (!is.null(soft_dependencies)) {
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if (!all(soft_dependencies %in% names(columns_available))) {
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if (!all(soft_dependencies %in% names(columns_available[!is.na(columns_available)]))) {
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# missing a soft dependency may lower the reliability
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missing <- soft_dependencies[!soft_dependencies %in% names(columns_available)]
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missing <- soft_dependencies[!soft_dependencies %in% names(columns_available[!is.na(columns_available)])]
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missing <- paste0("`", missing, "` (", ab_name(missing, tolower = TRUE), ")")
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warning('Reliability might be improved if these antimicrobial results would be available too: ', paste(missing, collapse = ", "),
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immediate. = TRUE,
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32
R/mo.R
32
R/mo.R
@ -557,22 +557,22 @@ exec_as.mo <- function(x,
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if (nchar(gsub("[^a-zA-Z]", "", x_trimmed[i])) < 3
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& !x_backup_without_spp[i] %like% "O?(26|103|104|104|111|121|145|157)") {
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# check if search term was like "A. species", then return first genus found with ^A
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if (x_backup[i] %like% "[a-z]+ species" | x_backup[i] %like% "[a-z] spp[.]?") {
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# get mo code of first hit
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found <- microorganismsDT[fullname %like% x_withspaces_start_only[i], mo]
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if (length(found) > 0) {
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mo_code <- found[1L] %>% strsplit("_") %>% unlist() %>% .[1:2] %>% paste(collapse = "_")
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found <- microorganismsDT[mo == mo_code, ..property][[1]]
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# return first genus that begins with x_trimmed, e.g. when "E. spp."
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if (length(found) > 0) {
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x[i] <- found[1L]
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if (initial_search == TRUE) {
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set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
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}
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next
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}
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}
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}
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# if (x_backup[i] %like% "[a-z]+ species" | x_backup[i] %like% "[a-z] spp[.]?") {
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# # get mo code of first hit
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# found <- microorganismsDT[fullname %like% x_withspaces_start_only[i], mo]
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# if (length(found) > 0) {
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# mo_code <- found[1L] %>% strsplit("_") %>% unlist() %>% .[1:2] %>% paste(collapse = "_")
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# found <- microorganismsDT[mo == mo_code, ..property][[1]]
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# # return first genus that begins with x_trimmed, e.g. when "E. spp."
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# if (length(found) > 0) {
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# x[i] <- found[1L]
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# if (initial_search == TRUE) {
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# set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
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# }
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# next
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# }
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# }
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# }
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# fewer than 3 chars and not looked for species, add as failure
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x[i] <- microorganismsDT[mo == "UNKNOWN", ..property][[1]]
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if (initial_search == TRUE) {
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@ -64,7 +64,8 @@
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#' mo_subspecies("E. coli") # ""
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#'
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#' ## colloquial properties
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#' mo_fullname("E. coli") # "Escherichia coli"
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#' mo_name("E. coli") # "Escherichia coli"
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#' mo_fullname("E. coli") # "Escherichia coli", same as mo_name()
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#' mo_shortname("E. coli") # "E. coli"
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#'
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#' ## other properties
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@ -131,6 +132,12 @@
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#'
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#' # get a list with the complete taxonomy (from kingdom to subspecies)
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#' mo_taxonomy("E. coli")
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mo_name <- function(x, language = get_locale(), ...) {
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mo_fullname(x = x, language = language, ... = ...)
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}
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#' @rdname mo_property
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#' @export
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mo_fullname <- function(x, language = get_locale(), ...) {
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x <- mo_validate(x = x, property = "fullname", ...)
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t(x, language = language)
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@ -31,7 +31,8 @@
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#' @param data a \code{data.frame} containing columns with class \code{rsi} (see \code{\link{as.rsi}})
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#' @param translate_ab a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations to, using \code{\link{ab_property}}
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#' @inheritParams ab_property
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#' @param combine_SI a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.
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#' @param combine_SI a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.
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#' @param combine_IR a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.
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#' @inheritSection as.rsi Interpretation of S, I and R
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#' @details \strong{Remember that you should filter your table to let it contain only first isolates!} Use \code{\link{first_isolate}} to determine them in your data set.
