Dedupe beta-coefficients and logistic-regression column metadata

R/create-Rmd-table.R

@@ -1,5 +1,5 @@
 create_Rmd_table <- function(file_type, file_metadata, column_metadata, column_category_metadata) {
-  column_metadata_rows <- column_metadata[column_metadata$fileName == file_type, ]
+  column_metadata_rows <- column_metadata[.matches_file_type(column_metadata$fileName, file_type), ]
   if(nrow(column_metadata_rows) == 0) {
     stop(glue::glue("No column metadata rows found for file {file_type}"))
   }

R/create-reference-Rmd.R

@@ -43,7 +43,7 @@ create_reference_Rmd <- function(
     )
 
     column_metadata_for_file <- column_metadata[
-      column_metadata$fileName == file_name,
+      .matches_file_type(column_metadata$fileName, file_name),
     ]
     if(nrow(column_metadata_for_file) == 0) {
       stop(paste("No column metadata found for file", file_name))

R/matches-file-type.R

@@ -0,0 +1,12 @@
+#' Tests the `fileName` column in the column metadata file for the existence of 
+#' a file
+#'
+#' @param files_names the fileName column
+#' @param file_type the file name to check for
+#'
+#' @return a logical vector
+#'
+#' @keywords internal
+.matches_file_type <- function(file_names, file_type) {
+  sapply(strsplit(file_names, ";"), function(names) file_type %in% names)
+}

R/validate-model-paramater-file.R

@@ -123,12 +123,12 @@ validate_file <- function(file,
                           column_metadata,
                           column_category_metadata) {
   current_file_metadata <- file_metadata[file_metadata$fileName == file_type,]
-  
+
   if (nrow(current_file_metadata) == 0) {
     stop(glue::glue("No rows found in file metadata for file type {file_type}"))
   }
-  
-  file_column_metadata <- column_metadata[column_metadata$fileName == file_type,]
+
+  file_column_metadata <- column_metadata[.matches_file_type(column_metadata$fileName, file_type),]
   if (nrow(file_column_metadata) == 0) {
     stop(glue::glue("No rows found in columns metadata for file type {file_type}"))
   }

docs/2-model-parameter-files.qmd

@@ -1,4 +1,5 @@
 ```{r echo=FALSE}
+source("../R/matches-file-type.R")
 source("../R/create-Rmd-table.R")
 ```
 

docs/5-reference.qmd

@@ -1,4 +1,5 @@
 ```{r, echo=FALSE, results='asis'}
+source("../R/matches-file-type.R")
 source("../R/create-reference-Rmd.R")
 
 file_metadata <- read.csv(

docs/_quarto.yml

@@ -3,6 +3,8 @@ project:
   output-dir: dist
   post-render: ./generate_llms_script.R
 
+quarto-required: ">=1.9.0"
+
 website:
   title: "Model Parameter Files"
   sidebar:

inst/metadata/column-metadata.csv

@@ -54,9 +54,9 @@ validate,value,The value to use when applying the validation,string,FALSE,,,,
 validate,error_handle,How to handle failed validations,category,FALSE,,,,
 validate,error_replace,Value to replace variables that fail validations whose errorHandle value is warning,string,FALSE,,,,
 validate,location,Which step in the scoring process the validation should be used,string,FALSE,,,,
-beta-coefficients,variable,The name of the variable whose beta coefficient the row contains. If this is the coefficient for the intercept then use the name "Intercept",string,FALSE,,,,
-beta-coefficients,coefficient,The beta coefficient,number,FALSE,,,,
-beta-coefficients,type,The statistical type of the variable,category,FALSE,,,,
+beta-coefficients;logistic-regression,variable,The name of the variable whose beta coefficient the row contains. If this is the coefficient for the intercept then use the name "Intercept",string,FALSE,,,,
+beta-coefficients;logistic-regression,coefficient,The beta coefficient,number,FALSE,,,,
+beta-coefficients;logistic-regression,type,The statistical type of the variable,category,FALSE,,,,
 baseline-hazards,time,The time upto which the baseline hazard should be used,number,FALSE,,,,
 baseline-hazards,baselineHazard,The baseline hazard value,number,FALSE,,,,
 survival_bins,catValue,The bin number,number,FALSE,,,,
@@ -66,6 +66,3 @@ tables,tableName,The name of the table,string,FALSE,,,,
 tables,tablePath,The path to the table relative to this file,string,FALSE,,,,
 simple-model,name,The name of the metadata,category,FALSE,,,,
 simple-model,value,The value of the metadata,string,FALSE,,,,
-logistic-regression,variable,The name of the variable whose beta coefficient the row contains. If this is the coefficient for the intercept then use the name "Intercept",string,FALSE,,,,
-logistic-regression,coefficient,The beta coefficient,number,FALSE,,,,
-logistic-regression,type,The statistical type of the variable,category,FALSE,,,,