read.csv warning 'EOF within quoted string' prevents complete reading of file
You need to disable quoting.
cit <- read.csv("citations.CSV", quote = "", row.names = NULL, stringsAsFactors = FALSE)str(cit)## 'data.frame': 112543 obs. of 13 variables:## $ row.names : chr "10.2307/675394" "10.2307/30007362" "10.2307/4254931" "10.2307/20537934" ...## $ id : chr "10.2307/675394\t" "10.2307/30007362\t" "10.2307/4254931\t" "10.2307/20537934\t" ...## $ doi : chr "Archaeological Inference and Inductive Confirmation\t" "Sound and Sense in Cath Almaine\t" "Oak Galls Preserved by the Eruption of Mount Vesuvius in A.D. 79_ and Their Probable Use\t" "The Arts Four Thousand Years Ago\t" ...## $ title : chr "Bruce D. Smith\t" "Tomás Ó Cathasaigh\t" "Hiram G. Larew\t" "\t" ...## $ author : chr "American Anthropologist\t" "Ériu\t" "Economic Botany\t" "The Illustrated Magazine of Art\t" ...## $ journaltitle : chr "79\t" "54\t" "41\t" "1\t" ...## $ volume : chr "3\t" "\t" "1\t" "3\t" ...## $ issue : chr "1977-09-01T00:00:00Z\t" "2004-01-01T00:00:00Z\t" "1987-01-01T00:00:00Z\t" "1853-01-01T00:00:00Z\t" ...## $ pubdate : chr "pp. 598-617\t" "pp. 41-47\t" "pp. 33-40\t" "pp. 171-172\t" ...## $ pagerange : chr "American Anthropological Association\tWiley\t" "Royal Irish Academy\t" "New York Botanical Garden Press\tSpringer\t" "\t" ...## $ publisher : chr "fla\t" "fla\t" "fla\t" "fla\t" ...## $ type : logi NA NA NA NA NA NA ...## $ reviewed.work: logi NA NA NA NA NA NA ...I think is because of this kind of lines (check "Thorn" and "Minus")
readLines("citations.CSV")[82][1] "10.2307/3642839,10.2307/3642839\t,\"Thorn\" and \"Minus\" in Hieroglyphic Luvian Orthography\t,H. Craig Melchert\t,Anatolian Studies\t,38\t,\t,1988-01-01T00:00:00Z\t,pp. 29-42\t,British Institute at Ankara\t,fla\t,\t,"
I'm a new-ish R user and thought I'd post this in case it helps anyone else. I was trying to read in data from a text file (separated with commas) that included a few Spanish characters and it took me forever to figure it out.I knew I needed to use UTF-8 encoding, set the header arg to TRUE, and that I need to set the sep arguemnt to ",", but then I still got hang ups. After reading this post I tried setting the fill arg to TRUE, but then got the same "EOF within quoted string" which I was able to fix in the same manner as above. My successful read.table looks like this:
target <- read.table("target2.txt", fill=TRUE, header=TRUE, quote="", sep=",", encoding="UTF-8")
The result has Spanish language characters and same dims I had originally, so I'm calling it a success! Thanks all!
In the R help section, as pointed out above, just disabling quoting altogether, by simply adding:
quote = "" to the read.csv() worked for me.
The error, "EOF within quoted string", occurred with:
> iproscan.53A.neg = read.csv("interproscan.53A.neg.n.csv", + colClasses=c(pb.id = "character", + genLoc = "character", + icode = "character", + length = "character", + proteinDB = "character", + protein.id = "character", + prot.desc = "character", + start = "character", + end = "character", + evalue = "character", + tchar = "character", + date = "character", + ipro.id = "character", + prot.name = "character", + go.cat = "character", + reactome.id= "character"), + as.is=T,header=F) Warning message: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : EOF within quoted string > dim(iproscan.53A.neg) [1] 69383 16And the file read in was missing 6,619 lines. But by disabling quoting
> iproscan.53A.neg = read.csv("interproscan.53A.neg.n.csv", + colClasses=c(pb.id = "character", + genLoc = "character", + icode = "character", + length = "character", + proteinDB = "character", + protein.id = "character", + prot.desc = "character", + start = "character", + end = "character", + evalue = "character", + tchar = "character", + date = "character", + ipro.id = "character", + prot.name = "character", + go.cat = "character", + reactome.id= "character"), + as.is=T,header=F,**quote=""**) > > dim(iproscan.53A.neg) [1] 76002 16Worked without error and all lines were successfully read in.