mirror of
https://github.com/msberends/AMR.git
synced 2025-07-12 23:01:51 +02:00
support veterinary MIC/disk translation
This commit is contained in:
80
R/zzz.R
80
R/zzz.R
@ -55,6 +55,7 @@ AMR_env$av_previously_coerced <- data.frame(
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av = character(0),
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stringsAsFactors = FALSE
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)
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AMR_env$host_preferred_order <- names(sort(table(AMR::clinical_breakpoints$host[!AMR::clinical_breakpoints$host %in% AMR::clinical_breakpoints$type]), decreasing = TRUE))
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AMR_env$sir_interpretation_history <- data.frame(
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datetime = Sys.time()[0],
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index = integer(0),
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@ -67,6 +68,7 @@ AMR_env$sir_interpretation_history <- data.frame(
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method = character(0),
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breakpoint_S_R = character(0),
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guideline = character(0),
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host = character(0),
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ref_table = character(0),
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stringsAsFactors = FALSE
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)
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@ -130,32 +132,33 @@ if (pkg_is_available("cli")) {
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s3_register("knitr::knit_print", "antibiogram")
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s3_register("knitr::knit_print", "formatted_bug_drug_combinations")
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# Support vctrs package for use in e.g. dplyr verbs
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# NOTE 2024-02-22 this is the right way - it should be 2 S3 classes in the second argument
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# S3: ab_selector
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s3_register("vctrs::vec_ptype2", "character.ab_selector")
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s3_register("vctrs::vec_ptype2", "ab_selector.character")
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s3_register("vctrs::vec_ptype2", "ab_selector.default")
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s3_register("vctrs::vec_ptype2", "ab_selector.ab_selector")
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s3_register("vctrs::vec_cast", "character.ab_selector")
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# S3: ab_selector_any_all
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s3_register("vctrs::vec_ptype2", "logical.ab_selector_any_all")
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s3_register("vctrs::vec_ptype2", "ab_selector_any_all.logical")
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s3_register("vctrs::vec_ptype2", "ab_selector_any_all.default")
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s3_register("vctrs::vec_ptype2", "ab_selector_any_all.ab_selector_any_all")
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s3_register("vctrs::vec_cast", "logical.ab_selector_any_all")
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# S3: ab
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s3_register("vctrs::vec_ptype2", "character.ab")
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s3_register("vctrs::vec_ptype2", "ab.character")
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s3_register("vctrs::vec_ptype2", "ab.default")
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s3_register("vctrs::vec_ptype2", "ab.ab")
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s3_register("vctrs::vec_cast", "character.ab")
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s3_register("vctrs::vec_cast", "ab.character")
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# S3: av
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s3_register("vctrs::vec_ptype2", "character.av")
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s3_register("vctrs::vec_ptype2", "av.character")
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s3_register("vctrs::vec_ptype2", "av.default")
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s3_register("vctrs::vec_ptype2", "av.av")
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s3_register("vctrs::vec_cast", "character.av")
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s3_register("vctrs::vec_cast", "av.character")
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# S3: mo
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s3_register("vctrs::vec_ptype2", "character.mo")
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s3_register("vctrs::vec_ptype2", "mo.character")
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s3_register("vctrs::vec_ptype2", "mo.default")
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s3_register("vctrs::vec_ptype2", "mo.mo")
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s3_register("vctrs::vec_cast", "character.mo")
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s3_register("vctrs::vec_cast", "mo.character")
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# S3: disk
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s3_register("vctrs::vec_ptype2", "integer.disk")
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s3_register("vctrs::vec_ptype2", "disk.integer")
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s3_register("vctrs::vec_ptype2", "disk.default")
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s3_register("vctrs::vec_ptype2", "disk.disk")
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s3_register("vctrs::vec_cast", "integer.disk")
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s3_register("vctrs::vec_cast", "disk.integer")
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s3_register("vctrs::vec_cast", "double.disk")
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@ -163,14 +166,19 @@ if (pkg_is_available("cli")) {
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s3_register("vctrs::vec_cast", "character.disk")
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s3_register("vctrs::vec_cast", "disk.character")
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# S3: mic
