Thank you for your patience.
This is the output of dput(head(d, 10))
structure(list(V1 = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L), .Label = "9.9761E+11,", class = "factor"), V2 = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "threat,", class = "factor"),
V3 = structure(c(1L, 28L, 37L, 48L, 55L, 63L, 73L, 88L, 2L,
20L), .Label = c("1,", "10,", "100,", "101,", "102,", "104,",
"107,", "108,", "109,", "110,", "111,", "112,", "113,", "114,",
"115,", "116,", "117,", "118,", "119,", "12,", "13,", "14,",
"15,", "16,", "17,", "18,", "19,", "2,", "20,", "21,", "22,",
"23,", "24,", "27,", "28,", "29,", "3,", "30,", "31,", "32,",
"33,", "34,", "35,", "36,", "37,", "38,", "39,", "4,", "42,",
"44,", "46,", "47,", "48,", "49,", "5,", "50,", "52,", "53,",
"54,", "55,", "57,", "59,", "6,", "60,", "61,", "62,", "63,",
"64,", "65,", "66,", "68,", "69,", "7,", "71,", "74,", "75,",
"76,", "78,", "81,", "82,", "83,", "84,", "85,", "86,", "87,",
"88,", "89,", "9,", "90,", "91,", "92,", "94,", "95,", "96,",
"97,", "98,"), class = "factor"), V4 = structure(c(1L, 2L,
1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L), .Label = c("1,", "2,"), class = "factor"),
V5 = structure(c(2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 2L), .Label = c("1,",
"2,"), class = "factor"), V6 = structure(c(2L, 1L, 2L, 2L,
1L, 2L, 2L, 1L, 2L, 2L), .Label = c("1,", "2,"), class = "factor"),
V7 = structure(c(2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L), .Label = c("1,",
"2,"), class = "factor"), V8 = structure(c(41L, 92L, 63L,
36L, 2L, 81L, 12L, 14L, 23L, 33L), .Label = c("abduction,",
"abortion,", "abuse,", "accident,", "addicted,", "agony,",
"anger,", "angry,", "anguish,", "assault,", "bankrupt,",
"bullet,", "burial,", "cancer,", "cemetery,", "coffin,",
"corpse,", "crash,", "crisis,", "cruel,", "death,", "defeated,",
"depressed,", "deserted,", "despair,", "destroy,", "disaster,",
"disloyal,", "distress,", "dreadful,", "drown,", "dull,",
"dump,", "emaciated,", "failure,", "fatigue,", "fault,",
"feeble,", "fever,", "filth,", "forlorn,", "germs,", "gloomy,",
"hardship,", "hell,", "helpless,", "horror,", "hostage,",
"hostile,", "hurt,", "idiot,", "infest,", "injury,", "irritable,",
"jail,", "killer,", "lonely,", "malaria,", "messy,", "misery,",
"mistake,", "morbid,", "murder,", "mutilate,", "pain,", "panic,",
"poison,", "prison,", "pus,", "rape,", "rat,", "rejected,",
"sad,", "scum,", "shame,", "sick,", "slap,", "snake,", "spider,",
"suicide,", "surgery,", "terrible,", "tormented,", "trash,",
"trauma,", "ugly,", "ulcer,", "unease,", "unhappy,", "useless,",
"victim,", "wasp,", "weep,", "worm,", "wound,"), class = "factor"),
V9 = structure(c(24L, 90L, 73L, 10L, 92L, 33L, 84L, 96L,
70L, 57L), .Label = c("alley,", "ankle,", "appliance,", "audience,",
"bandage,", "bathroom,", "bookcase,", "border,", "branch,",
"cabinet,", "category,", "clean,", "cliff,", "cold,", "consider,",
"consoled,", "context,", "country,", "crop,", "dentist,",
"detail,", "dinner,", "doctor,", "dynamic,", "easygoing,",
"elbow,", "energetic,", "farm,", "faucet,", "flat,", "flowing,",
"fork,", "freezer,", "glass,", "grass,", "guess,", "humble,",
