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(v1.3.0.9018) language corrections

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dr. M.S. (Matthijs) Berends committed 2020-09-14 12:21:23 +02:00
1 parent 0f6760d427
commit 7b6dd676f7
30 files changed
+364 -252
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data-raw/ab.md5
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37a7be09e34b5ec657a4bad94f45f355
data-raw/av.md5
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7b6649442069d3d121f61ca3ff01843a
data-raw/internals.R
+78 -45
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@@ -25,19 +25,19 @@
# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
skip = 10,
sep = "\t",
stringsAsFactors = FALSE,
header = TRUE,
strip.white = TRUE,
na = c(NA, "", NULL))
skip = 10,
sep = "\t",
stringsAsFactors = FALSE,
header = TRUE,
strip.white = TRUE,
na = c(NA, "", NULL))
# take the order of the reference.rule_group column in the original data file
eucast_rules_file$reference.rule_group <- factor(eucast_rules_file$reference.rule_group,
levels = unique(eucast_rules_file$reference.rule_group),
ordered = TRUE)
eucast_rules_file <- dplyr::arrange(eucast_rules_file,
reference.rule_group,
reference.rule)
reference.rule_group,
reference.rule)
eucast_rules_file$reference.rule_group <- as.character(eucast_rules_file$reference.rule_group)
# Translations ----
@@ -62,7 +62,8 @@ microorganisms.translation <- readRDS("data-raw/microorganisms.translation.rds")
usethis::use_data(eucast_rules_file, translations_file, microorganisms.translation,
internal = TRUE,
overwrite = TRUE,
version = 2)
version = 2,
compress = "xz")
# Remove from global environment ----
rm(eucast_rules_file)
@@ -70,51 +71,83 @@ rm(translations_file)
rm(microorganisms.translation)
# Save to raw data to repository ----
write_md5 <- function(object) {
writeLines(digest::digest(object, "md5"), file(paste0("data-raw/", deparse(substitute(object)), ".md5")))
}
changed_md5 <- function(object) {
tryCatch({
conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
compared <- digest::digest(object, "md5") != readLines(con = conn)
close(conn)
compared
}, error = function(e) TRUE)
}
usethis::ui_done(paste0("Saving raw data to {usethis::ui_value('/data-raw/')}"))
devtools::load_all(quiet = TRUE)
# give official names to ABs and MOs
rsi <- dplyr::mutate(rsi_translation, ab = ab_name(ab), mo = mo_name(mo))
try(saveRDS(rsi, "data-raw/rsi_translation.rds", version = 2), silent = TRUE)
try(write.table(rsi, "data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_sas(rsi, "data-raw/rsi_translation.sas"), silent = TRUE)
try(haven::write_sav(rsi, "data-raw/rsi_translation.sav"), silent = TRUE)
try(haven::write_dta(rsi, "data-raw/rsi_translation.dta"), silent = TRUE)
try(openxlsx::write.xlsx(rsi, "data-raw/rsi_translation.xlsx"), silent = TRUE)
if (changed_md5(rsi)) {
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)
try(haven::write_sas(rsi, "data-raw/rsi_translation.sas"), silent = TRUE)
try(haven::write_sav(rsi, "data-raw/rsi_translation.sav"), silent = TRUE)
try(haven::write_dta(rsi, "data-raw/rsi_translation.dta"), silent = TRUE)
try(openxlsx::write.xlsx(rsi, "data-raw/rsi_translation.xlsx"), silent = TRUE)
}
mo <- dplyr::mutate_if(microorganisms, ~!is.numeric(.), as.character)
try(saveRDS(mo, "data-raw/microorganisms.rds", version = 2), silent = TRUE)
try(write.table(mo, "data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_sas(mo, "data-raw/microorganisms.sas"), silent = TRUE)
try(haven::write_sav(mo, "data-raw/microorganisms.sav"), silent = TRUE)
