/
.Rhistory
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/
.Rhistory
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blogdown:::serve_site()
install.packages("blogdown")
install.packages("blogdown")
install.packages("blogdown")
install.packages("blogdown")
blogdown:::serve_site()
install.packages("xfun")
blogdown:::serve_site()
install.packages("blogdown")
install.packages("blogdown")
blogdown::install_hugo()
blogdown::hugo_version()
install.packages("xfun")
blogdown::hugo_version()
blogdown::install_hugo()
blogdown::serve_site()
blogdown:::serve_site()
library(blogdown)
blogdown::serve_site()
blogdown::build_site(build_rmd = 'newfile')
?blogdown::build_site
blogdown::build_site(build_rmd = T)
blogdown::new_post("passive_mi", ext =".Rmd", tags = c("Multiple imputation", "passive imputation", "missing items", "questionnaire data"))
blogdown::build_site(build_rmd = 'newfile')
blogdown::serve_site()
blogdown::build_site(build_rmd = 'newfile')
?blogdown::build_site
blogdown::serve_site
blogdown::serve_site()
blogdown::stop_server()
blogdown::serve_site()
blogdown::serve_site()
blogdown::build_site(build_rmd = 'newfile')
blogdown::serve_site()
blogdown::build_site(build_rmd = 'newfile')
blogdown::serve_site()
blogdown::stop_server()
blogdown::serve_site()
blogdown::stop_server()
blogdown::serve_site()
blogdown::build_site(build_rmd = 'newfile')
blogdown::build_site(build_rmd = 'content/post')
blogdown::build_site(build_rmd = 'content/post/2022-03-02-passive-mi')
blogdown::build_site(build_rmd = 'content/post/2022-03-02-passive-mi/index.Rmd')
blogdown::serve_site()
blogdown::build_site(build_rmd = 'content/post/2022-03-02-passive-mi')
blogdown::build_site(build_rmd = 'content/post/2022-03-02-passive-mi')
blogdown::build_site(build_rmd = 'content/post/2022-03-02-passive-mi/index.Rmd')
blogdown::build_site(build_rmd = 'content/post/2021-03-24-agreement-poli/index.Rmd')
blogdown::build_site(build_rmd = 'content/post/2022-03-02-passive-mi/index.Rmd')
blogdown::build_site(build_rmd = 'content/post/2021-03-24-agreement-poli/index.Rmd')
blogdown::build_site(build_rmd = 'content/post/2021-03-24-agreement-dich/index.Rmd')
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
# The function: bibtex_2academic
bibtex_2academic <- function(bibfile,
outfold,
abstract = TRUE,
overwrite = FALSE) {
if (!require("pacman")) install.packages("pacman")
pacman::p_load(RefManageR, dplyr, stringr, anytime, tidyr, stringi)
# Import the bibtex file and convert to data.frame
mypubs <- ReadBib(bibfile, check = "warn", .Encoding = "UTF-8") %>%
as.data.frame()
mypubs <- mypubs %>%
mutate(mainref = journal)
mypubs$mainref <- mypubs$mainref %>% replace_na('') #otherwise it appears "NA" in post
mypubs$abstract <- mypubs$abstract %>% replace_na('(Abstract not available)') #otherwise it appears "NA" in post
# mypubs$annotation <- mypubs$annotation %>% replace_na('image_preview = ""') #otherwise
# Customize Zotero extra field (here "annotation") in order to leave there the additional information for the md file
#clean backslashes generated by conversion of underline characters in links (_)
mypubs$annotation<- gsub(
pattern = ('\\\\'),
replacement = '',
x = mypubs$annotation
)
mypubs$abstract<- gsub(
pattern = ('\\\\'),
replacement = '',
x = mypubs$abstract
)
mypubs$mainref<- gsub(
pattern = ('\\\\'),
replacement = '',
x = mypubs$mainref
)
# Customize for more than one editor
mypubs$editor<- gsub(
