I use modified hugo-finite theme for this website. The theme supports listing of published articles. Each of such articles or papers is represented by a markdown file (*.md) holding all the citation information. The citation information inside markdown files has to be in YAML (or TOML) format. It is all present in the front matter of the files. Front matter is the part starting and ending with lines containing only three dashes (---).
To generate the list of such *.md files I first gathered all relevant DOI identifiers:
dois <- c("10.1002/cyto.a.21148",
"10.18637/jss.v076.i10",
"10.1182/blood-2016-07-725861",
"10.1002/ijc.30263",
"10.1016/j.canlet.2016.04.016",
"10.1074/mcp.M115.054593",
"10.1016/j.diff.2015.11.003",
"10.1182/blood-2015-07-655159",
"10.1038/leu.2015.213",
"10.1073/pnas.1508680112",
"10.1161/CIRCRESAHA.116.304393",
"10.1186/s13045-014-0094-0",
"10.1038/leu.2013.354",
"10.1371/journal.pone.0047155",
"10.1002/cyto.a.22011",
"10.1038/sj.bjc.6605821",
"10.1016/j.leukres.2005.10.008")Having the DOIs I used rcrossref to retrieve citation info for each DOI and yaml package to conevert it to yaml format. After that a number of awful hackish things happened (the code is below) to arrive at hugo-finite friendly underscore_separated_paper_title.md files. The files were saved in content/publication/ folder. The code includes among other things the addition of url_doi parameter to get links to paper publisher source.
library("rcrossref")
library("yaml")
library("anytime")
for(ii in 1:length(dois)) {
## get doi reference with rcrossref:
ref_md <- cr_cn(dois = dois[ii], format = "citeproc-json")
ref_md <- as.yaml(ref_md)
ref_md <- unlist(strsplit(ref_md, "\n"))
## change and construct yaml fields
url_doi <- gsub("URL:", "url_doi:", grep("^URL: ", ref_md, value = TRUE))
doi <- gsub("DOI:", "doi:", grep("^DOI: ", ref_md, value = TRUE))
# authors from first occurance of "author:", the second are authors of cited work
authors <- ref_md[(grep("author:", ref_md)[1]+1):(grep(" affiliation:", ref_md)[1]-1)]
authors <- apply(matrix(authors, ncol = 2)[-1, ] , 1 , paste , collapse = " ")
authors <- gsub(" - ", " ", authors)
authors <- gsub(" -", "-", authors)
authors <- c("authors:", authors)
if (length(grep("published-online:", ref_md)) >0 ) {
published <- "published-online:"
} else if (length(grep("published-print:", ref_md)) >0 ) {
published <- "published-print:"
}
published_date <- ref_md[grep(published, ref_md):length(ref_md)]
published_date <- gsub(" ", " ", published_date)
published_date <- published_date[1:(grep("^ ", published_date, invert = TRUE)[2]-1)]
published_date <- paste0(gsub("[^0-9\\.]", "", published_date), collapse = "-")
published_date <- gsub("^-+", "", published_date)
# if (is.na(as.Date(as.character(published_date),format="%Y-%m-%d"))) published_date <- as.character(anydate(published_date))
if (is.na(as.Date(as.character(anydate(published_date))))) {
published_date <- as.Date(as.character(published_date),format="%Y-%m-%d")
} else {
published_date <- as.character(anydate(published_date))
}
ref_date <- paste0("date: ", published_date)
## make article journal ciation field (e.g. "<em>Cytometry Part A</em>, 81A('1'):25-34")
ref_cit <- paste(paste0("<em>", strsplit(ref_md[grep("^container-title:", ref_md)], ": ")[[1]][2], "</em>, "),
if (length(grep("volume:", ref_md)) > 0) strsplit(ref_md[grep("volume:", ref_md)], ": ")[[1]][2],
if (length(grep("issue:", ref_md)) > 0) paste0("(", strsplit(ref_md[grep("issue:", ref_md)], ": ")[[1]][2], ")"),
if (length(grep("page:", ref_md)) > 0) paste0(":", strsplit(ref_md[grep("page:", ref_md)], ": ")[[1]][2]),
sep = "")
ref_cit <- gsub("'", "", ref_cit)
ref_cit <- paste0("citation: ", ref_cit)
# the title gets spread over several lines
ref_title <- ref_md[grep("^title: ", ref_md):length(ref_md)]
ref_title <- gsub(" ", " ", ref_title)
ref_title <- paste0(ref_title[1:(grep("^ ", ref_title, invert = TRUE)[2]-1)], collapse = "")
ref_md <- gsub("^title: ", "title-spread: ", ref_md) # changing the original title
## make hugo-finite theme compliant *.md files from reference:
ref_hugo_md <- c(ref_title, url_doi, doi, authors, ref_date, ref_cit, ref_md)
if (length(grep("bstract:", ref_md)) == 0) {
ref_abstract <- gsub("^title: ", "abstract: ", ref_title)
ref_hugo_md <- c(ref_abstract, ref_hugo_md)
}
ref_hugo_md <- c("---", ref_hugo_md, "---")
# hugo-finite does not like type: and URL: in lines (just needs proper type??, relative urls??)
ref_hugo_md <- ref_hugo_md[-grep("^URL: ", ref_hugo_md)]
ref_hugo_md <- ref_hugo_md[-grep("^type: ", ref_hugo_md)]
## save the resulting ref_hugo_md into *.md file
ref_name <- gsub("/", "_", gsub("'", "", gsub(" ", "_", paste(gsub("^title: ", "", grep("^title: ", ref_hugo_md, value = TRUE)[1])))))
if (!file.exists(paste0("content/publication/", ref_name, ".md"))) {
write.table(ref_hugo_md, file = paste0("content/publication/", ref_name, ".md"),
quote = FALSE, row.names = FALSE, col.names = FALSE)
print(paste(ii, ":", dois[ii], "---", ref_name))
}
}For notes on DOIs and their content retrieval see crosscite.org