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new tibble export

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dr. M.S. (Matthijs) Berends
2022-08-27 20:49:37 +02:00
parent 164886f50b
commit 303d61b473
115 changed files with 836 additions and 996 deletions
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data-raw/AMR_latest.tar.gz
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data-raw/Loinc.csv
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@ -71673,7 +71673,7 @@
"7553-1","Origanum vulgare Ab.IgG","ACnc","Pt","Ser","Qn","","ALLERGY","2.27","MIN","","ACTIVE","","1","","","","","","Y","","ABS; Aby; Allergen; Allergens; ALLERGY TESTING; Antby; Anti; Antibodies; Antibody; Arbitrary concentration; Autoantibodies; Autoantibody; f283; Immune globulin G; Immunoglobulin G; Oregano; Oreganum; Point in time; QNT; Quan; Quant; Quantitative; Random; Rf283; Serum; SR","Oregano IgG Qn","Both","","","","","Oregano IgG Ab [Units/volume] in Serum","","","","","","","0","0","0","","","","","","1.0h(2)","","Oregano IgG Qn (S)"
"75531-4","Enrollment basis","Type","Pt","^Patient","Nom","","SURVEY.PCORNET","2.50","MIN","","ACTIVE","","4","","","","","","","","Nominal; Point in time; Random; Survey; SURVEY.PCORNET; Typ","Enrollment basis","Observation","","","","","Enrollment basis","","","","","","","0","0","0","","","","","","2.50","",""
"75532-2","Applicable accrediting agency for unit","Type","Pt","{Nursing unit}","Nom","NMMDS","SURVEY.NMMDS","2.50","MIN","Types of accreditation that are appropriate or applicable to a unit or service. The unit may or may not have received the accreditation.","ACTIVE","","4","","","","","","","","Nominal; Nursing Management Minimum Data Set; Point in time; Random; Survey; SURVEY.NMMDS; Typ","","Observation","","","Copyright © 2006 Diane Huber and Connie Delaney. Used with permission.","","Applicable accrediting agency for unit [NMMDS]","","","","","","","0","0","0","","NMMDS","","","","2.50","",""
"75533-0","Accreditation, certification, & licensure panel","-","Pt","{Nursing unit}","-","NMMDS","PANEL.SURVEY.NMMDS","2.52","MIN","The set of terms in this panel are used to indicate quality assurance organizations of the nursing delivery unit/service by 3 different quality measure categories: accreditation, certification and licensure. Accreditation is a seal of approval given by private, nationally recognized groups that check on the quality of care at health care facilities and organizations. Health care organizations must meet certain quality standards in order to be accredited. Certification is the formal recognition of the knowledge, skills, and experience demonstrated by the achievement of standards that are identified by the profession² (ANA, 2009). Licensure is the granting of authority to practice² (ANA, 2009). State agencies determine the requirements for licensure and examine the competency necessary to meet quality standards.","ACTIVE","","4","","","","","","","","Nursing Management Minimum Data Set; Pan; PANEL.SURVEY.NMMDS; Panl; Pnl; Point in time; Random; Survey; SURVEY.NMMDS","","","","","Copyright © 2006 Diane Huber and Connie Delaney. Used with permission.","","NMMDS accreditation, certification, and licensure panel [NMMDS]","","","","","","","0","0","0","","NMMDS","Panel","","","2.50","",""
"75533-0","Accreditation, certification, & licensure panel","-","Pt","{Nursing unit}","-","NMMDS","PANEL.SURVEY.NMMDS","2.52","MIN","The set of terms in this panel are used to indicate quality assurance organizations of the nursing delivery unit/service by 3 different quality measure categories: accreditation, certification and licensure. Accreditation is a seal of approval given by private, nationally recognized groups that check on the quality of care at health care facilities and organizations. Health care organizations must meet certain quality standards in order to be accredited. Certification is the formal recognition of the knowledge, skills, and experience demonstrated by the achievement of standards that are identified by the profession² (ANA, 2009). Licensure is the granting of authority to practise² (ANA, 2009). State agencies determine the requirements for licensure and examine the competency necessary to meet quality standards.","ACTIVE","","4","","","","","","","","Nursing Management Minimum Data Set; Pan; PANEL.SURVEY.NMMDS; Panl; Pnl; Point in time; Random; Survey; SURVEY.NMMDS","","","","","Copyright © 2006 Diane Huber and Connie Delaney. Used with permission.","","NMMDS accreditation, certification, and licensure panel [NMMDS]","","","","","","","0","0","0","","NMMDS","Panel","","","2.50","",""
"75534-8","Accreditation received","Type","Pt","{Nursing unit}","Nom","NMMDS","SURVEY.NMMDS","2.50","MIN","Types of accreditation obtained by a unit to demonstrate quality of care. Accreditation is a seal of approval given by private, nationally recognized groups that check on the quality of care at health care facilities and organizations. Health care organizations must meet certain quality standards in order to be accredited.","ACTIVE","","4","","","","","","","","Nominal; Nursing Management Minimum Data Set; Point in time; Random; Survey; SURVEY.NMMDS; Typ","","Observation","","","Copyright © 2006 Diane Huber and Connie Delaney. Used with permission.","","Accreditation received [NMMDS]","","","","","","","0","0","0","","NMMDS","","","","2.50","",""
"75535-5","Certification received","Type","Pt","{Nursing unit}","Nom","NMMDS","SURVEY.NMMDS","2.50","MIN","Types of certification obtained by a unit to demonstrate quality care.","ACTIVE","","4","","","","","","","","Nominal; Nursing Management Minimum Data Set; Point in time; Random; Survey; SURVEY.NMMDS; Typ","","Observation","","","Copyright © 2006 Diane Huber and Connie Delaney. Used with permission.","","Certification received [NMMDS]","","","","","","","0","0","0","","NMMDS","","","","2.50","",""
"75536-3","Applicable certification agency for unit","Type","Pt","{Nursing unit}","Nom","NMMDS","SURVEY.NMMDS","2.50","MIN","Types of certification that are appropriate or applicable to a unit or service. The unit may or may not have received the certification.","ACTIVE","","4","","","","","","","","Nominal; Nursing Management Minimum Data Set; Point in time; Random; Survey; SURVEY.NMMDS; Typ","","Observation","","","Copyright © 2006 Diane Huber and Connie Delaney. Used with permission.","","Applicable certification agency for unit [NMMDS]","","","","","","","0","0","0","","NMMDS","","","","2.50","",""

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data-raw/_language_update.R
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@ -55,7 +55,7 @@ lang_env$TRANSLATIONS <- utils::read.delim(file = "data-raw/translations.tsv",
quote = "")
lang_env$LANGUAGES_SUPPORTED_NAMES <- c(list(en = list(exonym = "English", endonym = "English")),
lapply(lang_env$TRANSLATIONS[, which(nchar(colnames(lang_env$TRANSLATIONS)) == 2)],
lapply(lang_env$TRANSLATIONS[, which(nchar(colnames(lang_env$TRANSLATIONS)) == 2), drop = FALSE],
function(x) list(exonym = x[1], endonym = x[2])))
lang_env$LANGUAGES_SUPPORTED <- names(lang_env$LANGUAGES_SUPPORTED_NAMES)

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data-raw/ex2.R
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@ -1,13 +0,0 @@
ex2 <- example_isolates
for (extra_id in seq_len(50)) {
ex2 <- ex2 %>%
bind_rows(example_isolates %>% mutate(patient_id = paste0(patient_id, extra_id)))
}
# randomly clear antibibiograms of 2%
clr <- sort(sample(x = seq_len(nrow(ex2)),
size = nrow(ex2) * 0.02))
for (row in which(is.rsi(ex2))) {
ex2[clr, row] <- NA_rsi_
}

