R/CreateCV.R
In bomeara/cv: Code for compiling CVs from ORCID
Defines functions
CreateSummaryMarkdown
CreateFundingMarkdown
CreateEmploymentMarkdown
CreateEducationMarkdown
GetInfoFromOrcid
CreateTeachingMarkdown
CreateHeadMarkdown
CreatePresentationsMarkdown
CreateMarkdown
FinalCompileCV
CreatePublicationsMarkdown
GetCollaborators
CreateServiceMarkdown
CreatePeopleMarkdown
CleanNames
Documented in
CleanNames
CreateEducationMarkdown
CreateEmploymentMarkdown
CreateFundingMarkdown
CreateHeadMarkdown
CreateMarkdown
CreatePeopleMarkdown
CreatePresentationsMarkdown
CreatePublicationsMarkdown
CreateServiceMarkdown
CreateSummaryMarkdown
CreateTeachingMarkdown
FinalCompileCV
GetCollaborators
GetInfoFromOrcid
#' Apostophes cause problems. This will fix them.
#' @param citations Bibtext formatted
#' @return Same object, but with curly quotes and similar evil symbols fixed
#' @export
CleanNames <- function(citations) {
# for (i in sequence(length(citations))) {
# citations[i] <- gsub("meara", "Meara", citations[i])
# citations[i] <- gsub("\\{'\\}", "'", citations[i])
# citations[i] <- gsub("\\{\\\\textquotesingle\\}", "'", citations[i])
# citations[i] <- gsub("O\\?Meara", "O'Meara", citations[i])
# citations[i] <- gsub("\\{\\\\\\^\\a\\}\\?\\?", "'", citations[i])
# }
return(citations)
}
#' Create a Markdown document of people in the lab from biographical info
#' @param infile The path to the text delimited file
#' @param outdir The directory to store the markdown file in
#' @export
CreatePeopleMarkdown <- function(infile = system.file("extdata", "people.txt", package="cv"), outdir=tempdir()) {
people <- read.delim2(infile, stringsAsFactors=FALSE)
people$Stop <- as.character(people$Stop)
people$Stop[is.na(people$Stop)] <- "present"
people$Duration <- paste(people$Start,"-",people$Stop, sep="")
people$Name <- paste(people$First,people$Last)
for (i in sequence(dim(people)[1])) {
if(nchar(people$URL[i])>3) {
people$Name[i] <- paste("[", people$First[i], " ",people$Last[i],"](",people$URL[i], ")", sep="")
}
}
cat('\n\n## Mentoring, Postdocs\n\nI have mentored numerous postdocs off of my own grants and/or as one of their chosen NIMBioS mentors. Note that NIMBioS postdocs pursue independent research projects but choose one faculty member to mentor them in math and another to mentor them in biology (I have served in both roles).', file=paste(outdir, "/people.md", sep=""), sep='\n', append=FALSE)
postdocs <- subset(people, Stage=="Postdoc")
postdocs <- postdocs[order(postdocs$Last),]
postdocs.pretty <- postdocs[,c("Name", "Duration", "NIMBioS", "CurrentPosition")]
names(postdocs.pretty)[4] <- "Current Position"
cat(capture.output(knitr::kable(postdocs.pretty, row.names=FALSE)), file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
cat('\n\n## Mentoring, Grad students in my lab\n\n ', file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
grads <- subset(people, Stage=="PhD student")
grads <- grads[order(grads$Last),]
grads.pretty <- grads[,c("Name","Stage", "Duration", "Note")]
names(grads.pretty)[3] <- "Time in Lab"
cat(capture.output(knitr::kable(grads.pretty, row.names=FALSE)), file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
cat('\n\n## Mentoring, Undergrad students in my lab\n\n ', file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
undergrads <- subset(people, Stage=="Undergrad")
undergrads <- undergrads[order(undergrads $Last),]
undergrads.pretty <- undergrads[,c("Name","Stage", "Duration", "Note")]
names(undergrads.pretty)[3] <- "Time in Lab"
cat(capture.output(knitr::kable(undergrads.pretty, row.names=FALSE)), file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
cat('\n\n## Mentoring, Grad student committees\n\nIn addition to my own students, of course.', file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
com <- subset(people, Stage=="Committee")
com <- com[order(com$Last),]
com.pretty <- com[,c("Name","Department")]
cat(capture.output(knitr::kable(com.pretty, row.names=FALSE)), file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
cat('\n\n## Mentoring, Faculty\n\nOur department now has faculty mentored by a committee of later career faculty. I have served on committees for folks hired after me.', file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
faculty <- subset(people, Stage=="Faculty")
faculty <- faculty[order(faculty$Last),]
faculty.pretty <- faculty[,c("Name", "Department")]
cat(capture.output(knitr::kable(faculty.pretty, row.names=FALSE)), file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
}
#' Create a Markdown document of service from biographical info
#' @param infile The path to the text delimited file
#' @param outdir The directory to store the markdown file in
#' @export
CreateServiceMarkdown <- function(infile = system.file("extdata", "service.txt", package="cv"), outdir=tempdir()) {
service <- read.delim2(infile, stringsAsFactors=FALSE)
cat('\n\n## Service\n\n', file=paste(outdir, "/service.md", sep=""), sep='\n', append=FALSE)
service$Service <- paste("*", service$Service)
cat(service$Service, file=paste(outdir, "/service.md", sep=""), sep='\n', append=TRUE)
}
#' Get collaborators from past time period
#' @param orcid.info The list of info from orcid
#' @param starting.year What year to start including collaborators
#' @param outdir The directory to store the temporary markdown file in
#' @return vector of the authors
#' @export
GetCollaborators <- function(orcid.info, starting.year=2013, outdir=tempdir()) {
lapply(unlist(CleanNames(orcid.info$journals)), write, paste(outdir, "/publications.bib", sep=""), append=TRUE)
publications <- RefManageR::ReadBib(paste(outdir, "/publications.bib", sep=""))
publications <- sort(publications, decreasing=TRUE, sorting="ynt")
publications <- publications[which(as.numeric(publications$year)>=starting.year)]
CollapseName <- function(x) {
x <- (unlist(x))
return(paste0(x[grepl("family", names(x))], ", ", paste(x[grepl("given", names(x))], collapse=" ")))
}
all.authors <- c()
all.publications <- c()
for (i in sequence(length(publications))) {
all.authors <- append(all.authors, sapply(publications[i]$author, CollapseName))
all.publications <- append(all.publications, rep(paste0(publications[i]$title, " (", publications[i]$year, ")"), length(publications[i]$author)))
}
#authors.df <- data.frame(coauthor=unlist(all.authors), publication=all.publications, stringsAsFactors=FALSE)
#all.aggregation <- aggregate(authors.df, by=list(authors.df$coauthor), FUN=paste, collapse="; ")[,-2]
#names(all.aggregation)[1] <- "coauthor"
#all.aggregation[,2] <- as.character(all.aggregation[,2])
#all.authors <- sort(all.authors)
#all.authors.table <- table(all.authors)
all.authors <- sort(unique(unlist(all.authors)))
return(all.authors)
}
#' Create a Markdown document of publications from orcid
#' @param orcid.info The list of info from orcid
#' @param outdir The directory to store the markdown file in
#' @param emphasis.name The name to bold in the publications list. Presumably your own.
#' @param scholar.id Your ID on Google Scholar. NULL if you don't want to use this.
#' @param impact.story..id Your ID on ImpactStory. NULL if you don't want to use this.
#' @param badges Vector of ImpactStory badge names you want to show (a lot are goofy: could do c('global_reach', 'depsy')).
#' @export
CreatePublicationsMarkdown <- function(orcid.info, outdir=tempdir(), emphasis.name = "O'Meara", scholar.id="vpjEkQwAAAAJ", impact.story.id = "0000-0002-0337-5997", badges=c()) {
#lapply(CleanNames(orcid.info$journals), write, paste(outdir, "/publications.bib", sep=""), append=TRUE)
#publications <- RefManageR::ReadBib(paste(outdir, "/publications.bib", sep=""))
#publications <- sort(publications, decreasing=TRUE, sorting="ynt")
#publications.text <- capture.output(print(publications, .opts=list(bib.style="authoryear", dashed=FALSE, max.names=100, style="markdown", sorting="none", no.print.fields=c("URL", "DOI"))))
#publications.text <- gsub(emphasis.name, paste('**', emphasis.name, '**', sep=""), publications.text)
#cat(CleanNames(orcid.info$other.products), file=paste(outdir, "/chapters.bib", sep=""))
#chapters <- RefManageR::ReadBib(paste(outdir, "/chapters.bib", sep=""))
#chapters <- sort(chapters, decreasing=TRUE, sorting="ynt")
#chapters.text <- capture.output(print(chapters, .opts=list(bib.style="authoryear", dashed=FALSE, max.names=100, style="markdown", sorting="none", no.print.fields=c("URL", "DOI"))))
#chapters.text <- gsub(emphasis.name, paste('**', emphasis.name, '**', sep=""), chapters.text)
chapters <- orcid.info$other.products[which(orcid.info$other.products$type=='book-chapter'),]
cat('\n\n## Publications', file=paste(outdir, "/publications.md", sep=""), sep='\n', append=FALSE)
if(!is.null(scholar.id)) {
g.profile <- NULL
try(g.profile <- scholar::get_profile(scholar.id))
if(!is.null(g.profile)) {
cat(paste("\n\nI would recommend reading a few of my best papers to get a sense of my work; good examples are [O'Meara, Smith, et al. (2016)](https://doi.org/10.1098/rspb.2015.2304) and [Beaulieu & O'Meara (2016)](https://doi.org/10.1093/sysbio/syw022). Metrics are not as great (for example, my work with software might get cited than someone else's work on a new discovery about evolution, but it is not clear that the former is 'better') , but I know some people find them useful, so:", ' According to Google Scholar, my work has been cited ', g.profile$total_cites, " times, and my h-index is ", g.profile$h_index, ". (Google Scholar tends to overestimate citations, however). If there were a journal of just my papers, its ", as.numeric(format(Sys.Date(), "%Y"))-1," impact factor would be ",round(orcid.info$impact.factor,3), ". Also note that I work under a very stringent criterion for when I get authorship -- I have to actively make a significant contribution to the research and writing to merit authorship. For example, in 2015-6, three lab members had papers in *Science* ([grad student Sam Borstein](http://science.sciencemag.org/content/350/6264/1077.long), [postdoc Nick Matzke](http://science.sciencemag.org/content/351/6268/28), and [postdoc Sandy Kawano](http://science.sciencemag.org/content/353/6295/154.full)) but I am, appropriately to my mind, not an author on any of these.", sep=""), file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
}
}
if(!is.null(impact.story.id)) {
i.profile <- NULL
try(i.profile <- jsonlite::fromJSON(txt=paste("https://impactstory.org/api/person/", impact.story.id, sep="")))
if(!is.null(i.profile)) {
if(any(i.profile$badges$name %in% badges)) {
cat(paste('\n\nAccording to NSF-funded [ImpactStory.org](https://impactstory.org/u/', impact.story.id, '), a source of altmetrics data (a measure of impact beyond citations), my work has various impacts:', sep=""), file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
for (badge.index in sequence(length(badges))) {
if(badges[badge.index] %in% i.profile$badges$name) {
matching.row <- which(i.profile$badges$name==badges[badge.index])
cat(paste('\n* ', gsub("Your", "My", gsub("your", "my", i.profile$badges$description[matching.row])), " ",i.profile$badges$context[matching.row], sep=""), file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
}
}
}
}
}
journals <- orcid.info$journals[order(orcid.info$journals$`publication-date.year.value`, decreasing=TRUE),]
journals.txt <- '| Authors | Year | Title, Journal | DOI | Citations |\n| -- | -- | -- | -- | -- |'
for (i in sequence(nrow(journals))) {
journals.txt <- paste0(journals.txt, "\n", "| ", journals$author[i], " | ", journals$`publication-date.year.value`[i], " | ", '"', journals$`title.title.value`[i], '"', " ", journals$`journal-title`[i], " ", journals$number[i], " | ", "[", journals$doi[i], "](https://doi.org/", journals$doi[i], ")", " | ", journals$scholar_citations[i], " | ")
}
chapters.txt <- '| Authors | Year | Title | Book |\n| -- | -- | -- | -- |'
for (i in sequence(nrow(chapters))) {
if(nchar(chapters$author[i])>0) {
chapters.txt <- paste0(chapters.txt, "\n", "| ", chapters$author[i], " | ", chapters$`publication-date.year.value`[i], " | ", '"', chapters$`title.title.value`[i], '"', " | ", chapters$`journal-title.value`[i], " | ")
}
}
packages.txt <- '### Packages \n\nSoftware developed in R (often associated with a publication, but not always)\n\n| Package | Authors | Description | Downloads |\n| -- | -- | -- | -- |'
packages <- orcid.info$packages
for (i in sequence(nrow(packages))) {
packages.txt <- paste0(packages.txt, "\n", "| ", packages$NAME[i], " | ", gsub(",,", ",", gsub(" \\[aut, cre\\]", "", gsub(" \\[aut\\]", "", gsub(" ", " ",gsub("\\n", ", ", packages$AUTHOR[i]))))), " | ", packages$DESC_SHORT[i], " | ", packages$downloads[i], " |")
}
cat('\n\n### Papers', file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
cat('\n\n', file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
cat(journals.txt, file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
cat('\n\n## Publications: Books or Book Chapters\n\n', file=paste(outdir, "/publications.md", sep=""), append=TRUE)
cat(chapters.txt, file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
cat(packages.txt, file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
}
#
# #' Create a Markdown document of publications from orcid
# #' @param orcid.info The list of info from orcid
# #' @param outdir The directory to store the markdown file in
# #' @param emphasis.name The name to bold in the publications list. Presumably your own.
# #' @param scholar.id Your ID on Google Scholar. NULL if you don't want to use this.
# #' @param impact.story..id Your ID on ImpactStory. NULL if you don't want to use this.
# #' @param badges Vector of ImpactStory badge names you want to show (a lot are goofy: could do c('global_reach', 'depsy')).
# #' @export
# CreatePublicationsMarkdown <- function(orcid.info, outdir=tempdir(), emphasis.name = "O'Meara", scholar.id="vpjEkQwAAAAJ", impact.story.id = "0000-0002-0337-5997", badges=c()) {
# lapply(CleanNames(orcid.info$journals), write, paste(outdir, "/publications.bib", sep=""), append=TRUE)
# publications <- RefManageR::ReadBib(paste(outdir, "/publications.bib", sep=""))
# publications <- sort(publications, decreasing=TRUE, sorting="ynt")
# publications.text <- capture.output(print(publications, .opts=list(bib.style="authoryear", dashed=FALSE, max.names=100, style="markdown", sorting="none", no.print.fields=c("URL", "DOI"))))
# publications.text <- gsub(emphasis.name, paste('**', emphasis.name, '**', sep=""), publications.text)
#
# cat(CleanNames(orcid.info$other.products), file=paste(outdir, "/chapters.bib", sep=""))
# chapters <- RefManageR::ReadBib(paste(outdir, "/chapters.bib", sep=""))
# chapters <- sort(chapters, decreasing=TRUE, sorting="ynt")
# chapters.text <- capture.output(print(chapters, .opts=list(bib.style="authoryear", dashed=FALSE, max.names=100, style="markdown", sorting="none", no.print.fields=c("URL", "DOI"))))
# chapters.text <- gsub(emphasis.name, paste('**', emphasis.name, '**', sep=""), chapters.text)
#
# cat('\n\n## Publications: Papers', file=paste(outdir, "/publications.md", sep=""), sep='\n', append=FALSE)
# if(!is.null(scholar.id)) {
# g.profile <- NULL
# try(g.profile <- scholar::get_profile(scholar.id))
# if(!is.null(g.profile)) {
# cat(paste('\n\nAccording to Google Scholar, my work has been cited ', g.profile$total_cites, " times, and my h-index is ", g.profile$h_index, ". (Google Scholar tends to overestimate citations, however). Also note that I work under a very stringent criterion for when I get authorship -- I have to actively make a significant contribution to the research and writing to merit authorship. For example, in 2015-6, three lab members had papers in *Science* ([grad student Sam Borstein](http://science.sciencemag.org/content/350/6264/1077.long), [postdoc Nick Matzke](http://science.sciencemag.org/content/351/6268/28), and [postdoc Sandy Kawano](http://science.sciencemag.org/content/353/6295/154.full)) but I am, appropriately to my mind, not an author on any of these.", sep=""), file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
# }
# }
#
# if(!is.null(impact.story.id)) {
# i.profile <- NULL
# try(i.profile <- jsonlite::fromJSON(txt=paste("https://impactstory.org/api/person/", impact.story.id, sep="")))
# if(!is.null(i.profile)) {
# if(any(i.profile$badges$name %in% badges)) {
# cat(paste('\n\nAccording to NSF-funded [ImpactStory.org](https://impactstory.org/u/', impact.story.id, '), a source of altmetrics data (a measure of impact beyond citations), my work has various impacts:', sep=""), file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
# for (badge.index in sequence(length(badges))) {
# if(badges[badge.index] %in% i.profile$badges$name) {
# matching.row <- which(i.profile$badges$name==badges[badge.index])
# cat(paste('\n* ', gsub("Your", "My", gsub("your", "my", i.profile$badges$description[matching.row])), " ",i.profile$badges$context[matching.row], sep=""), file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
#
# }
# }
# }
# }
# }
# #cat('\n\n###Papers', file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
# cat('\n\n', file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
# cat(publications.text, file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
# cat('\n\n## Publications: Books or Book Chapters\n\n', file=paste(outdir, "/publications.md", sep=""), append=TRUE)
# cat(chapters.text, file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
# }
#' Compile a set of markdown documents and convert with pandoc
#' @param input Vector of markdown documents
#' @param outdir The directory to store the output in
#' @param css The css file with formatting info.
#' @param output The output base file name. You'll receive <output>.pdf and <output>.html files.
#' @param open.files If TRUE, open the output files
#' @export
#FinalCompileCV <- function(input = c("head.md", "summary.md", "education.md", "employment.md", "publications.md", "teaching.md", "funding.md", "service.md", "postdocs.md", "gradstudents.md", "undergradstudents.md", "gradcommittees.md", "software.md", "presentations.md"), output="OMearaCV.pdf") {
FinalCompileCV <- function(input = c("head.md", "summary.md", "education.md", "employment.md", "publications.md", "teaching.md", "funding.md", "presentations.md", "people.md", "service.md"), outdir=tempdir(), css = system.file("extdata", "format.css", package="cv"), output="OMearaCV", open.files=TRUE) {
original.wd <- getwd()
setwd(outdir)
system(paste("pandoc --css ", css, " -o ", output, ".html ", paste(input, collapse=" "), sep=""))
print(paste("HTML file ", output, ".html has been created in ", outdir, sep=""))
system(paste("wkhtmltopdf ", output, ".html ", output, ".pdf", sep=""))
print(paste("PDF file ", output, ".pdf has been created in ", outdir, sep=""))
#system(paste("pandoc --css ", css, " -o ", output, "_pandoc.pdf ", paste(input, collapse=" "), sep=""))
system(paste("pandoc --css ", css, " -o ", output, ".md ", paste(input, collapse=" "), sep=""))
system(paste("pandoc -reference-doc ", system.file("extdata", "reference.docx", package="cv"), " -o ", output, ".docx ", paste(input, collapse=" "), sep=""))
print(paste("MS Word file ", output, ".docx has been created in ", outdir, sep=""))
system(paste("pandoc -o ", output, "_fromword.pdf ", paste0(output, ".docx"), sep=""))
if(open.files) {
system(paste0("open ", output, ".docx"))
system(paste0("open ", output, ".pdf"))
system(paste0("open ", output, ".html"))
system(paste0("open ."))