try(haven::write_dta(mo, "data-raw/microorganisms.dta"), silent = TRUE)
try(openxlsx::write.xlsx(mo, "data-raw/microorganisms.xlsx"), silent = TRUE)
if (changed_md5(mo)) {
write_md5(mo)
try(saveRDS(mo, "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)
try(haven::write_sas(mo, "data-raw/microorganisms.sas"), silent = TRUE)
try(haven::write_sav(mo, "data-raw/microorganisms.sav"), silent = TRUE)
try(haven::write_dta(mo, "data-raw/microorganisms.dta"), silent = TRUE)
try(openxlsx::write.xlsx(mo, "data-raw/microorganisms.xlsx"), silent = TRUE)
}
try(saveRDS(microorganisms.old, "data-raw/microorganisms.old.rds", version = 2), silent = TRUE)
try(write.table(microorganisms.old, "data-raw/microorganisms.old.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_sas(microorganisms.old, "data-raw/microorganisms.old.sas"), silent = TRUE)
try(haven::write_sav(microorganisms.old, "data-raw/microorganisms.old.sav"), silent = TRUE)
try(haven::write_dta(microorganisms.old, "data-raw/microorganisms.old.dta"), silent = TRUE)
try(openxlsx::write.xlsx(microorganisms.old, "data-raw/microorganisms.old.xlsx"), silent = TRUE)
if (changed_md5(microorganisms.old)) {
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)
try(haven::write_sas(microorganisms.old, "data-raw/microorganisms.old.sas"), silent = TRUE)
try(haven::write_sav(microorganisms.old, "data-raw/microorganisms.old.sav"), silent = TRUE)
try(haven::write_dta(microorganisms.old, "data-raw/microorganisms.old.dta"), silent = TRUE)
try(openxlsx::write.xlsx(microorganisms.old, "data-raw/microorganisms.old.xlsx"), silent = TRUE)
}
ab <- dplyr::mutate_if(antibiotics, ~!is.numeric(.), as.character)
try(saveRDS(ab, "data-raw/antibiotics.rds", version = 2), silent = TRUE)
try(write.table(ab, "data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_sas(ab, "data-raw/antibiotics.sas"), silent = TRUE)
try(haven::write_sav(ab, "data-raw/antibiotics.sav"), silent = TRUE)
try(haven::write_dta(ab, "data-raw/antibiotics.dta"), silent = TRUE)
try(openxlsx::write.xlsx(ab, "data-raw/antibiotics.xlsx"), silent = TRUE)
if (changed_md5(ab)) {
write_md5(ab)
try(saveRDS(ab, "data-raw/antibiotics.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(ab, "data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_sas(ab, "data-raw/antibiotics.sas"), silent = TRUE)
try(haven::write_sav(ab, "data-raw/antibiotics.sav"), silent = TRUE)
try(haven::write_dta(ab, "data-raw/antibiotics.dta"), silent = TRUE)
try(openxlsx::write.xlsx(ab, "data-raw/antibiotics.xlsx"), silent = TRUE)
}
av <- dplyr::mutate_if(antivirals, ~!is.numeric(.), as.character)
try(saveRDS(av, "data-raw/antivirals.rds", version = 2), silent = TRUE)
try(write.table(av, "data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_sas(av, "data-raw/antivirals.sas"), silent = TRUE)
try(haven::write_sav(av, "data-raw/antivirals.sav"), silent = TRUE)
try(haven::write_dta(av, "data-raw/antivirals.dta"), silent = TRUE)
try(openxlsx::write.xlsx(av, "data-raw/antivirals.xlsx"), silent = TRUE)
if (changed_md5(av)) {
write_md5(av)
try(saveRDS(av, "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)
try(haven::write_sas(av, "data-raw/antivirals.sas"), silent = TRUE)
try(haven::write_sav(av, "data-raw/antivirals.sav"), silent = TRUE)
try(haven::write_dta(av, "data-raw/antivirals.dta"), silent = TRUE)
try(openxlsx::write.xlsx(av, "data-raw/antivirals.xlsx"), silent = TRUE)
}
try(saveRDS(intrinsic_resistant, "data-raw/intrinsic_resistant.rds", version = 2), silent = TRUE)
try(write.table(intrinsic_resistant, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_sas(intrinsic_resistant, "data-raw/intrinsic_resistant.sas"), silent = TRUE)
