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NA command in a 'for' loop

17 messages · Michael Dewey, Rui Barradas, Bert Gunter +4 more

Helen Sawaya
# 
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
Rui Barradas
# 
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



?s 20:52 de 19/04/20, Helen Sawaya escreveu:
Helen Sawaya
# 
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)..
Michael Dewey
# 
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:

  
    
  


  


      

    

    

      
      

        


  

        

      Helen Sawaya
    

    

      
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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.

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Rui Barradas
    

    

      
      #
    

  


  

      
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

?s 17:48 de 20/04/20, Helen Sawaya escreveu:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Jim Lemon
    

    

      
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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 <ruipbarradas at sapo.pt> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Helen Sawaya
    

    

      
      #
    

  


  

      
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

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Jim Lemon
    

    

      
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Hi Helen,
I can follow you this far:

# just read in the data from your example
d<-read.csv(text="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",
header=FALSE,stringsAsFactors=FALSE)
# get rows of d you want
d2<-d[d$V13==1,]
d2
congruent<-(d2$V4 == 1)
congruent

and things are as I expect even though I have shortened the code somewhat.
I'm not familiar with the "get_tlbs" function which I can find on GitHub
but not on CRAN, so if this:

x<-get_tlbs(d2$V14,congruent,prior_weights=NULL,method="weighted",
 fill_gaps = FALSE)

gives you the "x" that you want, I think we're close.

Jim

On Tue, Apr 21, 2020 at 1:53 PM Helen Sawaya <helensawaya at hotmail.com>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Bert Gunter
    

    

      
      #
    

  


  

      
Please follow Rui's advice and use dput to provide a small
reproducible example. You ask folks here to to help but won't make the
effort to enable them to do so, at least not without wasting a lot of
time trying to guess what's going on. And post in plain text, not
HTML. That is just common courtesy to follow the conventions of the
list.

Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

        
On Mon, Apr 20, 2020 at 8:53 PM Helen Sawaya <helensawaya at hotmail.com> wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Rui Barradas
    

    

      
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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

?s 04:52 de 21/04/20, Helen Sawaya escreveu:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Helen Sawaya
    

    

      
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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..

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      William Dunlap
    

    

      
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Read the files with read.csv(filename) or read.table(sep=",", filename) so
the commas don't become part of the R data.frame.

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Tue, Apr 21, 2020 at 10:17 AM Helen Sawaya <helensawaya at hotmail.com>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Rui Barradas
    

    

      
      #
    

  


  

      
Hello,

Much better, you have "," at the end of your data elements so nothing is 
working.

The following 3 instructions

1. remove those commas,
2. create a logical vector trying to guess which columns are numeric
3. coerce those columns to numeric.


d[] <- lapply(d, function(x){sub(",$", "", x)})
not_num <- sapply(d, function(x) all(is.na(as.numeric(as.character(x)))))
d[!not_num] <- lapply(d[!not_num], function(x) as.numeric(as.character(x)))



Then, if you want just d$V13 == 0 to become NA, this will do it.


is.na(d[["V13"]]) <- d[["V13"]] == 0


If you want to do this to all numeric columns, try


d[!not_num] <- lapply(d[!not_num], function(x){
   is.na(x) <- x == 0
   x
})


Hope this helps,

Rui Barradas


?s 18:11 de 21/04/20, Helen Sawaya escreveu:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Jim Lemon
    

    

      
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Hi Helen,

            

      
      
      
    

        
operations you are performing are giving you the results you want. If so,
then we can tackle the multiple input files. As I don't have the library
you are using, I cannot access the function "get_tbls", so please replace:

# load whatever library you are using here
with
library(xxxx)
where xxxx is the name of the library

Then run the following script and tell us if you get your expected output

d<-read.table(
text="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",
header=FALSE,sep=",",stringsAsFactors=FALSE)
# look at at d, is it what you expect?
d
# let d2 be the rows of d where V13 is non-zero
d2<-d[d$V13!=0,]
# look at at d2, is it what you expect?
d2
congruent <-(d2$V4 == 1)
# look at at congruent, is it what you expect?
congruent
# load whatever library you are using here
x<-get_tlbs(d2$V14,congruent,prior_weights=NULL,method="weighted",
 fill_gaps = FALSE)
# look at at x, is it what you expect?
x
write.table(x,file="test_output.txt",quote=FALSE,row.names=FALSE)}
# open "test_output.txt" in a text editor. Is it what you want?

Jim

On Wed, Apr 22, 2020 at 3:11 AM Helen Sawaya <helensawaya at hotmail.com>
wrote:

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Helen Sawaya
    

    

      
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Thank you all. Your suggestions worked. As you said, the problem appeared to have been the commas that were part of the data frame.

Thanks again ?

        

      
      
    

  
  


  


      

    

    
1 day later

    

      
      

        


  

        

      Richard O'Keefe
    

    

      
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You now say that you "want to get rid of" the rows
where V13 is 0.
  d1 <- d[d$V13 != 0,]
returns you a new data frame d1 containing all the
rows of d where V13 is not 0.

        
On Tue, 21 Apr 2020 at 15:53, Helen Sawaya <helensawaya at hotmail.com> wrote: