├── .Rbuildignore ├── .gitattributes ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── DESCRIPTION ├── NAMESPACE ├── R ├── biosketchr-package.R ├── nih_biosketch.R ├── nsf_biosketch.R └── utils.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── biosketchr.Rproj ├── docs ├── 404.html ├── CODE_OF_CONDUCT.html ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── authors.html ├── docsearch.css ├── docsearch.js ├── favicon-16x16.png ├── favicon-32x32.png ├── favicon.ico ├── index.html ├── link.svg ├── logo.png ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── biosketchr-package.html │ ├── figures │ ├── biosketchr_hex.png │ ├── logo.png │ ├── pdf_output_example.png │ ├── select_template.png │ └── skeleton_rmd.png │ ├── index.html │ ├── make_datetbl.html │ ├── make_numbered_citations.html │ └── nih_biosketch.html ├── inst ├── example-data │ ├── appointments-nsf.xlsx │ └── positions-honors-nih.xlsx └── rmarkdown │ └── templates │ ├── nih_biosketch │ ├── resources │ │ └── template.tex │ ├── skeleton │ │ ├── nihbiosketch.cls │ │ ├── skeleton.Rmd │ │ ├── skeleton.pdf │ │ ├── skeleton.tex │ │ └── yourbibfile.bib │ └── template.yaml │ └── nsf_biosketch │ ├── resources │ └── template.tex │ ├── skeleton │ ├── skeleton.Rmd │ └── yourbibfile.bib │ └── template.yaml ├── man ├── biosketchr-package.Rd ├── figures │ ├── logo.png │ ├── pdf_output_example.png │ ├── select_template.png │ └── skeleton_rmd.png ├── make_datetbl_nih.Rd ├── make_datetbl_nsf.Rd ├── make_numbered_citations.Rd ├── nih_biosketch.Rd └── nsf_biosketch.Rd └── pkgdown └── favicon ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── favicon-16x16.png ├── favicon-32x32.png └── favicon.ico /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^README\.Rmd$ 2 | ^LICENSE\.md$ 3 | \.Rproj$ 4 | ^\.Rproj\.user$ 5 | ^\.travis\.yml$ 6 | ^_pkgdown\.yml$ 7 | ^docs$ 8 | ^pkgdown$ 9 | ^CODE_OF_CONDUCT\.md$ 10 | ^\.github$ 11 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | # Auto detect text files and perform LF normalization 2 | * text=auto 3 | -------------------------------------------------------------------------------- /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | -------------------------------------------------------------------------------- /.github/workflows/R-CMD-check.yaml: -------------------------------------------------------------------------------- 1 | # Workflow derived from https://github.com/r-lib/actions/tree/master/examples 2 | # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help 3 | on: 4 | push: 5 | branches: [main, master] 6 | pull_request: 7 | branches: [main, master] 8 | 9 | name: R-CMD-check 10 | 11 | jobs: 12 | R-CMD-check: 13 | runs-on: ubuntu-latest 14 | env: 15 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} 16 | R_KEEP_PKG_SOURCE: yes 17 | steps: 18 | - uses: actions/checkout@v2 19 | 20 | - uses: r-lib/actions/setup-r@v1 21 | with: 22 | use-public-rspm: true 23 | 24 | - uses: r-lib/actions/setup-r-dependencies@v1 25 | with: 26 | extra-packages: rcmdcheck 27 | 28 | - uses: r-lib/actions/check-r-package@v1 29 | 30 | - name: Show testthat output 31 | if: always() 32 | run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true 33 | shell: bash 34 | 35 | - name: Upload check results 36 | if: failure() 37 | uses: actions/upload-artifact@main 38 | with: 39 | name: ${{ runner.os }}-r${{ matrix.config.r }}-results 40 | path: check 41 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | ## Core latex/pdflatex auxiliary files: 2 | *.aux 3 | *.lof 4 | *.log 5 | *.lot 6 | *.fls 7 | *.out 8 | *.toc 9 | 10 | ## Intermediate documents: 11 | *.dvi 12 | *-converted-to.* 13 | # these rules might exclude image files for figures etc. 14 | # *.ps 15 | # *.eps 16 | # *.pdf 17 | 18 | ## Bibliography auxiliary files (bibtex/biblatex/biber): 19 | *.bbl 20 | *.bcf 21 | *.blg 22 | *-blx.aux 23 | *-blx.bib 24 | *.brf 25 | *.run.xml 26 | 27 | ## Build tool auxiliary files: 28 | *.fdb_latexmk 29 | *.synctex 30 | *.synctex.gz 31 | *.synctex.gz(busy) 32 | *.pdfsync 33 | 34 | ## Auxiliary and intermediate files from other packages: 35 | 36 | # algorithms 37 | *.alg 38 | *.loa 39 | 40 | # achemso 41 | acs-*.bib 42 | 43 | # amsthm 44 | *.thm 45 | 46 | # beamer 47 | *.nav 48 | *.snm 49 | *.vrb 50 | 51 | #(e)ledmac/(e)ledpar 52 | *.end 53 | *.[1-9] 54 | *.[1-9][0-9] 55 | *.[1-9][0-9][0-9] 56 | *.[1-9]R 57 | *.[1-9][0-9]R 58 | *.[1-9][0-9][0-9]R 59 | *.eledsec[1-9] 60 | *.eledsec[1-9]R 61 | *.eledsec[1-9][0-9] 62 | *.eledsec[1-9][0-9]R 63 | *.eledsec[1-9][0-9][0-9] 64 | *.eledsec[1-9][0-9][0-9]R 65 | 66 | # glossaries 67 | *.acn 68 | *.acr 69 | *.glg 70 | *.glo 71 | *.gls 72 | 73 | # gnuplottex 74 | *-gnuplottex-* 75 | 76 | # hyperref 77 | *.brf 78 | 79 | # knitr 80 | *-concordance.tex 81 | *.tikz 82 | *-tikzDictionary 83 | 84 | # listings 85 | *.lol 86 | 87 | # makeidx 88 | *.idx 89 | *.ilg 90 | *.ind 91 | *.ist 92 | 93 | # minitoc 94 | *.maf 95 | *.mtc 96 | *.mtc0 97 | 98 | # minted 99 | _minted* 100 | *.pyg 101 | 102 | # morewrites 103 | *.mw 104 | 105 | # nomencl 106 | *.nlo 107 | 108 | # sagetex 109 | *.sagetex.sage 110 | *.sagetex.py 111 | *.sagetex.scmd 112 | 113 | # sympy 114 | *.sout 115 | *.sympy 116 | sympy-plots-for-*.tex/ 117 | 118 | # todonotes 119 | *.tdo 120 | 121 | # xindy 122 | *.xdy 123 | 124 | # WinEdt 125 | *.bak 126 | *.sav 127 | .Rproj.user 128 | 129 | .DS_Store 130 | -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- 1 | # Contributor Code of Conduct 2 | 3 | As contributors and maintainers of this project, we pledge to respect all people who 4 | contribute through reporting issues, posting feature requests, updating documentation, 5 | submitting pull requests or patches, and other activities. 6 | 7 | We are committed to making participation in this project a harassment-free experience for 8 | everyone, regardless of level of experience, gender, gender identity and expression, 9 | sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion. 10 | 11 | Examples of unacceptable behavior by participants include the use of sexual language or 12 | imagery, derogatory comments or personal attacks, trolling, public or private harassment, 13 | insults, or other unprofessional conduct. 14 | 15 | Project maintainers have the right and responsibility to remove, edit, or reject comments, 16 | commits, code, wiki edits, issues, and other contributions that are not aligned to this 17 | Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 18 | from the project team. 19 | 20 | Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by 21 | opening an issue or contacting one or more of the project maintainers. 22 | 23 | This Code of Conduct is adapted from the Contributor Covenant 24 | (https://www.contributor-covenant.org), version 1.0.0, available at 25 | https://contributor-covenant.org/version/1/0/0/. 26 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: biosketchr 2 | Type: Package 3 | Title: biosketchr 4 | Version: 0.1.5 5 | Authors@R: c(person("Tyson S.", "Barrett", 6 | role=c("aut","cre"), 7 | email = "t.barrett88@gmail.com", 8 | comment = c(ORCID = "0000-0002-2137-1391")), 9 | person("Daniel", "Anderson", 10 | role=c("aut"), 11 | email = "daniela@uoregon.edu", 12 | comment = c(ORCID = "https://orcid.org/0000-0003-4699-4680")) 13 | ) 14 | Maintainer: Tyson S. Barrett 15 | Description: Provides the template and functions that make creating a 16 | Biosketch for NIH and NSF proposals easier. 17 | Imports: 18 | rmarkdown, 19 | knitr, 20 | yaml 21 | Suggests: 22 | dplyr 23 | License: GPL-2 24 | Encoding: UTF-8 25 | LazyData: true 26 | RoxygenNote: 6.1.1 27 | -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 1 | # Generated by roxygen2: do not edit by hand 2 | 3 | export(make_datetbl_nih) 4 | export(make_datetbl_nsf) 5 | export(make_numbered_citations) 6 | export(nih_biosketch) 7 | export(nsf_biosketch) 8 | import(yaml) 9 | -------------------------------------------------------------------------------- /R/biosketchr-package.R: -------------------------------------------------------------------------------- 1 | #' @keywords internal 2 | "_PACKAGE" 3 | 4 | # The following block is used by usethis to automatically manage 5 | # roxygen namespace tags. Modify with care! 6 | ## usethis namespace: start 7 | ## usethis namespace: end 8 | NULL 9 | -------------------------------------------------------------------------------- /R/nih_biosketch.R: -------------------------------------------------------------------------------- 1 | #' NIH Biosketch format. 2 | #' 3 | #' Format for creating NIH Biosketches. Does not use an official template but should approximate the format required by NIH. Is built on the template created by Paul Magwene found here: https://github.com/pmagwene/latex-nihbiosketch. 4 | #' 5 | #' @inheritParams rmarkdown::pdf_document 6 | #' @param ... Additional arguments to \code{rmarkdown::pdf_document} 7 | #' 8 | #' @return R Markdown output format to pass to 9 | #' \code{\link[rmarkdown:render]{render}} 10 | #' 11 | #' @details Possible arguments for the YAML header are: 12 | #' \itemize{ 13 | #' \item \code{name} Your Full Name 14 | #' \item \code{eracommons} Your ERA Commons ID 15 | #' \item \code{position} Description of your research position 16 | #' \item \code{education} Your education attainment (include any Bachelors, Masters, Doctorate, Postdoc). Several items are required for the education: 1) degree, 2) school, 3) date, and 4) field. 17 | #' \item \code{researchsupport} Both \code{ongoing} and \code{completed} research support received. Several items are required for the research support for both ongoing and completed: 1) grant, 2) PI, 3) dates, 4) title, 5) description, and 6) role. 18 | #' \item \code{bibliography} The name of the bib file 19 | #' \item \code{bibliographystyle} The bib style 20 | #' \item \code{output} Should be one of the formats from \code{biosketchr} 21 | #' } 22 | #' 23 | #' 24 | #' @import yaml 25 | #' 26 | #' @export 27 | nih_biosketch <- function(..., highlight = NULL, citation_package = "none") { 28 | 29 | # Find template in biosketchr 30 | template_file <- 31 | system.file("rmarkdown", "templates", "nih_biosketch", 32 | file.path("resources", "template.tex"), 33 | package = "biosketchr") 34 | 35 | # Check template file exists 36 | .check_template(template_file) 37 | 38 | # Render the pdf_document with parameters 39 | pdf <- 40 | rmarkdown::pdf_document( 41 | ..., 42 | template = template_file, 43 | highlight = highlight, 44 | citation_package = citation_package 45 | ) 46 | 47 | # Documentation of inherits 48 | pdf$inherits <- "pdf_document" 49 | 50 | # Check pre-rendered output 51 | .check_pdf(pdf) 52 | 53 | # Return pre-rendered output 54 | pdf 55 | } 56 | 57 | #' Format positions data into a table for NIH 58 | #' 59 | #' Transforms a standard R data frame into a LaTeX \code{datetbl}. 60 | #' 61 | #' @param d Dataset including the information 62 | #' @param start_date Name of column denoting the year the position started or honor was awarded 63 | #' @param end_date Name of column denoting the year the position ended 64 | #' @param description Name of column describing the full description of the position/honor, including title, department, university, and location 65 | #' @param order Optional integer argument listing the order of entries 66 | #' @param trailing_dashes If end date is empty, should the start date have trailing dashes? Defaults to \code{TRUE}. 67 | #' 68 | #' @return LaTex \code{datetbl} 69 | #' @export 70 | 71 | make_datetbl_nih <- function(d, start_date, end_date, description, 72 | order = NULL, trailing_dashes = TRUE) { 73 | if(!is.null(order)) { 74 | d <- d[order(d[["order"]]), ] 75 | } 76 | 77 | description <- gsub("\\&", "\\\\&", d[["description"]]) 78 | pasted <- with(d, paste0(start_date, "--", end_date, " & ", 79 | description, " \\\\")) 80 | pasted <- gsub("NA ", " ", pasted) 81 | 82 | if(!trailing_dashes) { 83 | pasted <- gsub("-- ", " ", pasted) 84 | } 85 | 86 | cat("\\begin{datetbl}", pasted, "\\end{datetbl}", sep = "\n") 87 | } 88 | 89 | 90 | #' Format Numbered Citations 91 | #' 92 | #' Formats a list of keys into a LaTeX \code{enumerated list} of references. 