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ReturnOfTheMinivan

Data for response to Donoghue & Edward's response to Beaulieu and O'Meara. We have more cupholders, and they come filled with data! [and cheerios]

data/AJB_recs1to500.txt and data/AJB_recs501to1000.txt have the info on the most recent 1000 articles in AJB (downloaded on Dec. 17 from Web of Knowledge). part of 2013 to Nov 2018.

  • 877 are articles
  • 90 are editorials
  • 14 are reviews
  • 9 are corrections
  • 6 are letters
  • 4 are news

Top authors: Soltis DE (15), Soltis PS (15), Ashman TL (10), Pires JC (9), Rothwell GW (9), Smith SA (8), Escudero M (8), Rudall PJ (7), Temescu AMF (7)

DI field has DOI

library(bibliometrix)
library(fulltext)


#setwd("/Users/bomeara/Documents/MyDocuments/GitClones/ReturnOfTheMinivan/data")

files <- list.files(pattern=".txt")
all.files <- data.frame()
for (i in seq_along(files)) {
  local.files <- bibliometrix::readFiles(files[i])
  local.files <- bibliometrix::convert2df(local.files, dbsource = "isi", format = "plaintext")
  if(i==1) {
    all.files <- local.files
  } else {
    all.files <- plyr::rbind.fill(all.files, local.files)
  }
}


fulltext::cache_options_set(path="../../../../../Users/bomeara/Documents/MyDocuments/GitClones/ReturnOfTheMinivan/data/pdfcache")
#fulltext::ft_get("10.1002/ajb2.1180") # gets the PDF
text <- fulltext::ft_extract(ft_get(all.files[1,"DI"]))$wiley$data # is all the text

You can edit this to get rid of the references field, then pass to rphylotastic to get names

To run

This uses drake to run the analyses. The necessary functions, packages, etc are described in scripts in the R directory. To rerun the analysis, just source("make.R") within R (or, better so it can run unattended: nohup R CMD BATCH make.R > nohup.out &).

Make sure you have all the relevant packages (from R/packages.R). For rphylotastic, remotes::install_github("phylotastic/rphylotastic").