Misc code simplifications

R/coh_data_wrangling.R

@@ -106,13 +106,15 @@ set_event_status <- function(data_set,
     col_names = outcome_date_col,
     status = c(1, 0)
   )
+
+  checkmate::assert_character(censoring_date_col,
+                              any.missing = FALSE, min.len = 1, null.ok = TRUE
+  )
+  checkmate::assert_names(
+    names(data_set), must.include = censoring_date_col
+  )
+
   if (!is.null(censoring_date_col)) {
-    checkmate::assert_character(censoring_date_col,
-      any.missing = FALSE, min.len = 1
-    )
-    checkmate::assert_names(
-      names(data_set), must.include = censoring_date_col
-    )
     data_set$outcome_status <- ifelse(
       (!is.na(data_set[[censoring_date_col]])) &
         (!is.na(data_set[[outcome_date_col]])) &
@@ -181,15 +183,15 @@ get_time_to_event <- function(data_set,
   )
 
   #Checks of censoring_date_col if provided
+  checkmate::assert_string(censoring_date_col, null.ok = TRUE)
+  checkmate::assert_names(
+    colnames(data_set),
+    must.include = censoring_date_col
+  )
   if (!is.null(censoring_date_col)) {
-    checkmate::assert_names(
-      colnames(data_set),
-      must.include = censoring_date_col
-    )
     checkmate::assert_date(
       data_set[[censoring_date_col]]
     )
-    checkmate::assert_string(censoring_date_col)
   }
 
   # check immnunization date col if asked

R/coh_eff_utils.R

@@ -9,7 +9,7 @@ extract_surv_model <- function(model, start_cohort, end_cohort) {
   tte <- seq(0, as.numeric(days) - 1, by = 1)
   res <- summary(model, times = tte, scale = 1)
   cols <- lapply(c(2:6, 8:16), function(x) res[x])
-  tbl <- do.call(data.frame, cols)
+  tbl <- data.frame(cols)
   tbl$date <- tbl$time + start_cohort
   return(tbl)
 }

R/coh_immunization.R

@@ -119,29 +119,28 @@ make_immunization <- function(data_set,
     len = 1L
   )
 
+  checkmate::assert_string(censoring_date_col, null.ok = TRUE)
+  checkmate::assert_names(
+    colnames(data_set),
+    must.include = censoring_date_col
+  )
   # check censoring_date_col if provided
   if (!is.null(censoring_date_col)) {
-    checkmate::assert_names(
-      colnames(data_set),
-      must.include = censoring_date_col
-    )
     checkmate::assert_date(
       data_set[[censoring_date_col]]
     )
-    checkmate::assert_string(censoring_date_col)
   }
 
   # check vacc_name_col if provided
-  if (!is.null(vacc_name_col)) {
-    checkmate::assert_names(
-      names(data_set),
-      must.include = c(vacc_name_col)
-    )
-    checkmate::assert_character(
-      vacc_name_col,
-      min.len = length(vacc_date_col)
-    )
-  }
+  checkmate::assert_character(
+    vacc_name_col,
+    min.len = length(vacc_date_col),
+    null.ok = TRUE
+  )
+  checkmate::assert_names(
+    names(data_set),
+    must.include = c(vacc_name_col)
+  )
 
   # warn on year of cohort end date date
   max_year <- 2100 # a plausible maximum year

R/coh_match.R

@@ -135,15 +135,15 @@ match_cohort <- function(data_set,
   )
 
   #Checks of censoring_date_col if provided
+  checkmate::assert_string(censoring_date_col, null.ok = TRUE)
+  checkmate::assert_names(
+    colnames(data_set),
+    must.include = censoring_date_col
+  )
   if (!is.null(censoring_date_col)) {
-    checkmate::assert_names(
-      colnames(data_set),
-      must.include = censoring_date_col
-    )
     checkmate::assert_date(
       data_set[[censoring_date_col]]
     )
-    checkmate::assert_string(censoring_date_col)
   }
 
   # `exact` and `nearest` cannot be NULL. At least one must be provided
@@ -153,26 +153,23 @@ match_cohort <- function(data_set,
   )
 
   # checks for `nearest`
-  if (!is.null(nearest)) {
-    checkmate::assert_numeric(
-      nearest,
-      any.missing = FALSE, min.len = 1, names = "named"
-    )
-    checkmate::assert_names(
-      names(data_set),
-      must.include = names(nearest)
-    )
-  }
-  # checks for `exact`. Not else, both can be non-NULL
-  if (!is.null(exact)) {
-    checkmate::assert_character(exact,
-      any.missing = FALSE, min.len = 1
-    )
-    checkmate::assert_names(
-      names(data_set),
-      must.include = exact
-    )
-  }
+  checkmate::assert_numeric(
+    nearest,
+    any.missing = FALSE, min.len = 1, names = "named", null.ok = TRUE
+  )
+  checkmate::assert_names(
+    names(data_set),
+    must.include = names(nearest)
+  )
+
+  # checks for `exact`
+  checkmate::assert_character(exact,
+    any.missing = FALSE, min.len = 1, null.ok = TRUE
+  )
+  checkmate::assert_names(
+    names(data_set),
+    must.include = exact
+  )
 
   # check date types
   checkmate::assert_date(

R/coh_match_utils.R

@@ -15,14 +15,7 @@ match_cohort_ <- function(data_set,
 
   #Formula
   variables <- c(exact, names(nearest))
-  formula <- paste0(vacc_status_col, " ~ ")
-  for (v in seq_along(variables)) {
-    if (v == 1) {
-      formula <- paste0(formula, variables[v])
-    } else {
-      formula <- paste0(formula, " + ", variables[v])
-    }
-  }
+  formula <- paste(vacc_status_col, "~", paste(variables, collapse = " + "))
   formula_eval <- eval(parse(text = formula))
 
   #Matching