pattern = (' and '),
replacement = ', ',
x = mypubs$editor
)
mypubs$editor<- stri_replace_last_fixed(mypubs$editor, ',', ' &')
# add characters between tags for properly render
mypubs$keywords<- gsub(
pattern = (','),
replacement = '","',
x = mypubs$keywords
)
#add line breaks for the different entries
# mypubs$annotation<-cat(stri_wrap(mypubs$annotation, whitespace_only = TRUE))
# assign "categories" to the different types of publications
mypubs <- mypubs %>%
dplyr::mutate(
pubtype = dplyr::case_when(bibtype == "Article" ~ "2",
bibtype == "Article in Press" ~ "2",
bibtype == "InProceedings" ~ "1",
bibtype == "Proceedings" ~ "1",
bibtype == "Conference" ~ "1",
bibtype == "Conference Paper" ~ "1",
bibtype == "MastersThesis" ~ "3",
bibtype == "PhdThesis" ~ "3",
bibtype == "Manual" ~ "4",
bibtype == "TechReport" ~ "4",
bibtype == "Book" ~ "5",
bibtype == "InCollection" ~ "6",
bibtype == "InBook" ~ "6",
bibtype == "Misc" ~ "0",
TRUE ~ "0"))
# create a function which populates the md template based on the info
# about a publication
create_md <- function(x) {
# define a date and create filename by appending date and start of title
if (!is.na(x[["year"]])) {
x[["date"]] <- paste0(x[["year"]], "-01-01")
} else {
x[["date"]] <- "2999-01-01"
}
filename <- paste(x[["date"]], x[["title"]] %>%
str_replace_all(fixed(" "), "_") %>%
str_remove_all(fixed(":")) %>%
str_sub(1, 20) %>%
paste0(".md"), sep = "_")
# start writing
if (!file.exists(file.path(outfold, filename)) | overwrite) {
fileConn <- file.path(outfold, filename)
write("+++", fileConn)
# Title and date
write(paste0("title = \"", x[["title"]], "\""), fileConn, append = T)
write(paste0("date = \"", anydate(x[["date"]]), "\""), fileConn, append = T)
# Authors. Comma separated list, e.g. `["Bob Smith", "David Jones"]`.
auth_hugo <- str_replace_all(x["author"], " and ", "\", \"")
auth_hugo <- stringi::stri_trans_general(auth_hugo, "latin-ascii")
write(paste0("authors = [\"", auth_hugo,"\"]"), fileConn, append = T)
# Publication type. Legend:
# 0 = Uncategorized, 1 = Conference paper, 2 = Journal article
# 3 = Manuscript, 4 = Report, 5 = Book, 6 = Book section
write(paste0("publication_types = [\"", x[["pubtype"]],"\"]"),
fileConn, append = T)
# Publication details
publication <- x[["mainref"]]
if (!is.na(x[["editor"]])) publication <- paste0(publication,
" In ", x[["editor"]], ": ")
if (!is.na(x[["booktitle"]])) publication <- paste0(publication,
x[["booktitle"]], ". ")
if (!is.na(x[["volume"]])) publication <- paste0(publication,
", ", x[["volume"]], "")
if (!is.na(x[["type"]])) publication <- paste0(publication,
x[["type"]], " ")
if (!is.na(x[["number"]])) publication <- paste0(publication,
"(", x[["number"]], ")")
if (!is.na(x[["pages"]])) publication <- paste0(publication,
" ", x[["pages"]], ".")
if (!is.na(x[["address"]])) publication <- paste0(publication,
" ", x[["address"]], ":")
if (!is.na(x[["institution"]])) publication <- paste0(publication,
" ", x[["institution"]])
if (!is.na(x[["publisher"]])) publication <- paste0(publication,
" ", x[["publisher"]])
if (!is.na(x[["doi"]])) publication <- paste0(publication,
" ", paste0("https://doi.org/",
x[["doi"]]))
if (!is.na(x[["isbn"]])) publication <- paste0(publication,
". ISBN: ", paste0(x[["isbn"]]))
write(paste0("publication = \"", publication,"\""), fileConn, append = T)
write(paste0("publication_short = \"", publication,"\""),fileConn, append = T)
