Extracting Body of Text from Research Articles; Several Attempted Methods - r

Question

I need to extract the body of texts from my corpus for text mining as my code now includes references, which bias my results. All coding is performed in R using RStudio. I have tried many techniques.
I have text mining code (of which only the first bit is included below), but recently found out that simply text mining a corpus of research articles is insufficient as the reference section will bias results; reference sections alone may provide another analysis, which would be a bonus.
EDIT: perhaps there is an R package that I am not aware of
My initial response was to clean the text formats after converting from pdf to text using Regex commands within quanteda. As a reference I was intending to follow: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005962&rev=1 . Their method confuses me not just in coding a parallel regex code, but in how to implement recognizing the last reference section to avoid cutting off portions of the text when "reference" appears prior to that section; I have been in contact with their team, but am waiting to learn more about their code since it appears they use a streamlined program now.
PubChunks and LAPDF-text were my next two options the latter of which is referenced in the paper above. In order to utilize the PubChunks package I need to convert all of my pdf (now converted to text) files into XML. This should be straightforward only the packages I found (fileToPDF, pdf2xml, trickypdf) did not appear to work; this seems to be a within-R concern. (Coding relating to trickypdf is included below).
For LAPDF-text, ...[see edit]... the code did not seem to run properly. There are also very limited resources out there for this package in terms of guides etc and they have shifted their focus to a larger package using different language that does happen to include LAPDF-text.
EDIT: I installed java 1.6 (SE 6) and Maven 2.0 then ran the LAPDF-text installer, which seemed to work. That being said, I am still having issues with this process and mvn commands recognizing folders though am continuing to work through it.
I am guessing there is someone else out there, as there are related research papers with similarly vague processes, who has done this before and has also got their hands dirty. Any recommendations is greatly appreciated.
Cheers
library(quanteda)
library(pdftools)
library(tm)
library(methods)
library(stringi) # regex pattern
library(stringr) # simpler than stringi ; uses stringi on backend
setwd('C:\\Users\\Hunter S. Baggen\\Desktop\\ZS_TestSet_04_05')
files <- list.files(pattern = 'pdf$')
summary(files)
files
# Length 63
corpus_tm <- Corpus(URISource(files),
readerControl = list(reader = readPDF()))
corpus_tm
# documents 63
inspect(corpus_tm)
meta(corpus_tm[[1]])
# convert tm::Corpus to quanteda::corpus
corpus_q <- corpus(corpus_tm)
summary(corpus_q, n = 2)
# Add Doc-level Variables here *by folder and meta-variable year
corpus_q
head(docvars(corpus_q))
metacorpus(corpus_q)
#_________
# extract segments ~ later to remove segments
# corpus_segment(x, pattern, valuetype, extract_pattern = TRUE)
corpus_q_refA <- corpus_reshape(corpus_q, to = "paragraphs", showmeta = TRUE)
corpus_q_refA
# Based upon Westergaard et al (15 Million texts; removing references)
corpus_q_refB <- corpus_trim(corpus_q, what = c('sentences'), exclude_pattern = '^\[\d+\]\s[A-Za-z]')
corpus_q_refB # ERROR with regex above
corpus_tm[1]
sum(str_detect(corpus_q, '^Referen'))
corpus_qB <- corpus_q
RemoveRef_B <- corpus_segment(corpus_q, pattern = 'Reference', valuetype = 'regex')
cbind(texts(RemoveRef_B), docvars(corpus_qB))
# -------------------------
# Idea taken from guide (must reference guide)
setGeneric('removeCitations', function(object, ...) standardGeneric('removeCitations'))
'removCitations'
setMethod('removeCitations', signature(object = 'PlainTextDocument'),
function(object, ...) {
c <- Content(object)
# remove citations tarting with '>'
# EG for > : citations <- grep('^[[:blank:]]*>.*', c) if (length(citations) > 0) c <- c[-citations]
# EG for -- : signatureStart <- grep('^-- $', c) if (length(signatureStart) > 0) c <- c[-(signatureStart:length(c))]
# using 15 mil removal guideline
citations <- grep('^\[\d+\]\s[A-Za-z]')
}
# TRICKY PDF download from github
library(pubchunks)
library(polmineR)
library(githubinstall)
library(devtools)
library(tm)
githubinstall('trickypdf') # input Y then 1 if want all related packages
# library(trickypdf)
# This time suggested I install via 'PolMine/trickypdf'
# Second attempt issue with RPoppler
install_github('PolMine/trickypdf')
library(trickypdf) # Not working
# Failed to install package 'Rpoppler' is not available for R 3.6.0
Short of the RPoppler issue above the initial description should be sufficient.
UPDATE: Having reached out to several research groups the TALN-UPF researchers got back to me and provided me with a pdfx java program that has allowed me to convert my pdfs easily into xml. Of course, now I learn that PubChunks is created with its sister program that extracts xmls from search engines and therefore is of little use to me. That being said, the TALN-UPF group will hopefully advise whether I can extract the body of each text via their other programs (Dr Inventor and Grobid). If this is possible then everything will be accomplished. Of course if not I will be back at RegEx.