Thank you all for your input.
This is an example of one data file (I have 74 data files):
2.90546E+11, threat, 1, 2, 1, 2, 1, death, stove,
NA, NA, 205, 0, 394
2.90546E+11, threat, 2, 2, 2, 1, 1, emaciated, shortened,
NA, NA, 205, 0, 502
2.90546E+11, threat, 3, 1, 1, 1, 2, mutilate, consider,
NA, NA, 205, 1, 468
2.90546E+11, threat, 6, 1, 2, 2, 1, weep, shop,
NA, NA, 203, 1, 345
2.90546E+11, threat, 9, 2, 1, 2, 2, tormented, easygoing,
NA, NA, 205, 1, 373
2.90546E+11, threat, 10, 1, 2, 2, 2, snake, table,
NA, NA, 205, 1, 343
2.90546E+11, threat, 11, 2, 2, 1, 1, crisis, faucet,
NA, NA, 203, 1, 437
2.90546E+11, threat, 12, 1, 1, 1, 1, victim, utensil,
NA, NA, 203, 1, 343
2.90546E+11, threat, 14, 1, 2, 2, 1, depressed, repentant,
NA, NA, 203, 1, 441
2.90546E+11, threat, 15, 2, 2, 1, 2, scum, shoe,
NA, NA, 205, 1, 475
Column 13 has values of 0s and 1s which my cognitive task outputted.
Column 14 is the reaction time (ms) data. I want to get rid of the rows
that contain zeros so I thought I'd first replace zeros with NAs then
use complete.cases function to get rid of the NAs. I also wanted to
apply other functions so I included them all in a loop. All work fine
except for the one where I try to turn the zeros to NAs.
Jim when I tried your mockdata example, it worked fine. But when I
translated it to my data, I still get zeros in the output. Can you
identify any mistranslations I'm doing?
txt.files<-list.files(".",pattern="dotprobe") #all my data files are
text files in one folder
for(tf in txt.files) {
d<-read.table(tf)
d[,13][d[,13]==0]<-NA #column 13 contains zeros
d<-d[ ,-c(10,11)] #get rid of columns 10 and 11
write.table(d,sub("[.]",".tlbs.",tf),quote=FALSE, row.names=FALSE)
}
That's an example of one of the output I get:
V1 V2 V3 V4 V5 V6 V7 V8 V9 V12 V13 V14
2.90546E+11, threat, 1, 2, 1, 2, 1, death, stove, 205, 0, 394
2.90546E+11, threat, 2, 2, 2, 1, 1, emaciated, shortened, 205, 0, 502
2.90546E+11, threat, 3, 1, 1, 1, 2, mutilate, consider, 205, 1, 468
2.90546E+11, threat, 6, 1, 2, 2, 1, weep, shop, 203, 1, 345
2.90546E+11, threat, 9, 2, 1, 2, 2, tormented, easygoing, 205, 1, 373
2.90546E+11, threat, 10, 1, 2, 2, 2, snake, table, 205, 1, 343
Columns 10 and 11 were deleted. But zeros were not replaced by NAs.
After all the data cleaning, the functions I'm interested in including
in the loop are: get_tlbs and summarize_bias (and these also work fine
in my loop).
Thanks again 🙂
Sincerely
Helen
------------------------------------------------------------------------
*From:* Jim Lemon <drjimle...@gmail.com>
*Sent:* Tuesday, April 21, 2020 2:52 AM
*To:* Rui Barradas <ruipbarra...@sapo.pt>
*Cc:* Helen Sawaya <helensaw...@hotmail.com>; Michael Dewey
<li...@dewey.myzen.co.uk>; r-help@R-project.org <r-help@r-project.org>
*Subject:* Re: [R] NA command in a 'for' loop
Hi Helen,
Your problem may lie in using row.names=TRUE. I was puzzled when an
extra column kept popping up in the output files. For reading in and
replacing zeros with NAs, this seems to work:
for(mockdata in 1:3) {
mdf<-data.frame(sample(2:20,10),sample(2:20,10),sample(0:1,10,TRUE))
write.table(mdf,file=paste0("threat",mockdata,".txt"),quote=FALSE,
row.names=FALSE,col.names=FALSE)
}
txt.files<-list.files(".",pattern="threat[1-3]")
for(tf in txt.files) {
d<-read.table(tf)
d[,3][d[,3]==0]<-NA
write.table(d,sub("[.]",".tbls.",tf),quote=FALSE,row.names=FALSE)
}
Jim
On Tue, Apr 21, 2020 at 7:57 AM Rui Barradas <ruipbarra...@sapo.pt> wrote:
Hello,
I believe the only way we have to see what is happening is for you to
post the output of
dput(head(d, 20)) # or 30
or, with d2 a subset of d that includes zeros,
dput(head(d2, 20))
Hope this helps,
Rui Barradas
Às 17:48 de 20/04/20, Helen Sawaya escreveu:
> I have one column that represents correct response versus error (correct
> is coded as 1 and error is coded as 0). Nowhere else in the dataset are
> there values of 0. The vector is treated as an integer.
