first edits

data-raw/Loinc.csv

@@ -53952,7 +53952,7 @@
 "58301-3","High blood pressure without toxemia during this pregnancy","Find","Pt","^Patient","Ord","","PHENX","2.65","MIN","","TRIAL","","2","","","Did you have High blood pressure without toxemia during this pregnancy?","PX040401020000","N","BP; Finding; Findings; Gestation; Gestations; Gravida; High BP WO toxemia during pregnancy; Ordinal; PhenX; Point in time; Pregnancies; QL; Qual; Qualitative; Random; Screen","High BP WO toxemia during pregnancy","","","","","High blood pressure without toxemia during this pregnancy","","","","Updated the PhenX ID from ""PhenX.<ID>"" to ""PX<ID>"" in Survey Question Source field to align with the variable identifier used in the PhenX Toolkit.","0","0","0","","","","","","2.30","",""
 "58302-1","Ever told by doctor that you had rheumatic heart or heart valve problems","Find","Pt","^Patient","Ord","","PHENX","2.65","MIN","","TRIAL","","2","","","Has a doctor ever told you that you had rheumatic heart or heart valve problems?","PX040501010000","N","Finding; Findings; Ordinal; PhenX; Point in time; QL; Qual; Qualitative; Random; Screen","Rheumatic heart or heart valve problems","","","","","Ever told by doctor that you had rheumatic heart or heart valve problems","","","","Updated the PhenX ID from ""PhenX.<ID>"" to ""PX<ID>"" in Survey Question Source field to align with the variable identifier used in the PhenX Toolkit.","0","0","0","","","","","","2.30","",""
 "58303-9","Ever told by doctor that you had angina","Find","Pt","^Patient","Ord","","PHENX","2.65","MIN","","TRIAL","","2","","","Has a doctor ever told you that you had angina?","PX040601010000","N","Finding; Findings; Ordinal; PhenX; Point in time; QL; Qual; Qualitative; Random; Screen","Angina","","","","","Ever told by doctor that you had angina","","","","Updated the PhenX ID from ""PhenX.<ID>"" to ""PX<ID>"" in Survey Question Source field to align with the variable identifier used in the PhenX Toolkit.","0","0","0","","","","","","2.30","",""
-"58304-7","Chest discomfort ever or since last exam or medical history update","TmStp","Pt","^Patient","Ord","","PHENX","2.65","MIN","","TRIAL","","2","","","Any chest discomfort ever/since last exam or medical history update?","PX040601020000","N","Chest discomfort ever/since last exam; Date and time; Hx; Ordinal; Past; PhenX; Point in time; QL; Qual; Qualitative; Random; Screen; Time stamp; Timestamp","Chest discomfort ever/since last exam","","","","","Chest discomfort ever or since last exam or medical history update","","","","Updated the PhenX ID from ""PhenX.<ID>"" to ""PX<ID>"" in Survey Question Source field to align with the variable identifier used in the PhenX Toolkit.","0","0","0","","","","","","2.30","",""
+"58304-7","Chest discomfort ever or since last exam or medical history update","TmStp","Pt","^Patient","Ord","","PHENX","2.65","MIN","","TRIAL","","2","","","Any chest discomfort eveSIRnce last exam or medical history update?","PX040601020000","N","Chest discomfort eveSIRnce last exam; Date and time; Hx; Ordinal; Past; PhenX; Point in time; QL; Qual; Qualitative; Random; Screen; Time stamp; Timestamp","Chest discomfort eveSIRnce last exam","","","","","Chest discomfort ever or since last exam or medical history update","","","","Updated the PhenX ID from ""PhenX.<ID>"" to ""PX<ID>"" in Survey Question Source field to align with the variable identifier used in the PhenX Toolkit.","0","0","0","","","","","","2.30","",""
