In federicomarini/plateletopedia: What the Package Does (One Line, Title Case)

Compiled date: r Sys.Date()

Last edited: 2021-07-14

License: r packageDescription("plateletopedia")[["License"]]

knitr::opts_chunk$set(
  collapse = TRUE,
  comment  = "#>",
  error    = FALSE,
  warning  = FALSE,
  eval     = FALSE,
  message  = FALSE,
  fig.width = 10
)
options(width = 100)
stopifnot(requireNamespace("htmltools"))
htmltools::tagList(rmarkdown::html_dependency_font_awesome())

---

The datasets {#datasets}

Accessing the Google Sheet where all the information is stored

library("googlesheets4")
options(gargle_oauth_email = "[e-mail]")
googlesheets4::gs4_auth()
# sheets_auth(token = drive_token())

# googlesheets4::sheets_find()

googlesheets4::gs4_get("18t3gpFH4gBGWeSlOfoYLHPXCu_t2xFaoUxJFbp0WZRY")

pltdatasets <- googlesheets4::range_read("18t3gpFH4gBGWeSlOfoYLHPXCu_t2xFaoUxJFbp0WZRY", 
                          sheet = "Sheet1")

pltdatasets$n_samples_pub <- as.character(pltdatasets$n_samples_pub)

DT::datatable(pltdatasets)

save(pltdatasets, file = "data/pltdatasets.RData")
readr::write_tsv(pltdatasets, file = "data/pltdatasets.tsv")

# # access the googledocs sheet
# # install.packages("googlesheets")
# library("googlesheets")
# gs_auth(new_user = TRUE)
# 
# library(dplyr)
# gs_ls() %>% View

# plt_sets <- gs_read(gs_title("Platelets_datasets_collection"))

# open up the different Pubmed IDs, to retrieve the doi
## not required after the first time :)

# once the doi is there, use rcrossref to get the full textual citation
# devtools::install_github("ropensci/rcrossref")
library("rcrossref")
View(pltdatasets)
## see here some documentation: https://github.com/ropensci/rcrossref
# cr_cn(dois = plt_sets$doi[31], format = "text", style = "apa")
# cr_cn(dois = pltdatasets$doi[36], format = "text", style = "apa")
# View(get_styles()) # and there search for something with 'no-et-al' to list all authors
# cr_cn(dois = plt_sets$DOI[36], format = "text", style = "american-medical-association-no-et-al")
all_crossref_infos <- cr_cn(dois = pltdatasets$doi, format = "text", style = "american-medical-association-no-et-al")

# store this info in a multi-line text document - even better if the exported file is in markdown, it is directly previewable
all_crossref_infos %>% unlist() %>% writeLines()

# writeLines(paste0("pubstatus_",Sys.Date(),"_exported.md"))

# this one gives some bibtex
cat(cr_cn(dois = pltdatasets$doi[36], format = "bibtex"))

cr_abstract(pltdatasets$doi[3])
# does not work...

federicomarini/plateletopedia documentation built on Dec. 20, 2021, 7:49 a.m.