I find this error message when I'm using xml in r

Question

Hi I'm working with xml in Rstudio. The objective is to convert a xml to an r data frame and I'm trying on the sample data called tides.xml in the package folder.

tides = system.file("exampleData", "tides.xml", package = "XML")

Maybe we can see the items in the first few columns are constant:

Something like this

                       origin
                   NOAA/NOS/CO-OPS
                   NOAA/NOS/CO-OPS
                   NOAA/NOS/CO-OPS
                   NOAA/NOS/CO-OPS
                   NOAA/NOS/CO-OPS
                   NOAA/NOS/CO-OPS
                   NOAA/NOS/CO-OPS

Therefore when I use

xmlToDataFrame(xmlRoot(tides.str))

it returns error:

Error in `[<-.data.frame`(`*tmp*`, i, names(nodes[[i]]), value = c("2010/11/13Sat06:08    AM4.74H",  : 
duplicate subscripts for columns

I know I can do something like this:

xmlToDataFrame(nodes = xmlChildren(xmlRoot(tides.str)[["data"]]))

to produce a data frame but it is just a subset and I need to manually insert the first few columns.

So I am thinking is there anything I can do to remove the error by just changing some of the arguments in xmlToDataFrame() function and using the whole xml data?

Thanks in advance.

Answer 1

I'm not sure if it's possible with xmlToDataFrame. But you can extract all the non-data nodes and turn it into a data.frame yourself without too much trouble.

library(XML)
tides = system.file("exampleData","tides.xml", package="XML")

tides.str<-xmlParse(tides)
detaildf<-xmlToDataFrame(nodes = getNodeSet(tides.str, "/datainfo/data/item"))

header <- getNodeSet(tides.str, "/datainfo/*[not(self::data)]")
headerdf <- as.data.frame(as.list(setNames(xmlSApply(header, xmlValue), 
    xmlSApply(header, xmlName))))

merge(headerdf, detaildf)

And then at the end we just "merge" the two parts to repeat the header for each line in the detail.