93 | #' 94 | #' @param ... keys from the`.bib` file in order of appearance in biosketch 95 | #' @param NIH Is the biosketch being produced for NIH? Defaults to \code{TRUE} and is currently the only option. 96 | #' 97 | #' @return LaTex \code{enumerated list} 98 | #' @export 99 | 100 | make_numbered_citations <- function(..., NIH = TRUE) { 101 | 102 | keys <- list(...) 103 | 104 | if(NIH) { 105 | .check_4_cites_nih(keys) 106 | } 107 | 108 | pasted <- paste0(" \\item \\bibentry{", keys, "}") 109 | 110 | cat("\\begin{enumerate}", pasted, "\\end{enumerate}", sep = "\n") 111 | } 112 | 113 | 114 | -------------------------------------------------------------------------------- /R/nsf_biosketch.R: -------------------------------------------------------------------------------- 1 | #' NSF Biosketch format. 2 | #' 3 | #' Format for creating NIH Biosketches. Does not use an official template but should approximate the format required by NIH. Is built on the template created by Paul Magwene found here: https://github.com/pmagwene/latex-nihbiosketch. 4 | #' 5 | #' @inheritParams rmarkdown::pdf_document 6 | #' @param ... Additional arguments to \code{rmarkdown::pdf_document} 7 | #' 8 | #' @return R Markdown output format to pass to 9 | #' \code{\link[rmarkdown:render]{render}} 10 | #' 11 | #' @details Possible arguments for the YAML header are: 12 | #' \itemize{ 13 | #' \item \code{name} Your Full Name (can include prefix such as Dr.) 14 | #' \item \code{department} Your current department 15 | #' \item \code{university} Your current university or company 16 | #' \item \code{email} Your current email 17 | #' \item \code{telephone} Your current telephone number 18 | #' \item \code{preparation} Both degrees earned and positions worked in relevant to proposal. Four items are required for the education: 1) location, 2) field, 3) degree, and 4) dates. 19 | #' \item \code{bibliography} The name of the bib file 20 | #' \item \code{bibliographystyle} The bib style 21 | #' \item \code{output} Should be one of the formats from \code{biosketchr} 22 | #' } 23 | #' 24 | #' 25 | #' @import yaml 26 | #' 27 | #' @export 28 | nsf_biosketch <- function(..., highlight = NULL, citation_package = "none") { 29 | 30 | # Find template in biosketchr 31 | template_file <- 32 | system.file("rmarkdown", "templates", "nsf_biosketch", 33 | file.path("resources", "template.tex"), 34 | package = "biosketchr") 35 | 36 | # Check template file exists 37 | .check_template(template_file) 38 | 39 | # Render the pdf_document with parameters 40 | pdf <- 41 | rmarkdown::pdf_document( 42 | ..., 43 | template = template_file, 44 | highlight = highlight, 45 | citation_package = citation_package 46 | ) 47 | 48 | # Documentation of inherits 49 | pdf$inherits <- "pdf_document" 50 | 51 | # Check pre-rendered output 52 | .check_pdf(pdf) 53 | 54 | # Return pre-rendered output 55 | pdf 56 | } 57 | 58 | 59 | 60 | #' Format positions data into a table for NSF 61 | #' 62 | #' Transforms a standard R data frame into a LaTeX \code{table}. 63 | #' 64 | #' @param d Dataset including the information 65 | #' @param start_date Name of column denoting the year the position started or honor was awarded 66 | #' @param end_date Name of column denoting the year the position ended 67 | #' @param position Name of column describing the name of the position 68 | #' @param location Name of column denoting the location of position 69 | #' @param order Optional integer argument listing the order of entries 70 | #' @param trailing_dashes If end date is empty, should the start date have trailing dashes? Defaults to \code{TRUE}. 71 | #' 72 | #' @return LaTex \code{itemize} 73 | #' @export 74 | 75 | make_datetbl_nsf <- function(d, start_date, end_date, position, location, 76 | order = NULL, trailing_dashes = TRUE) { 77 | if(!is.null(order)) { 78 | d <- d[order(d[["order"]]), ] 79 | } 80 | 81 | d[] <- lapply(d, function(x) gsub( "\\&", "\\\\&", x)) 82 | 83 | pasted <- with(d, paste0(" \\item[", start_date, "--", end_date, ":] \n ", 84 | "\\textbf{", position, "}, \n ", 85 | location, " \n")) 86 | pasted <- gsub("NA ", " ", pasted) 87 | 88 | if(!trailing_dashes) { 89 | pasted <- gsub("-- ", " ", pasted) 90 | } 91 | 92 | cat("\\begin{itemize}[label={\\quad 9999--9999:},leftmargin=*,itemsep=0pt]", 93 | pasted, 94 | "\\end{itemize}", 95 | sep = "\n") 96 | } 97 | 98 | 99 | 100 | -------------------------------------------------------------------------------- /R/utils.R: -------------------------------------------------------------------------------- 1 | 2 | 3 | .check_template <-function(template, file){ 4 | if (template == "") 5 | stop("Couldn't find template file for biosketchr", call. = FALSE) 6 | } 7 | 8 | .check_pdf <- function(pdf){ 9 | # Stop if null 10 | if (is.null(pdf)) 11 | stop("Something went wrong, possibly in the yaml. Does it have all the necessary components? ", call. = FALSE) 12 | } 13 | 14 | .check_4_cites_nih <- function(x){ 15 | if (length(x) > 4) 16 | warning("Only 4 references are allowed in NIH biosketch.", call. = FALSE) 17 | } 18 | -------------------------------------------------------------------------------- /README.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | output: github_document 3 | --- 4 | 5 | 6 | 7 | ```{r setup, include = FALSE} 8 | knitr::opts_chunk$set( 9 | collapse = TRUE, 10 | comment = "#>", 11 | fig.path = "man/figures/README-", 12 | out.width = "100%" 13 | ) 14 | devtools::load_all() 15 | ``` 16 | 17 | # `biosketchr` `v`r packageVersion("biosketchr")`` 18 | 19 | 20 | [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental) 21 | [![Build Status](https://travis-ci.com/TysonStanley/biosketchr.svg?branch=master)](https://travis-ci.com/TysonStanley/biosketchr) 22 | [![R-CMD-check](https://github.com/TysonStanley/biosketchr/workflows/R-CMD-check/badge.svg)](https://github.com/TysonStanley/biosketchr/actions) 23 | 24 | 25 | 26 | 27 | 28 | The goal of `biosketchr` is to make two aspects of creating a Biosketch for either NIH (National Institutes of Health in the United States) or NSF (National Science Foundation in the United States) better: 29 | 30 | 1. Formatting of the biosketch is automatically done for you 31 | 2. The citations are automatically formatted and inserted in the document 32 | 33 | ## Installation 34 | 35 | You can install `biosketchr` with: 36 | 37 | ``` r 38 | remotes::install_github("tysonstanley/biosketchr") 39 | ``` 40 | 41 | ## LaTeX 42 | 43 | #### NIH Template 44 | 45 | The template was created by Paul M. Magwene and can be found at: [github.com/pmagwene/latex-nihbiosketch](https://github.com/pmagwene/latex-nihbiosketch). 46 | 47 | #### NSF Template 48 | 49 | The template was created by Theodore P. Pavlic and can be found [here](http://phaseportrait.blogspot.co.uk/2013/02/latex-template-for-nsf-style.html). 50 | 51 | ## Example 52 | 53 | To start, you'll want to select the appropriate template (for this example, the NIH one) from the `biosketchr` package. This will create a folder with whatever name you choose that contains an `Rmd` file, the appropriate `.cls` file, and a `.bib` file. 54 | 55 | 56 | 57 | The `.Rmd` file will open automatically showing you this template. 58 | 59 | 60 | 61 | This is where you'll do all the editing, writing your statement, fill in education, etc. You'll also want to edit the `yourbibfile.bib` file with your citations that you want to include in the biosketch. 62 | 63 | When you `knit` this, it will produce a PDF file in the same folder that is formatted like the appropriate biosketch. This PDF will look something like the following: 64 | 65 | 66 | 67 | A very similar process works for the NSF template, with slighty different fields in the skeleton RMarkdown file. 68 | 69 | Enjoy biosketching with RMarkdown! 70 | 71 | 72 | ## Note 73 | 74 | The package is still undergoing some development and we would love feedback on any aspect that doesn't work as expected. 75 | 76 | We also want to thank the [`rticles`](https://github.com/rstudio/rticles) package for showing how to create RMarkdown templates such as in `biosketchr`. 77 | 78 | Please note that the 'biosketchr' project is released with a 79 | [Contributor Code of Conduct](CODE_OF_CONDUCT.md). 80 | By contributing to this project, you agree to abide by its terms. 81 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | # `biosketchr` `v0.1.5` 5 | 6 | 7 | 8 | [![Lifecycle: 9 | experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental) 10 | [![Build 11 | Status](https://travis-ci.com/TysonStanley/biosketchr.svg?branch=master)](https://travis-ci.com/TysonStanley/biosketchr) 12 | [![R-CMD-check](https://github.com/TysonStanley/biosketchr/workflows/R-CMD-check/badge.svg)](https://github.com/TysonStanley/biosketchr/actions) 13 | 14 | 15 | The goal of `biosketchr` is to make two aspects of creating a Biosketch 16 | for either NIH (National Institutes of Health in the United States) or 17 | NSF (National Science Foundation in the United States) better: 18 | 19 | 1. Formatting of the biosketch is automatically done for you 20 | 2. The citations are automatically formatted and inserted in the 21 | document 22 | 23 | ## Installation 24 | 25 | You can install `biosketchr` with: 26 | 27 | ``` r 28 | remotes::install_github("tysonstanley/biosketchr") 29 | ``` 30 | 31 | ## LaTeX 32 | 33 | #### NIH Template 34 | 35 | The template was created by Paul M. Magwene and can be found at: 36 | [github.com/pmagwene/latex-nihbiosketch](https://github.com/pmagwene/latex-nihbiosketch). 37 | 38 | #### NSF Template 39 | 40 | The template was created by Theodore P. Pavlic and can be found 41 | [here](http://phaseportrait.blogspot.co.uk/2013/02/latex-template-for-nsf-style.html). 42 | 43 | ## Example 44 | 45 | To start, you’ll want to select the appropriate template (for this 46 | example, the NIH one) from the `biosketchr` package. This will create a 47 | folder with whatever name you choose that contains an `Rmd` file, the 48 | appropriate `.cls` file, and a `.bib` file. 49 | 50 | 51 | 52 | The `.Rmd` file will open automatically showing you this template. 53 | 54 | 55 | 56 | This is where you’ll do all the editing, writing your statement, fill in 57 | education, etc. You’ll also want to edit the `yourbibfile.bib` file with 58 | your citations that you want to include in the biosketch. 59 | 60 | When you `knit` this, it will produce a PDF file in the same folder that 61 | is formatted like the appropriate biosketch. This PDF will look 62 | something like the following: 63 | 64 | 65 | 66 | A very similar process works for the NSF template, with slighty 67 | different fields in the skeleton RMarkdown file. 68 | 69 | Enjoy biosketching with RMarkdown! 70 | 71 | ## Note 72 | 73 | The package is still undergoing some development and we would love 74 | feedback on any aspect that doesn’t work as expected. 75 | 76 | We also want to thank the 77 | [`rticles`](https://github.com/rstudio/rticles) package for showing how 78 | to create RMarkdown templates such as in `biosketchr`. 79 | 80 | Please note that the ‘biosketchr’ project is released with a 81 | [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to 82 | this project, you agree to abide by its terms. 83 | -------------------------------------------------------------------------------- /_pkgdown.yml: -------------------------------------------------------------------------------- 1 | destination: docs 2 | -------------------------------------------------------------------------------- /biosketchr.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: Sweave 13 | LaTeX: XeLaTeX 14 | 15 | BuildType: Package 16 | PackageUseDevtools: Yes 17 | PackageInstallArgs: --no-multiarch --with-keep.source 18 | -------------------------------------------------------------------------------- /docs/404.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | Page not found (404) • biosketchr 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 60 | 61 | 62 | 63 | 64 | 65 | 66 |
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Developed by Tyson S. Barrett, Daniel Anderson.

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Contributor Code of Conduct

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As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.

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We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.

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Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.

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Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed from the project team.

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Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.

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This Code of Conduct is adapted from the Contributor Covenant (https://www.contributor-covenant.org), version 1.0.0, available at https://contributor-covenant.org/version/1/0/0/.

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Developed by Tyson S. Barrett, Daniel Anderson.

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Site built with pkgdown 1.4.1.

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140 | 141 | 142 | 143 | 144 | 145 | 146 | 147 | 148 | -------------------------------------------------------------------------------- /docs/apple-touch-icon-120x120.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/apple-touch-icon-120x120.png -------------------------------------------------------------------------------- /docs/apple-touch-icon-152x152.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/apple-touch-icon-152x152.png -------------------------------------------------------------------------------- /docs/apple-touch-icon-180x180.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/apple-touch-icon-180x180.png -------------------------------------------------------------------------------- /docs/apple-touch-icon-60x60.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/apple-touch-icon-60x60.png -------------------------------------------------------------------------------- /docs/apple-touch-icon-76x76.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/apple-touch-icon-76x76.png -------------------------------------------------------------------------------- /docs/apple-touch-icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/apple-touch-icon.png -------------------------------------------------------------------------------- /docs/authors.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | Authors • biosketchr 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 60 | 61 | 62 | 63 | 64 | 65 | 66 |
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Authors

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    Tyson S. Barrett. Author, maintainer. ORCID 116 |

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    Daniel Anderson. Author. ORCID 120 |

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Developed by Tyson S. Barrett, Daniel Anderson.

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Site built with pkgdown 1.4.1.

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141 | 142 | 143 | 144 | 145 | 146 | 147 | 148 | 149 | -------------------------------------------------------------------------------- /docs/docsearch.css: -------------------------------------------------------------------------------- 1 | /* Docsearch -------------------------------------------------------------- */ 2 | /* 3 | Source: https://github.com/algolia/docsearch/ 4 | License: MIT 5 | */ 6 | 7 | .algolia-autocomplete { 8 | display: block; 9 | -webkit-box-flex: 1; 10 | -ms-flex: 1; 11 | flex: 1 12 | } 13 | 14 | .algolia-autocomplete .ds-dropdown-menu { 15 | width: 100%; 16 | min-width: none; 17 | max-width: none; 18 | padding: .75rem 0; 19 | background-color: #fff; 20 | background-clip: padding-box; 21 | border: 1px solid rgba(0, 0, 0, .1); 22 | box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175); 23 | } 24 | 25 | @media (min-width:768px) { 26 | .algolia-autocomplete .ds-dropdown-menu { 27 | width: 175% 28 | } 29 | } 30 | 31 | .algolia-autocomplete .ds-dropdown-menu::before { 32 | display: none 33 | } 34 | 35 | .algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] { 36 | padding: 0; 37 | background-color: rgb(255,255,255); 38 | border: 0; 39 | max-height: 80vh; 40 | } 41 | 42 | .algolia-autocomplete .ds-dropdown-menu .ds-suggestions { 43 | margin-top: 0 44 | } 45 | 46 | .algolia-autocomplete .algolia-docsearch-suggestion { 47 | padding: 0; 48 | overflow: visible 49 | } 50 | 51 | .algolia-autocomplete .algolia-docsearch-suggestion--category-header { 52 | padding: .125rem 1rem; 53 | margin-top: 0; 54 | font-size: 1.3em; 55 | font-weight: 500; 56 | color: #00008B; 57 | border-bottom: 0 58 | } 59 | 60 | .algolia-autocomplete .algolia-docsearch-suggestion--wrapper { 61 | float: none; 62 | padding-top: 0 63 | } 64 | 65 | .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column { 66 | float: none; 67 | width: auto; 68 | padding: 0; 69 | text-align: left 70 | } 71 | 72 | .algolia-autocomplete .algolia-docsearch-suggestion--content { 73 | float: none; 74 | width: auto; 75 | padding: 0 76 | } 77 | 78 | .algolia-autocomplete .algolia-docsearch-suggestion--content::before { 79 | display: none 80 | } 81 | 82 | .algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header { 83 | padding-top: .75rem; 84 | margin-top: .75rem; 85 | border-top: 1px solid rgba(0, 0, 0, .1) 86 | } 87 | 88 | .algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column { 89 | display: block; 90 | padding: .1rem 1rem; 91 | margin-bottom: 0.1; 92 | font-size: 1.0em; 93 | font-weight: 400 94 | /* display: none */ 95 | } 96 | 97 | .algolia-autocomplete .algolia-docsearch-suggestion--title { 98 | display: block; 99 | padding: .25rem 1rem; 100 | margin-bottom: 0; 101 | font-size: 0.9em; 102 | font-weight: 400 103 | } 104 | 105 | .algolia-autocomplete .algolia-docsearch-suggestion--text { 106 | padding: 0 1rem .5rem; 107 | margin-top: -.25rem; 108 | font-size: 0.8em; 109 | font-weight: 400; 110 | line-height: 1.25 111 | } 112 | 113 | .algolia-autocomplete .algolia-docsearch-footer { 114 | width: 110px; 115 | height: 20px; 116 | z-index: 3; 117 | margin-top: 10.66667px; 118 | float: right; 119 | font-size: 0; 120 | line-height: 0; 121 | } 122 | 123 | .algolia-autocomplete .algolia-docsearch-footer--logo { 124 | background-image: url("data:image/svg+xml;utf8,"); 125 | background-repeat: no-repeat; 126 | background-position: 50%; 127 | background-size: 100%; 128 | overflow: hidden; 129 | text-indent: -9000px; 130 | width: 100%; 131 | height: 100%; 132 | display: block; 133 | transform: translate(-8px); 134 | } 135 | 136 | .algolia-autocomplete .algolia-docsearch-suggestion--highlight { 137 | color: #FF8C00; 138 | background: rgba(232, 189, 54, 0.1) 139 | } 140 | 141 | 142 | .algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight { 143 | box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5) 144 | } 145 | 146 | .algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content { 147 | background-color: rgba(192, 192, 192, .15) 148 | } 149 | -------------------------------------------------------------------------------- /docs/docsearch.js: -------------------------------------------------------------------------------- 1 | $(function() { 2 | 3 | // register a handler to move the focus to the search bar 4 | // upon pressing shift + "/" (i.e. "?") 5 | $(document).on('keydown', function(e) { 6 | if (e.shiftKey && e.keyCode == 191) { 7 | e.preventDefault(); 8 | $("#search-input").focus(); 9 | } 10 | }); 11 | 12 | $(document).ready(function() { 13 | // do keyword highlighting 14 | /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */ 15 | var mark = function() { 16 | 17 | var referrer = document.URL ; 18 | var paramKey = "q" ; 19 | 20 | if (referrer.indexOf("?") !== -1) { 21 | var qs = referrer.substr(referrer.indexOf('?') + 1); 22 | var qs_noanchor = qs.split('#')[0]; 23 | var qsa = qs_noanchor.split('&'); 24 | var keyword = ""; 25 | 26 | for (var i = 0; i < qsa.length; i++) { 27 | var currentParam = qsa[i].split('='); 28 | 29 | if (currentParam.length !== 2) { 30 | continue; 31 | } 32 | 33 | if (currentParam[0] == paramKey) { 34 | keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20")); 35 | } 36 | } 37 | 38 | if (keyword !== "") { 39 | $(".contents").unmark({ 40 | done: function() { 41 | $(".contents").mark(keyword); 42 | } 43 | }); 44 | } 45 | } 46 | }; 47 | 48 | mark(); 49 | }); 50 | }); 51 | 52 | /* Search term highlighting ------------------------------*/ 53 | 54 | function matchedWords(hit) { 55 | var words = []; 56 | 57 | var hierarchy = hit._highlightResult.hierarchy; 58 | // loop to fetch from lvl0, lvl1, etc. 59 | for (var idx in hierarchy) { 60 | words = words.concat(hierarchy[idx].matchedWords); 61 | } 62 | 63 | var content = hit._highlightResult.content; 64 | if (content) { 65 | words = words.concat(content.matchedWords); 66 | } 67 | 68 | // return unique words 69 | var words_uniq = [...new Set(words)]; 70 | return words_uniq; 71 | } 72 | 73 | function updateHitURL(hit) { 74 | 75 | var words = matchedWords(hit); 76 | var url = ""; 77 | 78 | if (hit.anchor) { 79 | url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor; 80 | } else { 81 | url = hit.url + '?q=' + escape(words.join(" ")); 82 | } 83 | 84 | return url; 85 | } 86 | -------------------------------------------------------------------------------- /docs/favicon-16x16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/favicon-16x16.png -------------------------------------------------------------------------------- /docs/favicon-32x32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/favicon-32x32.png -------------------------------------------------------------------------------- /docs/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/favicon.ico -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | biosketchr • biosketchr 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 27 | 28 | 29 |
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71 | biosketchr v0.1.3 72 |

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The goal of biosketchr is to make two aspects of creating a Biosketch better:

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  1. Formatting of the biosketch is automatically done for you
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  2. The citations are automatically formatted and inserted in the document
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82 | Installation

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You can install biosketchr with:

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remotes::install_github("tysonstanley/biosketchr")
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88 | LaTeX

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The template was created by Paul M. Magwene and can be found at: github.com/pmagwene/latex-nihbiosketch.

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93 | Example

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To start, you’ll want to select the appropriate template (currently only the NIH one) from the biosketchr package. This will create a folder with whatever name you choose that contains an Rmd file, the appropriate .cls file, and a .bib file.

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The .Rmd file will open automatically showing you this template.

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This is where you’ll do all the editing, writing your statement, fill in education, etc. You’ll also want to edit the yourbibfile.bib file with your citations that you want to include in the biosketch.

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When you knit this, it will produce a PDF file in the same folder that is formatted like the appropriate biosketch. This PDF will look something like the following:

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Enjoy biosketching with RMarkdown!

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105 | Note

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The package is still undergoing some development and we would love feedback on any aspect that doesn’t work as expected.

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We also want to thank the rticles package for showing how to create RMarkdown templates such as in biosketchr.

