CODEWITHSUNDEEP
r
logicForPresident
logicForPresident

Reputation: 311

Using a function to add a column in R data.frame

I am trying to write a function in R which lumps species columns together within a data.frame.

(To elaborate a bit on what I'm doing...I have a data frame with multiple plant species for multiple sites and years. Some of the species were misidentified, so I'd like to group to a more general level (e.g. spp a and spp b were mixed up throughout the years; so I'd like to create a new column called spp.ab in which the data for spp a and b are lumped together)).

Example:

spp.a spp.b
  1     0
  2     3
  0     4
  3     2
  4     5

I'd like to eventually end up with a single column that displays the maximum from value from the two species:

spp.ab
  1
  3
  4
  3
  5

I've started writing a function which does this; however, I'm having troubling adding the new column to my data set and dropping the old ones. Could someone tell me what's wrong with my code?

lump <- function(db, spp.list, new.spp) { #input spp.list as c('spp.a', 'spp.b', ...)
  mini.db <- subset(db, select=spp.list);
  newcol <- as.vector(apply(mini.db, 1, max, na.rm=T));
  db$new.spp <- newcol
  db <- db[,names(db) %in% spp.list]
  return(db)
}

When I call the function as such

test <- lump(db, c('spp.a', 'spp.b'), spp.ab)
test

all that pops up is the mini.db. Am I missing something with return()?

For reference, db is the database, spp.list is the species I want to lump together, and new.spp is what I would like the new column named.

Thanks for any help,
Paul

Upvotes: 3

Views: 7308

Answers (2)

A5C1D2H2I1M1N2O1R2T1
A5C1D2H2I1M1N2O1R2T1

Reputation: 193687

While it seems like you've found your answer, I would suggest, instead, the pmax function:

> with(db, pmax(spp.a, spp.b))
[1] 1 3 4 3 5

You can use this with within or transform to mimic your function:

out <- within(db, spp.ab <- pmax(spp.a, spp.b))
out
#   spp.a spp.b spp.ab
# 1     1     0      1
# 2     2     3      3
# 3     0     4      4
# 4     3     2      3
# 5     4     5      5

Upvotes: 2

logicForPresident
logicForPresident

Reputation: 311

I've figured it out...stupid mistake, of course. Here is the code that works:

lump <- function(db, spp.list, new.spp) { #input spp.list as a c('spp.a', 'spp.b', ...), and new.spp must be in quotes (e.g. 'new.spp')
    mini.db <- subset(db, select=spp.list);
    newcol <- as.vector(apply(mini.db, 1, max, na.rm=T));
    newcol[newcol==-Inf] <- NA;
    db[new.spp] <- newcol;
    db <- db[, !names(db) %in% spp.list];
    return(as.data.frame(db));
 }

The key is in the db[new.spp] <- newcol; line. Apparently using this works, but using db$new.spp <- newcol does not. I also then added a ! to the line db <- db[,!names(db) %in% spp.list]. This was my biggest mistake.

Upvotes: 3

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