R：在 mapply 中的 function 中填充 data.frame

Question

A data.frame df1 is queried (fuzzy match) against another data.frame df2 with agrep . Via iterating over its output (a list called matches holding the row number of the respective matches in df2 ), df1 is populated with affiliated values from df2 . The goal is a function that is passed to mapply ; however, in all my attempts df1 remains unchanged.

In a for-loop, the code works as expected and populates df1 with the affiliated variables from df2 . Still, I would be interested how to solve this with a function that is passed to mapply .

First, the two data.frames:

df1 <- structure(list(Species = c("Alisma plantago-aquatica", "Alnus glutinosa",
                                  "Carex davalliana", "Carex echinata",
                                  "Carex elata"),
                      CheckPoint = c(NA, NA, NA, NA, NA),
                      L = c(NA, NA, NA, NA, NA),
                      R = c(NA, NA, NA, NA, NA),
                      K = c(NA, NA, NA, NA, NA)),
                 row.names = c(NA, 5L), class = "data.frame")

df2 <- structure(list(Species = c("Alisma gramineum", "Alisma lanceolatum",
                                  "Alisma plantago-aquatica", "Alnus glutinosa",
                                  "Alnus incana", "Alnus viridis",
                                  "Carex davalliana", "Carex depauperata",
                                  "Carex diandra", "Carex digitata",
                                  "Carex dioica", "Carex distans",
                                  "Carex disticha", "Carex echinata",
                                  "Carex elata"),
                      L = c(7L, 7L, 7L, 5L, 6L, 7L, 9L, 4L, 8L, 3L, 9L, 9L, 8L,
                            8L, 8L),
                      R = c(7L, 7L, 5L, 5L, 4L, 3L, 4L, 7L, 6L, NA, 4L, 6L, 6L,
                            NA, NA),
                      K = c(6L, 2L, NA, 3L, 5L, 4L, 4L, 2L, 7L, 4L, NA, 3L, NA,
                            3L, 2L)),
                 row.names = seq(1:15), class = "data.frame")

Then, fuzzy match by Species :

matches <- lapply(df1$Species, agrep, x = df2$Species, value = FALSE,
                 max.distance = c(deletions = 0,
                                  insertions = 1,
                                  substitutions = 1))

Populating df1 with the values from df2 works as expected:

for (i in 1:dim(df1)[1]){
  df1[i, 2:5] <- df2[matches[[i]], ]
  }

In contrast to my approach with mapply that does return the correct values, although as a list of dissasembled values that are never written into df1 . No combination (with or without return(df1) , writing it into another variable nor desparate attempts with the state of SIMPLIFY or USE.NAMES ) yielded the desired results.

populatedf1 <- function(matches, index){
    df1[index, 2:5] <- df2[matches, ]
  #return(df1)
  }

mapply(populatedf1, matches, seq_along(matches), SIMPLIFY = FALSE,
              USE.NAMES = FALSE)

Would be great if someone knows the solution or could point me into a certain direction, thanks: :)

Answer 1

Actually, you would not need any loop here ( for or mapply ) if you replace lapply with sapply (so that it returns a vector instead of list) and then do a direct assignment.

matches <- sapply(df1$Species, agrep, x = df2$Species, value = FALSE,
                   max.distance = c(deletions = 0,
                                    insertions = 1,
                                   substitutions = 1))

df1[, 2:5] <- df2[matches,]
df1

#                   Species               CheckPoint L  R  K
#1 Alisma plantago-aquatica Alisma plantago-aquatica 7  5 NA
#2          Alnus glutinosa          Alnus glutinosa 5  5  3
#3         Carex davalliana         Carex davalliana 9  4  4
#4           Carex echinata           Carex echinata 8 NA  3
#5              Carex elata              Carex elata 8 NA  2

---

As far as your approach is concerned you can use Map or mapply with SIMPLIFY = FALSE and bring the list of dataframes into one dataframe using do.call and rbind and then assign.

df1[, 2:5] <- do.call(rbind, Map(populatedf1, matches, seq_along(matches)))