"icebox,", "industry,", "invisible,", "jug,", "lighting,",
"lion,", "listen,", "little,", "machine,", "metal,", "month,",
"mushroom,", "napkin,", "news,", "noisy,", "north,", "nudge,",
"number,", "numerous,", "obey,", "odd,", "oval,", "plant,",
"possible,", "pot,", "public,", "puzzled,", "quarter,", "rational,",
"ready,", "reflect,", "reliable,", "repentant,", "sand,",
"school,", "secret,", "series,", "shark,", "shoe,", "shop,",
"shortened,", "skyline,", "stable,", "storm,", "stove,",
"table,", "theory,", "tower,", "truck,", "upgrade,", "upright,",
"utensil,", "vest,", "vision,", "volcano,", "walk,", "watchful,",
"window,", "winter,"), class = "factor"), V10 = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "NA,", class = "factor"),
V11 = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "NA,",
class = "factor"),
V12 = structure(c(2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L), .Label =
c("203,",
"205,"), class = "factor"), V13 = structure(c(1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "1,", class = "factor"),
V14 = c(4063L, 4914L, 1508L, 1819L, 1228L, 992L, 1898L, 1174L,
1294L, 1417L)), row.names = c(NA, 10L), class = "data.frame”)
When I use the following:
all.files <- list.files(".")
txt.files <- grep("threat.txt",all.files,value=T)
for(i in txt.files) {
d<-read.table(i, header=FALSE)
d[] <- lapply(d, function(x) {is.na(x) <- x == 0; x})
write.table(d,paste0(i, "trial.txt"), quote=FALSE, row.names=FALSE)}
I get this (an example of one of the output files with zeros in V13):
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14
3.17903E+11, threat, 1, 1, 2, 2, 1, useless, flowing, NA, NA, 203, 1, 949
3.17903E+11, threat, 3, 2, 2, 1, 1, hostage, skyline, NA, NA, 203, 1, 1116
3.17903E+11, threat, 4, 1, 1, 1, 2, messy, ready, NA, NA, 205, 1, 1277
3.17903E+11, threat, 6, 2, 1, 2, 2, emaciated, shortened, NA, NA, 205, 1, 691
3.17903E+11, threat, 7, 1, 1, 1, 1, abuse, plant, NA, NA, 203, 1, 660
3.17903E+11, threat, 8, 2, 1, 2, 2, tormented, easygoing, NA, NA, 205, 1, 812
3.17903E+11, threat, 9, 1, 2, 2, 2, hurt, sand, NA, NA, 205, 1, 917
3.17903E+11, threat, 10, 1, 1, 1, 1, surgery, freezer, NA, NA, 203, 1, 1829
3.17903E+11, threat, 12, 2, 2, 1, 2, accident, category, NA, NA, 205, 1, 821
3.17903E+11, threat, 13, 2, 1, 2, 2, terrible, energetic, NA, NA, 205, 1, 783
3.17903E+11, threat, 14, 1, 2, 2, 1, wound, storm, NA, NA, 203, 1, 813
3.17903E+11, threat, 15, 1, 1, 1, 2, victim, utensil, NA, NA, 205, 1, 1132
3.17903E+11, threat, 16, 2, 2, 1, 2, bankrupt, lighting, NA, NA, 203, 0, 1510
3.17903E+11, threat, 17, 1, 1, 1, 2, anguish, country, NA, NA, 203, 0, 811
3.17903E+11, threat, 18, 2, 2, 1, 1, snake, table, NA, NA, 203, 1, 805
3.17903E+11, threat, 19, 1, 1, 1, 2, slap, crop, NA, NA, 205, 1, 1180
3.17903E+11, threat, 20, 2, 1, 2, 2, scum, shoe, NA, NA, 205, 1, 792
3.17903E+11, threat, 21, 1, 2, 2, 1, weep, shop, NA, NA, 203, 1, 870
3.17903E+11, threat, 23, 2, 1, 2, 1, spider, border, NA, NA, 203, 1, 871
str(d) gives me the following:
'data.frame': 96 obs. of 14 variables:
$ V1 : Factor w/ 1 level "9.9761E+11,": 1 1 1 1 1 1 1 1 1 1 ...
