Fix PK/PD breakpoints

data-raw/clin_break.md5

@@ -1 +1 @@
-e150d98b724ad979e176058c4197c469
+ad4649f72b21de1c1828c0686c754f20

data-raw/reproduction_of_clinical_breakpoints.R

@@ -33,7 +33,7 @@
 library(dplyr)
 library(readr)
 library(tidyr)
-library(AMR)
+devtools::load_all()
 
 # Install the WHONET 2022 software on Windows (http://www.whonet.org/software.html),
 # and copy the folder C:\WHONET\Resources to the data-raw/WHONET/ folder
@@ -140,14 +140,17 @@ whonet_antibiotics <- read_tsv("data-raw/WHONET/Resources/Antibiotics.txt", na =
 
 breakpoints <- whonet_breakpoints %>%
   mutate(code = toupper(ORGANISM_CODE)) %>%
-  left_join(microorganisms.codes)
+  left_join(bind_rows(microorganisms.codes,
+                      # GEN (Generic) and ALL (All) are PK/PD codes
+                      data.frame(code = c("ALL", "GEN"),
+                                 mo = rep(as.mo("UNKNOWN"), 2))))
 # these ones lack a MO name, they cannot be used:
 unknown <- breakpoints %>%
   filter(is.na(mo)) %>%
   pull(code) %>%
   unique()
-whonet_organisms %>% 
-  filter(toupper(ORGANISM_CODE) %in% unknown)
+breakpoints %>% 
+  filter(code %in% unknown)
 breakpoints <- breakpoints %>% 
   filter(!is.na(mo))
 
@@ -244,6 +247,11 @@ breakpoints_new %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "B_[OR
 # compare with current version
 clinical_breakpoints %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
 
+# check dimensions
+dim(breakpoints_new)
+dim(clinical_breakpoints)
+
+
 # Save to package ----
 
 clinical_breakpoints <- breakpoints_new

man/as.sir.Rd

@@ -163,7 +163,7 @@ After using \code{\link[=as.sir]{as.sir()}}, you can use the \code{\link[=eucast
 
 \subsection{Machine-Readable Clinical Breakpoints}{
 
-The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 17 918 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
+The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 18 271 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
 }
 
 \subsection{Other}{

man/clinical_breakpoints.Rd

@@ -5,7 +5,7 @@
 \alias{clinical_breakpoints}
 \title{Data Set with Clinical Breakpoints for SIR Interpretation}
 \format{
-A \link[tibble:tibble]{tibble} with 17 918 observations and 11 variables:
+A \link[tibble:tibble]{tibble} with 18 271 observations and 11 variables:
 \itemize{
 \item \code{guideline}\cr Name of the guideline
 \item \code{method}\cr Either "DISK" or "MIC"