How do I replace values within a data frame with a string in R?

Question

short version: How do I replace values within a data frame with a string found within another data frame?

longer version: I'm a biologist working with many species of bees. I have a data set with many thousands of bees. Each row has a unique bee ID # along with all the relevant info about that specimen (data of capture, GPS location, etc). The species information for each bee has not been entered because it takes a long time to ID them. When IDing, I end up with boxes of hundred of bees, all of the same species. I enter these into a separate data frame. I am trying to write code that will update the original data file with species information (family, genus, species, sex, etc) as I ID the bees. Currently, in the original data file, the species info is blank and is interpreted as NA within R. I want to have R find all unique bee ID #'s and fill in the species info, but I am having trouble figuring out how to replace the NA values with a string (eg "Andrenidae")

Here is a simple example of what I am trying to do:

rawData<-data.frame(beeID=c(1:20),family=rep(NA,20))
speciesInfo<-data.frame(beeID=seq(1,20,3),family=rep("Andrenidae",7))

rawData[rawData$beeID == 4,"family"]  <- speciesInfo[speciesInfo$beeID == 4,"family"]

So, I am replacing things as I want, but with a number rather than the family name (a string). What I would eventually like to do is write a little loop to add in all the species info, eg:

for (i in speciesInfo$beeID){
  rawData[rawData$beeID == i,"family"]  <- speciesInfo[speciesInfo$beeID == i,"family"]
}

Thanks in advance for any advice!

Cheers,

Zak

EDIT:

I just noticed that the first two methods below add a new column each time, which would cause problems if I needed to add species info multiple times (which I typically do). For example:

rawData<-data.frame(beeID=c(1:20),family=rep(NA,20))
Andrenidae<-data.frame(beeID=seq(1,20,3),family=rep("Andrenidae",7))
Halictidae<-data.frame(beeID=seq(1,20,3)+1,family=rep("Halictidae",7))

# using join
library(plyr)
rawData <- join(rawData, Andrenidae, by = "beeID", type = "left")
rawData <- join(rawData, Halictidae, by = "beeID", type = "left")

# using merge
rawData <- merge(x=rawData,y=Andrenidae,by='beeID',all.x=T,all.y=F)
rawData <- merge(x=rawData,y=Halictidae,by='beeID',all.x=T,all.y=F)

Is there a way to either collapse the columns so that I have one, unified data frame? Or a way to update the rawData rather than adding a new column each time? Thanks in advance!

Answer 1

Here is a function I think will work for you. This uses match to find and index of values in your annotation dataframe, and then replaces the values in the rawData.

replaceID <- function(to,from,mergeBy,values){
  x <- match(from[,mergeBy],to[,mergeBy])
  to[,values][x] <- as.character(from[,values])
  return(to)
}
> rawData <- replaceID(rawData,Halictidae,"beeID","family")
> rawData
   beeID     family
1      1       <NA>
2      2 Halictidae
3      3       <NA>
4      4       <NA>
5      5 Halictidae
6      6       <NA>
7      7       <NA>
8      8 Halictidae
9      9       <NA>
10    10       <NA>
11    11 Halictidae
12    12       <NA>
13    13       <NA>
14    14 Halictidae
15    15       <NA>
16    16       <NA>
17    17 Halictidae
18    18       <NA>
19    19       <NA>
20    20 Halictidae

Answer 2

Another option is to use ?join in package plyr

    library(plyr)
#Adding family ahead of time was unnecessary so I'll remove it alongside the join.
join(rawData, speciesInfo, by = "beeID", type = "left")[,-2]
   beeID     family
1      1 Andrenidae
2      2       <NA>
3      3       <NA>
4      4 Andrenidae
5      5       <NA>
6      6       <NA>
7      7 Andrenidae
8      8       <NA>
9      9       <NA>
10    10 Andrenidae
11    11       <NA>
12    12       <NA>
13    13 Andrenidae
14    14       <NA>
15    15       <NA>
16    16 Andrenidae
17    17       <NA>
18    18       <NA>
19    19 Andrenidae
20    20       <NA>

Update

# If you anticipate adding new species over time, 
# simply rbind those into a single reference data.frame to merge with your rawData. 
# Like so:
library(plyr)
rawData <- join(rawData, rbind(Andrenidae, Halictidae), by = "beeID", type = "left")