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data-raw/exploratory_data_analysis_test.R
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@ -1,28 +0,0 @@
library(dplyr)
example_isolates %>%
select(mo, where(is.rsi)) %>%
tidyr::pivot_longer(cols = where(is.rsi)) %>%
# remove intrisic R
filter(!paste(mo, name) %in% AMR:::INTRINSIC_R) %>%
mutate(name = as.ab(name),
value = ifelse(value == "R", 1, 0),
class = ab_group(name)) %>%
group_by(mo, class) %>%
summarise(n = n(),
res = mean(value, na.rm = TRUE)) %>%
filter(n > 30, !is.na(res))
df <- example_isolates
search_mo <- "B_ESCHR_COLI"
intrinsic_res <- INTRINSIC_R[INTRINSIC_R %like% search_mo]
intrinsic_res <- gsub(".* (.*)", "\\1", intrinsic_res)
x <- df %>%
select(mo, where(is.rsi)) %>%
filter(mo == search_mo) %>%
# at least 30 results available
select(function(x) sum(!is.na(x)) >= 30) %>%
# remove intrisic R
select(!matches(paste(intrinsic_res, collapse = "|")))

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data-raw/pre-commit-hook.R
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@ -29,7 +29,7 @@
library(dplyr, warn.conflicts = FALSE)
devtools::load_all(quiet = TRUE)
set_AMR_locale("en")
suppressMessages(set_AMR_locale("en"))
old_globalenv <- ls(envir = globalenv())
@ -69,7 +69,7 @@ TRANSLATIONS <- utils::read.delim(file = "data-raw/translations.tsv",
quote = "")
LANGUAGES_SUPPORTED_NAMES <- c(list(en = list(exonym = "English", endonym = "English")),
lapply(TRANSLATIONS[, which(nchar(colnames(TRANSLATIONS)) == 2)],
lapply(TRANSLATIONS[, which(nchar(colnames(TRANSLATIONS)) == 2), drop = FALSE],
function(x) list(exonym = x[1], endonym = x[2])))
LANGUAGES_SUPPORTED <- names(LANGUAGES_SUPPORTED_NAMES)
@ -122,7 +122,7 @@ create_MO_fullname_lower <- function() {
MO_lookup$species,
MO_lookup$subspecies)))
ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname", drop = TRUE])
MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
MO_lookup$fullname_lower
}
@ -208,49 +208,50 @@ create_AB_lookup <- function() {
AB_LOOKUP <- create_AB_lookup()
# Export to package as internal data ----
usethis::use_data(EUCAST_RULES_DF,
TRANSLATIONS,
LANGUAGES_SUPPORTED_NAMES,
LANGUAGES_SUPPORTED,
MO_CONS,
MO_COPS,
MO_STREP_ABCG,
MO_FULLNAME_LOWER,
MO_PREVALENT_GENERA,
AB_LOOKUP,
AB_AMINOGLYCOSIDES,
AB_AMINOPENICILLINS,
AB_ANTIFUNGALS,
AB_ANTIMYCOBACTERIALS,
AB_CARBAPENEMS,
AB_CEPHALOSPORINS,
AB_CEPHALOSPORINS_1ST,
AB_CEPHALOSPORINS_2ND,
AB_CEPHALOSPORINS_3RD,
AB_CEPHALOSPORINS_4TH,
AB_CEPHALOSPORINS_5TH,
AB_CEPHALOSPORINS_EXCEPT_CAZ,
AB_FLUOROQUINOLONES,
AB_LIPOGLYCOPEPTIDES,
AB_GLYCOPEPTIDES,
AB_GLYCOPEPTIDES_EXCEPT_LIPO,
AB_LINCOSAMIDES,
AB_MACROLIDES,
AB_OXAZOLIDINONES,
AB_PENICILLINS,
AB_POLYMYXINS,
AB_QUINOLONES,
AB_STREPTOGRAMINS,
AB_TETRACYCLINES,
AB_TETRACYCLINES_EXCEPT_TGC,
AB_TRIMETHOPRIMS,
AB_UREIDOPENICILLINS,
AB_BETALACTAMS,
DEFINED_AB_GROUPS,
internal = TRUE,
overwrite = TRUE,
version = 2,
compress = "xz")
usethis::ui_info(paste0("Saving {usethis::ui_value('sysdata.rda')} to {usethis::ui_value('R/')}"))
suppressMessages(usethis::use_data(EUCAST_RULES_DF,
TRANSLATIONS,
LANGUAGES_SUPPORTED_NAMES,
LANGUAGES_SUPPORTED,
MO_CONS,
MO_COPS,
MO_STREP_ABCG,
MO_FULLNAME_LOWER,
MO_PREVALENT_GENERA,
AB_LOOKUP,
AB_AMINOGLYCOSIDES,
AB_AMINOPENICILLINS,
AB_ANTIFUNGALS,
AB_ANTIMYCOBACTERIALS,
AB_CARBAPENEMS,
AB_CEPHALOSPORINS,
AB_CEPHALOSPORINS_1ST,
AB_CEPHALOSPORINS_2ND,
AB_CEPHALOSPORINS_3RD,
AB_CEPHALOSPORINS_4TH,
AB_CEPHALOSPORINS_5TH,
AB_CEPHALOSPORINS_EXCEPT_CAZ,
AB_FLUOROQUINOLONES,
AB_LIPOGLYCOPEPTIDES,
AB_GLYCOPEPTIDES,
AB_GLYCOPEPTIDES_EXCEPT_LIPO,
AB_LINCOSAMIDES,
AB_MACROLIDES,
AB_OXAZOLIDINONES,
AB_PENICILLINS,
AB_POLYMYXINS,
AB_QUINOLONES,
AB_STREPTOGRAMINS,
AB_TETRACYCLINES,
AB_TETRACYCLINES_EXCEPT_TGC,
AB_TRIMETHOPRIMS,
AB_UREIDOPENICILLINS,
AB_BETALACTAMS,
DEFINED_AB_GROUPS,
internal = TRUE,
overwrite = TRUE,
version = 2,
compress = "xz"))
# Export data sets to the repository in different formats -----------------
@ -285,7 +286,7 @@ rsi <- rsi_translation %>%
mutate(mo_name = mo_name(mo, language = NULL), .after = mo) %>%
mutate(ab_name = ab_name(ab, language = NULL), .after = ab)
if (changed_md5(rsi)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('rsi_translation')} to {usethis::ui_value('/data-raw/')}"))
usethis::ui_info(paste0("Saving {usethis::ui_value('rsi_translation')} to {usethis::ui_value('data-raw/')}"))
write_md5(rsi)
try(saveRDS(rsi, "data-raw/rsi_translation.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(rsi, "data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
@ -298,7 +299,7 @@ if (changed_md5(rsi)) {
}
if (changed_md5(microorganisms)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms')} to {usethis::ui_value('/data-raw/')}"))
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms')} to {usethis::ui_value('data-raw/')}"))
write_md5(microorganisms)
try(saveRDS(microorganisms, "data-raw/microorganisms.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(mo, "data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
@ -315,7 +316,7 @@ if (changed_md5(microorganisms)) {
}
if (changed_md5(microorganisms.old)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.old')} to {usethis::ui_value('/data-raw/')}"))
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.old')} to {usethis::ui_value('data-raw/')}"))
write_md5(microorganisms.old)
try(saveRDS(microorganisms.old, "data-raw/microorganisms.old.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(microorganisms.old, "data-raw/microorganisms.old.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
@ -329,7 +330,7 @@ if (changed_md5(microorganisms.old)) {
ab <- dplyr::mutate_if(antibiotics, ~!is.numeric(.), as.character)
if (changed_md5(ab)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('antibiotics')} to {usethis::ui_value('/data-raw/')}"))
usethis::ui_info(paste0("Saving {usethis::ui_value('antibiotics')} to {usethis::ui_value('data-raw/')}"))
write_md5(ab)
try(saveRDS(antibiotics, "data-raw/antibiotics.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(antibiotics, "data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
@ -343,7 +344,7 @@ if (changed_md5(ab)) {
av <- dplyr::mutate_if(antivirals, ~!is.numeric(.), as.character)
if (changed_md5(av)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('antivirals')} to {usethis::ui_value('/data-raw/')}"))
usethis::ui_info(paste0("Saving {usethis::ui_value('antivirals')} to {usethis::ui_value('data-raw/')}"))
write_md5(av)
try(saveRDS(antivirals, "data-raw/antivirals.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(av, "data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
@ -360,7 +361,7 @@ intrinsicR <- data.frame(microorganism = mo_name(intrinsic_resistant$mo, languag
antibiotic = ab_name(intrinsic_resistant$ab, language = NULL),
stringsAsFactors = FALSE)
if (changed_md5(intrinsicR)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('intrinsic_resistant')} to {usethis::ui_value('/data-raw/')}"))
usethis::ui_info(paste0("Saving {usethis::ui_value('intrinsic_resistant')} to {usethis::ui_value('data-raw/')}"))
write_md5(intrinsicR)
try(saveRDS(intrinsicR, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(intrinsicR, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
@ -373,7 +374,7 @@ if (changed_md5(intrinsicR)) {
}
if (changed_md5(dosage)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('dosage')} to {usethis::ui_value('/data-raw/')}"))
usethis::ui_info(paste0("Saving {usethis::ui_value('dosage')} to {usethis::ui_value('data-raw/')}"))
write_md5(dosage)
try(saveRDS(dosage, "data-raw/dosage.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(dosage, "data-raw/dosage.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
@ -385,7 +386,7 @@ if (changed_md5(dosage)) {
try(arrow::write_parquet(dosage, "data-raw/dosage.parquet"), silent = TRUE)
}
reset_AMR_locale()
suppressMessages(reset_AMR_locale())
# remove leftovers from global env
current_globalenv <- ls(envir = globalenv())

