How to specify end of header line with read.table - r

Question

I have ASCII files with data separated by $ signs.
There are 23 columns in the data, the first row is of column names, but there is inconsistency between the line endings, which causes R to import the data improperly, by shift the data left-wise with respect to their columns.
Header line:
ISR$CASE$I_F_COD$FOLL_SEQ$IMAGE$EVENT_DT$MFR_DT$FDA_DT$REPT_COD$MFR_NUM$MFR_SNDR$AGE$AGE_COD$GNDR_COD$E_SUB$WT$WT_COD$REPT_DT$OCCP_COD$DEATH_DT$TO_MFR$CONFID$REPORTER_COUNTRY
which does not end with a $ sign.
First row line:
7215577$8135839$I$$7215577-0$20101011$$20110104$DIR$$$67$YR$F$N$220$LBS$20110102$CN$$N$Y$UNITED STATES$
Which does end with a $ sign.
My import command:
read.table(filename, header=TRUE, sep="$", comment.char="", header=TRUE, quote="")
My guess is that the inconsistency between the line endings causes R to think that the records have one column more than the header, thus making the first column as a row.names column, which is not correct. Adding the specification row.names=NULL does not fix the issue.
If I manually add a $ sign in the file the problem is solved, but this is infeasible as the issue occurs in hundreds of files. Is there a way to specify how to read the header line? Do I have any alternative?
Additional info: the headers change across different files, so I cannot set my own vector of column names

Answer 1

Create a dummy test file:
cat("ISR$CASE$I_F_COD$FOLL_SEQ$IMAGE$EVENT_DT$MFR_DT$FDA_DT$REPT_COD$MFR_NUM$MFR_SNDR$AGE$AGE_COD$GNDR_COD$E_SUB$WT$WT_COD$REPT_DT$OCCP_COD$DEATH_DT$TO_MFR$CONFID$REPORTER_COUNTRY\n7215577$8135839$I$$7215577-0$20101011$$20110104$DIR$$$67$YR$F$N$220$LBS$20110102$CN$$N$Y$UNITED STATES$",
file="deleteme.txt",
"\n")
Solution using gsub:
First read the file as text and then edit its content:
file_path <- "deleteme.txt"
fh <- file(file_path)
file_content <- readLines(fh)
close(fh)
Either add a $ at the end of header row:
file_content[1] <- paste0(file_content, "$")
Or remove $ from the end of all rows:
file_content <- gsub("\\$$", "", file_content)
Then we write the fixed file back to disk:
cat(paste0(file_content, collapse="\n"), file=paste0("fixed_", file_path), "\n")
Now we can read the file:
df <- read.table(paste0("fixed_", file_path), header=TRUE, sep="$", comment.char="", quote="", stringsAsFactors=FALSE)
And get the desired structure:
str(df)
'data.frame': 1 obs. of 23 variables:
$ ISR : int 7215577
$ CASE : int 8135839
$ I_F_COD : chr "I"
$ FOLL_SEQ : logi NA
$ IMAGE : chr "7215577-0"
$ EVENT_DT : int 20101011
$ MFR_DT : logi NA
$ FDA_DT : int 20110104
$ REPT_COD : chr "DIR"
$ MFR_NUM : logi NA
$ MFR_SNDR : logi NA
$ AGE : int 67
$ AGE_COD : chr "YR"
$ GNDR_COD : logi FALSE
$ E_SUB : chr "N"
$ WT : int 220
$ WT_COD : chr "LBS"
$ REPT_DT : int 20110102
$ OCCP_COD : chr "CN"
$ DEATH_DT : logi NA
$ TO_MFR : chr "N"
$ CONFID : chr "Y"
$ REPORTER_COUNTRY: chr "UNITED STATES "