}
setwd(original.wd)
}
#' Create a Markdown document from biographical info
#' @param orcid.info The list of info from orcid
#' @param outdir The directory to store the markdown file in
#' @param emphasis.name The name to bold in the publications list. Presumably your own.
#' @param scholar.id Your ID on Google Scholar. NULL if you don't want to use this.
#' @param impact.story..id Your ID on ImpactStory. NULL if you don't want to use this.
#' @export
CreateMarkdown <- function(orcid.info = GetInfoFromOrcid(), outdir=tempdir(), emphasis.name="O'Meara", scholar.id="vpjEkQwAAAAJ", impact.story.id = "0000-0002-0337-5997") {
CreateSummaryMarkdown(orcid.info, outdir)
CreateEducationMarkdown(orcid.info, outdir)
CreateEmploymentMarkdown(orcid.info, outdir)
CreateFundingMarkdown(orcid.info, outdir)
CreatePublicationsMarkdown(orcid.info, outdir, emphasis.name, scholar.id, impact.story.id)
CreatePeopleMarkdown(outdir=outdir)
CreateServiceMarkdown(outdir=outdir)
CreatePresentationsMarkdown(outdir=outdir)
CreateHeadMarkdown(outdir=outdir)
CreateTeachingMarkdown(outdir=outdir)
}
#' Copy the presentations markdown
#' @param outdir The directory to store the markdown file in
#' @export
CreatePresentationsMarkdown <- function(outdir = tempdir()) {
file.copy(system.file("extdata", "presentations.md", package="cv"), outdir)
}
#' Copy the head markdown
#' @param outdir The directory to store the markdown file in
#' @export
CreateHeadMarkdown <- function(outdir = tempdir()) {
file.copy(system.file("extdata", "head.md", package="cv"), outdir)
}
#' Copy the teaching markdown
#' @param outdir The directory to store the markdown file in
#' @export
CreateTeachingMarkdown <- function(outdir = tempdir()) {
file.copy(system.file("extdata", "teaching.md", package="cv"), outdir)
}
#' Pull in info from ORCID
#' @param id Your ORCID id
#' @param scholar_id Your Google Scholar id
#' @param package_author_name A string to search for your packages on CRAN
#' @return A list of info from ORCID
#' @export
GetInfoFromOrcid <- function(id="0000-0002-0337-5997", scholar_id = "vpjEkQwAAAAJ", package_author_name = "Meara") {
#me <- rorcid::orcid_id(id)
#me.pubs <- rorcid::works(me)
#journal.info <- subset(me.pubs, type=="journal-article")
#journal.dois <- c()
# for (i in sequence(nrow(journal.info))) {
# info.df <- journal.info$`external-ids.external-id`[[i]]
# info.df <- subset(info.df, `external-id-type`=="doi")
# if(nrow(info.df)>=1) {
# journal.dois <- append(journal.dois, info.df$`external-id-value`[1])
# }
# }
#my.dois <- rorcid::identifiers(rorcid::works(me))
#journals <- rcrossref::cr_cn(dois = journal.dois, format = "bibtex", .progress="text")
# TO DO: Make sure all entries are bibtex
#journals <- me.pubs$'work-citation.citation'[which(me.pubs$'work-type'=="journal-article")]
print("Pulling in citations from orcid")
citations <- unlist(rorcid::orcid_citations(id)$citation)
cat(citations, file=file.path(tempdir(), "me.bib"), sep="\n\n")
bibs <- as.data.frame(bib2df::bib2df(file.path(tempdir(), "me.bib")), stringsAsFactors=FALSE)
bibs <- bibs[!duplicated(bibs$DOI),]
print("Pulling in info from Google scholar")
scholar <- scholar::get_publications(scholar_id)
print("Pulling in all works from orcid")
publications <- rorcid::orcid_works(id, format="application/json")[[1]][[1]]
publications <- publications[order(publications$`publication-date.month.value`),]
publications <- publications[!duplicated(tolower(publications$title.title.value)),]
publications$doi <- ""
publications$author <- ""
publications$number <- ""
publications$author_scholar <- ""
bibs$TITLE_CLEAN <- gsub('\\textendash', '-', gsub('}', "", gsub('{', "", bibs$TITLE, fixed=TRUE), fixed=TRUE), fixed=TRUE)
for (i in sequence(nrow(publications))) {
ref.info <- publications$`external-ids.external-id`[[i]]
best.match <- agrep(publications$title.title.value[i],bibs$TITLE_CLEAN, ignore.case=TRUE, max.distance=0.5)
if(length(best.match)>1) {
best.match <- which.min(adist(publications$title.title.value[i],bibs$TITLE_CLEAN, ignore.case=TRUE))
}
if(length(ref.info$`external-id-value`[which(ref.info$`external-id-type`=="doi")])>0) {
publications$doi[i] <- ref.info$`external-id-value`[which(ref.info$`external-id-type`=="doi")]
} else {
if(length(best.match)==1) {
publications$doi[i] <- bibs$DOI[best.match]
}
}
if(length(best.match)==1) {
publications$doi[i] <- bibs$DOI[best.match]
#publications$author[i] <- bibs$AUTHOR[best.match]
publications$author[i] <- gsub('\\{\\\\textquotesingle\\}', "'", paste(bibs$AUTHOR[[best.match]], collapse=", "))
publications$author[i] <- gsub("{\\'{e}}", "é", publications$author[i], fixed=TRUE)
publications$author[i] <- gsub("{\\'{a}}", "á", publications$author[i], fixed=TRUE)
publications$author[i] <- gsub("{\\'{o}}", "ó", publications$author[i], fixed=TRUE)
publications$author[i] <- gsub("{'}", "'", publications$author[i], fixed=TRUE)
}
}
# for (i in sequence(nrow(publications))) {
# best.match <- agrep(publications$title.title.value[i],bibs$TITLE)
# if(length(best.match)>1) {
# best.match <- which.min(adist(publications$title.title.value[i],bibs$TITLE))
# }
# if(length(best.match)==1) {
# publications$author[i] <- gsub('\\{\\\\textquotesingle\\}', "'", paste(bibs$AUTHOR[[best.match]], collapse=", "))
# }
# }
for (i in sequence(nrow(publications))) {
best.match <- agrep(publications$title.title.value[i],scholar$title, ignore.case=TRUE)
if(length(best.match)>1) {
best.match <- which.min(adist(publications$title.title.value[i],scholar$title, ignore.case=TRUE))
}
if(length(best.match)==1) {
publications$author_scholar[i] <- as.character(scholar$author)[best.match]
publications$number[i] <- as.character(scholar$number)[best.match]
}
}
publications$scholar_citations <- NA
for (i in sequence(nrow(publications))) {
# print(i)
# print(publications$title.title.value[i])
best.match <- agrep(tolower(publications$title.title.value[i]),tolower(scholar$title), ignore.case=TRUE)
if(length(best.match)>1) {
best.match <- which.min(adist(tolower(publications$title.title.value[i]),tolower(scholar$title), ignore.case=TRUE))
}
#print(scholar$title[best.match])
#print(paste0("Cites ", scholar$cites[best.match]))
if(length(best.match)==1) {
publications$scholar_citations[i] <- scholar$cites[best.match]
}
}
print("Pulling in all R packages from CRAN")
packages <- as.data.frame(packagefinder::exploreFields(package_author_name, c("Maintainer", "Authors@R", "Author"), "or", "like"))
total_dl <- function(x) {
return(sum(cranlogs::cran_downloads(packages=x,from="2005-01-01")$count))
}
packages$downloads <- sapply(packages$NAME, total_dl)
journals <- subset(publications, type=="journal-article")
other.products <- subset(publications, type!="journal-article")
#other.products.raw <- rorcid::orcid_works(id, put_code=other.products.raw$`put-code`)[[1]]
#other.products <- other.products.raw[[1]]$`work.citation.citation-value`
activities <- rorcid::orcid_activities(id)[[1]]
funding <- plyr::rbind.fill(activities$funding$group$`funding-summary`)
funding <- funding[order(funding$`start-date.year.value`, decreasing = TRUE),]
# funding.full <- data.frame()
# for (i in sequence(nrow(funding))) {
# local.funding <- rorcid::orcid_fundings(id, put_code=funding$`put-code`[i])[[1]]
# }
#affiliations <- activities$affiliation
educations <- rorcid::orcid_educations(id)[[1]]$`affiliation-group`
education <- as.data.frame(matrix(unlist(educations$summaries), nrow=length(educations$summaries), byrow=TRUE))
colnames(education) <- gsub("education-summary.", "", names(educations$summaries[[1]]))
#education <- activities$educations$`education-summary`
education <- education[order(education$'end-date.year.value', decreasing=TRUE),]
employments <- rorcid::orcid_employments(id)[[1]]$`affiliation-group`
employment <- data.frame()
for (i in sequence(length(employments$summaries))) {
employment <- plyr::rbind.fill(employment, as.data.frame(employments$summaries[[i]], stringsAsFactors=FALSE))
}
colnames(employment) <- gsub("employment-summary.", "", colnames(employment))
employment <- employment[order(employment$'start-date.year.value', decreasing=TRUE),]
current.year <- as.numeric(format(Sys.Date(), "%Y"))
citation.year <- current.year - 1
paper.years <- c(citation.year-1, citation.year-2)
scholar_previous2 <- scholar[which(scholar$year %in% paper.years),]
scholar_previous2$number <- as.character(scholar_previous2$number)
scholar_previous2$journal <- as.character(scholar_previous2$journal)
scholar_previous2 <- scholar_previous2[which(nchar(scholar_previous2$journal)>0),]
scholar_previous2 <- scholar_previous2[which(nchar(scholar_previous2$number)>0),]
impact.citations <- 0
for (i in sequence(nrow(scholar_previous2))) {
ach <- get_article_cite_history(scholar_id, scholar_previous2$pubid[i])
impact.citations <- sum(impact.citations, ach$cites[which(ach$year==citation.year)], na.rm=TRUE)
}
impact.factor <- impact.citations / nrow(scholar_previous2)
#employment <- activities$employments$`employment-summary`
# employment <- employment[order(employment $'start-date.year.value', decreasing=TRUE),]
return(list(journals=journals, other.products=other.products, funding=funding, education=education, employment=employment, id=id, packages=packages, impact.factor=impact.factor, bibs=bibs, scholar=scholar))
