refac: move data simulation validation functions to validation module

R/simulate_serosurvey.R

@@ -415,55 +415,6 @@ check_age_constraints <- function(df) {
   return(TRUE)
 }
 
-validate_survey <- function(survey_features) {
-
-  if (!is.data.frame(survey_features) || !all(c("age_min", "age_max", "sample_size") %in% names(survey_features))) {
-    stop("survey_features must be a dataframe with columns 'age_min', 'age_max', and 'sample_size'.")
-  }
-
-  # check that the age_max of a bin does not coincide with
-  # the age min of a different bin
-  is_age_ok <- check_age_constraints(survey_features)
-  if(!is_age_ok)
-    stop("Age bins in a survey are inclusive of both bounds, so the age_max of
-         one bin cannot equal the age_min of another.")
-}
-
-validate_foi_df <- function(foi_df, cnames_additional) {
-  if (!is.data.frame(foi_df) || !all(cnames_additional %in% names(foi_df)) || ncol(foi_df) != (1 + length(cnames_additional))) {
-    if(length(cnames_additional) == 1)
-      message_end <- paste0(" and ", cnames_additional, ".")
-    else
-      message_end <- paste0(", ", paste(cnames_additional, collapse=" and "), ".")
-    message_beginning <- "foi must be a dataframe with columns foi"
-    stop(paste0(message_beginning, message_end))
-  }
-}
-
-validate_seroreversion_rate <- function(seroreversion_rate) {
-  if (!is.numeric(seroreversion_rate) || seroreversion_rate < 0) {
-    stop("seroreversion_rate must be a non-negative numeric value.")
-  }
-}
-
-validate_survey_and_foi_consistency <- function(
-    survey_features,
-    foi_df
-) {
-  max_age_foi_df <- nrow(foi_df)
-  if(max_age_foi_df > max(survey_features$age_max))
-    stop("maximum age implicit in foi_df should not exceed max age in survey_features.")
-}
-
-validate_survey_and_foi_consistency_age_time <- function(
-    survey_features,
-    foi_df
-) {
-  max_age_foi_df <- max(foi_df$year) - min(foi_df$year) + 1
-  if(max_age_foi_df > max(survey_features$age_max))
-    stop("maximum age implicit in foi_df should not exceed max age in survey_features.")
-}
-
 generate_seropositive_counts_by_age_bin <- function(
     probability_seropositive_by_age,
     sample_size_by_age_random,

R/validation.R

@@ -55,3 +55,51 @@ validate_serosurvey <- function(serosurvey) {
 
   return(serosurvey)
 }
+
+validate_survey <- function(survey_features) {
+
+  if (!is.data.frame(survey_features) || !all(c("age_min", "age_max", "sample_size") %in% names(survey_features))) {
+    stop("survey_features must be a dataframe with columns 'age_min', 'age_max', and 'sample_size'.")
+  }
+
+  # check that the age_max of a bin does not coincide with
+  # the age min of a different bin
+  is_age_ok <- check_age_constraints(survey_features)
+  if(!is_age_ok)
+    stop("Age bins in a survey are inclusive of both bounds, so the age_max of one bin cannot equal the age_min of another.")
+}
+
+validate_foi_df <- function(foi_df, cnames_additional) {
+  if (!is.data.frame(foi_df) || !all(cnames_additional %in% names(foi_df)) || ncol(foi_df) != (1 + length(cnames_additional))) {
+    if(length(cnames_additional) == 1)
+      message_end <- paste0(" and ", cnames_additional, ".")
+    else
+      message_end <- paste0(", ", paste(cnames_additional, collapse=" and "), ".")
+    message_beginning <- "foi must be a dataframe with columns foi"
+    stop(paste0(message_beginning, message_end))
+  }
+}
+
+validate_seroreversion_rate <- function(seroreversion_rate) {
+  if (!is.numeric(seroreversion_rate) || seroreversion_rate < 0) {
+    stop("seroreversion_rate must be a non-negative numeric value.")
+  }
+}
+
+validate_survey_and_foi_consistency <- function(
+    survey_features,
+    foi_df
+) {
+  max_age_foi_df <- nrow(foi_df)
+  if(max_age_foi_df > max(survey_features$age_max))
+    stop("maximum age implicit in foi_df should not exceed max age in survey_features.")
+}
+
+validate_survey_and_foi_consistency_age_time <- function(
+    survey_features,
+    foi_df
+) {
+  max_age_foi_df <- max(foi_df$year) - min(foi_df$year) + 1
+  if(max_age_foi_df > max(survey_features$age_max))
+    stop("maximum age implicit in foi_df should not exceed max age in survey_features.")
+}