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Please note that the ‘biosketchr’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

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Developed by Tyson S. Barrett, Daniel Anderson.

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Site built with pkgdown 1.4.1.

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155 | 156 | 157 | 158 | 159 | 160 | 161 | -------------------------------------------------------------------------------- /docs/link.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 5 | 8 | 12 | 13 | -------------------------------------------------------------------------------- /docs/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/logo.png -------------------------------------------------------------------------------- /docs/pkgdown.css: -------------------------------------------------------------------------------- 1 | /* Sticky footer */ 2 | 3 | /** 4 | * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/ 5 | * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css 6 | * 7 | * .Site -> body > .container 8 | * .Site-content -> body > .container .row 9 | * .footer -> footer 10 | * 11 | * Key idea seems to be to ensure that .container and __all its parents__ 12 | * have height set to 100% 13 | * 14 | */ 15 | 16 | html, body { 17 | height: 100%; 18 | } 19 | 20 | body > .container { 21 | display: flex; 22 | height: 100%; 23 | flex-direction: column; 24 | } 25 | 26 | body > .container .row { 27 | flex: 1 0 auto; 28 | } 29 | 30 | footer { 31 | margin-top: 45px; 32 | padding: 35px 0 36px; 33 | border-top: 1px solid #e5e5e5; 34 | color: #666; 35 | display: flex; 36 | flex-shrink: 0; 37 | } 38 | footer p { 39 | margin-bottom: 0; 40 | } 41 | footer div { 42 | flex: 1; 43 | } 44 | footer .pkgdown { 45 | text-align: right; 46 | } 47 | footer p { 48 | margin-bottom: 0; 49 | } 50 | 51 | img.icon { 52 | float: right; 53 | } 54 | 55 | img { 56 | max-width: 100%; 57 | } 58 | 59 | /* Fix bug in bootstrap (only seen in firefox) */ 60 | summary { 61 | display: list-item; 62 | } 63 | 64 | /* Typographic tweaking ---------------------------------*/ 65 | 66 | .contents .page-header { 67 | margin-top: calc(-60px + 1em); 68 | } 69 | 70 | /* Section anchors ---------------------------------*/ 71 | 72 | a.anchor { 73 | margin-left: -30px; 74 | display:inline-block; 75 | width: 30px; 76 | height: 30px; 77 | visibility: hidden; 78 | 79 | background-image: url(./link.svg); 80 | background-repeat: no-repeat; 81 | background-size: 20px 20px; 82 | background-position: center center; 83 | } 84 | 85 | .hasAnchor:hover a.anchor { 86 | visibility: visible; 87 | } 88 | 89 | @media (max-width: 767px) { 90 | .hasAnchor:hover a.anchor { 91 | visibility: hidden; 92 | } 93 | } 94 | 95 | 96 | /* Fixes for fixed navbar --------------------------*/ 97 | 98 | .contents h1, .contents h2, .contents h3, .contents h4 { 99 | padding-top: 60px; 100 | margin-top: -40px; 101 | } 102 | 103 | /* Sidebar --------------------------*/ 104 | 105 | #sidebar { 106 | margin-top: 30px; 107 | position: -webkit-sticky; 108 | position: sticky; 109 | top: 70px; 110 | } 111 | #sidebar h2 { 112 | font-size: 1.5em; 113 | margin-top: 1em; 114 | } 115 | 116 | #sidebar h2:first-child { 117 | margin-top: 0; 118 | } 119 | 120 | #sidebar .list-unstyled li { 121 | margin-bottom: 0.5em; 122 | } 123 | 124 | .orcid { 125 | height: 16px; 126 | /* margins are required by official ORCID trademark and display guidelines */ 127 | margin-left:4px; 128 | margin-right:4px; 129 | vertical-align: middle; 130 | } 131 | 132 | /* Reference index & topics ----------------------------------------------- */ 133 | 134 | .ref-index th {font-weight: normal;} 135 | 136 | .ref-index td {vertical-align: top;} 137 | .ref-index .icon {width: 40px;} 138 | .ref-index .alias {width: 40%;} 139 | .ref-index-icons .alias {width: calc(40% - 40px);} 140 | .ref-index .title {width: 60%;} 141 | 142 | .ref-arguments th {text-align: right; padding-right: 10px;} 143 | .ref-arguments th, .ref-arguments td {vertical-align: top;} 144 | .ref-arguments .name {width: 20%;} 145 | .ref-arguments .desc {width: 80%;} 146 | 147 | /* Nice scrolling for wide elements --------------------------------------- */ 148 | 149 | table { 150 | display: block; 151 | overflow: auto; 152 | } 153 | 154 | /* Syntax highlighting ---------------------------------------------------- */ 155 | 156 | pre { 157 | word-wrap: normal; 158 | word-break: normal; 159 | border: 1px solid #eee; 160 | } 161 | 162 | pre, code { 163 | background-color: #f8f8f8; 164 | color: #333; 165 | } 166 | 167 | pre code { 168 | overflow: auto; 169 | word-wrap: normal; 170 | white-space: pre; 171 | } 172 | 173 | pre .img { 174 | margin: 5px 0; 175 | } 176 | 177 | pre .img img { 178 | background-color: #fff; 179 | display: block; 180 | height: auto; 181 | } 182 | 183 | code a, pre a { 184 | color: #375f84; 185 | } 186 | 187 | a.sourceLine:hover { 188 | text-decoration: none; 189 | } 190 | 191 | .fl {color: #1514b5;} 192 | .fu {color: #000000;} /* function */ 193 | .ch,.st {color: #036a07;} /* string */ 194 | .kw {color: #264D66;} /* keyword */ 195 | .co {color: #888888;} /* comment */ 196 | 197 | .message { color: black; font-weight: bolder;} 198 | .error { color: orange; font-weight: bolder;} 199 | .warning { color: #6A0366; font-weight: bolder;} 200 | 201 | /* Clipboard --------------------------*/ 202 | 203 | .hasCopyButton { 204 | position: relative; 205 | } 206 | 207 | .btn-copy-ex { 208 | position: absolute; 209 | right: 0; 210 | top: 0; 211 | visibility: hidden; 212 | } 213 | 214 | .hasCopyButton:hover button.btn-copy-ex { 215 | visibility: visible; 216 | } 217 | 218 | /* headroom.js ------------------------ */ 219 | 220 | .headroom { 221 | will-change: transform; 222 | transition: transform 200ms linear; 223 | } 224 | .headroom--pinned { 225 | transform: translateY(0%); 226 | } 227 | .headroom--unpinned { 228 | transform: translateY(-100%); 229 | } 230 | 231 | /* mark.js ----------------------------*/ 232 | 233 | mark { 234 | background-color: rgba(255, 255, 51, 0.5); 235 | border-bottom: 2px solid rgba(255, 153, 51, 0.3); 236 | padding: 1px; 237 | } 238 | 239 | /* vertical spacing after htmlwidgets */ 240 | .html-widget { 241 | margin-bottom: 10px; 242 | } 243 | 244 | /* fontawesome ------------------------ */ 245 | 246 | .fab { 247 | font-family: "Font Awesome 5 Brands" !important; 248 | } 249 | 250 | /* don't display links in code chunks when printing */ 251 | /* source: https://stackoverflow.com/a/10781533 */ 252 | @media print { 253 | code a:link:after, code a:visited:after { 254 | content: ""; 255 | } 256 | } 257 | -------------------------------------------------------------------------------- /docs/pkgdown.js: -------------------------------------------------------------------------------- 1 | /* http://gregfranko.com/blog/jquery-best-practices/ */ 2 | (function($) { 3 | $(function() { 4 | 5 | $('.navbar-fixed-top').headroom(); 6 | 7 | $('body').css('padding-top', $('.navbar').height() + 10); 8 | $(window).resize(function(){ 9 | $('body').css('padding-top', $('.navbar').height() + 10); 10 | }); 11 | 12 | $('body').scrollspy({ 13 | target: '#sidebar', 14 | offset: 60 15 | }); 16 | 17 | $('[data-toggle="tooltip"]').tooltip(); 18 | 19 | var cur_path = paths(location.pathname); 20 | var links = $("#navbar ul li a"); 21 | var max_length = -1; 22 | var pos = -1; 23 | for (var i = 0; i < links.length; i++) { 24 | if (links[i].getAttribute("href") === "#") 25 | continue; 26 | // Ignore external links 27 | if (links[i].host !== location.host) 28 | continue; 29 | 30 | var nav_path = paths(links[i].pathname); 31 | 32 | var length = prefix_length(nav_path, cur_path); 33 | if (length > max_length) { 34 | max_length = length; 35 | pos = i; 36 | } 37 | } 38 | 39 | // Add class to parent
  • , and enclosing
  • if in dropdown 40 | if (pos >= 0) { 41 | var menu_anchor = $(links[pos]); 42 | menu_anchor.parent().addClass("active"); 43 | menu_anchor.closest("li.dropdown").addClass("active"); 44 | } 45 | }); 46 | 47 | function paths(pathname) { 48 | var pieces = pathname.split("/"); 49 | pieces.shift(); // always starts with / 50 | 51 | var end = pieces[pieces.length - 1]; 52 | if (end === "index.html" || end === "") 53 | pieces.pop(); 54 | return(pieces); 55 | } 56 | 57 | // Returns -1 if not found 58 | function prefix_length(needle, haystack) { 59 | if (needle.length > haystack.length) 60 | return(-1); 61 | 62 | // Special case for length-0 haystack, since for loop won't run 63 | if (haystack.length === 0) { 64 | return(needle.length === 0 ? 0 : -1); 65 | } 66 | 67 | for (var i = 0; i < haystack.length; i++) { 68 | if (needle[i] != haystack[i]) 69 | return(i); 70 | } 71 | 72 | return(haystack.length); 73 | } 74 | 75 | /* Clipboard --------------------------*/ 76 | 77 | function changeTooltipMessage(element, msg) { 78 | var tooltipOriginalTitle=element.getAttribute('data-original-title'); 79 | element.setAttribute('data-original-title', msg); 80 | $(element).tooltip('show'); 81 | element.setAttribute('data-original-title', tooltipOriginalTitle); 82 | } 83 | 84 | if(ClipboardJS.isSupported()) { 85 | $(document).ready(function() { 86 | var copyButton = ""; 87 | 88 | $(".examples, div.sourceCode").addClass("hasCopyButton"); 89 | 90 | // Insert copy buttons: 91 | $(copyButton).prependTo(".hasCopyButton"); 92 | 93 | // Initialize tooltips: 94 | $('.btn-copy-ex').tooltip({container: 'body'}); 95 | 96 | // Initialize clipboard: 97 | var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { 98 | text: function(trigger) { 99 | return trigger.parentNode.textContent; 100 | } 101 | }); 102 | 103 | clipboardBtnCopies.on('success', function(e) { 104 | changeTooltipMessage(e.trigger, 'Copied!'); 105 | e.clearSelection(); 106 | }); 107 | 108 | clipboardBtnCopies.on('error', function() { 109 | changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); 110 | }); 111 | }); 112 | } 113 | })(window.jQuery || window.$) 114 | -------------------------------------------------------------------------------- /docs/pkgdown.yml: -------------------------------------------------------------------------------- 1 | pandoc: '2.5' 2 | pkgdown: 1.4.1 3 | pkgdown_sha: ~ 4 | articles: [] 5 | 6 | -------------------------------------------------------------------------------- /docs/reference/biosketchr-package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | biosketchr: biosketchr — biosketchr-package • biosketchr 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 62 | 63 | 64 | 65 | 66 | 67 | 68 |
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    biosketchr: biosketchr

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    Provides the template and functions that make creating a Biosketch easier.

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    Developed by Tyson S. Barrett, Daniel Anderson.

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    Site built with pkgdown 1.4.1.