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#'
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@ -242,6 +242,8 @@
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<a href="#new" class="anchor"></a>New</h4>
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<ul>
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<li>Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><a href="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><a href="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
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<li>Function <code><a href="../reference/mo_property.html">mo_name()</a></code> as alias of <code><a href="../reference/mo_property.html">mo_fullname()</a></code>
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</li>
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</ul>
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</div>
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<div id="changed" class="section level4">
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@ -285,7 +285,11 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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</tr>
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<tr>
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<th>combine_SI</th>
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<td><p>a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now <code>TRUE</code>.</p></td>
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<td><p>a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now <code>TRUE</code>.</p></td>
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</tr>
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<tr>
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<th>combine_IR</th>
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<td><p>a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter <code>combine_SI</code>.</p></td>
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</tr>
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</table>
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</tr>
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<tr>
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<th>combine_SI</th>
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<td><p>a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now <code>TRUE</code>.</p></td>
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<td><p>a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now <code>TRUE</code>.</p></td>
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</tr>
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<tr>
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<th>combine_IR</th>
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<td><p>a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter <code>combine_SI</code>.</p></td>
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</tr>
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<tr>
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<th>language</th>
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@ -373,7 +373,7 @@
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</tr><tr>
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<td>
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<p><code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
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<p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
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</td>
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<td><p>Property of a microorganism</p></td>
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</tr><tr>
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@ -241,7 +241,9 @@
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</div>
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<pre class="usage"><span class='fu'>mo_fullname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
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<pre class="usage"><span class='fu'>mo_name</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
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<span class='fu'>mo_fullname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
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<span class='fu'>mo_shortname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
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@ -364,7 +366,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<span class='fu'>mo_subspecies</span>(<span class='st'>"E. coli"</span>) <span class='co'># ""</span>
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<span class='co'>## colloquial properties</span>
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<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli"</span>
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<span class='fu'>mo_name</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli"</span>
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<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli", same as mo_name()</span>
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<span class='fu'>mo_shortname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "E. coli"</span>
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<span class='co'>## other properties</span>
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@ -295,7 +295,11 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
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</tr>
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<tr>
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<th>combine_SI</th>
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<td><p>a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now <code>TRUE</code>.</p></td>
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<td><p>a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now <code>TRUE</code>.</p></td>
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</tr>
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<tr>
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<th>combine_IR</th>
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<td><p>a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter <code>combine_SI</code>.</p></td>
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</tr>
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</table>
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@ -43,7 +43,9 @@ count_df(data, translate_ab = "name", language = get_locale(),
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\item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{combine_SI}{a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
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\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
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\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.}
|
||||
}
|
||||
\value{
|
||||
Integer
|
||||
|
@ -50,7 +50,9 @@ labels_rsi_count(position = NULL, x = "Antibiotic",
|
||||
|
||||
\item{translate_ab}{a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations to, using \code{\link{ab_property}}}
|
||||
|
||||
\item{combine_SI}{a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
|
||||
\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
|
||||
|
||||
\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.}
|
||||
|
||||
\item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
|
||||
|
||||
|
@ -2,6 +2,7 @@
|
||||
% Please edit documentation in R/mo_property.R
|
||||
\name{mo_property}
|
||||
\alias{mo_property}
|
||||
\alias{mo_name}
|
||||
\alias{mo_fullname}
|
||||
\alias{mo_shortname}
|
||||
\alias{mo_subspecies}
|
||||
@ -22,6 +23,8 @@
|
||||
\alias{mo_url}
|
||||
\title{Property of a microorganism}
|
||||
\usage{
|
||||
mo_name(x, language = get_locale(), ...)
|
||||
|
||||
mo_fullname(x, language = get_locale(), ...)
|
||||
|
||||
mo_shortname(x, language = get_locale(), ...)
|
||||
@ -132,7 +135,8 @@ mo_species("E. coli") # "coli"
|
||||
mo_subspecies("E. coli") # ""
|
||||
|
||||
## colloquial properties
|
||||
mo_fullname("E. coli") # "Escherichia coli"
|
||||
mo_name("E. coli") # "Escherichia coli"
|
||||
mo_fullname("E. coli") # "Escherichia coli", same as mo_name()
|
||||
mo_shortname("E. coli") # "E. coli"
|
||||
|
||||
## other properties
|
||||
|
@ -49,7 +49,9 @@ portion_df(data, translate_ab = "name", language = get_locale(),
|
||||
|
||||
\item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
|
||||
|
||||
\item{combine_SI}{a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
|
||||
\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
|
||||
|
||||
\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.}
|
||||
}
|
||||
\value{
|
||||
Double or, when \code{as_percent = TRUE}, a character.