> ------------------------------------------------------------------------
> *From:* Michael Dewey <li...@dewey.myzen.co.uk>
> *Sent:* Monday, April 20, 2020 7:35 PM
> *To:* Helen Sawaya <helensaw...@hotmail.com>; Rui Barradas
> <ruipbarra...@sapo.pt>; r-help@R-project.org <r-help@R-project.org>
> *Subject:* Re: [R] NA command in a 'for' loop
> Just a thought Helen but is x being treated as a real and what you think
> are zero and are printed as zero are in fact some very small number? If
> so you need to alter your test appropriately.
>
> Michael
>
> On 20/04/2020 17:25, Helen Sawaya wrote:
>> Thank you for your reply.
>>
>> I tried d[] <- lapply(d, function(x) {is.na(x) <- x == 0; x})
>> but I am still getting zeros instead of NAs in my output..
>>
>> I wonder if the problem is that some of my data files don't have any zeros
(participants made no errors)..
>> ________________________________
>> From: Rui Barradas <ruipbarra...@sapo.pt>
>> Sent: Monday, April 20, 2020 9:05 AM
>> To: Helen Sawaya <helensaw...@hotmail.com>; r-help@R-project.org
<r-help@R-project.org>
>> Subject: Re: [R] NA command in a 'for' loop
>>
>> Hello,
>>
>> Instead of
>>
>> d[d == 0] <- NA
>>
>> try
>>
>> d[] <- lapply(d, function(x) {is.na(x) <- x == 0; x})
>>
>>
>> Also, in the first for loop
>>
>> paste(i, sep = "")
>>
>> does nothing, it's the same as i.
>> And the same for
>>
>> (d2$V4 == 1) == TRUE
>>
>> Since (d2$V4 == 1) already is FALSE/TRUE there is no need for
>>
>> (.) == TRUE
>>
>>
>> Hope this helps,
>>
>> Rui Barradas
>>
>>
>>
>> Às 20:52 de 19/04/20, Helen Sawaya escreveu:
>>> Dear R experts,
>>>
>>> I am using a 'for' loop to apply commands to multiple datasets (each file is one
participant). The only one not working is the command that identifies zeros in my datasets and
changes them to NAs. But when I look at the output, zeros ("0") are still present.
Surprisingly, the functions work fine when I apply them to a single
> dataset (outside the loop). I've tried:
>>>
>>> all.files <- list.files(".")
>>> txt.files <- grep("threat.txt",all.files,value=T)
>>>
>>> for(i in txt.files){
>>> d <- read.table(paste(i,sep=""),header=F)
>>> d[d==0] <- NA #replace zeros with NA
>>> write.table(d, paste0(i,".tlbs.txt"), quote=FALSE, row.names=TRUE)}
>>> d<-d[ ,-c(10,11)]
>>> d2<-d[complete.cases(d), ]
>>> d2$V4<-as.numeric(d2$V4)
>>> congruent <- (d2$V4 == 1) == TRUE
>>> x <- get_tlbs(d2$V14, congruent, prior_weights = NULL, method =
"weighted", fill_gaps = FALSE)
>>> write.table(x, paste0(i,".tlbs.txt"), quote=FALSE, row.names=TRUE)}
>>>
>>> I've also tried:
>>>
>>> for(i in txt.files){
>>> d <- read.table(paste(i,sep=""),header=F)
>>> if (0 %in% d)
>>> {replace_with_na(d,replace = list(x = 0))} # replace zeros with NA
>>> d<-d[ ,-c(10,11)]
>>> d2<-d[complete.cases(d), ]
>>> d2$V4<-as.numeric(d2$V4)
>>> congruent <- (d2$V4 == 1) == TRUE
>>> x <- get_tlbs(d2$V14, congruent, prior_weights = NULL, method =
"weighted", fill_gaps = FALSE)
>>> write.table(x, paste0(i,".summaryoutput.txt"), quote=FALSE,
row.names=TRUE)}
>>>
>>> Thank you for your help.
>>> Sincerely
>>> Helen
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
> --
> Michael
> http://www.dewey.myzen.co.uk/home.html
______________________________________________
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