}
#' Create a Markdown document of education from biographical info
#' @param orcid.info The list of info from orcid
#' @param outdir The directory to store the markdown file in
#' @export
CreateEducationMarkdown <- function(orcid.info, outdir=tempdir()) {
education.string <- '\n\n## Education'
for (i in sequence(dim(orcid.info$education)[1])) {
education.string <- paste(education.string, '\n\n', orcid.info$education[i,]$organization.name, ': ', orcid.info$education[i,]$'role-title', " (", orcid.info$education[i,]$'end-date.year.value', ")", sep='')
if(!is.na(orcid.info$education$'department-name')[i]) {
education.string <- paste(education.string, ' in ', orcid.info$education[i,]$'department-name', sep='')
}
}
cat(education.string, file=paste(outdir, "/education.md", sep=""))
}
#' Create a Markdown document of employment history from biographical info
#' @param orcid.info The list of info from orcid
#' @param outdir The directory to store the markdown file in
#' @export
CreateEmploymentMarkdown <- function(orcid.info, outdir=tempdir()) {
employment.string <- '\n\n## Employment'
orcid.info$employment$'end-date.year.value'[which(is.na(orcid.info$employment$'end-date.year.value'))] <- "Present"
for (i in sequence(dim(orcid.info$employment)[1])) {
employment.string <- paste(employment.string, '\n\n', orcid.info$employment[i,]$'start-date.year.value', '-', orcid.info$employment[i,]$'end-date.year.value', ": ", orcid.info$employment[i,]$'role-title', ", ", sep='')
if(!is.na(orcid.info$employment$'department-name')[i]) {
employment.string <- paste(employment.string, "Dept. of ", orcid.info$employment[i,]$'department-name', ", ", sep='')
}
employment.string <- paste(employment.string, orcid.info$employment[i,]$'organization.name', ", ", orcid.info$employment[i,]$'organization.address.city', ", ", orcid.info$employment[i,]$'organization.address.region', sep="")
}
cat(employment.string, file=paste(outdir, "/employment.md", sep=""))
}
#' Create a Markdown document of funding from biographical info
#' @param orcid.info The list of info from orcid
#' @param outdir The directory to store the markdown file in
#' @export
CreateFundingMarkdown <- function(orcid.info, outdir=tempdir(), additional.te = "This is all in addition to other **funding my students have gotten** (NSF EAPSI grant, fellowships from NIMBioS and PEER (an NIH-funded program at UTK), Google Summer of Code funding), **funding for workshops or working groups** (from NIMBioS and the Society for Systematic Biologists), and **funding I got before my faculty position** (NESCent postdoctoral fellowship, NSF DDIG, NSF GRF, and various internal grants at UC Davis).") {
funding.string <- '\n\n## Funding\n\n'
funding.string <- paste(funding.string, additional.te, sep="")
funding.full <- list()
total.funding <- 0
for (i in sequence(nrow(orcid.info$funding))) {
local.funding <- rorcid::orcid_fundings(orcid.info$id, put_code=orcid.info$funding$`put-code`[i])[[1]]
total.funding <- total.funding + as.numeric(local.funding$amount$value)
funding.full[[i]] <- local.funding
}
funding.string <- paste(funding.string, paste(" Total external funding, so far, as a faculty member is $", prettyNum(total.funding, big.mark=",", scientific=FALSE), ".", sep=""), sep="")
funding.string <- paste(funding.string, '\n\n| Year | Title | Funder | Amount |\n| ---- | ------------------------------ | -------- | ------ |', sep="")
# orcid.info$funding <- orcid.info$funding[order(orcid.info$funding$'start-date.year.value', decreasing=TRUE),]
for (i in sequence(length(funding.full))) {
organization <- funding.full[[i]]$organization$name
if (grepl("National Science Foundation", organization, ignore.case=FALSE)) {
organization <- 'NSF'
}
if (grepl("National Institutes of Health", organization, ignore.case=FALSE)) {
organization <- 'NIH'
}
funding.string <- paste(funding.string, '\n| ', funding.full[[i]]$`start-date`$year$value, ' | ', funding.full[[i]]$title$title$value, ' | ', organization, ' | $', prettyNum(as.numeric(funding.full[[i]]$amount$value), big.mark=",", scientific=FALSE), ' |', sep="")
# funding.string <- paste(funding.string, '\n\n', orcid.info$funding[i,]$'funding-title.title.value', " ", orcid.info$funding[i,]$organization.name, ': ', orcid.info$funding[i,]$'role-title', " (", orcid.info$funding[i,]$'end-date.year.value', "): $", orcid.info$funding[i,]$'amount.value', sep='')
# if(!is.null(orcid.info$funding$'department-name')[i]) {
# funding.string <- paste(funding.string, ' in ', orcid.info$funding[i,]$'department-name', sep='')
# }
}
cat(funding.string, file=paste(outdir, "/funding.md", sep=""))
}
#' Create a Markdown document to summarize me
#' @param orcid.info The list of info from orcid
#' @param outdir The directory to store the markdown file in
#' @param publications.offset How to change the publication count.
#'
#' You may want an offset if some of your publications shouldn't count.
#' For example, I have two Nature "papers" that are actually corrigendia,
#' that is, corrections for errors. Shouldn't really count, I think.
#' @export
CreateSummaryMarkdown <- function(orcid.info, outdir=tempdir(), publications.offset=-2, prominent.pubs='*Science, Nature, Ann. Rev Ecology, Evolution & Systematics, Systematic Biology, Evolution*, etc.') {
results <- data.frame(matrix(nrow=6, ncol=2))
colnames(results) <- c("", "")
results[1,1] <- '**Publications**'
results[1,2] <- paste(nrow(orcid.info$journals)+publications.offset, " journal articles, including ", prominent.pubs, sep="")
results[2,1] <- '**Teaching**'
results[2,2] <- "Approximately 2 courses per year on average, ranging from large introductory biology courses to small graduate seminars"
results[3,1] <- '**Mentoring**'
people <- read.delim2(system.file("extdata", "people.txt", package="cv"), stringsAsFactors=FALSE)
results[3,2] <- paste(sum(grepl("PhD student", people$Stage)), " PhD students, ", sum(grepl("Postdoc", people$Stage)), " postdocs, ", sum(grepl("Faculty", people$Stage)), " faculty, ", "and served on ", sum(grepl("Committee", people$Stage)), " graduate student committees", sep="")
results[4,1] <- '**Service/Outreach**'
results[4,2] <- 'Darwin Day TN advisor, curator of R phylogenetics task view, instructor at workshops in Sweden, Switzerland, Brazil, and various US locations (Ohio, TN, NC)'
results[5,1] <- '**Leadership**'
results[5,2] <- 'Associate Head for Dept. of Ecology & Evolutionary Biology, 2016-present; Associate Director for the National Institute for Mathematical and Biological Synthesis, 2016-2018; Code of Conduct Committee for SSE/SSB/ASN, 2018-present; Communications Director for the Society of Systematic Biologists, 2016-2017; Society of Systematic Biologists Council, 2012-2014; iEvoBio co-organizer, 2014-2016.'
results[6,1] <- '**Funding**'
total.funding <- 0
for (i in sequence(nrow(orcid.info$funding))) {
local.funding <- rorcid::orcid_fundings(orcid.info$id, put_code=orcid.info$funding$`put-code`[i])[[1]]
total.funding <- total.funding + as.numeric(local.funding$amount$value)
}
results[6,2] <- paste("$",round((1e-6)*total.funding,2), "M in external support, including ", sum(grepl("National Science Foundation", orcid.info$funding$organization.name)), " NSF grants (including a CAREER grant) plus funding from iPlant and Encyclopedia of Life", sep="")
scholar.id="vpjEkQwAAAAJ"
impact.story.id = "0000-0002-0337-5997"
g.profile <- scholar::get_profile(scholar.id)
github.user <- jsonlite::fromJSON(txt="https://api.github.com/users/bomeara")
i.profile <- jsonlite::fromJSON(txt=paste("https://impactstory.org/api/person/", impact.story.id, sep=""))
i.sources <- i.profile$sources
#results[7,1] <- '**Altmetrics**'
#results[7,2] <- paste("Number of citations = ", g.profile$total_cites, "; h-index = ", g.profile$h_index, "; ", github.user$public_repos, " public github repos; Erdős number = 4; papers have been tweeted about ", subset(i.sources, source_name=="twitter")$posts_count, " times, and have been mentioned ", subset(i.sources, source_name=="news")$posts_count, " times in the news", sep="")
cat('\n\n## Summary\n\n ', file=paste(outdir, "/summary.md", sep=""), sep='\n', append=FALSE)
cat(capture.output(knitr::kable(results, row.names=FALSE)), file=paste(outdir, "/summary.md", sep=""), sep='\n', append=TRUE)
}
bomeara/cv documentation built on March 24, 2022, 1:26 a.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions CreateSummaryMarkdown CreateFundingMarkdown CreateEmploymentMarkdown CreateEducationMarkdown GetInfoFromOrcid CreateTeachingMarkdown CreateHeadMarkdown CreatePresentationsMarkdown CreateMarkdown FinalCompileCV CreatePublicationsMarkdown GetCollaborators CreateServiceMarkdown CreatePeopleMarkdown CleanNames
Documented in CleanNames CreateEducationMarkdown CreateEmploymentMarkdown CreateFundingMarkdown CreateHeadMarkdown CreateMarkdown CreatePeopleMarkdown CreatePresentationsMarkdown CreatePublicationsMarkdown CreateServiceMarkdown CreateSummaryMarkdown CreateTeachingMarkdown FinalCompileCV GetCollaborators GetInfoFromOrcid
#' Apostophes cause problems. This will fix them.
#' @param citations Bibtext formatted
#' @return Same object, but with curly quotes and similar evil symbols fixed
#' @export
CleanNames <- function(citations) {
# for (i in sequence(length(citations))) {
# citations[i] <- gsub("meara", "Meara", citations[i])
# citations[i] <- gsub("\\{'\\}", "'", citations[i])
# citations[i] <- gsub("\\{\\\\textquotesingle\\}", "'", citations[i])
# citations[i] <- gsub("O\\?Meara", "O'Meara", citations[i])
# citations[i] <- gsub("\\{\\\\\\^\\a\\}\\?\\?", "'", citations[i])
# }
return(citations)
}
#' Create a Markdown document of people in the lab from biographical info
#' @param infile The path to the text delimited file
#' @param outdir The directory to store the markdown file in
#' @export
CreatePeopleMarkdown <- function(infile = system.file("extdata", "people.txt", package="cv"), outdir=tempdir()) {
people <- read.delim2(infile, stringsAsFactors=FALSE)
people$Stop <- as.character(people$Stop)
people$Stop[is.na(people$Stop)] <- "present"
people$Duration <- paste(people$Start,"-",people$Stop, sep="")
people$Name <- paste(people$First,people$Last)
for (i in sequence(dim(people)[1])) {
if(nchar(people$URL[i])>3) {
people$Name[i] <- paste("[", people$First[i], " ",people$Last[i],"](",people$URL[i], ")", sep="")
}
}
cat('\n\n## Mentoring, Postdocs\n\nI have mentored numerous postdocs off of my own grants and/or as one of their chosen NIMBioS mentors. Note that NIMBioS postdocs pursue independent research projects but choose one faculty member to mentor them in math and another to mentor them in biology (I have served in both roles).', file=paste(outdir, "/people.md", sep=""), sep='\n', append=FALSE)
postdocs <- subset(people, Stage=="Postdoc")
postdocs <- postdocs[order(postdocs$Last),]
postdocs.pretty <- postdocs[,c("Name", "Duration", "NIMBioS", "CurrentPosition")]
names(postdocs.pretty)[4] <- "Current Position"
cat(capture.output(knitr::kable(postdocs.pretty, row.names=FALSE)), file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
cat('\n\n## Mentoring, Grad students in my lab\n\n ', file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
grads <- subset(people, Stage=="PhD student")
grads <- grads[order(grads$Last),]
grads.pretty <- grads[,c("Name","Stage", "Duration", "Note")]
names(grads.pretty)[3] <- "Time in Lab"
cat(capture.output(knitr::kable(grads.pretty, row.names=FALSE)), file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
cat('\n\n## Mentoring, Undergrad students in my lab\n\n ', file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
undergrads <- subset(people, Stage=="Undergrad")
undergrads <- undergrads[order(undergrads $Last),]
undergrads.pretty <- undergrads[,c("Name","Stage", "Duration", "Note")]
names(undergrads.pretty)[3] <- "Time in Lab"
cat(capture.output(knitr::kable(undergrads.pretty, row.names=FALSE)), file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
cat('\n\n## Mentoring, Grad student committees\n\nIn addition to my own students, of course.', file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
com <- subset(people, Stage=="Committee")
com <- com[order(com$Last),]
com.pretty <- com[,c("Name","Department")]
cat(capture.output(knitr::kable(com.pretty, row.names=FALSE)), file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
cat('\n\n## Mentoring, Faculty\n\nOur department now has faculty mentored by a committee of later career faculty. I have served on committees for folks hired after me.', file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
faculty <- subset(people, Stage=="Faculty")
faculty <- faculty[order(faculty$Last),]
faculty.pretty <- faculty[,c("Name", "Department")]
cat(capture.output(knitr::kable(faculty.pretty, row.names=FALSE)), file=paste(outdir, "/people.md", sep=""), sep='\n', append=TRUE)
}
#' Create a Markdown document of service from biographical info
#' @param infile The path to the text delimited file
#' @param outdir The directory to store the markdown file in
#' @export
CreateServiceMarkdown <- function(infile = system.file("extdata", "service.txt", package="cv"), outdir=tempdir()) {
service <- read.delim2(infile, stringsAsFactors=FALSE)
cat('\n\n## Service\n\n', file=paste(outdir, "/service.md", sep=""), sep='\n', append=FALSE)
service$Service <- paste("*", service$Service)
cat(service$Service, file=paste(outdir, "/service.md", sep=""), sep='\n', append=TRUE)
}
#' Get collaborators from past time period
#' @param orcid.info The list of info from orcid
#' @param starting.year What year to start including collaborators
#' @param outdir The directory to store the temporary markdown file in
#' @return vector of the authors
#' @export
GetCollaborators <- function(orcid.info, starting.year=2013, outdir=tempdir()) {
lapply(unlist(CleanNames(orcid.info$journals)), write, paste(outdir, "/publications.bib", sep=""), append=TRUE)
publications <- RefManageR::ReadBib(paste(outdir, "/publications.bib", sep=""))
publications <- sort(publications, decreasing=TRUE, sorting="ynt")
publications <- publications[which(as.numeric(publications$year)>=starting.year)]
CollapseName <- function(x) {
x <- (unlist(x))
return(paste0(x[grepl("family", names(x))], ", ", paste(x[grepl("given", names(x))], collapse=" ")))
}
all.authors <- c()
all.publications <- c()
for (i in sequence(length(publications))) {
all.authors <- append(all.authors, sapply(publications[i]$author, CollapseName))
all.publications <- append(all.publications, rep(paste0(publications[i]$title, " (", publications[i]$year, ")"), length(publications[i]$author)))
}
#authors.df <- data.frame(coauthor=unlist(all.authors), publication=all.publications, stringsAsFactors=FALSE)
#all.aggregation <- aggregate(authors.df, by=list(authors.df$coauthor), FUN=paste, collapse="; ")[,-2]
#names(all.aggregation)[1] <- "coauthor"
#all.aggregation[,2] <- as.character(all.aggregation[,2])
#all.authors <- sort(all.authors)
#all.authors.table <- table(all.authors)
all.authors <- sort(unique(unlist(all.authors)))
return(all.authors)
}
#' Create a Markdown document of publications from orcid
#' @param orcid.info The list of info from orcid
#' @param outdir The directory to store the markdown file in
#' @param emphasis.name The name to bold in the publications list. Presumably your own.
#' @param scholar.id Your ID on Google Scholar. NULL if you don't want to use this.
#' @param impact.story..id Your ID on ImpactStory. NULL if you don't want to use this.
#' @param badges Vector of ImpactStory badge names you want to show (a lot are goofy: could do c('global_reach', 'depsy')).
