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Editorial Team
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Asked: 2026-06-04T08:55:27+00:00

There are good answers on SO about how to use readHTMLTable from the XML

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There are good answers on SO about how to use readHTMLTable from the XML package and I did that with regular http pages, however I am not able to solve my problem with https pages.

I am trying to read table on this website (url string):

library(RTidyHTML)
library(XML)
url <- "https://ned.nih.gov/search/ViewDetails.aspx?NIHID=0010121048"
h = htmlParse(url)
tables <- readHTMLTable(url)

But I get this error: File https://ned.nih.gov/search/Vi…does not exist.

I tried to get past the https problem with this (first 2 lines below)(from using google to find solution (like here:http://tonybreyal.wordpress.com/2012/01/13/r-a-quick-scrape-of-top-grossing-films-from-boxofficemojo-com/).

This trick helps to see more of the page, but any attempts to extract the table are not working. Any advice appreciated. I need the table fields like Organization, Organizational Title, Manager.

 #attempt to get past the https problem 
 raw <- getURL(url, followlocation = TRUE, cainfo = system.file("CurlSSL", "cacert.pem", package = "RCurl"))
 head(raw)
[1] "\r\n<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">\n<html xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\" lang=\"en\">\n<head>\n<meta http-equiv=\"Content-Type\" content=\"text/html; 
...
 h = htmlParse(raw)
Error in htmlParse(raw) : File ...
tables <- readHTMLTable(raw)
Error in htmlParse(doc) : File ...
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1 Answer

  1. Editorial Team

    The new package httr provides a wrapper around RCurl to make it easier to scrape all kinds of pages.

    Still, this page gave me a fair amount of trouble. The following works, but no doubt there are easier ways of doing it.

    library("httr")
library("XML")

# Define certicificate file
cafile <- system.file("CurlSSL", "cacert.pem", package = "RCurl")

# Read page
page <- GET(
  "https://ned.nih.gov/", 
  path="search/ViewDetails.aspx", 
  query="NIHID=0010121048",
  config(cainfo = cafile)
)

# Use regex to extract the desired table
x <- text_content(page)
tab <- sub('.*(<table class="grid".*?>.*</table>).*', '\\1', x)

# Parse the table
readHTMLTable(tab)

    The results:

    $ctl00_ContentPlaceHolder_dvPerson
                V1                                      V2
1      Legal Name:                    Dr Francis S Collins
2  Preferred Name:                      Dr Francis Collins
3          E-mail:                 francis.collins@nih.gov
4        Location: BG 1 RM 1261 CENTER DRBETHESDA MD 20814
5       Mail Stop:                                       Â
6           Phone:                            301-496-2433
7             Fax:                                       Â
8              IC:             OD (Office of the Director)
9    Organization:            Office of the Director (HNA)
10 Classification:                                Employee
11            TTY:                                       Â

    Get httr here: http://cran.r-project.org/web/packages/httr/index.html

    EDIT: Useful page with FAQ about the RCurl package: http://www.omegahat.org/RCurl/FAQ.html

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