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
>
> ______________________________________________
> 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]]
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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