#' @export
CreatePublicationsMarkdown <- function(orcid.info, outdir=tempdir(), emphasis.name = "O'Meara", scholar.id="vpjEkQwAAAAJ", impact.story.id = "0000-0002-0337-5997", badges=c()) {
#lapply(CleanNames(orcid.info$journals), write, paste(outdir, "/publications.bib", sep=""), append=TRUE)
#publications <- RefManageR::ReadBib(paste(outdir, "/publications.bib", sep=""))
#publications <- sort(publications, decreasing=TRUE, sorting="ynt")
#publications.text <- capture.output(print(publications, .opts=list(bib.style="authoryear", dashed=FALSE, max.names=100, style="markdown", sorting="none", no.print.fields=c("URL", "DOI"))))
#publications.text <- gsub(emphasis.name, paste('**', emphasis.name, '**', sep=""), publications.text)
#cat(CleanNames(orcid.info$other.products), file=paste(outdir, "/chapters.bib", sep=""))
#chapters <- RefManageR::ReadBib(paste(outdir, "/chapters.bib", sep=""))
#chapters <- sort(chapters, decreasing=TRUE, sorting="ynt")
#chapters.text <- capture.output(print(chapters, .opts=list(bib.style="authoryear", dashed=FALSE, max.names=100, style="markdown", sorting="none", no.print.fields=c("URL", "DOI"))))
#chapters.text <- gsub(emphasis.name, paste('**', emphasis.name, '**', sep=""), chapters.text)
chapters <- orcid.info$other.products[which(orcid.info$other.products$type=='book-chapter'),]
cat('\n\n## Publications', file=paste(outdir, "/publications.md", sep=""), sep='\n', append=FALSE)
if(!is.null(scholar.id)) {
g.profile <- NULL
try(g.profile <- scholar::get_profile(scholar.id))
if(!is.null(g.profile)) {
cat(paste("\n\nI would recommend reading a few of my best papers to get a sense of my work; good examples are [O'Meara, Smith, et al. (2016)](https://doi.org/10.1098/rspb.2015.2304) and [Beaulieu & O'Meara (2016)](https://doi.org/10.1093/sysbio/syw022). Metrics are not as great (for example, my work with software might get cited than someone else's work on a new discovery about evolution, but it is not clear that the former is 'better') , but I know some people find them useful, so:", ' According to Google Scholar, my work has been cited ', g.profile$total_cites, " times, and my h-index is ", g.profile$h_index, ". (Google Scholar tends to overestimate citations, however). If there were a journal of just my papers, its ", as.numeric(format(Sys.Date(), "%Y"))-1," impact factor would be ",round(orcid.info$impact.factor,3), ". Also note that I work under a very stringent criterion for when I get authorship -- I have to actively make a significant contribution to the research and writing to merit authorship. For example, in 2015-6, three lab members had papers in *Science* ([grad student Sam Borstein](http://science.sciencemag.org/content/350/6264/1077.long), [postdoc Nick Matzke](http://science.sciencemag.org/content/351/6268/28), and [postdoc Sandy Kawano](http://science.sciencemag.org/content/353/6295/154.full)) but I am, appropriately to my mind, not an author on any of these.", sep=""), file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
}
}
if(!is.null(impact.story.id)) {
i.profile <- NULL
try(i.profile <- jsonlite::fromJSON(txt=paste("https://impactstory.org/api/person/", impact.story.id, sep="")))
if(!is.null(i.profile)) {
if(any(i.profile$badges$name %in% badges)) {
cat(paste('\n\nAccording to NSF-funded [ImpactStory.org](https://impactstory.org/u/', impact.story.id, '), a source of altmetrics data (a measure of impact beyond citations), my work has various impacts:', sep=""), file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
for (badge.index in sequence(length(badges))) {
if(badges[badge.index] %in% i.profile$badges$name) {
matching.row <- which(i.profile$badges$name==badges[badge.index])
cat(paste('\n* ', gsub("Your", "My", gsub("your", "my", i.profile$badges$description[matching.row])), " ",i.profile$badges$context[matching.row], sep=""), file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
}
}
}
}
}
journals <- orcid.info$journals[order(orcid.info$journals$`publication-date.year.value`, decreasing=TRUE),]
journals.txt <- '| Authors | Year | Title, Journal | DOI | Citations |\n| -- | -- | -- | -- | -- |'
for (i in sequence(nrow(journals))) {
journals.txt <- paste0(journals.txt, "\n", "| ", journals$author[i], " | ", journals$`publication-date.year.value`[i], " | ", '"', journals$`title.title.value`[i], '"', " ", journals$`journal-title`[i], " ", journals$number[i], " | ", "[", journals$doi[i], "](https://doi.org/", journals$doi[i], ")", " | ", journals$scholar_citations[i], " | ")
}
chapters.txt <- '| Authors | Year | Title | Book |\n| -- | -- | -- | -- |'
for (i in sequence(nrow(chapters))) {
if(nchar(chapters$author[i])>0) {
chapters.txt <- paste0(chapters.txt, "\n", "| ", chapters$author[i], " | ", chapters$`publication-date.year.value`[i], " | ", '"', chapters$`title.title.value`[i], '"', " | ", chapters$`journal-title.value`[i], " | ")
}
}
packages.txt <- '### Packages \n\nSoftware developed in R (often associated with a publication, but not always)\n\n| Package | Authors | Description | Downloads |\n| -- | -- | -- | -- |'
packages <- orcid.info$packages
for (i in sequence(nrow(packages))) {
packages.txt <- paste0(packages.txt, "\n", "| ", packages$NAME[i], " | ", gsub(",,", ",", gsub(" \\[aut, cre\\]", "", gsub(" \\[aut\\]", "", gsub(" ", " ",gsub("\\n", ", ", packages$AUTHOR[i]))))), " | ", packages$DESC_SHORT[i], " | ", packages$downloads[i], " |")
}
cat('\n\n### Papers', file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
cat('\n\n', file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
cat(journals.txt, file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
cat('\n\n## Publications: Books or Book Chapters\n\n', file=paste(outdir, "/publications.md", sep=""), append=TRUE)
cat(chapters.txt, file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
cat(packages.txt, file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
}
#
# #' Create a Markdown document of publications from orcid
# #' @param orcid.info The list of info from orcid
# #' @param outdir The directory to store the markdown file in
# #' @param emphasis.name The name to bold in the publications list. Presumably your own.
# #' @param scholar.id Your ID on Google Scholar. NULL if you don't want to use this.
# #' @param impact.story..id Your ID on ImpactStory. NULL if you don't want to use this.
# #' @param badges Vector of ImpactStory badge names you want to show (a lot are goofy: could do c('global_reach', 'depsy')).
# #' @export
# CreatePublicationsMarkdown <- function(orcid.info, outdir=tempdir(), emphasis.name = "O'Meara", scholar.id="vpjEkQwAAAAJ", impact.story.id = "0000-0002-0337-5997", badges=c()) {
# lapply(CleanNames(orcid.info$journals), write, paste(outdir, "/publications.bib", sep=""), append=TRUE)
# publications <- RefManageR::ReadBib(paste(outdir, "/publications.bib", sep=""))
# publications <- sort(publications, decreasing=TRUE, sorting="ynt")
# publications.text <- capture.output(print(publications, .opts=list(bib.style="authoryear", dashed=FALSE, max.names=100, style="markdown", sorting="none", no.print.fields=c("URL", "DOI"))))
# publications.text <- gsub(emphasis.name, paste('**', emphasis.name, '**', sep=""), publications.text)
#
# cat(CleanNames(orcid.info$other.products), file=paste(outdir, "/chapters.bib", sep=""))
# chapters <- RefManageR::ReadBib(paste(outdir, "/chapters.bib", sep=""))
# chapters <- sort(chapters, decreasing=TRUE, sorting="ynt")
# chapters.text <- capture.output(print(chapters, .opts=list(bib.style="authoryear", dashed=FALSE, max.names=100, style="markdown", sorting="none", no.print.fields=c("URL", "DOI"))))
# chapters.text <- gsub(emphasis.name, paste('**', emphasis.name, '**', sep=""), chapters.text)
#
# cat('\n\n## Publications: Papers', file=paste(outdir, "/publications.md", sep=""), sep='\n', append=FALSE)
# if(!is.null(scholar.id)) {
# g.profile <- NULL
# try(g.profile <- scholar::get_profile(scholar.id))
# if(!is.null(g.profile)) {
# cat(paste('\n\nAccording to Google Scholar, my work has been cited ', g.profile$total_cites, " times, and my h-index is ", g.profile$h_index, ". (Google Scholar tends to overestimate citations, however). Also note that I work under a very stringent criterion for when I get authorship -- I have to actively make a significant contribution to the research and writing to merit authorship. For example, in 2015-6, three lab members had papers in *Science* ([grad student Sam Borstein](http://science.sciencemag.org/content/350/6264/1077.long), [postdoc Nick Matzke](http://science.sciencemag.org/content/351/6268/28), and [postdoc Sandy Kawano](http://science.sciencemag.org/content/353/6295/154.full)) but I am, appropriately to my mind, not an author on any of these.", sep=""), file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
# }
# }
#
# if(!is.null(impact.story.id)) {
# i.profile <- NULL
# try(i.profile <- jsonlite::fromJSON(txt=paste("https://impactstory.org/api/person/", impact.story.id, sep="")))
# if(!is.null(i.profile)) {
# if(any(i.profile$badges$name %in% badges)) {
# cat(paste('\n\nAccording to NSF-funded [ImpactStory.org](https://impactstory.org/u/', impact.story.id, '), a source of altmetrics data (a measure of impact beyond citations), my work has various impacts:', sep=""), file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
# for (badge.index in sequence(length(badges))) {
# if(badges[badge.index] %in% i.profile$badges$name) {
# matching.row <- which(i.profile$badges$name==badges[badge.index])
# cat(paste('\n* ', gsub("Your", "My", gsub("your", "my", i.profile$badges$description[matching.row])), " ",i.profile$badges$context[matching.row], sep=""), file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
#
# }
# }
# }
# }
# }
# #cat('\n\n###Papers', file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
# cat('\n\n', file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
# cat(publications.text, file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
# cat('\n\n## Publications: Books or Book Chapters\n\n', file=paste(outdir, "/publications.md", sep=""), append=TRUE)
# cat(chapters.text, file=paste(outdir, "/publications.md", sep=""), sep='\n', append=TRUE)
# }
#' Compile a set of markdown documents and convert with pandoc
#' @param input Vector of markdown documents
#' @param outdir The directory to store the output in
#' @param css The css file with formatting info.
#' @param output The output base file name. You'll receive <output>.pdf and <output>.html files.
#' @param open.files If TRUE, open the output files
#' @export
#FinalCompileCV <- function(input = c("head.md", "summary.md", "education.md", "employment.md", "publications.md", "teaching.md", "funding.md", "service.md", "postdocs.md", "gradstudents.md", "undergradstudents.md", "gradcommittees.md", "software.md", "presentations.md"), output="OMearaCV.pdf") {
FinalCompileCV <- function(input = c("head.md", "summary.md", "education.md", "employment.md", "publications.md", "teaching.md", "funding.md", "presentations.md", "people.md", "service.md"), outdir=tempdir(), css = system.file("extdata", "format.css", package="cv"), output="OMearaCV", open.files=TRUE) {
original.wd <- getwd()
setwd(outdir)
system(paste("pandoc --css ", css, " -o ", output, ".html ", paste(input, collapse=" "), sep=""))
print(paste("HTML file ", output, ".html has been created in ", outdir, sep=""))
system(paste("wkhtmltopdf ", output, ".html ", output, ".pdf", sep=""))
print(paste("PDF file ", output, ".pdf has been created in ", outdir, sep=""))
#system(paste("pandoc --css ", css, " -o ", output, "_pandoc.pdf ", paste(input, collapse=" "), sep=""))
system(paste("pandoc --css ", css, " -o ", output, ".md ", paste(input, collapse=" "), sep=""))
system(paste("pandoc -reference-doc ", system.file("extdata", "reference.docx", package="cv"), " -o ", output, ".docx ", paste(input, collapse=" "), sep=""))
print(paste("MS Word file ", output, ".docx has been created in ", outdir, sep=""))
system(paste("pandoc -o ", output, "_fromword.pdf ", paste0(output, ".docx"), sep=""))
if(open.files) {
system(paste0("open ", output, ".docx"))
system(paste0("open ", output, ".pdf"))
system(paste0("open ", output, ".html"))
system(paste0("open ."))