 "5830-5","Adenovirus Ag","PrThr","Pt","Tiss","Ord","IF","MICRO","2.73","MIN","","ACTIVE","","1","","","","","","ACIF; Adeno virus; Anticomplement Immunofluorescence; Antigen; Antigens; DFA; FA; Fluorescent antibody; Fluoresent; HAdV; ID; IFA; Immune fluorescence; Immunoflour; Immunofluor; Immunofluorescence; Infectious Disease; InfectiousDisease; Microbiology; Ordinal; Point in time; PR; QL; Qual; Qualitative; Random; Screen; Time Resolved Fluorescence; Tissue; Tissue, unspecified; TRF","HAdV Ag Tiss Ql IF","Both","","","","Adenovirus Ag [Presence] in Tissue by Immunofluorescence","","","","The PrThr property is used for LOINC terms whose results are reported using an ordered categorical scale, regardless of whether or not an internal threshold was used to make that determination. This change was approved by the Laboratory LOINC Committee in June 2016.","12067","0","0","","","","","","1.0","","Adenovirus Ag IF Ql (Tiss)"
 "58305-4","Chest discomfort with exertion or excitement","Find","Pt","^Patient","Ord","","PHENX","2.65","MIN","","TRIAL","","2","","","","PX040601030000","N","Chest discomf W exertion/excitement; Finding; Findings; Ordinal; PhenX; Point in time; QL; Qual; Qualitative; Random; Screen","Chest discomf W exertion/excitement","","","","","Chest discomfort with exertion or excitement","","","","Updated the PhenX ID from ""PhenX.<ID>"" to ""PX<ID>"" in Survey Question Source field to align with the variable identifier used in the PhenX Toolkit.","0","0","0","","","","","","2.30","",""
 "58306-2","Chest discomfort when quiet or resting","Find","Pt","^Patient","Ord","","PHENX","2.65","MIN","","TRIAL","","2","","","","PX040601040000","N","Finding; Findings; Ordinal; PhenX; Point in time; QL; Qual; Qualitative; Random; Screen","Chest discomfort when quiet or resting","","","","","Chest discomfort when quiet or resting","","","","Updated the PhenX ID from ""PhenX.<ID>"" to ""PX<ID>"" in Survey Question Source field to align with the variable identifier used in the PhenX Toolkit.","0","0","0","","","","","","2.30","",""
@@ -58634,7 +58634,7 @@
 "62660-6","PhenX - hormonal therapy protocol 100701","-","Pt","^Patient","-","PhenX","PANEL.PHENX","2.66","NAM","Female participants are asked whether they have ever used Evista® or Nolvadex® and then asked length of time they used it as well as whether they are currently using it. They are asked whether they are using any over-the-counter preparations for hormone replacement or post-menopause symptoms. Lastly, they are asked about their use of prescription female hormones (number of months taken, types, dosage). Note: PhenX staff removed embedded dates of original study for clarity of Toolkit users.","TRIAL","","2","","","","PX100701","N","Pan; Panel; PANEL.PHENX; Panl; Pnl; Point in time; Random","Hormonal therapy proto","","","","","PhenX - hormonal therapy protocol 100701","","","","Updated the PhenX ID from ""PhenX.<ID>"" to ""PX<ID>"" in Survey Question Source field to align with the variable identifier used in the PhenX Toolkit.; Added the PhenX protocol ID to the Component to clearly define the protocol version for which this panel is based upon.","0","0","0","","","Panel","","","2.36","",""
 "6266-1","Lycopersicon lycopersicum Ab.IgE","ACnc","Pt","Ser","Qn","","ALLERGY","2.73","MIN","","ACTIVE","","1","","","","","Y","ABS; Aby; Allergen; Allergens; ALLERGY TESTING; Antby; Anti; Antibodies; Antibody; Arbitrary concentration; Autoantibodies; Autoantibody; f25; Immune globulin E; Immunoglobulin E; Lycopersicon esculatum; Lycopersicon lycopersicon; Point in time; QNT; Quan; Quant; Quantitative; Random; Serum; SR; Tomato; UniversalLabOrders","Tomato IgE Qn","Both","","","kIU/L; kU/L","Tomato IgE Ab [Units/volume] in Serum","k[IU]/L","","","","1964","0","0","","","","","","1.0d","","Tomato IgE Qn (S)"