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    153 | 154 | 155 | 156 | 157 | 158 | 159 | 160 | 161 | -------------------------------------------------------------------------------- /docs/reference/figures/biosketchr_hex.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/reference/figures/biosketchr_hex.png -------------------------------------------------------------------------------- /docs/reference/figures/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/reference/figures/logo.png -------------------------------------------------------------------------------- /docs/reference/figures/pdf_output_example.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/reference/figures/pdf_output_example.png -------------------------------------------------------------------------------- /docs/reference/figures/select_template.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/reference/figures/select_template.png -------------------------------------------------------------------------------- /docs/reference/figures/skeleton_rmd.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/docs/reference/figures/skeleton_rmd.png -------------------------------------------------------------------------------- /docs/reference/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | Function reference • biosketchr 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 60 | 61 | 62 | 63 | 64 | 65 | 66 |
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    Reference

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    All functions

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    make_datetbl()

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    Format positions data into a table

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    make_numbered_citations()

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    Format Numbered Citations

    143 |

    nih_biosketch()

    144 |

    NIH Biosketch format.

    149 |
    150 | 151 | 157 |
    158 | 159 | 160 |
    161 |
    162 |

    Developed by Tyson S. Barrett, Daniel Anderson.

    163 |
    164 | 165 |
    166 |

    Site built with pkgdown 1.4.1.

    167 |
    168 | 169 |
    170 |
    171 | 172 | 173 | 174 | 175 | 176 | 177 | 178 | 179 | -------------------------------------------------------------------------------- /docs/reference/make_datetbl.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | Format positions data into a table — make_datetbl • biosketchr 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 61 | 62 | 63 | 64 | 65 | 66 | 67 |
    68 |
    69 | 103 | 104 | 105 | 106 |
    107 | 108 |
    109 |
    110 |
    111 |

    Format positions data into a table

    112 | 113 | 114 |
    115 | 116 |
    117 |

    Transforms a standard R data frame into a LaTeX datetbl.

    118 |
    119 | 120 | 
    make_datetbl(d, start_date, end_date, description, order = NULL,
121 |   trailing_dashes = TRUE)
    122 | 123 |

    Arguments

    124 | 125 | 126 | 127 | 128 | 129 | 130 | 131 | 132 | 133 | 134 | 135 | 136 | 137 | 138 | 139 | 140 | 141 | 142 | 143 | 144 | 145 | 146 | 147 | 148 | 149 | 150 |
    d

    Dataset including the information

    start_date

    Name of column denoting the year the position started or honor was awarded

    end_date

    Name of column denoting the year the position ended

    description

    Name of column describing the full description of the position/honor, including title, department, university, and location

    order

    Optional integer argument listing the order of entries

    trailing_dashes

    If end date is empty, should the start date have trailing dashes? Defaults to TRUE.

    151 | 152 |

    Value

    153 | 154 |

    LaTex datetbl

    155 | 156 |
    157 | 165 |
    166 | 167 | 168 |
    169 |
    170 |

    Developed by Tyson S. Barrett, Daniel Anderson.

    171 |
    172 | 173 |
    174 |

    Site built with pkgdown 1.4.1.

    175 |
    176 | 177 |
    178 |
    179 | 180 | 181 | 182 | 183 | 184 | 185 | 186 | 187 | -------------------------------------------------------------------------------- /docs/reference/make_numbered_citations.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | Format Numbered Citations — make_numbered_citations • biosketchr 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 61 | 62 | 63 | 64 | 65 | 66 | 67 |
    68 |
    69 | 103 | 104 | 105 | 106 |
    107 | 108 |
    109 |
    110 |
    111 |

    Format Numbered Citations

    112 | 113 | 114 |
    115 | 116 |
    117 |

    Formats a list of keys into a LaTeX enumerated list of references.

    118 |
    119 | 120 | 
    make_numbered_citations(...)
    121 | 122 |

    Arguments

    123 | 124 | 125 | 126 | 127 | 128 | 129 |
    ...

    keys from the`.bib` file in order of appearance in biosketch

    130 | 131 |

    Value

    132 | 133 |

    LaTex enumerated list

    134 | 135 |
    136 | 144 |
    145 | 146 | 147 |
    148 |
    149 |

    Developed by Tyson S. Barrett, Daniel Anderson.

    150 |
    151 | 152 |
    153 |

    Site built with pkgdown 1.4.1.

    154 |
    155 | 156 |
    157 |
    158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | -------------------------------------------------------------------------------- /docs/reference/nih_biosketch.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | NIH Biosketch format. — nih_biosketch • biosketchr 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 61 | 62 | 63 | 64 | 65 | 66 | 67 |
    68 |
    69 | 103 | 104 | 105 | 106 |
    107 | 108 |
    109 |
    110 |
    111 |

    NIH Biosketch format.

    112 | 113 | 114 |
    115 | 116 |
    117 |

    Format for creating NIH Biosketches. Does not use an official template but should approximate the format required by NIH. Is built on the template created by Paul Magwene found here: https://github.com/pmagwene/latex-nihbiosketch.

    118 |
    119 | 120 | 
    nih_biosketch(..., highlight = NULL, citation_package = "none")
    121 | 122 |

    Arguments

    123 | 124 | 125 | 126 | 127 | 128 | 129 | 130 | 131 | 134 | 135 | 136 | 137 | 139 | 140 |
    ...

    Additional arguments to rmarkdown::pdf_document

    highlight

    Syntax highlighting style. Supported styles include 132 | "default", "tango", "pygments", "kate", "monochrome", "espresso", 133 | "zenburn", and "haddock". Pass NULL to prevent syntax highlighting.

    citation_package

    The LaTeX package to process citations, natbib 138 | or biblatex. Use none if neither package is to be used.

    141 | 142 |

    Value

    143 | 144 |

    R Markdown output format to pass to 145 | render

    146 |

    Details

    147 | 148 |

    Possible arguments for the YAML header are:

      149 |

    • name Your Full Name

      • 150 |

    • eracommons Your ERA Commons ID

      • 151 |

    • position Description of your research position

      • 152 |

    • education Your education attainment (include any Bachelors, Masters, Doctorate, Postdoc). Several items are required for the education: 1) degree, 2) school, 3) date, and 4) field.

      • 153 |

    • researchsupport Both ongoing and completed research support received. Several items are required for the research support for both ongoing and completed: 1) grant, 2) PI, 3) dates, 4) title, 5) description, and 6) role.

      • 154 |

    • bibliography The name of the bib file

      • 155 |

    • bibliographystyle The bib style

      • 156 |

    • output Should be one of the formats from biosketchr

      • 157 |
    158 | 159 | 160 |

    Examples

    161 | 
    
162 | if (FALSE) {
163 | library(rmarkdown)
164 | draft("MyArticle.Rmd", template = "nih_biosketch", package = "biosketchr")
165 | }
    166 |
    167 | 177 |
    178 | 179 | 180 |
    181 |
    182 |

    Developed by Tyson S. Barrett, Daniel Anderson.

    183 |
    184 | 185 |
    186 |

    Site built with pkgdown 1.4.1.

