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readHTMLTable seems pretty robust, but when I try to use it on this page, I get an error.

Any ideas what it means or how I could get around it? The page's biggest table is nested inside another table... is that a problem? 

> tables<-readHTMLTable(myURL, header=NA,a.data.frame=TRUE)
Error in htmlParse(doc) : 
  error in creating parser for http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi
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    $\begingroup$ Move to StackOverflow? $\endgroup$
    – kmm
    Feb 10, 2011 at 16:23
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    $\begingroup$ I think it is Ok to answer this question here. We do have a R tag. $\endgroup$
    – suncoolsu
    Feb 10, 2011 at 16:58

1 Answer 1

Reset to default
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The table in question seems to need use of a Javascript button to download. If you just want this particular data then save it as the offered untitle.txt or something else (it is basically tab-delimited) and then 

tables           <- read.delim("untitle.txt", skip=1)
colnames(tables) <- c(colnames(tables)[-1],"junk")
tables$junk      <- NULL

seems to give you what I believe you want. The second and third lines of the R code are to deal with "## Columns:" which starts the second line of the file and upsets read.delim() when trying to get the column names.

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  • $\begingroup$ wow thanks - that was it - i hadn't even considered the possibility :) $\endgroup$
    – shigeta
    Feb 12, 2011 at 4:23

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