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s3_register("vctrs::vec_ptype2", "mic.default")
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s3_register("vctrs::vec_ptype2", "mic.mic")
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s3_register("vctrs::vec_cast", "character.mic")
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s3_register("vctrs::vec_cast", "double.mic")
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s3_register("vctrs::vec_cast", "integer.mic")
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s3_register("vctrs::vec_cast", "mic.character")
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s3_register("vctrs::vec_cast", "mic.double")
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s3_register("vctrs::vec_cast", "mic.integer")
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s3_register("vctrs::vec_math", "mic")
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s3_register("vctrs::vec_arith", "mic")
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# S3: sir
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s3_register("vctrs::vec_ptype2", "character.sir")
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s3_register("vctrs::vec_ptype2", "sir.character")
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s3_register("vctrs::vec_ptype2", "sir.default")
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s3_register("vctrs::vec_ptype2", "sir.sir")
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s3_register("vctrs::vec_cast", "character.sir")
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s3_register("vctrs::vec_cast", "sir.character")
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@ -192,26 +200,34 @@ if (pkg_is_available("cli")) {
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.onAttach <- function(lib, pkg) {
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# if custom ab option is available, load it
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if (!is.null(getOption("AMR_custom_ab")) && file.exists(getOption("AMR_custom_ab", default = ""))) {
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packageStartupMessage("Adding custom antimicrobials from '", getOption("AMR_custom_ab"), "'...", appendLF = FALSE)
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x <- readRDS_AMR(getOption("AMR_custom_ab"))
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tryCatch(
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{
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suppressWarnings(suppressMessages(add_custom_antimicrobials(x)))
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packageStartupMessage("OK.")
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},
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error = function(e) packageStartupMessage("Failed: ", e$message)
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)
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if (getOption("AMR_custom_ab") %unlike% "[.]rds$") {
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packageStartupMessage("The file with custom antimicrobials must be an RDS file. Set the option `AMR_custom_ab` to another path.")
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} else {
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packageStartupMessage("Adding custom antimicrobials from '", getOption("AMR_custom_ab"), "'...", appendLF = FALSE)
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x <- readRDS_AMR(getOption("AMR_custom_ab"))
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tryCatch(
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{
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suppressWarnings(suppressMessages(add_custom_antimicrobials(x)))
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packageStartupMessage("OK.")
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},
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error = function(e) packageStartupMessage("Failed: ", e$message)
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)
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}
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}
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# if custom mo option is available, load it
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if (!is.null(getOption("AMR_custom_mo")) && file.exists(getOption("AMR_custom_mo", default = ""))) {
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packageStartupMessage("Adding custom microorganisms from '", getOption("AMR_custom_mo"), "'...", appendLF = FALSE)
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x <- readRDS_AMR(getOption("AMR_custom_mo"))
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tryCatch(
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{
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suppressWarnings(suppressMessages(add_custom_microorganisms(x)))
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packageStartupMessage("OK.")
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},
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error = function(e) packageStartupMessage("Failed: ", e$message)
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)
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if (getOption("AMR_custom_mo") %unlike% "[.]rds$") {
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packageStartupMessage("The file with custom microorganisms must be an RDS file. Set the option `AMR_custom_mo` to another path.")
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} else {
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packageStartupMessage("Adding custom microorganisms from '", getOption("AMR_custom_mo"), "'...", appendLF = FALSE)
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x <- readRDS_AMR(getOption("AMR_custom_mo"))
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tryCatch(
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{
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suppressWarnings(suppressMessages(add_custom_microorganisms(x)))
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packageStartupMessage("OK.")
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},
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error = function(e) packageStartupMessage("Failed: ", e$message)
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)
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}
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}
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}
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