# Getting ecology and evolution journal titles from R

August 31, 2012
By

(This article was first published on Recology - R, and kindly contributed to R-bloggers)

So I want to mine some #altmetrics data for some research I'm thinking about doing. The steps would be:

• Get journal titles for ecology and evolution journals.
• Get DOI's for all papers in all the above journal titles.
• Get altmetrics data on each DOI.
• Do some fancy analyses.
• Make som pretty figs.
• Write up results.

It's early days, so jus working on the first step. However, getting a list of journals in ecology and evolution is frustratingly hard. This turns out to not be that easy if you are (1) trying to avoid Thomson Reuters, and (2) want a machine interface way to do it (read: API).

Unfortunately, Mendeley's API does not have methods for getting a list of journals by field, or at least I don't know how to do it using their API. No worries though - Crossref comes to save the day. Here's my attempt at this using the Crossref OAI-PMH.

### I wrote a little while loop to get journal titles from the Crossref OAI-PMH. This takes a while to run, but at least it works on my machine - hopefully yours too!

library(XML)
library(RCurl)

token <- "characters"  # define a iterator, also used for gettingn the resumptionToken
nameslist <- list()  # define empty list to put joural titles in to
while (is.character(token) == TRUE) {
baseurl <- "http://oai.crossref.org/OAIHandler?verb=ListSets"
if (token == "characters") {
tok2 <- NULL
} else {
tok2 <- paste("&resumptionToken=", token, sep = "")
}
query <- paste(baseurl, tok2, sep = "")
crsets <- xmlToList(xmlParse(getURL(query)))
names <- as.character(sapply(crsets[[4]], function(x) x[["setName"]]))
nameslist[[token]] <- names
if (class(try(crsets[[2]]$.attrs[["resumptionToken"]])) == "try-error") { stop("no more data") } else token <- crsets[[2]]$.attrs[["resumptionToken"]]
}


### Yay! Hopefully it worked if you tried it. Let's see how long the list of journal titles is.

sapply(nameslist, length)  # length of each list

                          characters c65ebc3f-b540-4672-9c00-f3135bf849e3
10001                                10001
6f61b343-a8f4-48f1-8297-c6f6909ca7f7
6864

allnames <- do.call(c, nameslist)  # combine to list
length(allnames)

[1] 26866


### Now, let's use some regex to pull out the journal titles that are likely ecology and evolutionary biology journals. The ^ symbol says "the string must start here". The \\s means whitespace. The [] lets you specify a set of letters you are looking for, e.g., [Ee] means capital EOR lowercase e. I threw in titles that had the words systematic and natrualist too. Tried to trim any whitespace as well using the stringr package.

library(stringr)

ecotitles <- as.character(allnames[str_detect(allnames, "^[Ee]cology|\\s[Ee]cology")])
evotitles <- as.character(allnames[str_detect(allnames, "^[Ee]volution|\\s[Ee]volution")])
systtitles <- as.character(allnames[str_detect(allnames, "^[Ss]ystematic|\\s[Ss]systematic")])
naturalist <- as.character(allnames[str_detect(allnames, "[Nn]aturalist")])

ecoevotitles <- unique(c(ecotitles, evotitles, systtitles, naturalist))  # combine to list
ecoevotitles <- str_trim(ecoevotitles, side = "both")  # trim whitespace, if any
length(ecoevotitles)

[1] 188

# Just the first ten titles
ecoevotitles[1:10]

 [1] "Microbial Ecology in Health and Disease"
[2] "Population Ecology"
[3] "Researches on Population Ecology"
[4] "Behavioral Ecology and Sociobiology"
[5] "Microbial Ecology"
[6] "Biochemical Systematics and Ecology"
[7] "FEMS Microbiology Ecology"
[8] "Journal of Experimental Marine Biology and Ecology"
[9] "Applied Soil Ecology"
[10] "Forest Ecology and Management"