$ V2 : Factor w/ 1 level "threat,": 1 1 1 1 1 1 1 1 1 1 ...
$ V3 : Factor w/ 96 levels "1,","10,","100,",..: 1 28 37 48 55 63 73 88 2 20
...
$ V4 : Factor w/ 2 levels "1,","2,": 1 2 1 2 2 2 2 2 1 1 ...
$ V5 : Factor w/ 2 levels "1,","2,": 2 2 2 1 2 1 1 2 2 2 ...
$ V6 : Factor w/ 2 levels "1,","2,": 2 1 2 2 1 2 2 1 2 2 ...
$ V7 : Factor w/ 2 levels "1,","2,": 2 1 2 2 2 2 1 2 1 2 ...
$ V8 : Factor w/ 95 levels "abduction,","abortion,",..: 41 92 63 36 2 81 12 14
23 33 ...
$ V9 : Factor w/ 96 levels "alley,","ankle,",..: 24 90 73 10 92 33 84 96 70 57
...
$ V10: Factor w/ 1 level "NA,": 1 1 1 1 1 1 1 1 1 1 ...
$ V11: Factor w/ 1 level "NA,": 1 1 1 1 1 1 1 1 1 1 ...
$ V12: Factor w/ 2 levels "203,","205,": 2 1 2 2 2 2 1 2 1 2 ...
$ V13: Factor w/ 1 level "1,": 1 1 1 1 1 1 1 1 1 1 ...
$ V14: int 4063 4914 1508 1819 1228 992 1898 1174 1294 1417 …
When I use this:
for(i in txt.files) {
d<-read.table(i, header=FALSE)
d2<-d[d$V13==1,]
write.table(d2,sub("[.]",".trial.",i),quote=FALSE,row.names=FALSE)
}
I get empty files:
str(d2)
'data.frame': 0 obs. of 14 variables:
$ V1 : Factor w/ 1 level "9.9761E+11,":
$ V2 : Factor w/ 1 level "threat,":
$ V3 : Factor w/ 96 levels "1,","10,","100,",..:
$ V4 : Factor w/ 2 levels "1,","2,":
$ V5 : Factor w/ 2 levels "1,","2,":
$ V6 : Factor w/ 2 levels "1,","2,":
$ V7 : Factor w/ 2 levels "1,","2,":
$ V8 : Factor w/ 95 levels "abduction,","abortion,",..:
$ V9 : Factor w/ 96 levels "alley,","ankle,",..:
$ V10: Factor w/ 1 level "NA,":
$ V11: Factor w/ 1 level "NA,":
$ V12: Factor w/ 2 levels "203,","205,":
$ V13: Factor w/ 1 level "1,":
$ V14: int
When I use as.integer to change V13 to an integer, the output of this column is
replaced by 1s and 2s..
> On Apr 21, 2020, at 1:14 AM, Rui Barradas <ruipbarra...@sapo.pt> wrote:
>
> Hello,
>
> Thanks for the data. But since the replacements still do not work, please
> post the output of
>
> dput(head(d, 10))
>
>
> in order for us to have an *exact* copy of the data structure.
> I had asked for 20 or 30 rows but given your post 10 are enough.
> With a way to exactly reproduce what you have, it will be much easier to try
> code and find a solution. I, and I believe most R users, will run
>
> str(d)
>
> as one of the first steps to know what is in that problem column. And go from
> there.
>
>
> Hope this helps,
>
> Rui Barradas
>
> Às 04:52 de 21/04/20, Helen Sawaya escreveu:
>> 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.
______________________________________________
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.
