Elegant way to merge many duplicated columns in R?

I have two dataframes that I need to merge in R. I can't really modify them before the merge, and they share many columns, but there are no overlapping values in the duplicated columns, if one row in one column has a value then the same row in the duplicated column is NA. After the merge, I have something that looks like this:

df1 <- data.frame(id = c(1,2,3,4),
                  Var1 = c(1,2,NA,NA),
                  Var2 = c("a","b",NA,NA))

df2 <- data.frame(id = c(1,2,3,4),
                  Var1 = c(NA,NA,3,4),
                  Var2 = c(NA,NA,"c","d"))

mergedData <- merge(df1, df2, by = "id")

mergedData <- mergedData[, c("Var1.x", "Var1.y", "Var2.x", "Var2.y")]

print(mergedData)
  Var1.x Var1.y Var2.x Var2.y
1      1     NA      a   <NA>
2      2     NA      b   <NA>
3     NA      3   <NA>      c
4     NA      4   <NA>      d

I wrote a function to use in other scripts that merges two columns and then removes one of them:

mergeColumns <- function(df, colToRemove, colToKeep) {
  df[[colToKeep]][is.na(df[[colToKeep]])] <- df[[colToRemove]][is.na(df[[colToKeep]])]
  df[[colToRemove]] <- NULL
  names(df)[names(df) %in% colToKeep] <- gsub(".x|.y", "", names(df)[names(df) %in% colToKeep])
  return(df)
}

This works fine (although I'm sure there is a cleaner approach) when working with single columns. However, in my merged dataframe I have many columns that need to be merged. I am not sure of the best way to do this. I thought about creating a dataframe of the columns that need to be merged and tried using the apply family of functions with no success (I sort of knew the approach below was unlikely to work but thought it might get me going in the right direction):

duplicatedColumns <- data.frame(colstoKeep = c("Var1.x", "Var2.x'"),
                                coltoRemove = c("Var1.y", "Var2.y"))

lapply(data, mergeColumns(duplicatedColumns$sampleIntakeCols, duplicatedColumns$rnaMetadataCols))
>Error in match.fun(FUN) : argument "FUN" is missing, with no default

Any insight into how I might be able to get this to work of a better approach would be much appreciated. Base R would be preferable. Thanks in advance.

you can use a loop or the apply family of functions. Try this:

mergedData <- data.frame(Var1.x = c(1,2,NA,NA),
                         Var1.y = c(NA,NA,1,2),
                         Var2.x = c("a", "b", NA, NA),
                         Var2.y = c(NA,NA,"c","d"))

duplicatedColumns <- data.frame(colstoKeep = c("Var1.x", "Var2.x"),
                                coltoRemove = c("Var1.y", "Var2.y"))

for (i in 1:nrow(duplicatedColumns)) {
  colToKeep <- duplicatedColumns$colstoKeep[i]
  colToRemove <- duplicatedColumns$coltoRemove[i]
  mergedData[[colToKeep]][is.na(mergedData[[colToKeep]])] <- mergedData[[colToRemove]][is.na(mergedData[[colToKeep]])]
  mergedData[[colToRemove]] <- NULL
  names(mergedData)[names(mergedData) == colToKeep] <- gsub(".x|.y", "", colToKeep)
}