    187 |
    188 | 189 |
    190 |
    191 | 192 | 193 | 194 | 195 | 196 | 197 | 198 | 199 | -------------------------------------------------------------------------------- /inst/example-data/appointments-nsf.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/inst/example-data/appointments-nsf.xlsx -------------------------------------------------------------------------------- /inst/example-data/positions-honors-nih.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/inst/example-data/positions-honors-nih.xlsx -------------------------------------------------------------------------------- /inst/rmarkdown/templates/nih_biosketch/resources/template.tex: -------------------------------------------------------------------------------- 1 | %% For Use With NIH Biosketch LaTeX Class 2 | %% Added to RMarkdown by Tyson S. Barrett, PhD 3 | 4 | % Document class and options 5 | \documentclass{nihbiosketch} 6 | \usepackage{natbib} 7 | \usepackage{bibentry} 8 | \bibliographystyle{$bibliographystyle$} 9 | \providecommand{\tightlist}{\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}} 10 | 11 | % Pandoc header 12 | $for(header-includes)$ 13 | $header-includes$ 14 | $endfor$ 15 | 16 | $preamble$ 17 | 18 | 19 | \name{$name$} 20 | \eracommons{$eracommons$} 21 | \position{$position$} 22 | 23 | 24 | \begin{document} 25 | 26 | 27 | 28 | $if(bibliography)$ 29 | \nobibliography{$for(bibliography)$$bibliography$$sep$,$endfor$} 30 | $endif$ 31 | 32 | 33 | $if(education)$ 34 | \begin{education} 35 | $for(education)$ 36 | $education.school$ & $education.degree$ & $education.date$ & $education.field$ \\ 37 | $endfor$ 38 | \end{education} 39 | $endif$ 40 | 41 | 42 | 43 | $body$ 44 | 45 | 46 | 47 | $if(myBibliography)$ 48 | \subsection*{Complete List of Published Work in MyBibliography:} 49 | \url{$myBibliography$} 50 | $endif$ 51 | 52 | $if(researchsupport)$ 53 | \section{Research Support} 54 | 55 | $if(researchsupport.ongoing)$ 56 | \subsection*{Ongoing Research Support} 57 | 58 | $for(researchsupport.ongoing)$ 59 | 60 | \grantinfo{$researchsupport.ongoing.grant$}{$researchsupport.ongoing.pi$}{$researchsupport.ongoing.dates$} 61 | {$researchsupport.ongoing.title$} 62 | {$researchsupport.ongoing.description$} 63 | {Role: $researchsupport.ongoing.role$} 64 | 65 | \bigskip 66 | $endfor$ 67 | 68 | $endif$ 69 | 70 | 71 | $if(researchsupport.completed)$ 72 | \subsection*{Completed Research Support} 73 | 74 | $for(researchsupport.completed)$ 75 | 76 | \grantinfo{$researchsupport.completed.grant$}{$researchsupport.completed.pi$}{$researchsupport.completed.dates$} 77 | {$researchsupport.completed.title$} 78 | {$researchsupport.completed.description$} 79 | {Role: $researchsupport.completed.role$} 80 | 81 | \bigskip 82 | $endfor$ 83 | 84 | $endif$ 85 | 86 | $endif$ 87 | 88 | 89 | $for(include-after)$ 90 | $include-after$ 91 | $endfor$ 92 | 93 | \end{document} 94 | -------------------------------------------------------------------------------- /inst/rmarkdown/templates/nih_biosketch/skeleton/nihbiosketch.cls: -------------------------------------------------------------------------------- 1 | %% nihbiosketch.cls 2 | %% Copyright 2015 Paul M. Magwene 3 | % 4 | % This work may be distributed and/or modified under the 5 | % conditions of the LaTeX Project Public License, either version 1.3 6 | % of this license or (at your option) any later version. 7 | % The latest version of this license is in 8 | % http://www.latex-project.org/lppl.txt 9 | % and version 1.3c or later is part of all distributions of LaTeX 10 | % version 008/05/04 or later. 11 | % 12 | % This work has the LPPL maintenance status `maintained'. 13 | % 14 | % The Current Maintainer of this work is Paul M. Magwene 15 | % 16 | % This work consists of the files nihbiosketch.cls 17 | 18 | 19 | \NeedsTeXFormat{LaTeX2e} 20 | \ProvidesClass{nihbiosketch}[2015/04/22 NIH Biosketch Class] 21 | 22 | %------------------------------------------------------------------------------ 23 | 24 | \ProcessOptions\relax 25 | \LoadClass[11pt,letterpaper]{article} 26 | 27 | %------------------------------------------------------------------------------ 28 | % Packages 29 | 30 | \RequirePackage{etoolbox} 31 | \RequirePackage[letterpaper]{geometry} 32 | \RequirePackage{ifxetex, ifluatex} % requires fontspec, so either XeTeX or LuaTeX 33 | \RequirePackage{fontspec} 34 | \setmainfont[Ligatures=TeX]{Arial} 35 | \RequirePackage{microtype} 36 | 37 | \RequirePackage{tabu} 38 | \RequirePackage{ifthen} 39 | \RequirePackage{ulem} 40 | 41 | \RequirePackage{enumitem} 42 | \setlist[enumerate,2]{label=\alph*.,itemsep=0pt,parsep=1pt,partopsep=1pt} 43 | 44 | 45 | \RequirePackage{titlesec} 46 | \renewcommand{\thesection}{\Alph{section}.} 47 | \titleformat{\section}[hang]{\normalfont\bfseries}{\thesection}{0.5em}{} % section style 48 | \titleformat{\subsection}[hang]{\normalfont\bfseries}{\thesubsection}{0.5em}{\uline} % subsection style 49 | \titleformat{\subsubsection}[hang]{\itshape}{\thesubsubsection}{0.5em}{} % subsubsection style 50 | 51 | \titlespacing{\section}{0pt}{2ex}{1ex} 52 | \titlespacing{\subsection}{0pt}{1.25ex}{0.5ex} 53 | \titlespacing{\subsubsection}{0pt}{1.25ex}{0.5ex} 54 | 55 | \PassOptionsToPackage{urlcolor=blue,colorlinks=true,breaklinks=true}{hyperref} 56 | \RequirePackage{hyperref} 57 | \urlstyle{same} 58 | 59 | %------------------------------------------------------------------------------ 60 | % New commands and environments 61 | 62 | \newcommand{\@name}{} 63 | \newcommand{\@eracommons}{} 64 | \newcommand{\@position}{} 65 | 66 | \newcommand{\name}[1]{\renewcommand{\@name}{#1}} 67 | \newcommand{\eracommons}[1]{\renewcommand{\@eracommons}{#1}} 68 | \newcommand{\position}[1]{\renewcommand{\@position}{#1}} 69 | 70 | \newcommand{\pgline}{\noindent\makebox[\linewidth]{\rule{\textwidth}{0.5pt}}\newline} 71 | 72 | \newcommand{\piinfo} 73 | {\pgline 74 | {\centering 75 | \textbf{BIOGRAPHICAL SKETCH}\\ 76 | {\footnotesize 77 | Provide the following information for the Senior/key personnel and other significant contributors.\\ 78 | Follow this format for each person. \textbf{DO NOT EXCEED FIVE PAGES}.\\}} 79 | \pgline 80 | NAME: \@name\\ 81 | \pgline 82 | eRA COMMONS USER NAME (credential, e.g., agency login): \@eracommons\\ 83 | \pgline 84 | POSITION TITLE: \@position\\ 85 | \pgline 86 | EDUCATION/TRAINING (\textit{Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable. Add/delete rows as necessary.})\\} 87 | 88 | \newcommand{\grantinfo}[6] 89 | {\begin{tabular}{@{}lll@{}} 90 | {#1} & {#2} & {#3} \\ 91 | \end{tabular} 92 | \newline{#4}\newline{#5}\newline{#6}} 93 | 94 | \newenvironment{education} 95 | {% 96 | \bgroup\centering 97 | \tabulinesep=1.5mm 98 | \begin{tabu} to \textwidth {X[3.73,l,m]|X[1,c,m]|X[1,c,m]|X[1.8,l,m]} 99 | \hline 100 | \rowfont[c]{} % for the header only we want all the text centered 101 | INSTITUTION AND LOCATION & 102 | DEGREE \newline (\textit{if applicable}) & 103 | Completion Date MM/YYYY & 104 | FIELD OF STUDY\\ 105 | \hline} 106 | {\end{tabu}\egroup} 107 | 108 | \newenvironment{datetbl} 109 | {\tabulinesep=0mm 110 | \begin{tabu} to 7.5in{X[1,l]X[6.5,l,p]}} 111 | {\end{tabu}} 112 | 113 | \newenvironment{statement} 114 | {\setlength\parindent{2em}} 115 | {\setlength\parindent{0pt}} 116 | 117 | 118 | %------------------------------------------------------------------------------ 119 | % setup document geometry 120 | 121 | % turn off page numbering 122 | \pagenumbering{gobble} 123 | 124 | % no paragraph indentation 125 | \setlength\parindent{0pt} 126 | 127 | \geometry{left=0.5in,right=0.5in,top=0.5in,bottom=0.5in} % this should be the last call 128 | 129 | %------------------------------------------------------------------------------ 130 | 131 | \AfterEndPreamble{\piinfo} 132 | 133 | -------------------------------------------------------------------------------- /inst/rmarkdown/templates/nih_biosketch/skeleton/skeleton.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | name: "Your Name" 3 | eracommons: "IDstuff" 4 | position: "Researcher" 5 | myBibliography: "url" 6 | education: 7 | - degree: "BS" 8 | school: "University State" 9 | date: "5/2000" 10 | field: "Psychology" 11 | - degree: "PhD" 12 | school: "University State" 13 | date: "5/2005" 14 | field: "Psychology" 15 | researchsupport: 16 | ongoing: 17 | - grant: "NIH R01 Numbers" 18 | pi: "You Are" 19 | dates: "Still Happening" 20 | title: "Life Changing Grant" 21 | description: "This is the stuff we are doing" 22 | role: "PI" 23 | - grant: "NIH R01 Numbers 2" 24 | pi: "You Are Also" 25 | dates: "Still Happening Also" 26 | title: "Life Changing Grant Also" 27 | description: "This is the stuff we are also doing" 28 | role: "PI" 29 | completed: 30 | - grant: "NIH R01 Numbers" 31 | pi: "You Were" 32 | dates: "Over" 33 | title: "Life Changing Grant Now Over" 34 | description: "This is the stuff we were doing" 35 | role: "PI" 36 | output: 37 | biosketchr::nih_biosketch: 38 | latex_engine: xelatex 39 | keep_tex: yes 40 | bibliography: yourbibfile.bib 41 | bibliographystyle: apalike 42 | --- 43 | 44 | ```{r global_options, include=FALSE} 45 | library(dplyr) 46 | library(biosketchr) 47 | 48 | ## This saves you from having to do this for every chunk 49 | knitr::opts_chunk$set(fig.path = 'figures/', 50 | echo = FALSE, 51 | warning = FALSE, 52 | message = FALSE, 53 | results = "asis") 54 | 55 | # load positions/honors data 56 | d <- readxl::read_xlsx(system.file("example-data", "positions-honors-nih.xlsx", 57 | package = "biosketchr")) 58 | 59 | ``` 60 | 61 | 64 | 65 | 66 | # Personal Statement {-} 67 | 68 | Your statement about your qualifications for the proposal goes here. Include up-to-four citations related to the statement (either using the `make_numbered_citations()` function as shown below with the appropriate keys from the `.bib` file or manually entered). This can often include any previous products from collaborations between the research team that is relevant to the current proposal. Ultimately, this is a space to show that you are competent capable of completing the proposed project. Feel free to erase all of this filler text. 69 | 70 | ```{r statement_citations} 71 | # replace these keys with your own 72 | make_numbered_citations("RCoreTeam", "RStudio", "biosketchr", "nihbiosketch") 73 | ``` 74 | 75 | 76 | # Positions and Honors {-} 77 | 78 | ## Positions and Employment {-} 79 | ```{r positions} 80 | d %>% 81 | filter(section == "positions") %>% 82 | make_datetbl_nih(start_date, end_date, description, order) 83 | ``` 84 | 85 | ## Other Experience and Professional Memberships {-} 86 | 87 | ```{r other_exp} 88 | d %>% 89 | filter(section == "other_exp") %>% 90 | make_datetbl_nih(start_date, end_date, description, order) 91 | ``` 92 | 93 | ## Honors {-} 94 | 95 | ```{r honors} 96 | d %>% 97 | filter(section == "honors") %>% 98 | make_datetbl_nih(start_date, end_date, description, order, FALSE) 99 | ``` 100 | 101 | # Contribution to Science {-} 102 | 103 | \begin{enumerate} 104 | 105 | \item Paragraph of contribution number 1. This should include a narrative about one of your main research lines. Below, cite up to four publications stemming from this contribution. Feel free to erase all of this filler text. 106 | 107 | ```{r contribution_citations1} 108 | # replace these keys with your own 109 | make_numbered_citations("RCoreTeam", "RStudio", "biosketchr", "nihbiosketch") 110 | ``` 111 | 112 | 113 | \item Paragraph of contribution number 2. This should include a narrative about one of your main research lines. Below, cite up to four publications stemming from this contribution. Feel free to erase all of this filler text. 114 | 115 | ```{r contribution_citations2} 116 | # replace these keys with your own 117 | make_numbered_citations("RCoreTeam", "RStudio", "biosketchr", "nihbiosketch") 118 | ``` 119 | 120 | \end{enumerate} 121 | 122 | 127 | 128 | 129 | 130 | 131 | -------------------------------------------------------------------------------- /inst/rmarkdown/templates/nih_biosketch/skeleton/skeleton.