# To keep you code clean, you could do this step ahead of time
species_list <- rbind(Andrenidae, Halictidae)
rawData <- join(rawData, species_list, by = "beeID", type = "left")

Answer 3

You could use the merge function, eg :

rawData <- data.frame(beeID=c(1:20),family=rep(NA,20))
speciesInfo <- data.frame(beeID=seq(1,20,3),
                          family=c(rep('Halictidae',4), rep("Andrenidae",3)))

merged <- merge(x=rawData,y=speciesInfo,by='beeID',all.x=T,all.y=F)
merged$family.x <- NULL # remove the family.x column
names(merged) <- c('beeID','family') # rename the columns

NB

It is not necessary to initialize rawData with the family column.
Merge function will add it automatically, eg :

rawData <- data.frame(beeID=c(1:20))
speciesInfo <- data.frame(beeID=seq(1,20,3),
                          family=c(rep('Halictidae',4), rep("Andrenidae",3)))

merged <- merge(x=rawData,y=speciesInfo,by='beeID',all.x=T,all.y=F)

> merged
   beeID     family
1      1 Halictidae
2      2       <NA>
3      3       <NA>
4      4 Halictidae
5      5       <NA>
6      6       <NA>
7      7 Halictidae
8      8       <NA>
9      9       <NA>
10    10 Halictidae
11    11       <NA>
12    12       <NA>
13    13 Andrenidae
14    14       <NA>
15    15       <NA>
16    16 Andrenidae
17    17       <NA>
18    18       <NA>
19    19 Andrenidae
20    20       <NA>

Answer 4

A data.table solution that will be memory and time efficient.

• Note that you need to have stringsAsFactors = F for rbindlist (a super-fast version of do.call(rbind,list) / rbind)
• I've added another column as dummy data to the rawData object and removed family.

Create the data -

rawData <- data.frame(beeID = c(1:20), other_stuff = sample(letters, 20), stringsAsFactors = F)
Andrenidae <- data.frame(beeID = seq(1, 20, 3), family = rep("Andrenidae", 7), stringsAsFactors = F)
Halictidae <- data.frame(beeID = seq(1, 20 , 3)+  1, family = rep("Halictidae", 7), stringsAsFactors = F)
library(data.table)
# convert to data.table
rawDT <- as.data.table(rawData)
# combine the list of Species-specific data.frames into a large data.table
speciesInfo <- rbindlist(list(Andrenidae, Halictidae))
# set the keys, to allow efficient use of data.table and its merging 
# abilities. The keys are the same for both 
setkeyv(rawDT, 'beeID')
setkeyv(speciesInfo, 'beeID')
# merge by key 
speciesInfo[rawDT, nomatch = NA]
## beeID     family other_stuff
## 1:     1 Andrenidae           s
## 2:     2 Halictidae           x
## 3:     3         NA           i
## 4:     4 Andrenidae           e
## 5:     5 Halictidae           v
## 6:     6         NA           q
## 7:     7 Andrenidae           w
## 8:     8 Halictidae           c
## 9:     9         NA           u
## 10:    10 Andrenidae           z
## 11:    11 Halictidae           y
## 12:    12         NA           a
## 13:    13 Andrenidae           l
## 14:    14 Halictidae           r
## 15:    15         NA           h
## 16:    16 Andrenidae           o
## 17:    17 Halictidae           n
## 18:    18         NA           g
## 19:    19 Andrenidae           p
## 20:    20 Halictidae           m

or

rawDT[speciesInfo]

##    beeID other_stuff     family
## 1:     1           s Andrenidae
## 2:     2           x Halictidae
## 3:     4           e Andrenidae
## 4:     5           v Halictidae
## 5:     7           w Andrenidae
## 6:     8           c Halictidae
## 7:    10           z Andrenidae
## 8:    11           y Halictidae
## 9:    13           l Andrenidae
## 10:   14           r Halictidae
## 11:   16           o Andrenidae
## 12:   17           n Halictidae
## 13:   19           p Andrenidae
## 14:   20           m Halictidae

Which ever is the data you are interested in