|
||||
|
@ -33,6 +33,9 @@ test_that("EUCAST rules work", {
|
||||
"reference.rule", "reference.rule_group"))
|
||||
|
||||
expect_error(suppressWarnings(eucast_rules(septic_patients, col_mo = "Non-existing")))
|
||||
expect_error(eucast_rules(x = "text"))
|
||||
expect_error(eucast_rules(data.frame(a = "test")))
|
||||
expect_error(eucast_rules(data.frame(mo = "test"), rules = "invalid rules set"))
|
||||
|
||||
expect_identical(colnames(septic_patients),
|
||||
colnames(suppressWarnings(eucast_rules(septic_patients))))
|
||||
|
@ -42,3 +42,10 @@ test_that("functions missing in older R versions work", {
|
||||
expect_equal(trimws(" test ", "l"), "test ")
|
||||
expect_equal(trimws(" test ", "r"), " test")
|
||||
})
|
||||
|
||||
test_that("looking up ab columns works", {
|
||||
expect_warning(generate_warning_abs_missing(c("AMP", "AMX")))
|
||||
expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
|
||||
expect_warning(get_column_abx(septic_patients, hard_dependencies = "FUS"))
|
||||
expect_warning(get_column_abx(septic_patients, soft_dependencies = "FUS"))
|
||||
})
|
||||
|
@ -200,6 +200,9 @@ test_that("as.mo works", {
|
||||
expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = FALSE))), "UNKNOWN")
|
||||
expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = TRUE))), "B_ESCHR_COL")
|
||||
expect_warning(as.mo("esco extra_text", allow_uncertain = TRUE))
|
||||
expect_equal(suppressWarnings(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AUR")
|
||||
expect_equal(suppressWarnings(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY")
|
||||
expect_equal(suppressWarnings(as.character(as.mo("Staphylococcus aureus unexisting", allow_uncertain = 3))), "B_STPHY")
|
||||
|
||||
# predefined reference_df
|
||||
expect_equal(as.character(as.mo("TestingOwnID",
|
||||
@ -244,4 +247,20 @@ test_that("as.mo works", {
|
||||
# summary
|
||||
expect_equal(length(summary(septic_patients$mo)), 6)
|
||||
|
||||
# other
|
||||
expect_equal(as.character(as.mo(c("xxx", "con", "na", "nan"), debug = TRUE)),
|
||||
rep(NA_character_, 4))
|
||||
|
||||
expect_equal(as.character(as.mo(c("other", "none", "unknown"))),
|
||||
rep("UNKNOWN", 3))
|
||||
|
||||
expect_null(mo_failures())
|
||||
expect_true(septic_patients %>% pull(mo) %>% is.mo())
|
||||
|
||||
expect_equal(get_mo_code("test", "mo"), "test")
|
||||
expect_equal(length(get_mo_code("Escherichia", "genus")),
|
||||
nrow(AMR::microorganisms[base::which(AMR::microorganisms[, "genus"] %in% "Escherichia"),]))
|
||||
|
||||
expect_error(translate_allow_uncertain(5))
|
||||
|
||||
})
|
||||
|
@ -31,6 +31,7 @@ test_that("mo_property works", {
|
||||
expect_equal(mo_species("E. coli"), "coli")
|
||||
expect_equal(mo_subspecies("E. coli"), "")
|
||||
expect_equal(mo_fullname("E. coli"), "Escherichia coli")
|
||||
expect_equal(mo_name("E. coli"), "Escherichia coli")
|
||||
expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
|
||||
expect_equal(mo_gramstain("E. coli", language = "en"), "Gram negative")
|
||||
expect_equal(class(mo_taxonomy("E. coli")), "list")
|
||||
@ -47,6 +48,8 @@ test_that("mo_property works", {
|
||||
expect_equal(mo_shortname("S. agalac"), "S. agalactiae")
|
||||
expect_equal(mo_shortname("S. agalac", Lancefield = TRUE), "GBS")
|
||||
|
||||
expect_true(mo_url("Escherichia coli") %like% "www.catalogueoflife.org")
|
||||
|
||||
# test integrity
|
||||
MOs <- AMR::microorganisms
|
||||
expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
|
||||
|
Loading…
Reference in New Issue
Block a user