 "62661-4","PhenX measure - human papillomavirus vaccine use","-","Pt","^Patient","-","PhenX","PANEL.PHENX","2.46","DEL","Questions to assess women's use of the human papillomavirus vaccine. These questions ascertain if a woman received the human papillomavirus vaccine and if so, the number of doses received. Use of the vaccine impacts a woman's risk of developing cervical cancer and the overall incidence rate of cervical cancer.","DEPRECATED","","2","","","","PhenX.100800","N","Measure - HPV vaccine use; Pan; Panel; PANEL.PHENX; Panl; Pnl; Point in time; Random","","","","","","Deprecated PhenX measure - human papillomavirus vaccine use","","","Measure terms were added to match PhenX hierarchy but make it difficult to locate protocols (which contain the set of variables you would use for a particular purpose).  They have been deprecated and mapped directly to protocols.","","0","0","0","","","","","","2.36","",""
-"62662-2","PhenX - human papillomavirus vaccine use protocol 100801","-","Pt","^Patient","-","PhenX","PANEL.PHENX","2.66","NAM","The interviewer asks the female participant whether she has ever received a human papillomavirus (HPV) vaccination. If she answers yes, the interviewer asks her age and how many shots she received. If the participant answers ""yes"" to question 1, the interviewer should complete the rest of the protocol. If the participant answers ""no"" then the protocol is deemed complete. The PhenX Working Group notes that GARDASIL® is also known as Silgard. European Medicines Agency. (September 25, 2009). Silgard European Public Assessment Report. Retrieved from http://www.emea.europa.eu/humandocs/Humans/EPAR/silgard/silgard.htm. Waknine, Yael. (October 2, 2006). International Approvals: Singulair and Gardasil/Silgard. Medscape Today. Retrieved from http://www.medscape.com/viewarticle/545374.","TRIAL","","2","","","","PX100801","N","HPV vaccine use proto; Pan; Panel; PANEL.PHENX; Panl; Pnl; Point in time; Random","HPV vaccine use proto","","","","","PhenX - human papillomavirus vaccine use protocol 100801","","","","Updated the PhenX ID from ""PhenX.<ID>"" to ""PX<ID>"" in Survey Question Source field to align with the variable identifier used in the PhenX Toolkit.; Added the PhenX protocol ID to the Component to clearly define the protocol version for which this panel is based upon.","0","0","0","","","Panel","","","2.36","",""
+"62662-2","PhenX - human papillomavirus vaccine use protocol 100801","-","Pt","^Patient","-","PhenX","PANEL.PHENX","2.66","NAM","The interviewer asks the female participant whether she has ever received a human papillomavirus (HPV) vaccination. If she answers yes, the interviewer asks her age and how many shots she received. If the participant answers ""yes"" to question 1, the interviewer should complete the rest of the protocol. If the participant answers ""no"" then the protocol is deemed complete. The PhenX Working Group notes that GARDASIL® is also known as Silgard. European Medicines Agency. (September 25, 2009). Silgard European Public Assessment Report. Retrieved from http://www.emea.europa.eu/humandocs/Humans/EPASIRlgard/silgard.htm. Waknine, Yael. (October 2, 2006). International Approvals: Singulair and Gardasil/Silgard. Medscape Today. Retrieved from http://www.medscape.com/viewarticle/545374.","TRIAL","","2","","","","PX100801","N","HPV vaccine use proto; Pan; Panel; PANEL.PHENX; Panl; Pnl; Point in time; Random","HPV vaccine use proto","","","","","PhenX - human papillomavirus vaccine use protocol 100801","","","","Updated the PhenX ID from ""PhenX.<ID>"" to ""PX<ID>"" in Survey Question Source field to align with the variable identifier used in the PhenX Toolkit.; Added the PhenX protocol ID to the Component to clearly define the protocol version for which this panel is based upon.","0","0","0","","","Panel","","","2.36","",""