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/inst/rmarkdown/templates/nih_biosketch/skeleton/skeleton.pdf -------------------------------------------------------------------------------- /inst/rmarkdown/templates/nih_biosketch/skeleton/skeleton.tex: -------------------------------------------------------------------------------- 1 | %% For Use With NIH Biosketch LaTeX Class 2 | %% Added to RMarkdown by Tyson S. Barrett, PhD 3 | 4 | % Document class and options 5 | \documentclass{nihbiosketch} 6 | \usepackage{natbib} 7 | \usepackage{bibentry} 8 | \bibliographystyle{apalike} 9 | \providecommand{\tightlist}{\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}} 10 | 11 | % Pandoc header 12 | 13 | 14 | 15 | 16 | \name{Your Name} 17 | \eracommons{IDstuff} 18 | \position{Researcher} 19 | 20 | 21 | \begin{document} 22 | 23 | 24 | 25 | \nobibliography{yourbibfile.bib} 26 | 27 | 28 | \begin{education} 29 | University State & BS & 5/2000 & Psychology \\ 30 | University State & PhD & 5/2005 & Psychology \\ 31 | \end{education} 32 | 33 | \nobibliography* 34 | 35 | \hypertarget{personal-statement}{% 36 | \section*{Personal Statement}\label{personal-statement}} 37 | \addcontentsline{toc}{section}{Personal Statement} 38 | 39 | Your statement about your qualifications for the proposal goes here. 40 | Include up-to-four citations related to the statement (either using the 41 | \texttt{make\_numbered\_citations()} function as shown below with the 42 | appropriate keys from the \texttt{.bib} file or manually entered). This 43 | can often include any previous products from collaborations between the 44 | research team that is relevant to the current proposal. Ultimately, this 45 | is a space to show that you are competent capable of completing the 46 | proposed project. Feel free to erase all of this filler text. 47 | 48 | \begin{enumerate} 49 | \item \bibentry{RCoreTeam} 50 | \item \bibentry{RStudio} 51 | \item \bibentry{biosketchr} 52 | \item \bibentry{nihbiosketch} 53 | \end{enumerate} 54 | 55 | \hypertarget{positions-and-honors}{% 56 | \section*{Positions and Honors}\label{positions-and-honors}} 57 | \addcontentsline{toc}{section}{Positions and Honors} 58 | 59 | \hypertarget{positions-and-employment}{% 60 | \subsection*{Positions and Employment}\label{positions-and-employment}} 61 | \addcontentsline{toc}{subsection}{Positions and Employment} 62 | 63 | \begin{datetbl} 64 | 2007-- & Associate Research Professor, Department of Psychology, University State, Somewhere Fantastic \\ 65 | 2002--2005 & Assistant Research Professor, Department of Psychology, University State, Somewhere Fantastic \\ 66 | 2000--2002 & Lecturer, Department of Psychology, A University, Somewhere Cool \\ 67 | 1998--2000 & Fellow, Somewhere Neat \\ 68 | \end{datetbl} 69 | 70 | \hypertarget{other-experience-and-professional-memberships}{% 71 | \subsection*{Other Experience and Professional 72 | Memberships}\label{other-experience-and-professional-memberships}} 73 | \addcontentsline{toc}{subsection}{Other Experience and Professional 74 | Memberships} 75 | 76 | \begin{datetbl} 77 | 2000-- & Member, Gerontological Society of America \\ 78 | 2000-- & Member, American Psychological Association \\ 79 | \end{datetbl} 80 | 81 | \hypertarget{honors}{% 82 | \subsection*{Honors}\label{honors}} 83 | \addcontentsline{toc}{subsection}{Honors} 84 | 85 | \begin{datetbl} 86 | 2009 & Award for Best of Something, A University, Somewhere Cool \\ 87 | 2004 & Excellence in Teaching, University State, Somewhere Fantastic \\ 88 | 2003 & Outstanding Person, University State, Somewhere Fantastic \\ 89 | \end{datetbl} 90 | 91 | \hypertarget{contribution-to-science}{% 92 | \section*{Contribution to Science}\label{contribution-to-science}} 93 | \addcontentsline{toc}{section}{Contribution to Science} 94 | 95 | \begin{enumerate} 96 | 97 | \item Paragraph of contribution number 1. This should include a narrative about one of your main research lines. Below, cite up to four publications stemming from this contribution. Feel free to erase all of this filler text. 98 | 99 | \begin{enumerate} 100 | \item \bibentry{RCoreTeam} 101 | \item \bibentry{RStudio} 102 | \item \bibentry{biosketchr} 103 | \item \bibentry{nihbiosketch} 104 | \end{enumerate} 105 | 106 | 107 | \item Paragraph of contribution number 2. This should include a narrative about one of your main research lines. Below, cite up to four publications stemming from this contribution. Feel free to erase all of this filler text. 108 | 109 | \begin{enumerate} 110 | \item \bibentry{RCoreTeam} 111 | \item \bibentry{RStudio} 112 | \item \bibentry{biosketchr} 113 | \item \bibentry{nihbiosketch} 114 | \end{enumerate} 115 | 116 | \end{enumerate} 117 | 118 | 119 | 120 | \subsection*{Complete List of Published Work in MyBibliography:} 121 | \url{url} 122 | 123 | \section{Research Support} 124 | 125 | \subsection*{Ongoing Research Support} 126 | 127 | 128 | \grantinfo{NIH R01 Numbers}{You Are}{Still Happening} 129 | {Life Changing Grant} 130 | {This is the stuff we are doing} 131 | {Role: PI} 132 | 133 | \bigskip 134 | 135 | \grantinfo{NIH R01 Numbers 2}{You Are Also}{Still Happening Also} 136 | {Life Changing Grant Also} 137 | {This is the stuff we are also doing} 138 | {Role: PI} 139 | 140 | \bigskip 141 | 142 | 143 | 144 | \subsection*{Completed Research Support} 145 | 146 | 147 | \grantinfo{NIH R01 Numbers}{You Were}{Over} 148 | {Life Changing Grant Now Over} 149 | {This is the stuff we were doing} 150 | {Role: PI} 151 | 152 | \bigskip 153 | 154 | 155 | 156 | 157 | 158 | \end{document} 159 | -------------------------------------------------------------------------------- /inst/rmarkdown/templates/nih_biosketch/skeleton/yourbibfile.bib: -------------------------------------------------------------------------------- 1 | 2 | @Manual{RCoreTeam, 3 | title = {R: A Language and Environment for Statistical Computing}, 4 | author = {{R Core Team}}, 5 | organization = {R Foundation for Statistical Computing}, 6 | address = {Vienna, Austria}, 7 | year = {2018}, 8 | url = {https://www.R-project.org/}, 9 | } 10 | 11 | @Manual{Rstudio, 12 | title = {RStudio: Integrated Development Environment for R}, 13 | author = {{RStudio Team}}, 14 | organization = {RStudio, Inc.}, 15 | address = {Boston, MA}, 16 | year = {2018}, 17 | url = {http://www.rstudio.com/}, 18 | } 19 | 20 | @Manual{biosketchr, 21 | title = {biosketchr: RMarkdown for Biosketches}, 22 | author = {Tyson S. Barrett and Daniel Anderson}, 23 | year = {2019}, 24 | note = {R package version 0.1.0}, 25 | } 26 | 27 | @Manual{nihbiosketch, 28 | title = {nihbiosketch}, 29 | author = {Paul M. Magwene}, 30 | year = {2015}, 31 | note = {LaTeX package}, 32 | } 33 | -------------------------------------------------------------------------------- /inst/rmarkdown/templates/nih_biosketch/template.yaml: -------------------------------------------------------------------------------- 1 | name: "NIH Biosketch" 2 | description: > 3 | Template for creating an NIH biosketch. 4 | create_dir: true 5 | -------------------------------------------------------------------------------- /inst/rmarkdown/templates/nsf_biosketch/resources/template.tex: -------------------------------------------------------------------------------- 1 | % Template Adapted from: 2 | % 3 | % NSF Biographical Sketch: Dr. Theodore P. Pavlic 4 | % 5 | % Copyright (c) 2013 by Theodore P. Pavlic 6 | % All rights reserved. 7 | % 8 | % Dr. Theodore P. Pavlic is not responsible for any changes made herein 9 | 10 | \documentclass[svgnames,11pt]{article} 11 | \usepackage[margin=1in]{geometry} 12 | \usepackage[T1]{fontenc} 13 | \usepackage{times} 14 | \renewcommand\thesection{(\alph{section})} 15 | \renewcommand\thesubsection{(\alph{subsection})} 16 | 17 | \usepackage{calc} 18 | 19 | \usepackage{lastpage} 20 | %\newcommand{\pageoflastpage}{Page {\thepage} of \pageref*{LastPage}} 21 | %\newcommand{\pageoflastpage}{{\thepage} of \pageref*{LastPage}} 22 | \newcommand{\pageoflastpage}{} 23 | 24 | % Redefine the plain pagestyle for the title page 25 | \makeatletter 26 | \let\oldps@plain\ps@plain 27 | \renewcommand{\ps@plain}{\oldps@plain% 28 | \renewcommand{\@evenfoot}{\hfil\pageoflastpage\hfil}% 29 | \renewcommand{\@oddfoot}{\@evenfoot}} 30 | \makeatother 31 | 32 | % Use fancy for non-title pages 33 | \usepackage{fancyhdr} 34 | \fancyhead{} 35 | \fancyfoot{} 36 | \cfoot{\pageoflastpage} 37 | \pagestyle{fancy} 38 | 39 | \usepackage{xspace} 40 | 41 | \usepackage[shortlabels]{enumitem} 42 | \usepackage{graphicx} 43 | \usepackage{varioref} 44 | \usepackage[% 45 | colorlinks=true,urlcolor=, 46 | pdfpagelabels=true,hypertexnames=true, 47 | plainpages=false,naturalnames=true, 48 | ]{hyperref} 49 | % 50 | \usepackage{url} 51 | \newcommand\doilink[1]{\href{http://dx.doi.org/#1}{#1}} 52 | \newcommand\doi[1]{doi:\doilink{#1}} 53 | 54 | % \makeatletter 55 | % \newlength{\bibhang} 56 | % \setlength{\bibhang}{1em} 57 | % \newlength{\bibsep} 58 | % {\@listi \global\bibsep\itemsep \global\advance\bibsep by\parsep} 59 | % \newlist{bibsection}{itemize}{3} 60 | % \setlist[bibsection]{label=,leftmargin={\bibhang+\widthof{[9]}},% 61 | % itemindent=-\bibhang, 62 | % itemsep=\bibsep,parsep=\z@,partopsep=0pt, 63 | % topsep=0pt} 64 | % \newlist{bibenum}{enumerate}{3} 65 | % \setlist[bibenum]{label=\textbf{\arabic*.},leftmargin={\bibhang+\widthof{[999]}},% 66 | % itemindent=-\bibhang, 67 | % itemsep=\bibsep,parsep=\z@,partopsep=0pt, 68 | % topsep=0pt} 69 | % \let\oldendbibenum\endbibenum 70 | % \def\endbibenum{\oldendbibenum\vspace{-.6\baselineskip}} 71 | % \let\oldendbibsection\endbibsection 72 | % \def\endbibsection{\oldendbibsection\vspace{-.6\baselineskip}} 73 | % \makeatother 74 | 75 | \title{% 76 | \vspace{-2\baselineskip} 77 | \normalsize 78 | Biographical Sketch\\ 79 | {\large\textbf{$name$}}\\ 80 | \vspace{0.5\baselineskip} 81 | \hrule 82 | \vspace{0.5\baselineskip} 83 | $department$, $university$, e-mail: \href{mailto:$email$}{$email$}, tel: $telephone$ 84 | \vspace{-1.5ex} 85 | } 86 | \date{} 87 | \author{} 88 | 89 | \newcommand{\ie}{i.e.\xspace} 90 | \newcommand{\eg}{e.g.\xspace} 91 | 92 | 93 | \usepackage{natbib} 94 | \usepackage{bibentry} 95 | \bibliographystyle{$bibliographystyle$} 96 | \providecommand{\tightlist}{\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}} 97 | 98 | 99 | $preamble$ 100 | 101 | 102 | \begin{document} 103 | 104 | 105 | $if(bibliography)$ 106 | \nobibliography{$for(bibliography)$$bibliography$$sep$,$endfor$} 107 | $endif$ 108 | 109 | 110 | \maketitle 111 | \vspace{-4\baselineskip} 112 | 113 | 114 | \subsection{Professional Preparation} 115 | 116 | $for(preparation)$ 117 | $preparation.location$; $preparation.field$; $preparation.degree$; $preparation.dates$ \\ 118 | $endfor$ 119 | 120 | 121 | 122 | $body$ 123 | 124 | 125 | 126 | $for(include-after)$ 127 | $include-after$ 128 | $endfor$ 129 | 130 | 131 | \end{document} 132 | -------------------------------------------------------------------------------- /inst/rmarkdown/templates/nsf_biosketch/skeleton/skeleton.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | name: "Your Name" 3 | department: "Department" 4 | university: "Somewhere Great" 5 | email: "email" 6 | telephone: "number" 7 | preparation: 8 | - location: "University or Company" 9 | field: "Your Field" 10 | degree: "Your degree earned" 11 | dates: "2000--2005" 12 | - location: "University or Company" 13 | field: "Your Field" 14 | degree: "Your degree earned" 15 | dates: "2005--2008" 16 | - location: "University or Company" 17 | field: "Your Field" 18 | degree: "Your degree earned" 19 | dates: "2008--2012" 20 | output: 21 | biosketchr::nsf_biosketch: 22 | latex_engine: xelatex 23 | keep_tex: yes 24 | bibliography: yourbibfile.bib 25 | bibliographystyle: apalike 26 | --- 27 | 28 | ```{r global_options, include=FALSE} 29 | library(biosketchr) 30 | 31 | ## This saves you from having to do this for every chunk 32 | knitr::opts_chunk$set(fig.path = 'figures/', 33 | echo = FALSE, 34 | warning = FALSE, 35 | message = FALSE, 36 | results = "asis") 37 | 38 | # load positions/honors data 39 | d <- readxl::read_xlsx(system.file("example-data", "appointments-nsf.xlsx", 40 | package = "biosketchr")) 41 | 42 | ``` 43 | 44 | 47 | 48 | 49 | ## Appointments 50 | 51 | ```{r statement_citations} 52 | make_datetbl_nsf(d, start_date, end_date, position, location, order) 53 | ``` 54 | 55 | 56 | ## Products 57 | 58 | ```{r contribution_citations1} 59 | # replace these keys with your own 60 | make_numbered_citations("RCoreTeam", "RStudio", "biosketchr", "nihbiosketch") 61 | ``` 62 | 63 | 64 | ## Synergistic Activities 65 | 66 | 1. **Conference service**: Organized some really neat conference collaborating with the editor of a journal that I like. Feel free to erase all this filler text. 67 | 68 | 2. **University service**: Baked cookies to raise money to help underrepresented college students. Feel free to erase all this filler text. 69 | 70 | 3. **Community service**: Did some great stuff for the community. Feel free to erase all this filler text. 71 | 72 | 4. **Mentoring**: Mentoring experience and awards. Feel free to erase all this filler text. 73 | 74 | 5. **Teaching**: Teaching experience and style (open resources?). Feel free to erase all this filler text. 75 | 76 | 77 | 78 | 79 | ## Collaborators \& Other Affiliations 80 | 81 | 1. **Collaborators and Co-Editors**: *University 1*: A list of names separated by semi-colons that I've collaborated with at University 1; *University 2*: A list of names separated by semi-colons that I've collaborated with at University 2 82 | 83 | 2. **Graduate Advisers and Postdoctoral Sponsors**: *University 1*: A list of names separated by semi-colons that I've collaborated with at University 1 84 | 85 | 86 | 87 | -------------------------------------------------------------------------------- /inst/rmarkdown/templates/nsf_biosketch/skeleton/yourbibfile.bib: -------------------------------------------------------------------------------- 1 | 2 | @Manual{RCoreTeam, 3 | title = {R: A Language and Environment for Statistical Computing}, 4 | author = {{R Core Team}}, 5 | organization = {R Foundation for Statistical Computing}, 6 | address = {Vienna, Austria}, 7 | year = {2018}, 8 | url = {https://www.R-project.org/}, 9 | } 10 | 11 | @Manual{Rstudio, 12 | title = {RStudio: Integrated Development Environment for R}, 13 | author = {{RStudio Team}}, 14 | organization = {RStudio, Inc.