}
setwd(original.wd)
}
#' Create a Markdown document from biographical info
#' @param orcid.info The list of info from orcid
#' @param outdir The directory to store the markdown file in
#' @param emphasis.name The name to bold in the publications list. Presumably your own.
#' @param scholar.id Your ID on Google Scholar. NULL if you don't want to use this.
#' @param impact.story..id Your ID on ImpactStory. NULL if you don't want to use this.
#' @export
CreateMarkdown <- function(orcid.info = GetInfoFromOrcid(), outdir=tempdir(), emphasis.name="O'Meara", scholar.id="vpjEkQwAAAAJ", impact.story.id = "0000-0002-0337-5997") {
CreateSummaryMarkdown(orcid.info, outdir)
CreateEducationMarkdown(orcid.info, outdir)
CreateEmploymentMarkdown(orcid.info, outdir)
CreateFundingMarkdown(orcid.info, outdir)
CreatePublicationsMarkdown(orcid.info, outdir, emphasis.name, scholar.id, impact.story.id)
CreatePeopleMarkdown(outdir=outdir)
CreateServiceMarkdown(outdir=outdir)
CreatePresentationsMarkdown(outdir=outdir)
CreateHeadMarkdown(outdir=outdir)
CreateTeachingMarkdown(outdir=outdir)
}
#' Copy the presentations markdown
#' @param outdir The directory to store the markdown file in
#' @export
CreatePresentationsMarkdown <- function(outdir = tempdir()) {
file.copy(system.file("extdata", "presentations.md", package="cv"), outdir)
}
#' Copy the head markdown
#' @param outdir The directory to store the markdown file in
#' @export
CreateHeadMarkdown <- function(outdir = tempdir()) {
file.copy(system.file("extdata", "head.md", package="cv"), outdir)
}
#' Copy the teaching markdown
#' @param outdir The directory to store the markdown file in
#' @export
CreateTeachingMarkdown <- function(outdir = tempdir()) {
file.copy(system.file("extdata", "teaching.md", package="cv"), outdir)
}
#' Pull in info from ORCID
#' @param id Your ORCID id
#' @param scholar_id Your Google Scholar id
#' @param package_author_name A string to search for your packages on CRAN
#' @return A list of info from ORCID
#' @export
GetInfoFromOrcid <- function(id="0000-0002-0337-5997", scholar_id = "vpjEkQwAAAAJ", package_author_name = "Meara") {
#me <- rorcid::orcid_id(id)
#me.pubs <- rorcid::works(me)
#journal.info <- subset(me.pubs, type=="journal-article")
#journal.dois <- c()
# for (i in sequence(nrow(journal.info))) {
# info.df <- journal.info$`external-ids.external-id`[[i]]
# info.df <- subset(info.df, `external-id-type`=="doi")
# if(nrow(info.df)>=1) {
# journal.dois <- append(journal.dois, info.df$`external-id-value`[1])
# }
# }
#my.dois <- rorcid::identifiers(rorcid::works(me))
#journals <- rcrossref::cr_cn(dois = journal.dois, format = "bibtex", .progress="text")
# TO DO: Make sure all entries are bibtex
#journals <- me.pubs$'work-citation.citation'[which(me.pubs$'work-type'=="journal-article")]
print("Pulling in citations from orcid")
citations <- unlist(rorcid::orcid_citations(id)$citation)
cat(citations, file=file.path(tempdir(), "me.bib"), sep="\n\n")
bibs <- as.data.frame(bib2df::bib2df(file.path(tempdir(), "me.bib")), stringsAsFactors=FALSE)
bibs <- bibs[!duplicated(bibs$DOI),]
print("Pulling in info from Google scholar")
scholar <- scholar::get_publications(scholar_id)
print("Pulling in all works from orcid")
publications <- rorcid::orcid_works(id, format="application/json")[[1]][[1]]
publications <- publications[order(publications$`publication-date.month.value`),]
publications <- publications[!duplicated(tolower(publications$title.title.value)),]
publications$doi <- ""
publications$author <- ""
publications$number <- ""
publications$author_scholar <- ""
bibs$TITLE_CLEAN <- gsub('\\textendash', '-', gsub('}', "", gsub('{', "", bibs$TITLE, fixed=TRUE), fixed=TRUE), fixed=TRUE)
for (i in sequence(nrow(publications))) {
ref.info <- publications$`external-ids.external-id`[[i]]
best.match <- agrep(publications$title.title.value[i],bibs$TITLE_CLEAN, ignore.case=TRUE, max.distance=0.5)
if(length(best.match)>1) {
best.match <- which.min(adist(publications$title.title.value[i],bibs$TITLE_CLEAN, ignore.case=TRUE))
}
if(length(ref.info$`external-id-value`[which(ref.info$`external-id-type`=="doi")])>0) {
publications$doi[i] <- ref.info$`external-id-value`[which(ref.info$`external-id-type`=="doi")]
} else {
if(length(best.match)==1) {
publications$doi[i] <- bibs$DOI[best.match]
}
}
if(length(best.match)==1) {
publications$doi[i] <- bibs$DOI[best.match]
#publications$author[i] <- bibs$AUTHOR[best.match]
publications$author[i] <- gsub('\\{\\\\textquotesingle\\}', "'", paste(bibs$AUTHOR[[best.match]], collapse=", "))
publications$author[i] <- gsub("{\\'{e}}", "é", publications$author[i], fixed=TRUE)
publications$author[i] <- gsub("{\\'{a}}", "á", publications$author[i], fixed=TRUE)
publications$author[i] <- gsub("{\\'{o}}", "ó", publications$author[i], fixed=TRUE)
publications$author[i] <- gsub("{'}", "'", publications$author[i], fixed=TRUE)
}
}
# for (i in sequence(nrow(publications))) {
# best.match <- agrep(publications$title.title.value[i],bibs$TITLE)
# if(length(best.match)>1) {
# best.match <- which.min(adist(publications$title.title.value[i],bibs$TITLE))
# }
# if(length(best.match)==1) {
# publications$author[i] <- gsub('\\{\\\\textquotesingle\\}', "'", paste(bibs$AUTHOR[[best.match]], collapse=", "))
# }
# }
for (i in sequence(nrow(publications))) {
best.match <- agrep(publications$title.title.value[i],scholar$title, ignore.case=TRUE)
if(length(best.match)>1) {
best.match <- which.min(adist(publications$title.title.value[i],scholar$title, ignore.case=TRUE))
}
if(length(best.match)==1) {
publications$author_scholar[i] <- as.character(scholar$author)[best.match]
publications$number[i] <- as.character(scholar$number)[best.match]
}
}
publications$scholar_citations <- NA
for (i in sequence(nrow(publications))) {
# print(i)
# print(publications$title.title.value[i])
best.match <- agrep(tolower(publications$title.title.value[i]),tolower(scholar$title), ignore.case=TRUE)
if(length(best.match)>1) {
best.match <- which.min(adist(tolower(publications$title.title.value[i]),tolower(scholar$title), ignore.case=TRUE))
}
#print(scholar$title[best.match])
#print(paste0("Cites ", scholar$cites[best.match]))
if(length(best.match)==1) {
publications$scholar_citations[i] <- scholar$cites[best.match]
}
}
print("Pulling in all R packages from CRAN")
packages <- as.data.frame(packagefinder::exploreFields(package_author_name, c("Maintainer", "Authors@R", "Author"), "or", "like"))
total_dl <- function(x) {
return(sum(cranlogs::cran_downloads(packages=x,from="2005-01-01")$count))
}
packages$downloads <- sapply(packages$NAME, total_dl)
journals <- subset(publications, type=="journal-article")
other.products <- subset(publications, type!="journal-article")
#other.products.raw <- rorcid::orcid_works(id, put_code=other.products.raw$`put-code`)[[1]]
#other.products <- other.products.raw[[1]]$`work.citation.citation-value`
activities <- rorcid::orcid_activities(id)[[1]]
funding <- plyr::rbind.fill(activities$funding$group$`funding-summary`)
funding <- funding[order(funding$`start-date.year.value`, decreasing = TRUE),]
# funding.full <- data.frame()
# for (i in sequence(nrow(funding))) {
# local.funding <- rorcid::orcid_fundings(id, put_code=funding$`put-code`[i])[[1]]
# }
#affiliations <- activities$affiliation
educations <- rorcid::orcid_educations(id)[[1]]$`affiliation-group`
education <- as.data.frame(matrix(unlist(educations$summaries), nrow=length(educations$summaries), byrow=TRUE))
colnames(education) <- gsub("education-summary.", "", names(educations$summaries[[1]]))
#education <- activities$educations$`education-summary`
education <- education[order(education$'end-date.year.value', decreasing=TRUE),]
employments <- rorcid::orcid_employments(id)[[1]]$`affiliation-group`
employment <- data.frame()
for (i in sequence(length(employments$summaries))) {
employment <- plyr::rbind.fill(employment, as.data.frame(employments$summaries[[i]], stringsAsFactors=FALSE))
}
colnames(employment) <- gsub("employment-summary.", "", colnames(employment))
employment <- employment[order(employment$'start-date.year.value', decreasing=TRUE),]
current.year <- as.numeric(format(Sys.Date(), "%Y"))
citation.year <- current.year - 1
paper.years <- c(citation.year-1, citation.year-2)
scholar_previous2 <- scholar[which(scholar$year %in% paper.years),]
scholar_previous2$number <- as.character(scholar_previous2$number)
scholar_previous2$journal <- as.character(scholar_previous2$journal)
scholar_previous2 <- scholar_previous2[which(nchar(scholar_previous2$journal)>0),]
scholar_previous2 <- scholar_previous2[which(nchar(scholar_previous2$number)>0),]
impact.citations <- 0
for (i in sequence(nrow(scholar_previous2))) {
ach <- get_article_cite_history(scholar_id, scholar_previous2$pubid[i])