 "62663-0","PhenX measure - male reproductive tract birth defects","-","Pt","^Patient","-","PhenX","PANEL.PHENX","2.46","DEL","Questions to determine whether a male participant has ever had certain conditions that could have developed in utero. Cryptorchidism is failure of one or both of the testes to descend into the scrotum. Hypospadius is a developmental anomaly in which the male urethra opens on the underside of the penis or on the perineum. The purpose of these questions is to determine whether the participant had ever had the following abnormalities that developed in utero: Cryptorchidism, Hypospadius, and/or other related conditions. These conditions are suspected of being hereditary and/or influenced by environmental factors, may reflect abnormalities of androgen production, and may be passed to offspring.","DEPRECATED","","2","","","","PhenX.100900","N","Measure male reproduct birth defects; Pan; Panel; PANEL.PHENX; Panl; Pnl; Point in time; Random","","","","","","Deprecated PhenX measure - male reproductive tract birth defects","","","Measure terms were added to match PhenX hierarchy but make it difficult to locate protocols (which contain the set of variables you would use for a particular purpose).  They have been deprecated and mapped directly to protocols.","","0","0","0","","","","","","2.36","",""
 "62664-8","PhenX - male reproductive tract birth defects protocol 100901","-","Pt","^Patient","-","PhenX","PANEL.PHENX","2.66","NAM","The male participant answers whether he was ever diagnosed with Cryptorchidism, Hypospadius and/or other related conditions. The questions were originally asked of partners of pregnant women but the WG recommends asking them of adult males. Note: Cryptorchidism is failure of one or both of the testes to descend into the scrotum. Hypospadius is a developmental anomaly in which the male urethra opens on the underside of the penis or on the perineum.","TRIAL","","2","","","","PX100901","N","Male reproductive birth defects proto; Pan; Panel; PANEL.PHENX; Panl; Pnl; Point in time; Random","Male reproductive birth defects proto","","","","","PhenX - male reproductive tract birth defects protocol 100901","","","","Updated the PhenX ID from ""PhenX.<ID>"" to ""PX<ID>"" in Survey Question Source field to align with the variable identifier used in the PhenX Toolkit.; Added the PhenX protocol ID to the Component to clearly define the protocol version for which this panel is based upon.","0","0","0","","","Panel","","","2.36","",""
 "62665-5","PhenX measure - male sexual function","-","Pt","^Patient","-","PhenX","PANEL.PHENX","2.46","DEL","Questions to determine whether a male participant has certain types of sexual function difficulties. The purpose of these questions is to determine whether the participant ever had sexual difficulties regarding erection and/or performance.","DEPRECATED","","2","","","","PhenX.101000","N","FCN; Func; Funct; Pan; Panel; PANEL.PHENX; Panl; Pnl; Point in time; Random","","","","","","Deprecated PhenX measure - male sexual function","","","Measure terms were added to match PhenX hierarchy but make it difficult to locate protocols (which contain the set of variables you would use for a particular purpose).  They have been deprecated and mapped directly to protocols.","","0","0","0","","","","","","2.36","",""

