Merge pull request #67 from istallworthy/run-through

catch NA
istallworthy · Sep 15, 2023 · a7a221c · a7a221c
2 parents c0e20e1 + 1eac1c8
commit a7a221c
Showing 1 changed file with 20 additions and 4 deletions.
diff --git a/R/assessBalance.R b/R/assessBalance.R
@@ -253,6 +253,10 @@ assessBalance <- function(home_dir, data, exposure, exposure_time_pts, outcome,
 
         bal_stats <- lapply(seq_len(m), function(k) {
           d <- as.data.frame(mice::complete(data, k))
+          if (which(is.na(d)) > 0){
+            stop("This code requires complete data. Consider imputation if missingness < 20% and is reasonably Missing at Random (MAR).",
+                 call. = FALSE)
+          }
           exposure_type <- ifelse(inherits(d[, paste0(exposure, '.',
                                                       exposure_time_pts[1])], "numeric"), "continuous", "binary")
 
@@ -270,7 +274,10 @@ assessBalance <- function(home_dir, data, exposure, exposure_time_pts, outcome,
 
         bal_stats <- lapply(seq_len(m), function(k) {
           d <- data[[k]]
-
+          if (which(is.na(d)) > 0){
+            stop("This code requires complete data. Consider imputation if missingness < 20% and is reasonably Missing at Random (MAR).",
+                 call. = FALSE)
+          }
           exposure_type <- ifelse(inherits(d[, paste0(exposure, '.',
                                                       exposure_time_pts[1])], "numeric"), "continuous", "binary")
 
@@ -333,7 +340,10 @@ assessBalance <- function(home_dir, data, exposure, exposure_time_pts, outcome,
       if (sum(duplicated(data$"ID")) > 0){
         stop("Please provide wide dataset with a single row per ID.", call. = FALSE)
       }
-
+      if (which(is.na(data)) > 0){
+        stop("This code requires complete data. Consider imputation if missingness < 20% and is reasonably Missing at Random (MAR).",
+             call. = FALSE)
+      }
       exposure_type <- ifelse(inherits(data[, paste0(exposure, '.', exposure_time_pts[1])], "numeric"), "continuous", "binary")
 
       bal_stats <- calcBalStats(home_dir, data, formulas, exposure, exposure_time_pts, outcome,
@@ -367,7 +377,10 @@ assessBalance <- function(home_dir, data, exposure, exposure_time_pts, outcome,
 
         bal_stats <- lapply(seq_len(m), function(k) {
           d <- as.data.frame(mice::complete(data, k))
-
+          if (which(is.na(d)) > 0){
+            stop("This code requires complete data. Consider imputation if missingness < 20% and is reasonably Missing at Random (MAR).",
+                 call. = FALSE)
+          }
           if (sum(duplicated(d$"ID")) > 0){
             stop("Please provide wide imputed datasets with a single row per ID.", call. = FALSE)
           }
@@ -384,7 +397,10 @@ assessBalance <- function(home_dir, data, exposure, exposure_time_pts, outcome,
         m = length(data)
         bal_stats <- lapply(seq_len(m), function(k) {
           d <- data[[k]]
-
+          if (which(is.na(d)) > 0){
+            stop("This code requires complete data. Consider imputation if missingness < 20% and is reasonably Missing at Random (MAR).",
+                 call. = FALSE)
+          }
           if (sum(duplicated(d$"ID")) > 0){
             stop("Please provide wide imputed datasets with a single row per ID.", call. = FALSE)
           }