```
# NOT RUN {
# List publishers included
ft_get_ls()
# }
# NOT RUN {
# If you just have DOIs and don't know the publisher
## PLOS
ft_get('10.1371/journal.pone.0086169')
# Collect all errors from across papers
# similarly can combine from different publishers as well
res <- ft_get(c('10.7554/eLife.03032', '10.7554/eLife.aaaa'), from = "elife")
res$elife$errors
## PeerJ
ft_get('10.7717/peerj.228')
ft_get('10.7717/peerj.228', type = "pdf")
## eLife
### xml
ft_get('10.7554/eLife.03032')
res <- ft_get(c('10.7554/eLife.03032', '10.7554/eLife.32763'),
from = "elife")
res$elife
respdf <- ft_get(c('10.7554/eLife.03032', '10.7554/eLife.32763'),
from = "elife", type = "pdf")
respdf$elife
elife_xml <- ft_get('10.7554/eLife.03032', from = "elife")
library(magrittr)
elife_xml %<>% ft_collect()
elife_xml$elife
### pdf
elife_pdf <- ft_get(c('10.7554/eLife.03032', '10.7554/eLife.32763'),
from = "elife", type = "pdf")
elife_pdf$elife
elife_pdf %<>% ft_collect()
elife_pdf %>% ft_extract()
## some BMC DOIs will work, but some may not, who knows
ft_get(c('10.1186/2049-2618-2-7', '10.1186/2193-1801-3-7'), from = "entrez")
## FrontiersIn
res <- ft_get(c('10.3389/fphar.2014.00109', '10.3389/feart.2015.00009'))
res
res$frontiersin
## Hindawi - via Entrez
res <- ft_get(c('10.1155/2014/292109','10.1155/2014/162024',
'10.1155/2014/249309'))
res
res$hindawi
res$hindawi$data$path
res %>% ft_collect() %>% .$hindawi
## F1000Research - via Entrez
x <- ft_get('10.12688/f1000research.6522.1')
## Two different publishers via Entrez - retains publisher names
res <- ft_get(c('10.1155/2014/292109', '10.12688/f1000research.6522.1'))
res$hindawi
res$f1000research
## Thieme -
### coverage is hit and miss, it's not great
ft_get('10.1055/s-0032-1316462')
## Pensoft
ft_get('10.3897/mycokeys.22.12528')
## Copernicus
out <- ft_get(c('10.5194/angeo-31-2157-2013', '10.5194/bg-12-4577-2015'))
out$copernicus
## arXiv - only pdf, you have to pass in the from parameter
res <- ft_get(x='cond-mat/9309029', from = "arxiv")
res$arxiv
res %>% ft_extract %>% .$arxiv
## bioRxiv - only pdf
res <- ft_get(x='10.1101/012476')
res$biorxiv
## AAAS - only pdf
res <- ft_get(x='10.1126/science.276.5312.548')
res$aaas
# The Royal Society
res <- ft_get("10.1098/rspa.2007.1849")
ft_get(c("10.1098/rspa.2007.1849", "10.1098/rstb.1970.0037",
"10.1098/rsif.2006.0142"))
## Karger Publisher
(x <- ft_get('10.1159/000369331'))
x$karger
## MDPI Publisher
(x <- ft_get('10.3390/nu3010063'))
x$mdpi
ft_get('10.3390/nu7085279')
ft_get(c('10.3390/nu3010063', '10.3390/nu7085279'))
# Scientific Societies
## this is a paywall article, you may not have access or you may
x <- ft_get("10.1094/PHYTO-04-17-0144-R")
x$scientificsocieties
# Informa
x <- ft_get("10.1080/03088839.2014.926032")
ft_get("10.1080/03088839.2013.863435")
## CogentOA - part of Inform/Taylor Francis now
ft_get('10.1080/23311916.2014.938430')
library(rplos)
(dois <- searchplos(q="*:*", fl='id',
fq=list('doc_type:full',"article_type:\"research article\""),
limit=5)$data$id)
ft_get(dois)
ft_get(c('10.7717/peerj.228','10.7717/peerj.234'))
# elife
ft_get('10.7554/eLife.04300', from='elife')
ft_get(c('10.7554/eLife.04300', '10.7554/eLife.03032'), from='elife')
## search for elife papers via Entrez
dois <- ft_search("elife[journal]", from = "entrez")
ft_get(dois)
# Frontiers in Pharmacology (publisher: Frontiers)
doi <- '10.3389/fphar.2014.00109'
ft_get(doi, from="entrez")
