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# TODO J.E.M. Flemming should be J.E. Mills Flemming
# TODO J.E. Mills Flemming needs to be fixed throughout refs.bib too
# TODO Earth2Oceans Derby needs to be manually fixed
# Need to fix all authors contributed equally and asterisks
library("bibtex")
d <- read.bib("refs.bib")
ref <- list()
for(i in seq_along(d)) {
name <- list()
x <- d[[i]]
# authors:
for(j in seq_along(x$author)) {
init <- paste0(paste(substr(x$author$given[[j]], 1, 1), collapse = "."), ".")
family <- x$author$family[[j]]
if(j == 1) {
name[[j]] <- paste0(family, ", ", init)
if(name[[j]] == "Anderson, S.C.") name[[j]] <- "**Anderson, S.C.**"
} else {
name[[j]] <- paste(init, family)
if(name[[j]] == "S.C. Anderson") name[[j]] <- "**S.C. Anderson**"
}
}
name0 <- paste0(paste0(name, collase = ""), collapse = ", ")
vol_num_p <- ""
if(!is.null(x$number) & !is.null(x$volume) & !is.null(x$pages)) {
vol_num_p <- paste0(x$volume, "(", x$number, "): ", x$pages)
}
# no number:
if(is.null(x$number) & !is.null(x$volume) & !is.null(x$pages)) {
vol_num_p <- paste0(x$volume, ": ", x$pages)
}
# no pages:
if(is.null(x$number) & !is.null(x$volume) & is.null(x$pages)) {
vol_num_p <- paste0(x$volume, "(", x$number, ")")
}
# no number or pages:
if(is.null(x$number) & !is.null(x$volume) & is.null(x$pages)) {
vol_num_p <- x$volume
}
# no vol, number, or pages:
if(is.null(x$number) & is.null(x$volume) & is.null(x$pages)) {
vol_num_p <- ""
}
if(vol_num_p != "" & !vol_num_p %in% c("In review", "In revision", "Submitted")) {
main <- paste0(paste0(name0, ". ", x$title, ". ", x$journal, ". ", vol_num_p), ".")
} else {
main <-paste0(name0, ". ", x$title, ". ", vol_num_p, ".")
}
if(!is.null(x$doi)) {
main <- paste0(main, " <http://doi.org/", x$doi, ">")
}
if(!is.null(x$pdf)) {
if(grepl("http", x$pdf)) {
main <- paste0(main, " ([PDF](", x$pdf, ")).")
} else {
main <- paste0(main,
" ([PDF](https://dl.dropboxusercontent.com/u/254940/papers/", x$pdf, ")).")
}
}
if(!is.null(x$note)) {
main <- paste0(main, " ", x$note, ".")
}
if(!is.null(x$altm)) {
if(x$altm == "TRUE") {
main <- paste0(main,
"\n <div class=\'altmetric-embed\' data-badge-type=\'1\' data-doi=\"",
x$doi, "\"></div>")
}
}
if(!is.null(x$f1000)) {
main <- paste0(main,
"\n <a href=\"http://f1000.com/prime/",
x$f1000,
"\" target=\"_blank\"><img src=\"http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif\" id=\"bg\"/></a>")
}
main <- paste0(x$year, "\n: ", main)
ref[[i]] <- main
}
ref <- paste(ref, collapse = "\n\n")
writeLines(ref, con = "papers.md")
# authors:
library(magrittr)
lapply(d, function(x) x$author$family) %>% unlist() %>%
gsub("\\\\\\*", "", .) %>% unique() %>% sort()