# Abstract and optional shortened version.
write(paste0("abstract = \"", x[["abstract"]], "\""), fileConn, append = T)
# if (abstract) {
# write(paste0("abstract = \"", x[["abstract"]],"\""), fileConn, append = T)
# } else {
# write("abstract = \"\"", fileConn, append = T)
# }
write(paste0("abstract_short = \"","\""), fileConn, append = T)
# Source document from Zotero URL field
if (!is.na(x[["url"]])) write(paste0("url_source = \"", x[["url"]], "\""), fileConn, append = T)
if (!is.na(x[["keywords"]])) write(paste0("tags = [\"", x[["keywords"]], "\"]"), fileConn, append = T)
# other possible fields are kept empty. They can be customized later by
# editing the created md
write("url_code = \"\"", fileConn, append = T)
write("image_preview = \"\"", fileConn, append = T)
write("selected = false", fileConn, append = T)
write("projects = []", fileConn, append = T)
#links
write("url_pdf = \"\"", fileConn, append = T)
write("url_preprint = \"\"", fileConn, append = T)
write("url_dataset = \"\"", fileConn, append = T)
write("url_project = \"\"", fileConn, append = T)
write("url_slides = \"\"", fileConn, append = T)
write("url_video = \"\"", fileConn, append = T)
write("url_poster = \"\"", fileConn, append = T)
#other stuff
write("math = true", fileConn, append = T)
write("highlight = true", fileConn, append = T)
# Featured image
write("[header]", fileConn, append = T)
write("image = \"\"", fileConn, append = T)
write("caption = \"\"", fileConn, append = T)
write("+++", fileConn, append = T)
# Any other relevant information from Zotero: write in the "Extra" field
if (!is.na(x[["annotation"]])) write(paste0(x[["annotation"]]), fileConn, append = T)
}
}
# apply the "create_md" function over the publications list to generate
# the different "md" files.
apply(mypubs, FUN = function(x) create_md(x), MARGIN = 1)
}
# Running the function
my_bibfile <- "content/publication/googlescholarexport.bib"
out_fold <- "content/publication"
bibtex_2academic(bibfile = my_bibfile,
outfold = out_fold,
abstract = TRUE,
overwrite = TRUE)
#From <https://raw.githubusercontent.com/juancarloscastillo/starter-hugo-academic/master/content/publication/bibtex_2academic.R>
bibtex_2academic(bibfile = my_bibfile,
outfold = out_fold,
abstract = TRUE,
overwrite = TRUE)
library(pacman)
bibtex_2academic(bibfile = my_bibfile,
outfold = out_fold,
abstract = TRUE,
overwrite = TRUE)
warnings()
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
bibfile
bibfile = my_bibfile
# Import the bibtex file and convert to data.frame
mypubs <- ReadBib(bibfile, check = "warn", .Encoding = "UTF-8") %>%
as.data.frame()
mypubs
head(mypubs)
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
mypubs$bibtype
table(mypubs$bibtype)
table(mypubs$bibtype, useNA = "always")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
names(mypubs)
source("content/publication/bibtex_2academic.R")
?ReadBib
if(!"doi" %in% names(mypubs)){mypubs$doi <- NA}
names(mypubs)
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
rlang::last_error()
mypubs$abstract
if(!"abstract" %in% names(mypubs)){mypubs$abstract <- NA}
mypubs$abstract
mypubs$abstract <- mypubs$abstract %>% replace_na('(Abstract not available)') #otherwise it appears "NA" in post
mypubs$abstract <- as.character(NA)
mypubs$abstract
mypubs$abstract <- mypubs$abstract %>% replace_na('(Abstract not available)') #otherwise it appears "NA" in post
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
source("content/publication/bibtex_2academic.R")
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
academic import --bibtex googlescholarexport.bib --publication-dir content/publication/new
academic import --bibtex content/publication/googlescholarexport.bib --publication-dir content/publication/new
academic import --bibtex content/publication/googlescholarexport.bib
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()
blogdown::serve_site()