4
data-raw/reproduction_of_antibiotics.R
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@ -138,7 +138,7 @@ abx2 <- abx2 %>% arrange(ab)
seqnr <- 0
# add follow up nrs
for (i in 2:nrow(abx2)) {
if (abx2[i, "ab"] == abx2[i - 1, "ab"]) {
if (abx2[i, "ab", drop = TRUE] == abx2[i - 1, "ab", drop = TRUE]) {
seqnr <- seqnr + 1
abx2[i, "seqnr"] <- seqnr
} else {
@ -147,7 +147,7 @@ for (i in 2:nrow(abx2)) {
}
for (i in 2:nrow(abx2)) {
if (!is.na(abx2[i, "seqnr"])) {
abx2[i, "ab"] <- paste0(abx2[i, "ab"], abx2[i, "seqnr"])
abx2[i, "ab"] <- paste0(abx2[i, "ab", drop = TRUE], abx2[i, "seqnr", drop = TRUE])
}
}
abx2 <- abx2 %>% select(-seqnr) %>% arrange(name)

6
data-raw/reproduction_of_example_isolates_unclean.R
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@ -92,7 +92,7 @@ example_isolates_unclean <- data_a %>%
example_isolates_unclean$patient_id <- sample(patients, size = nrow(example_isolates_unclean), replace = TRUE)
example_isolates_unclean <- example_isolates_unclean %>%
select(patient_id, hospital, date, bacteria, everything())
usethis::use_data(example_isolates_unclean, overwrite = TRUE)
select(patient_id, hospital, date, bacteria, everything()) %>%
dataset_UTF8_to_ASCII()
usethis::use_data(example_isolates_unclean, overwrite = TRUE, internal = FALSE, version = 2, compress = "xz")

2
data-raw/reproduction_of_intrinsic_resistant.R
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@ -36,7 +36,7 @@ int_resis <- eucast_rules(int_resis,
is.na(have_these_values) & reference.version == 3.3),
info = FALSE)
int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R"))] %>%
int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R")), drop = FALSE] %>%
tidyr::pivot_longer(-mo) %>%
filter(value == "R") %>%
select(mo, ab = name)

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