try(haven::write_sav(intrinsic_resistant, "data-raw/intrinsic_resistant.sav"), silent = TRUE)
try(haven::write_dta(intrinsic_resistant, "data-raw/intrinsic_resistant.dta"), silent = TRUE)
try(openxlsx::write.xlsx(intrinsic_resistant, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
if (changed_md5(intrinsic_resistant)) {
write_md5(intrinsic_resistant)
try(saveRDS(intrinsic_resistant, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(intrinsic_resistant, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_sas(intrinsic_resistant, "data-raw/intrinsic_resistant.sas"), silent = TRUE)
try(haven::write_sav(intrinsic_resistant, "data-raw/intrinsic_resistant.sav"), silent = TRUE)
try(haven::write_dta(intrinsic_resistant, "data-raw/intrinsic_resistant.dta"), silent = TRUE)
try(openxlsx::write.xlsx(intrinsic_resistant, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
}
rm(write_md5)
rm(changed_md5)
data-raw/intrinsic_resistant.md5
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6915f562bd64e546e1d57741a2a5ad27
data-raw/microorganisms.old.md5
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617b59b8ac3bd1aad7847aafc328f0f3
data-raw/mo.md5
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a5b85c5b3d37d6330865dfe09ef9b354
data-raw/rsi.md5
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0ac715df4f94c8704ae1d9bf56913312
data-raw/translations.tsv
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@@ -27,6 +27,7 @@ de vegetative vegetativ FALSE FALSE
de ([([ ]*?)group \\1Gruppe FALSE FALSE
de ([([ ]*?)Group \\1Gruppe FALSE FALSE
de no .*growth keine? .*wachstum FALSE TRUE
de no|not keine? FALSE TRUE
nl Coagulase-negative Staphylococcus Coagulase-negatieve Staphylococcus FALSE FALSE
nl Coagulase-positive Staphylococcus Coagulase-positieve Staphylococcus FALSE FALSE
@@ -58,6 +59,8 @@ nl antibiotic antibioticum FALSE FALSE
nl Antibiotic Antibioticum FALSE FALSE
nl Drug Middel FALSE FALSE
nl drug middel FALSE FALSE
nl no .*growth geen .*groei FALSE TRUE
nl no|not geen|niet FALSE TRUE
es Coagulase-negative Staphylococcus Staphylococcus coagulasa negativo FALSE FALSE
es Coagulase-positive Staphylococcus Staphylococcus coagulasa positivo FALSE FALSE
@@ -86,6 +89,8 @@ es biotype biotipo FALSE FALSE
es vegetative vegetativo FALSE FALSE
es ([([ ]*?)group \\1grupo FALSE FALSE
es ([([ ]*?)Group \\1Grupo FALSE FALSE
es no .*growth no .*crecimientonon FALSE TRUE
es no|not no|sin FALSE TRUE
it Coagulase-negative Staphylococcus Staphylococcus negativo coagulasi FALSE FALSE
it Coagulase-positive Staphylococcus Staphylococcus positivo coagulasi FALSE FALSE
@@ -112,6 +117,8 @@ it biotype biotipo FALSE FALSE
it vegetative vegetativo FALSE FALSE
it ([([ ]*?)group \\1gruppo FALSE FALSE
it ([([ ]*?)Group \\1Gruppo FALSE FALSE
it no .*growth sem .*crescimento FALSE TRUE
it no|not sem FALSE TRUE
fr Coagulase-negative Staphylococcus Staphylococcus à coagulase négative FALSE FALSE
fr Coagulase-positive Staphylococcus Staphylococcus à coagulase positif FALSE FALSE
@@ -137,6 +144,8 @@ fr biogroup biogroupe FALSE FALSE
fr vegetative végétatif FALSE FALSE
fr ([([ ]*?)group \\1groupe FALSE FALSE
fr ([([ ]*?)Group \\1Groupe FALSE FALSE
fr no .*growth pas .*croissance FALSE TRUE
fr no|not non FALSE TRUE
pt Coagulase-negative Staphylococcus Staphylococcus coagulase negativo FALSE FALSE
pt Coagulase-positive Staphylococcus Staphylococcus coagulase positivo FALSE FALSE
@@ -163,6 +172,8 @@ pt biotype biótipo FALSE FALSE
pt vegetative vegetativo FALSE FALSE
pt ([([ ]*?)group \\1grupo FALSE FALSE
pt ([([ ]*?)Group \\1Grupo FALSE FALSE