data-raw/_pre_commit_hook.R

@@ -369,20 +369,20 @@ changed_md5 <- function(object) {
 }
 
 # give official names to ABs and MOs
-rsi <- rsi_translation %>%
+rsi <- clinical_breakpoints %>%
   mutate(mo_name = mo_name(mo, language = NULL, keep_synonyms = TRUE, info = FALSE), .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('clinical_breakpoints')} 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)
-  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)
-  try(arrow::write_feather(rsi, "data-raw/rsi_translation.feather"), silent = TRUE)
-  try(arrow::write_parquet(rsi, "data-raw/rsi_translation.parquet"), silent = TRUE)
+  try(saveRDS(rsi, "data-raw/clinical_breakpoints.rds", version = 2, compress = "xz"), silent = TRUE)
+  try(write.table(rsi, "data-raw/clinical_breakpoints.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
+  try(haven::write_sas(rsi, "data-raw/clinical_breakpoints.sas"), silent = TRUE)
+  try(haven::write_sav(rsi, "data-raw/clinical_breakpoints.sav"), silent = TRUE)
+  try(haven::write_dta(rsi, "data-raw/clinical_breakpoints.dta"), silent = TRUE)
+  try(openxlsx::write.xlsx(rsi, "data-raw/clinical_breakpoints.xlsx"), silent = TRUE)
+  try(arrow::write_feather(rsi, "data-raw/clinical_breakpoints.feather"), silent = TRUE)
+  try(arrow::write_parquet(rsi, "data-raw/clinical_breakpoints.parquet"), silent = TRUE)
 }
 
 if (changed_md5(microorganisms)) {

data-raw/microorganisms.txt

@@ -45554,7 +45554,7 @@
 "B_STRPT_ORLX"	"Streptococcus oriloxodontae"	"accepted"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"oriloxodontae"	""	"species"	"Shinozaki-Kuwahara et al., 2014"	"LPSN"	"792340"	"517118"					1.5	""
 "B_STRPT_ORSS"	"Streptococcus orisasini"	"accepted"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"orisasini"	""	"species"	"Takada et al., 2013"	"LPSN"	"790987"	"517118"					1.5	""
 "B_STRPT_ORSR"	"Streptococcus orisratti"	"accepted"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"orisratti"	""	"species"	"Zhu et al., 2000"	"LPSN"	"781365"	"517118"					1.5	"438034004"
-"B_STRPT_RSIS"	"Streptococcus orisuis"	"accepted"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"orisuis"	""	"species"	"Takada et al., 2007"	"LPSN"	"781314"	"517118"					1.5	"6441000146108"
+"B_STRPT_sirS"	"Streptococcus orisuis"	"accepted"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"orisuis"	""	"species"	"Takada et al., 2007"	"LPSN"	"781314"	"517118"					1.5	"6441000146108"
 "B_STRPT_OVIS"	"Streptococcus ovis"	"accepted"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"ovis"	""	"species"	"Collins et al., 2001"	"LPSN"	"781366"	"517118"					1.5	"438035003"
 "B_STRPT_OVBR"	"Streptococcus ovuberis"	"accepted"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"ovuberis"	""	"species"	"Zamora et al., 2017"	"LPSN"	"796216"	"517118"					1.5	""
 "B_STRPT_PCFC"	"Streptococcus pacificus"	"accepted"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"pacificus"	""	"species"	"Volokhov et al., 2021"	"LPSN"	"19573"	"517118"					1.5	""

data-raw/read_EUCAST.R

@@ -230,7 +230,7 @@ read_EUCAST <- function(sheet, file, guideline_name) {
       mo = ifelse(mo == "", mo_sheet, mo)
     ) %>%
     filter(!(is.na(breakpoint_S) & is.na(breakpoint_R))) %>%
-    # comply with rsi_translation for now
+    # comply with clinical_breakpoints for now
     transmute(guideline,
       method,
       site = case_when(
@@ -285,7 +285,7 @@ for (i in 2:length(sheets_to_analyse)) {
 }
 
 # 2021-07-12 fix for Morganellaceae (check other lines too next time)
-morg <- rsi_translation %>%
+morg <- clinical_breakpoints %>%
   as_tibble() %>%
   filter(
     ab == "IPM",
@@ -298,7 +298,7 @@ morg[which(morg$method == "MIC"), "breakpoint_R"] <- 4
 morg[which(morg$method == "DISK"), "breakpoint_S"] <- 50
 morg[which(morg$method == "DISK"), "breakpoint_R"] <- 19
 