}, 15 | address = {Boston, MA}, 16 | year = {2018}, 17 | url = {http://www.rstudio.com/}, 18 | } 19 | 20 | @Manual{biosketchr, 21 | title = {biosketchr: RMarkdown for Biosketches}, 22 | author = {Tyson S. Barrett and Daniel Anderson}, 23 | year = {2019}, 24 | note = {R package version 0.1.0}, 25 | } 26 | 27 | @Manual{nihbiosketch, 28 | title = {nihbiosketch}, 29 | author = {Paul M. Magwene}, 30 | year = {2015}, 31 | note = {LaTeX package}, 32 | } 33 | -------------------------------------------------------------------------------- /inst/rmarkdown/templates/nsf_biosketch/template.yaml: -------------------------------------------------------------------------------- 1 | name: "NSF Biosketch" 2 | description: > 3 | Template for creating an NSF biosketch. 4 | create_dir: true 5 | -------------------------------------------------------------------------------- /man/biosketchr-package.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/biosketchr-package.R 3 | \docType{package} 4 | \name{biosketchr-package} 5 | \alias{biosketchr} 6 | \alias{biosketchr-package} 7 | \title{biosketchr: biosketchr} 8 | \description{ 9 | \if{html}{\figure{logo.png}{options: align='right'}} 10 | 11 | Provides the template and functions that make creating a 12 | Biosketch for NIH and NSF proposals easier. 13 | } 14 | \author{ 15 | \strong{Maintainer}: Tyson S. Barrett \email{t.barrett@aggiemail.usu.edu} (0000-0002-2137-1391) 16 | 17 | Authors: 18 | \itemize{ 19 | \item Daniel Anderson \email{daniela@uoregon.edu} (https://orcid.org/0000-0003-4699-4680) 20 | } 21 | 22 | } 23 | \keyword{internal} 24 | -------------------------------------------------------------------------------- /man/figures/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/man/figures/logo.png -------------------------------------------------------------------------------- /man/figures/pdf_output_example.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/man/figures/pdf_output_example.png -------------------------------------------------------------------------------- /man/figures/select_template.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/man/figures/select_template.png -------------------------------------------------------------------------------- /man/figures/skeleton_rmd.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/man/figures/skeleton_rmd.png -------------------------------------------------------------------------------- /man/make_datetbl_nih.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/nih_biosketch.R 3 | \name{make_datetbl_nih} 4 | \alias{make_datetbl_nih} 5 | \title{Format positions data into a table for NIH} 6 | \usage{ 7 | make_datetbl_nih(d, start_date, end_date, description, order = NULL, 8 | trailing_dashes = TRUE) 9 | } 10 | \arguments{ 11 | \item{d}{Dataset including the information} 12 | 13 | \item{start_date}{Name of column denoting the year the position started or honor was awarded} 14 | 15 | \item{end_date}{Name of column denoting the year the position ended} 16 | 17 | \item{description}{Name of column describing the full description of the position/honor, including title, department, university, and location} 18 | 19 | \item{order}{Optional integer argument listing the order of entries} 20 | 21 | \item{trailing_dashes}{If end date is empty, should the start date have trailing dashes? Defaults to \code{TRUE}.} 22 | } 23 | \value{ 24 | LaTex \code{datetbl} 25 | } 26 | \description{ 27 | Transforms a standard R data frame into a LaTeX \code{datetbl}. 28 | } 29 | -------------------------------------------------------------------------------- /man/make_datetbl_nsf.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/nsf_biosketch.R 3 | \name{make_datetbl_nsf} 4 | \alias{make_datetbl_nsf} 5 | \title{Format positions data into a table for NSF} 6 | \usage{ 7 | make_datetbl_nsf(d, start_date, end_date, position, location, 8 | order = NULL, trailing_dashes = TRUE) 9 | } 10 | \arguments{ 11 | \item{d}{Dataset including the information} 12 | 13 | \item{start_date}{Name of column denoting the year the position started or honor was awarded} 14 | 15 | \item{end_date}{Name of column denoting the year the position ended} 16 | 17 | \item{position}{Name of column describing the name of the position} 18 | 19 | \item{location}{Name of column denoting the location of position} 20 | 21 | \item{order}{Optional integer argument listing the order of entries} 22 | 23 | \item{trailing_dashes}{If end date is empty, should the start date have trailing dashes? Defaults to \code{TRUE}.} 24 | } 25 | \value{ 26 | LaTex \code{itemize} 27 | } 28 | \description{ 29 | Transforms a standard R data frame into a LaTeX \code{table}. 30 | } 31 | -------------------------------------------------------------------------------- /man/make_numbered_citations.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/nih_biosketch.R 3 | \name{make_numbered_citations} 4 | \alias{make_numbered_citations} 5 | \title{Format Numbered Citations} 6 | \usage{ 7 | make_numbered_citations(..., NIH = TRUE) 8 | } 9 | \arguments{ 10 | \item{...}{keys from the`.bib` file in order of appearance in biosketch} 11 | 12 | \item{NIH}{Is the biosketch being produced for NIH? Defaults to \code{TRUE} and is currently the only option.} 13 | } 14 | \value{ 15 | LaTex \code{enumerated list} 16 | } 17 | \description{ 18 | Formats a list of keys into a LaTeX \code{enumerated list} of references. 19 | } 20 | -------------------------------------------------------------------------------- /man/nih_biosketch.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/nih_biosketch.R 3 | \name{nih_biosketch} 4 | \alias{nih_biosketch} 5 | \title{NIH Biosketch format.} 6 | \usage{ 7 | nih_biosketch(..., highlight = NULL, citation_package = "none") 8 | } 9 | \arguments{ 10 | \item{...}{Additional arguments to \code{rmarkdown::pdf_document}} 11 | 12 | \item{highlight}{Syntax highlighting style. Supported styles include 13 | "default", "tango", "pygments", "kate", "monochrome", "espresso", 14 | "zenburn", and "haddock". Pass \code{NULL} to prevent syntax highlighting.} 15 | 16 | \item{citation_package}{The LaTeX package to process citations, \code{natbib} 17 | or \code{biblatex}. Use \code{none} if neither package is to be used.} 18 | } 19 | \value{ 20 | R Markdown output format to pass to 21 | \code{\link[rmarkdown:render]{render}} 22 | } 23 | \description{ 24 | Format for creating NIH Biosketches. Does not use an official template but should approximate the format required by NIH. Is built on the template created by Paul Magwene found here: https://github.com/pmagwene/latex-nihbiosketch. 25 | } 26 | \details{ 27 | Possible arguments for the YAML header are: 28 | \itemize{ 29 | \item \code{name} Your Full Name 30 | \item \code{eracommons} Your ERA Commons ID 31 | \item \code{position} Description of your research position 32 | \item \code{education} Your education attainment (include any Bachelors, Masters, Doctorate, Postdoc). Several items are required for the education: 1) degree, 2) school, 3) date, and 4) field. 33 | \item \code{researchsupport} Both \code{ongoing} and \code{completed} research support received. Several items are required for the research support for both ongoing and completed: 1) grant, 2) PI, 3) dates, 4) title, 5) description, and 6) role. 34 | \item \code{bibliography} The name of the bib file 35 | \item \code{bibliographystyle} The bib style 36 | \item \code{output} Should be one of the formats from \code{biosketchr} 37 | } 38 | } 39 | -------------------------------------------------------------------------------- /man/nsf_biosketch.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/nsf_biosketch.R 3 | \name{nsf_biosketch} 4 | \alias{nsf_biosketch} 5 | \title{NSF Biosketch format.} 6 | \usage{ 7 | nsf_biosketch(..., highlight = NULL, citation_package = "none") 8 | } 9 | \arguments{ 10 | \item{...}{Additional arguments to \code{rmarkdown::pdf_document}} 11 | 12 | \item{highlight}{Syntax highlighting style. Supported styles include 13 | "default", "tango", "pygments", "kate", "monochrome", "espresso", 14 | "zenburn", and "haddock". Pass \code{NULL} to prevent syntax highlighting.} 15 | 16 | \item{citation_package}{The LaTeX package to process citations, \code{natbib} 17 | or \code{biblatex}. Use \code{none} if neither package is to be used.} 18 | } 19 | \value{ 20 | R Markdown output format to pass to 21 | \code{\link[rmarkdown:render]{render}} 22 | } 23 | \description{ 24 | Format for creating NIH Biosketches. Does not use an official template but should approximate the format required by NIH. Is built on the template created by Paul Magwene found here: https://github.com/pmagwene/latex-nihbiosketch. 25 | } 26 | \details{ 27 | Possible arguments for the YAML header are: 28 | \itemize{ 29 | \item \code{name} Your Full Name (can include prefix such as Dr.) 30 | \item \code{department} Your current department 31 | \item \code{university} Your current university or company 32 | \item \code{email} Your current email 33 | \item \code{telephone} Your current telephone number 34 | \item \code{preparation} Both degrees earned and positions worked in relevant to proposal. Four items are required for the education: 1) location, 2) field, 3) degree, and 4) dates. 35 | \item \code{bibliography} The name of the bib file 36 | \item \code{bibliographystyle} The bib style 37 | \item \code{output} Should be one of the formats from \code{biosketchr} 38 | } 39 | } 40 | -------------------------------------------------------------------------------- /pkgdown/favicon/apple-touch-icon-120x120.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/pkgdown/favicon/apple-touch-icon-120x120.png -------------------------------------------------------------------------------- /pkgdown/favicon/apple-touch-icon-152x152.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/pkgdown/favicon/apple-touch-icon-152x152.png -------------------------------------------------------------------------------- /pkgdown/favicon/apple-touch-icon-180x180.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/pkgdown/favicon/apple-touch-icon-180x180.png -------------------------------------------------------------------------------- /pkgdown/favicon/apple-touch-icon-60x60.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/pkgdown/favicon/apple-touch-icon-60x60.png -------------------------------------------------------------------------------- /pkgdown/favicon/apple-touch-icon-76x76.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/pkgdown/favicon/apple-touch-icon-76x76.png -------------------------------------------------------------------------------- /pkgdown/favicon/apple-touch-icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/pkgdown/favicon/apple-touch-icon.png -------------------------------------------------------------------------------- /pkgdown/favicon/favicon-16x16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/pkgdown/favicon/favicon-16x16.png -------------------------------------------------------------------------------- /pkgdown/favicon/favicon-32x32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/pkgdown/favicon/favicon-32x32.png -------------------------------------------------------------------------------- /pkgdown/favicon/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TysonStanley/biosketchr/dd5896fe0d8d715c15b05c2c663fd1f1758d2d55/pkgdown/favicon/favicon.ico --------------------------------------------------------------------------------