# Hindawi Journals
ft_get(c('10.1155/2014/292109','10.1155/2014/162024','10.1155/2014/249309'),
from='entrez')
# Frontiers Publisher - Frontiers in Aging Nueroscience
res <- ft_get("10.3389/fnagi.2014.00130", from='entrez')
res$entrez
# Search entrez, get some DOIs
(res <- ft_search(query='ecology', from='entrez'))
res$entrez$data$doi
ft_get(res$entrez$data$doi[1], from='entrez')
ft_get(res$entrez$data$doi[1:3], from='entrez')
# Search entrez, and pass to ft_get()
(res <- ft_search(query='ecology', from='entrez'))
ft_get(res)
# elsevier, ugh
## set the environment variable Sys.setenv(ELSEVIER_TDM_KEY = "your key")
### an open access article
ft_get(x = "10.1016/j.trac.2016.01.027", from = "elsevier")
### non open access article
#### If you don't have access, by default you get abstract only, and we
##### treat it as an error as we assume you want full text
ft_get(x = "10.1016/j.trac.2016.05.027", from = "elsevier")
#### If you want to retain whatever Elsevier gives you
##### set "retain_non_ft = TRUE"
ft_get(x = "10.1016/j.trac.2016.05.027", from = "elsevier",
elsevieropts = list(retain_non_ft = TRUE))
# sciencedirect
## set the environment variable Sys.setenv(ELSEVIER_TDM_KEY = "your key")
ft_get(x = "10.1016/S0140-6736(13)62329-6", from = "sciencedirect")
# wiley, ugh
## set the environment variable Sys.setenv(WILEY_TDM_KEY = "your key")
ft_get(x = "10.1006/asle.2001.0035", from = "wiley", type = "pdf")
## xml
ft_get(x = "10.1111/evo.13812", from = "wiley")
## highwire fiasco paper
ft_get(x = "10.3732/ajb.1300053", from = "wiley")
ft_get(x = "10.3732/ajb.1300053", from = "wiley", type = "pdf")
# IEEE, ugh
ft_get('10.1109/TCSVT.2012.2221191', type = "pdf")
# AIP Publishing
ft_get('10.1063/1.4967823', try_unknown = TRUE)
# PNAS
ft_get('10.1073/pnas.1708584115', try_unknown = TRUE)
# American Society for Microbiology
ft_get('10.1128/cvi.00178-17')
# American Society of Clinical Oncology
ft_get('10.1200/JCO.18.00454')
# American Institute of Physics
ft_get('10.1063/1.4895527')
# American Chemical Society
ft_get(c('10.1021/la903074z', '10.1021/jp048806z'))
# Royal Society of Chemistry
ft_get('10.1039/c8cc06410e')
# From ft_links output
## Crossref
(res2 <- ft_search(query = 'ecology', from = 'crossref', limit = 3,
crossrefopts = list(filter = list(has_full_text=TRUE, member=98))))
(out <- ft_links(res2))
(ress <- ft_get(x = out, type = "pdf"))
ress$crossref
(x <- ft_links("10.1111/2041-210X.12656", "crossref"))
(y <- ft_get(x))
## Cambridge
x <- ft_get("10.1017/s0922156598230305")
x$cambridge
z <- ft_get("10.1017/jmo.2019.20")
z$cambridge
m <- ft_get("10.1017/S0266467419000270")
m$cambridge
## No publisher plugin provided yet
ft_get('10.1037/10740-005')
### no link available for this DOI
res <- ft_get('10.1037/10740-005', try_unknown = TRUE)
res[[1]]
# Get a progress bar - off by default
library(rplos)
(dois <- searchplos(q="*:*", fl='id',
fq=list('doc_type:full',"article_type:\"research article\""),
limit=5)$data$id)
## when articles not already downloaded you see the progress bar
b <- ft_get(dois, progress = TRUE)
## if articles already downloaded/cached, normally we through messages
## saying so
b <- ft_get(dois, progress = FALSE)
## but if a progress bar is requested, then the messages are suppressed
b <- ft_get(dois, progress = TRUE)
# curl options
ft_get("10.1371/journal.pcbi.1002487", verbose = TRUE)
ft_get('10.3897/mycokeys.22.12528', from = "pensoft", verbose = TRUE)
# }
```

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