-rsi_translation <- rsi_translation %>%
+clinical_breakpoints <- clinical_breakpoints %>%
   bind_rows(morg) %>%
   bind_rows(morg %>%
     mutate(guideline = "EUCAST 2020")) %>%

data-raw/reproduction_of_clinical_breakpoints.R

@@ -28,7 +28,7 @@
 # ==================================================================== #
 
 # This script runs in under a minute and renews all guidelines of CLSI and EUCAST!
-# Run it with source("data-raw/reproduction_of_rsi_translation.R")
+# Run it with source("data-raw/reproduction_of_clinical_breakpoints.R")
 
 library(dplyr)
 library(readr)
@@ -206,11 +206,11 @@ breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- b
 # check again
 breakpoints_new %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
 # compare with current version
-rsi_translation %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
+clinical_breakpoints %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
 
 # Save to package ----
 
-rsi_translation <- breakpoints_new
-usethis::use_data(rsi_translation, overwrite = TRUE, compress = "xz", version = 2)
-rm(rsi_translation)
+clinical_breakpoints <- breakpoints_new
+usethis::use_data(clinical_breakpoints, overwrite = TRUE, compress = "xz", version = 2)
+rm(clinical_breakpoints)
 devtools::load_all(".")

data-raw/reproduction_of_intrinsic_resistant.R

@@ -31,7 +31,7 @@ library(AMR)
 library(dplyr)
 int_resis <- data.frame(mo = microorganisms$mo, stringsAsFactors = FALSE)
 for (i in seq_len(nrow(antibiotics))) {
-  int_resis$new <- as.rsi("S")
+  int_resis$new <- as.sir("S")
   colnames(int_resis)[ncol(int_resis)] <- antibiotics$ab[i]
 }
 
@@ -43,7 +43,7 @@ int_resis <- eucast_rules(int_resis,
   info = FALSE
 )
 
-int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R")), drop = FALSE] %>%
+int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.sir(x) | x == "R")), drop = FALSE] %>%
   tidyr::pivot_longer(-mo) %>%
   filter(value == "R") %>%
   select(mo, ab = name)

data-raw/reproduction_of_microorganisms.R

@@ -1333,7 +1333,7 @@ rm(microorganisms)
 
 # and check: these codes should not be missing (will otherwise throw a unit test error):
 AMR::microorganisms.codes %>% filter(!mo %in% taxonomy$mo)
-AMR::rsi_translation %>% filter(!mo %in% taxonomy$mo)
+AMR::clinical_breakpoints %>% filter(!mo %in% taxonomy$mo)
 AMR::example_isolates %>% filter(!mo %in% taxonomy$mo)
 AMR::intrinsic_resistant %>% filter(!mo %in% taxonomy$mo)
 
@@ -1342,10 +1342,10 @@ devtools::load_all(".")
 
 
 # reset previously changed mo codes
-if (!identical(rsi_translation$mo, as.mo(rsi_translation$mo, language = NULL))) {
-  rsi_translation$mo <- as.mo(rsi_translation$mo, language = NULL)
-  usethis::use_data(rsi_translation, overwrite = TRUE, version = 2, compress = "xz")
-  rm(rsi_translation)
+if (!identical(clinical_breakpoints$mo, as.mo(clinical_breakpoints$mo, language = NULL))) {
+  clinical_breakpoints$mo <- as.mo(clinical_breakpoints$mo, language = NULL)
+  usethis::use_data(clinical_breakpoints, overwrite = TRUE, version = 2, compress = "xz")
+  rm(clinical_breakpoints)
 }
 
 if (!identical(microorganisms.codes$mo, as.mo(microorganisms.codes$mo, language = NULL))) {