Changing entries of column of type "factor"/Adding a new level to a factor

On Aug 27, 2012, at 12:18 PM, Bert Gunter wrote:

Well ...See below.

-- Cheers, Bert

On Mon, Aug 27, 2012 at 9:19 AM, David Winsemius <dwinsemius at comcast.net>
wrote:

On Aug 27, 2012, at 3:09 AM, Fridolin wrote:

What is a smart way to change an entry inside a column of a dataframe or
matrix which is of type "factor"?

Here is my script incl. input data:

#set working directory:
setwd("K:/R")

#read in data:
input<-read.table("Exampleinput.txt", sep="\t", header=TRUE)

#check data:
input

 Ind      M1      M2      M3
1    1   96/98 120/120     0/0
2    2 102/108 120/124 305/305
3    3  96/108 120/120     0/0
4    4     0/0 116/120 300/305
5    5  96/108 120/130 300/305
6    6   98/98 116/120 300/305
7    7  98/108 120/120 305/305
8    8  98/108 120/120 305/305
9    9  98/102 120/124 300/300
10  10 108/108 120/120 305/305

str(input)

'data.frame':   10 obs. of  4 variables:
$ Ind: int  1 2 3 4 5 6 7 8 9 10
$ M1 : Factor w/ 8 levels "0/0","102/108",..: 5 2 4 1 4 8 7 7 6 3
$ M2 : Factor w/ 4 levels "116/120","120/120",..: 2 3 2 1 4 1 2 2 3 2
$ M3 : Factor w/ 4 levels "0/0","300/300",..: 1 4 1 3 3 3 4 4 2 4

#replace 0/0 by 999/999:
for (r in 1:10)

+   for (c in 2:4)
+     if (input[r,c]=="0/0") input[r,c]<-"999/999"
Warnmeldungen:
1: In `[<-.factor`(`*tmp*`, iseq, value = "999/999") :
invalid factor level, NAs generated
2: In `[<-.factor`(`*tmp*`, iseq, value = "999/999") :
invalid factor level, NAs generated
3: In `[<-.factor`(`*tmp*`, iseq, value = "999/999") :
invalid factor level, NAs generated

input

 Ind      M1      M2      M3
1    1   96/98 120/120    <NA>
2    2 102/108 120/124 305/305
3    3  96/108 120/120    <NA>
4    4    <NA> 116/120 300/305
5    5  96/108 120/130 300/305
6    6   98/98 116/120 300/305
7    7  98/108 120/120 305/305
8    8  98/108 120/120 305/305
9    9  98/102 120/124 300/300
10  10 108/108 120/120 305/305


I want to replace all "0/0" by "999/999". My code should work for
columns
of
type "character" and "integer". But to make it work for a
"factor"-column
I
would need to add the new level of "999/999" at first, I guess. How do I
add
a new level?

?levels

levels(input$M1) <- c(levels(input$M1), "999/999")

This adds an additional level; then you have to replace the "0/0"
level with this one; then you have to call levels again to remove the
"0/0" level.

Then do it this way (different from what I thought was originally desired):

x <- factor(letters[1:3])
levels(x) <- c("d", levels(x)[2:3])
x

[1] d b c
Levels: d b c

I think the following slight tweak may be preferred, as illustrated
with a little example (opinions?):

x <- factor(letters[1:3])
x

[1] a b c
Levels: a b c

## create a new levels vector

newlvl <- levels(x)
newlvl[newlvl == "a"] <- "d"

## Create the new factor and replace the old with it

x <- factor(newlvl[x])
x

[1] d b c
Levels: b c d

Note, however, as Bill D. said, in either case your level ordering --
which will be used, e.g. in printing and displaying -- will be weird.

So the above method might be what you expect. Several options are now
available to the questioner.

--
David.

--

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

--

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:

http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

David Winsemius, MD
Alameda, CA, USA