pt no .*growth sem .*crescimento FALSE TRUE
pt no|not sem FALSE TRUE
de clavulanic acid Clavulansäure FALSE TRUE
1 lang pattern replacement fixed ignore.case
27 de ([([ ]*?)group \\1Gruppe FALSE FALSE
28 de ([([ ]*?)Group \\1Gruppe FALSE FALSE
29 de no .*growth keine? .*wachstum FALSE TRUE
30 de no|not keine? FALSE TRUE
31 nl Coagulase-negative Staphylococcus Coagulase-negatieve Staphylococcus FALSE FALSE
32 nl Coagulase-positive Staphylococcus Coagulase-positieve Staphylococcus FALSE FALSE
33 nl Beta-haemolytic Streptococcus Beta-hemolytische Streptococcus FALSE FALSE
59 nl Drug Middel FALSE FALSE
60 nl drug middel FALSE FALSE
61 es nl Coagulase-negative Staphylococcus no .*growth Staphylococcus coagulasa negativo geen .*groei FALSE FALSE TRUE
62 nl no|not geen|niet FALSE TRUE
63 es Coagulase-negative Staphylococcus Staphylococcus coagulasa negativo FALSE FALSE
64 es Coagulase-positive Staphylococcus Staphylococcus coagulasa positivo FALSE FALSE
65 es Beta-haemolytic Streptococcus Streptococcus Beta-hemolítico FALSE FALSE
66 es unknown Gram-negatives Gram negativos desconocidos FALSE FALSE
89 es ([([ ]*?)Group \\1Grupo FALSE FALSE
90 it es Coagulase-negative Staphylococcus no .*growth Staphylococcus negativo coagulasi no .*crecimientonon FALSE FALSE TRUE
91 it es Coagulase-positive Staphylococcus no|not Staphylococcus positivo coagulasi no|sin FALSE FALSE TRUE
92 it Coagulase-negative Staphylococcus Staphylococcus negativo coagulasi FALSE FALSE
93 it Coagulase-positive Staphylococcus Staphylococcus positivo coagulasi FALSE FALSE
94 it Beta-haemolytic Streptococcus Streptococcus Beta-emolitico FALSE FALSE
95 it unknown Gram-negatives Gram negativi sconosciuti FALSE FALSE
96 it unknown Gram-positives Gram positivi sconosciuti FALSE FALSE
117 fr it Coagulase-negative Staphylococcus no .*growth Staphylococcus à coagulase négative sem .*crescimento FALSE FALSE TRUE
118 fr it Coagulase-positive Staphylococcus no|not Staphylococcus à coagulase positif sem FALSE FALSE TRUE
119 fr Beta-haemolytic Streptococcus Coagulase-negative Staphylococcus Streptococcus Bêta-hémolytique Staphylococcus à coagulase négative FALSE FALSE
120 fr Coagulase-positive Staphylococcus Staphylococcus à coagulase positif FALSE FALSE
121 fr Beta-haemolytic Streptococcus Streptococcus Bêta-hémolytique FALSE FALSE
122 fr unknown Gram-negatives Gram négatifs inconnus FALSE FALSE
123 fr unknown Gram-positives Gram positifs inconnus FALSE FALSE
124 fr unknown name nom inconnu FALSE FALSE
144 pt fr Coagulase-positive Staphylococcus no|not Staphylococcus coagulase positivo non FALSE FALSE TRUE
145 pt Beta-haemolytic Streptococcus Coagulase-negative Staphylococcus Streptococcus Beta-hemolítico Staphylococcus coagulase negativo FALSE FALSE
146 pt unknown Gram-negatives Coagulase-positive Staphylococcus Gram negativos desconhecidos Staphylococcus coagulase positivo FALSE FALSE
147 pt Beta-haemolytic Streptococcus Streptococcus Beta-hemolítico FALSE FALSE
148 pt unknown Gram-negatives Gram negativos desconhecidos FALSE FALSE
149 pt unknown Gram-positives Gram positivos desconhecidos FALSE FALSE
150 pt unknown name nome desconhecido FALSE FALSE
151 pt unknown kingdom reino desconhecido FALSE FALSE
172 nl de Adefovir dipivoxil clavulanic acid Adefovir Clavulansäure FALSE TRUE
173 nl Aldesulfone sodium 4-aminosalicylic acid Aldesulfon 4-aminosalicylzuur
174 nl Amikacin Adefovir dipivoxil Amikacine Adefovir
175 nl Aldesulfone sodium Aldesulfon
176 nl Amikacin Amikacine
177 nl Amoxicillin Amoxicilline
178 nl Amoxicillin/beta-lactamase inhibitor Amoxicilline/enzymremmer
179 nl Amphotericin B Amfotericine B