Read csv file with hidden or invisible character ^M

Question

I am attempting unsuccessfully to read a *.csv file containing hidden or invisible characters. The file contents are shown here:

my.data2 <- read.table(text          


        

Answer 1

Here's a solution using scan to read the data, matrix to structure it, and data.frame to make it into a data frame:

readF <- function(path, nfields=4){    
    m = matrix(
          gsub(",","",scan(path,what=rep("",nfields))),
              ncol=nfields,byrow=TRUE)
    d = data.frame(m[-1,])
    names(d)=m[1,]
    d
}

So first check the file duplicates your problem :

> read.csv("./invisible.delimiter2.csv")
            Common.name    Scientific.name Stuff1 Stuff2
1         Greylag.Goose        Anser.anser              
2                   AAC                 rr              
3            Snow.Goose                                 
4    Anser.caerulescens                                 
5                   AAC                 rr              
6  Greater.Canada.Goose  Branta.canadensis    AAC     rr
7        Barnacle.Goose   Branta.leucopsis              
8                   AAC                 rr              
9           Brent.Goose    Branta.bernicla              
10                  AAC                 rr        

and then see if my function solves it:

> readF("./invisible.delimiter2.csv")
Read 24 items
           Common.name    Scientific.name Stuff1 Stuff2
1        Greylag.Goose        Anser.anser    AAC     rr
2           Snow.Goose Anser.caerulescens    AAC     rr
3 Greater.Canada.Goose  Branta.canadensis    AAC     rr
4       Barnacle.Goose   Branta.leucopsis    AAC     rr
5          Brent.Goose    Branta.bernicla    AAC     rr

Feel free to pick the function apart to see how it works.

I suspect the source of the problem is that the ^M is in the field data, and because you're fields aren't quoted then R can't tell if its a real line end or one in a field. There's some notes about embedded newlines in quoted fields in the documentation for read.csv etc.