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add Python package to repo

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dr. M.S. (Matthijs) Berends
2024-11-21 10:06:26 +01:00
parent f424c39474
commit 87271d261a
16 changed files with 1417 additions and 34 deletions
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24
R/sir.R
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@ -970,6 +970,7 @@ as_sir_method <- function(method_short,
warning_("The following animal host(s) could not be coerced: ", vector_and(host.bak[is.na(host) & !is.na(host.bak)]), immediate = TRUE)
message() # new line
}
# TODO add a switch to turn this off? In interactive sessions perhaps ask the user. Default should be On.
if (breakpoint_type == "animal" && message_not_thrown_before("as.sir", "host_missing_breakpoints")) {
if (guideline_coerced %like% "CLSI") {
message_("Please note that in the absence of specific veterinary breakpoints for certain animal hosts, the CLSI guideline VET09 will be applied where possible.\n\n")
@ -1053,6 +1054,8 @@ as_sir_method <- function(method_short,
)
}
}
# TODO set uti to specimen column here
if (length(ab) == 1 && ab %like% paste0("as.", method_short)) {
stop_("No unambiguous name was supplied about the antibiotic (argument `ab`). See ?as.sir.", call = FALSE)
@ -1238,6 +1241,8 @@ as_sir_method <- function(method_short,
new_sir <- rep(NA_sir_, length(rows))
# find different mo properties, as fast as possible
# TODO in case of VET09, we need to keep E. coli, also when users have Proteus in their data set
# TODO look up which species, at least E. coli - also Staph or Strep?
mo_current_genus <- AMR_env$MO_lookup$mo[match(AMR_env$MO_lookup$genus[match(mo_current, AMR_env$MO_lookup$mo)], AMR_env$MO_lookup$fullname)]
mo_current_family <- AMR_env$MO_lookup$mo[match(AMR_env$MO_lookup$family[match(mo_current, AMR_env$MO_lookup$mo)], AMR_env$MO_lookup$fullname)]
mo_current_order <- AMR_env$MO_lookup$mo[match(AMR_env$MO_lookup$order[match(mo_current, AMR_env$MO_lookup$mo)], AMR_env$MO_lookup$fullname)]
@ -1262,6 +1267,7 @@ as_sir_method <- function(method_short,
)
# gather all available breakpoints for current MO
# TODO for VET09 do not filter out E. coli and such
breakpoints_current <- breakpoints %pm>%
subset(ab == ab_current) %pm>%
subset(mo %in% c(
@ -1271,14 +1277,17 @@ as_sir_method <- function(method_short,
mo_current_other
))
# TODO are operators considered??
# This seems to not work well: as.sir(as.mic(c(4, ">4", ">=4", 8, ">8", ">=8")), ab = "AMC", mo = "E. coli", breakpoint_type = "animal", host = "dogs", guideline = "CLSI 2024")
## fall-back methods for veterinary guidelines ----
if (breakpoint_type == "animal" && !host_current %in% breakpoints_current$host) {
if (guideline_coerced %like% "CLSI") {
# VET09 says that staph/strep/enterococcus BP can be extrapolated to all Gr+ cocci except for intrinsic resistance, so take all Gr+ cocci:
all_gram_pos_genera <- c("B_STPHY", "B_STRPT", "B_PPTST", "B_AERCC", "B_MCRCCC", "B_TRPRL")
gram_plus_cocci_vet09 <- microorganisms$mo[microorganisms$genus %in% c("Staphylococcus", "Streptococcus", "Peptostreptococcus", "Aerococcus", "Micrococcus") & microorganisms$rank == "genus"] # TODO should probably include genera that were either of these before
# HUMAN SUBSTITUTES
if (ab_current == "AZM" && mo_current_genus %in% all_gram_pos_genera && host_current %in% c("dogs", "cats", "horse")) {
if (ab_current == "AZM" && mo_current_genus %in% gram_plus_cocci_vet09 && host_current %in% c("dogs", "cats", "horse")) {
# azithro can take human breakpoints for these agents
breakpoints_current <- breakpoints_current %pm>% subset(host == "human")
notes_current <- c(notes_current, paste0("Using ", font_bold("human"), " breakpoints for ", ab_formatted, " in Gram-positive cocci based on CLSI VET09."))
@ -1290,7 +1299,7 @@ as_sir_method <- function(method_short,
# cefta can take human breakpoints for these agents
breakpoints_current <- breakpoints_current %pm>% subset(host == "human")
notes_current <- c(notes_current, paste0("Using ", font_bold("human"), " breakpoints for ", ab_formatted, " in Enterobacterales and ", font_italic("P. aeruginosa"), " based on CLSI VET09."))
} else if (ab_current == "ERY" && mo_current_genus %in% all_gram_pos_genera && host_current %in% c("dogs", "cats", "horse")) {
} else if (ab_current == "ERY" && mo_current_genus %in% gram_plus_cocci_vet09 && host_current %in% c("dogs", "cats", "horse")) {
# erythro can take human breakpoints for these agents
breakpoints_current <- breakpoints_current %pm>% subset(host == "human")
notes_current <- c(notes_current, paste0("Using ", font_bold("human"), " breakpoints for ", ab_formatted, " in Gram-positive cocci based on CLSI VET09."))
@ -1298,7 +1307,7 @@ as_sir_method <- function(method_short,
# imipenem can take human breakpoints for these agents
breakpoints_current <- breakpoints_current %pm>% subset(host == "human")
notes_current <- c(notes_current, paste0("Using ", font_bold("human"), " breakpoints for ", ab_formatted, " in Enterobacterales and ", font_italic("P. aeruginosa"), " based on CLSI VET09."))
} else if (ab_current == "LNZ" && mo_current_genus %in% all_gram_pos_genera && host_current %in% c("dogs", "cats")) {
} else if (ab_current == "LNZ" && mo_current_genus %in% gram_plus_cocci_vet09 && host_current %in% c("dogs", "cats")) {
# linezolid can take human breakpoints for these agents
breakpoints_current <- breakpoints_current %pm>% subset(host == "human")
notes_current <- c(notes_current, paste0("Using ", font_bold("human"), " breakpoints for ", ab_formatted, " in staphylococci/enterococci based on CLSI VET09."))
@ -1306,11 +1315,11 @@ as_sir_method <- function(method_short,
# nitro can take human breakpoints for these agents
breakpoints_current <- breakpoints_current %pm>% subset(host == "human")
notes_current <- c(notes_current, paste0("Using ", font_bold("human"), " breakpoints for ", ab_formatted, " based on CLSI VET09."))
} else if (ab_current == "PEN" && mo_current_genus %in% all_gram_pos_genera && host_current %in% c("dogs", "cats")) {
} else if (ab_current == "PEN" && mo_current_genus %in% gram_plus_cocci_vet09 && host_current %in% c("dogs", "cats")) {
# penicillin can take human breakpoints for these agents
breakpoints_current <- breakpoints_current %pm>% subset(host == "human")
notes_current <- c(notes_current, paste0("Using ", font_bold("human"), " breakpoints for ", ab_formatted, " in Gram-positive cocci based on CLSI VET09."))
} else if (ab_current == "RIF" && mo_current_genus %in% all_gram_pos_genera && host_current %in% c("dogs", "cats")) {
} else if (ab_current == "RIF" && mo_current_genus %in% gram_plus_cocci_vet09 && host_current %in% c("dogs", "cats")) {
# rifampicin can take human breakpoints for staphylococci
breakpoints_current <- breakpoints_current %pm>% subset(host == "human")
notes_current <- c(notes_current, paste0("Using ", font_bold("human"), " breakpoints for ", ab_formatted, " in staphylococci based on CLSI VET09."))
@ -1325,7 +1334,8 @@ as_sir_method <- function(method_short,
} else if (host_current %in% c("dogs", "cats") && (mo_current_genus %in% c("B_AMYCS", "B_NOCRD", "B_CMPYL", "B_CRYNB", "B_ENTRC", "B_MYCBC", "B_PSDMN", "B_AERMN") | mo_current_class == "B_[CLS]_BTPRTBCT" | mo_current == "B_LISTR_MNCY")) {
# dog breakpoints if no canine/feline
breakpoints_current <- breakpoints_current %pm>% subset(host == "human")
# TODO do we still have dogs breakpoints at this point???
breakpoints_current <- breakpoints_current %pm>% subset(host == "human") # WRONG
notes_current <- c(notes_current, paste0("Using ", font_bold("human"), " breakpoints for ", mo_formatted, " based on CLSI VET09."))
} else {