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(v1.5.0.9014) only_rsi_columns, is.rsi.eligible improvement

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dr. M.S. (Matthijs) Berends
2021-02-02 23:57:35 +01:00
parent 20d638c193
commit 2eca8c3f01
246 changed files with 1171 additions and 965 deletions
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data-raw/AMR_1.5.0.9013.tar.gz → data-raw/AMR_1.5.0.9014.tar.gz
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data-raw/internals.R → data-raw/_internals.R
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@ -1,6 +1,6 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
@ -20,11 +20,11 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# Run this file to update the package using:
# source("data-raw/internals.R")
# source("data-raw/_internals.R")
library(dplyr, warn.conflicts = FALSE)
devtools::load_all(quiet = TRUE)
@ -74,6 +74,15 @@ create_AB_lookup <- function() {
AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name)
AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name)
AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name)
AB_lookup$generalised_all <- unname(lapply(as.list(as.data.frame(t(AB_lookup[,
c("ab", "atc", "cid", "name",
colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]),
drop = FALSE]),
stringsAsFactors = FALSE)),
function(x) {
x <- generalise_antibiotic_name(unname(unlist(x)))
x[x != ""]
}))
AB_lookup
}

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data-raw/loinc.R
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@ -1,6 +1,6 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
@ -20,7 +20,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# last updated: 20 January 2020 - Loinc_2.67

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data-raw/poorman_prepend.R
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@ -1,6 +1,6 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
@ -20,7 +20,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# ------------------------------------------------

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data-raw/read_EUCAST.R
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@ -1,6 +1,6 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
@ -20,7 +20,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
library(openxlsx)

4
data-raw/reproduction_of_antibiotics.R
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@ -1,6 +1,6 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
@ -20,7 +20,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
library(dplyr)

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data-raw/reproduction_of_antivirals.R
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@ -1,6 +1,6 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
@ -20,7 +20,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# get all data from the WHOCC website

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data-raw/reproduction_of_dosage.R
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@ -1,6 +1,6 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
@ -20,7 +20,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
library(dplyr)

4
data-raw/reproduction_of_example_isolates_unclean.R
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@ -1,6 +1,6 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
@ -20,7 +20,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
patients <- unlist(lapply(LETTERS, paste0, 1:10))

4
data-raw/reproduction_of_intrinsic_resistant.R
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@ -1,6 +1,6 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
@ -20,7 +20,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
library(AMR)

6
data-raw/reproduction_of_microorganisms.R
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@ -1,6 +1,6 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
@ -20,7 +20,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# Reproduction of the `microorganisms` data set
@ -925,7 +925,7 @@ usethis::use_data(rsi_translation, overwrite = TRUE, version = 2)
usethis::use_data(microorganisms.codes, overwrite = TRUE, version = 2)
saveRDS(microorganisms.translation, file = "data-raw/microorganisms.translation.rds", version = 2)
# to save microorganisms.translation internally to the package
source("data-raw/internals.R")
source("data-raw/_internals.R")
# load new data sets again
devtools::load_all(".")

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data-raw/snomed.R
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@ -1,6 +1,6 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
@ -20,7 +20,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
library(AMR)