impact.citations <- sum(impact.citations, ach$cites[which(ach$year==citation.year)], na.rm=TRUE)
}
impact.factor <- impact.citations / nrow(scholar_previous2)
#employment <- activities$employments$`employment-summary`
# employment <- employment[order(employment $'start-date.year.value', decreasing=TRUE),]
return(list(journals=journals, other.products=other.products, funding=funding, education=education, employment=employment, id=id, packages=packages, impact.factor=impact.factor, bibs=bibs, scholar=scholar))
}
#' Create a Markdown document of education from biographical info
#' @param orcid.info The list of info from orcid
#' @param outdir The directory to store the markdown file in
#' @export
CreateEducationMarkdown <- function(orcid.info, outdir=tempdir()) {
education.string <- '\n\n## Education'
for (i in sequence(dim(orcid.info$education)[1])) {
education.string <- paste(education.string, '\n\n', orcid.info$education[i,]$organization.name, ': ', orcid.info$education[i,]$'role-title', " (", orcid.info$education[i,]$'end-date.year.value', ")", sep='')
if(!is.na(orcid.info$education$'department-name')[i]) {
education.string <- paste(education.string, ' in ', orcid.info$education[i,]$'department-name', sep='')
}
}
cat(education.string, file=paste(outdir, "/education.md", sep=""))
}
#' Create a Markdown document of employment history from biographical info
#' @param orcid.info The list of info from orcid
#' @param outdir The directory to store the markdown file in
#' @export
CreateEmploymentMarkdown <- function(orcid.info, outdir=tempdir()) {
employment.string <- '\n\n## Employment'
orcid.info$employment$'end-date.year.value'[which(is.na(orcid.info$employment$'end-date.year.value'))] <- "Present"
for (i in sequence(dim(orcid.info$employment)[1])) {
employment.string <- paste(employment.string, '\n\n', orcid.info$employment[i,]$'start-date.year.value', '-', orcid.info$employment[i,]$'end-date.year.value', ": ", orcid.info$employment[i,]$'role-title', ", ", sep='')
if(!is.na(orcid.info$employment$'department-name')[i]) {
employment.string <- paste(employment.string, "Dept. of ", orcid.info$employment[i,]$'department-name', ", ", sep='')
}
employment.string <- paste(employment.string, orcid.info$employment[i,]$'organization.name', ", ", orcid.info$employment[i,]$'organization.address.city', ", ", orcid.info$employment[i,]$'organization.address.region', sep="")
}
cat(employment.string, file=paste(outdir, "/employment.md", sep=""))
}
#' Create a Markdown document of funding from biographical info
#' @param orcid.info The list of info from orcid
#' @param outdir The directory to store the markdown file in
#' @export
CreateFundingMarkdown <- function(orcid.info, outdir=tempdir(), additional.te = "This is all in addition to other **funding my students have gotten** (NSF EAPSI grant, fellowships from NIMBioS and PEER (an NIH-funded program at UTK), Google Summer of Code funding), **funding for workshops or working groups** (from NIMBioS and the Society for Systematic Biologists), and **funding I got before my faculty position** (NESCent postdoctoral fellowship, NSF DDIG, NSF GRF, and various internal grants at UC Davis).") {
funding.string <- '\n\n## Funding\n\n'
funding.string <- paste(funding.string, additional.te, sep="")
funding.full <- list()
total.funding <- 0
for (i in sequence(nrow(orcid.info$funding))) {
local.funding <- rorcid::orcid_fundings(orcid.info$id, put_code=orcid.info$funding$`put-code`[i])[[1]]
total.funding <- total.funding + as.numeric(local.funding$amount$value)
funding.full[[i]] <- local.funding
}
funding.string <- paste(funding.string, paste(" Total external funding, so far, as a faculty member is $", prettyNum(total.funding, big.mark=",", scientific=FALSE), ".", sep=""), sep="")
funding.string <- paste(funding.string, '\n\n| Year | Title | Funder | Amount |\n| ---- | ------------------------------ | -------- | ------ |', sep="")
# orcid.info$funding <- orcid.info$funding[order(orcid.info$funding$'start-date.year.value', decreasing=TRUE),]
for (i in sequence(length(funding.full))) {
organization <- funding.full[[i]]$organization$name
if (grepl("National Science Foundation", organization, ignore.case=FALSE)) {
organization <- 'NSF'
}
if (grepl("National Institutes of Health", organization, ignore.case=FALSE)) {
organization <- 'NIH'
}
funding.string <- paste(funding.string, '\n| ', funding.full[[i]]$`start-date`$year$value, ' | ', funding.full[[i]]$title$title$value, ' | ', organization, ' | $', prettyNum(as.numeric(funding.full[[i]]$amount$value), big.mark=",", scientific=FALSE), ' |', sep="")
# funding.string <- paste(funding.string, '\n\n', orcid.info$funding[i,]$'funding-title.title.value', " ", orcid.info$funding[i,]$organization.name, ': ', orcid.info$funding[i,]$'role-title', " (", orcid.info$funding[i,]$'end-date.year.value', "): $", orcid.info$funding[i,]$'amount.value', sep='')
# if(!is.null(orcid.info$funding$'department-name')[i]) {
# funding.string <- paste(funding.string, ' in ', orcid.info$funding[i,]$'department-name', sep='')
# }
}
cat(funding.string, file=paste(outdir, "/funding.md", sep=""))
}
#' Create a Markdown document to summarize me
#' @param orcid.info The list of info from orcid
#' @param outdir The directory to store the markdown file in
#' @param publications.offset How to change the publication count.
#'
#' You may want an offset if some of your publications shouldn't count.
#' For example, I have two Nature "papers" that are actually corrigendia,
#' that is, corrections for errors. Shouldn't really count, I think.
#' @export
CreateSummaryMarkdown <- function(orcid.info, outdir=tempdir(), publications.offset=-2, prominent.pubs='*Science, Nature, Ann. Rev Ecology, Evolution & Systematics, Systematic Biology, Evolution*, etc.') {
results <- data.frame(matrix(nrow=6, ncol=2))
colnames(results) <- c("", "")
results[1,1] <- '**Publications**'
results[1,2] <- paste(nrow(orcid.info$journals)+publications.offset, " journal articles, including ", prominent.pubs, sep="")
results[2,1] <- '**Teaching**'
results[2,2] <- "Approximately 2 courses per year on average, ranging from large introductory biology courses to small graduate seminars"
results[3,1] <- '**Mentoring**'
people <- read.delim2(system.file("extdata", "people.txt", package="cv"), stringsAsFactors=FALSE)
results[3,2] <- paste(sum(grepl("PhD student", people$Stage)), " PhD students, ", sum(grepl("Postdoc", people$Stage)), " postdocs, ", sum(grepl("Faculty", people$Stage)), " faculty, ", "and served on ", sum(grepl("Committee", people$Stage)), " graduate student committees", sep="")
results[4,1] <- '**Service/Outreach**'
results[4,2] <- 'Darwin Day TN advisor, curator of R phylogenetics task view, instructor at workshops in Sweden, Switzerland, Brazil, and various US locations (Ohio, TN, NC)'
results[5,1] <- '**Leadership**'
results[5,2] <- 'Associate Head for Dept. of Ecology & Evolutionary Biology, 2016-present; Associate Director for the National Institute for Mathematical and Biological Synthesis, 2016-2018; Code of Conduct Committee for SSE/SSB/ASN, 2018-present; Communications Director for the Society of Systematic Biologists, 2016-2017; Society of Systematic Biologists Council, 2012-2014; iEvoBio co-organizer, 2014-2016.'
results[6,1] <- '**Funding**'
total.funding <- 0
for (i in sequence(nrow(orcid.info$funding))) {
local.funding <- rorcid::orcid_fundings(orcid.info$id, put_code=orcid.info$funding$`put-code`[i])[[1]]
total.funding <- total.funding + as.numeric(local.funding$amount$value)
}
results[6,2] <- paste("$",round((1e-6)*total.funding,2), "M in external support, including ", sum(grepl("National Science Foundation", orcid.info$funding$organization.name)), " NSF grants (including a CAREER grant) plus funding from iPlant and Encyclopedia of Life", sep="")
scholar.id="vpjEkQwAAAAJ"
impact.story.id = "0000-0002-0337-5997"
g.profile <- scholar::get_profile(scholar.id)
github.user <- jsonlite::fromJSON(txt="https://api.github.com/users/bomeara")
i.profile <- jsonlite::fromJSON(txt=paste("https://impactstory.org/api/person/", impact.story.id, sep=""))
i.sources <- i.profile$sources
#results[7,1] <- '**Altmetrics**'
#results[7,2] <- paste("Number of citations = ", g.profile$total_cites, "; h-index = ", g.profile$h_index, "; ", github.user$public_repos, " public github repos; Erdős number = 4; papers have been tweeted about ", subset(i.sources, source_name=="twitter")$posts_count, " times, and have been mentioned ", subset(i.sources, source_name=="news")$posts_count, " times in the news", sep="")
cat('\n\n## Summary\n\n ', file=paste(outdir, "/summary.md", sep=""), sep='\n', append=FALSE)
cat(capture.output(knitr::kable(results, row.names=FALSE)), file=paste(outdir, "/summary.md", sep=""), sep='\n', append=TRUE)
}
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