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Implement extensive support for antiviral agents support (#77)

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This commit is contained in:
Dr. Matthijs Berends
2022-11-13 08:46:10 +01:00
committed by GitHub
parent d2edcf51ad
commit 496c08d851
46 changed files with 1966 additions and 1563 deletions
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17
R/zzz.R
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@ -50,6 +50,11 @@ AMR_env$ab_previously_coerced <- data.frame(
ab = character(0),
stringsAsFactors = FALSE
)
AMR_env$av_previously_coerced <- data.frame(
x = character(0),
av = character(0),
stringsAsFactors = FALSE
)
AMR_env$rsi_interpretation_history <- data.frame(
datetime = Sys.time()[0],
index = integer(0),
@ -87,11 +92,13 @@ if (utf8_supported && !is_latex) {
# developers of the vctrs package:
# https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
s3_register("pillar::pillar_shaft", "ab")
s3_register("pillar::pillar_shaft", "av")
s3_register("pillar::pillar_shaft", "mo")
s3_register("pillar::pillar_shaft", "rsi")
s3_register("pillar::pillar_shaft", "mic")
s3_register("pillar::pillar_shaft", "disk")
s3_register("tibble::type_sum", "ab")
s3_register("tibble::type_sum", "av")
s3_register("tibble::type_sum", "mo")
s3_register("tibble::type_sum", "rsi")
s3_register("tibble::type_sum", "mic")
@ -129,6 +136,11 @@ if (utf8_supported && !is_latex) {
s3_register("vctrs::vec_ptype2", "ab.character")
s3_register("vctrs::vec_cast", "character.ab")
s3_register("vctrs::vec_cast", "ab.character")
# S3: av
s3_register("vctrs::vec_ptype2", "character.av")
s3_register("vctrs::vec_ptype2", "av.character")
s3_register("vctrs::vec_cast", "character.av")
s3_register("vctrs::vec_cast", "av.character")
# S3: mo
s3_register("vctrs::vec_ptype2", "character.mo")
s3_register("vctrs::vec_ptype2", "mo.character")
@ -168,6 +180,7 @@ if (utf8_supported && !is_latex) {
# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
AMR_env$AB_lookup <- create_AB_lookup()
AMR_env$AV_lookup <- create_AV_lookup()
AMR_env$MO_lookup <- create_MO_lookup()
}
@ -190,6 +203,10 @@ create_AB_lookup <- function() {
cbind(AMR::antibiotics, AB_LOOKUP)
}
create_AV_lookup <- function() {
cbind(AMR::antivirals, AV_LOOKUP)
}
create_MO_lookup <- function() {
MO_lookup <- AMR::microorganisms