knitr::opts_chunk$set( message = FALSE, echo = TRUE, warning = FALSE, comment = FALSE, collapse = TRUE, comment = "#>" ) options(rmarkdown.html_vignette.check_title = FALSE)
library(NMFSReports)
Here, I'll show a basic script that you can quickly run to get started.
# 1. Load the NMFSReports Library library(devtools) devtools::install_github("EmilyMarkowitz-NOAA/NMFSReports", force = TRUE) library(NMFSReports) # 2. Build your report NMFSReports::buildReport( sections = c("abstract", "introduction", "history", "methods", "results", "results_discussion", "endmatter", "presentation"), report_authors = "Me, Myself, and I", report_title = "The best report ever", styles_reference_pptx = "refppt_nmfs", styles_reference_docx = "refdoc_noaa_tech_memo", bibliography.bib = "bib_example", csl = "bulletin-of-marine-science" ) # 3. Run your run.R file source("./code/run.R")
More details about each option and step of the process is below!
Do everyone here a favor and create a new R project or at least set up a working directory (setwd()
). There will be a lot of file management here...
To build your intitial architecture for your new NOAA Tech Memo or Report, simply run the below script:
Default = "". Here, put the title of your report. You can change this later in the run.R
file in needed.
report_title = "My Awesome Report!"
Here, add the first and last name of everyone who is producing the report. You can change this later in the run.R
file in needed.
report_authors = "Me, Myself, and I"
Let's first think about what you want/need your Tech Memo to look like. For my purposes, I'll assume that you need the below sections:
# list the sections (that you will have different rmd scripts for) in order and with no spaces sections <- c("frontmatter", # This is a specific template that matches the NOAA Template "abstract", # This, and all others unless otherwise mentioned, come from the same plain-slate document but are appropriately named and linked up in the 'run' file. "introduction", "methods", "results", "discussion", "endmatter" # This is a specific template that will document all of your citations throughout the report, the R packages you used to create this report. I'm biased, but please give credit where credit is due! There are also spots here to list people's ORCID numbers and acknowlegements. )
styles_reference_docx
is a document style reference guide is essentially a word document where you have defined each style. Either use a local document (insert "path") or some of the pre-made templates ("refdoc_noaa_tech_memo" or "refdoc_fisheries_economics_of_the_us"). Default = "refdoc_noaa_tech_memo"
To edit the stlyes in your word document, check out this resource.
Here's what they look like:
styles_reference_pptx
is a document style reference guide is essentially a word document where you have defined each style. Either use NULL to not have a presentation, a local document (insert full path to local document), or a pre-made template ("refpptx_nmfs"). Default = "refpptx_nmfs". You can change this later by renaming the file in the code folder.
Here's what they look like:
csl
is a citation style. Either use a local document (insert "path") or some of the pre-made templates ("apa" or "bulletin-of-marine-science"). Default = "apa" because it was easy to find.
A primer on creating and modifying CSL styles can be found at http://citationstyles.org/downloads/primer.html. A repository of CSL styles can be found at https://github.com/citation-style-language/styles. See also http://zotero.org/styles for easy browsing.
csl = "bulletin-of-marine-science" # it looks something like this: csl0 <- base::readLines(system.file("cite","bulletin-of-marine-science.csl", package="NMFSReports")) head(csl0)
bibliography.bib
: Either use a local document (.bib format; insert full "path") or the example file from the package ("bib_example"). Default = "bib_example".
csl = "bib_example" # it looks something like this: bib <- base::readLines(system.file("rmd","bib_example.bib", package="NMFSReports")) bib
Now, magic! Now for the sake of the vignette, I can't actually run it here, but below is a picture of what this looks like:
NMFSReports::buildReport( sections = sections, report_authors = report_authors, report_title = report_title, styles_reference_pptx = styles_reference_pptx, styles_reference_docx = styles_reference_docx, bibliography.bib = bibliography.bib, csl = csl )
library(NMFSReports) # Input variables for buildReport() sections = c("coverpage", # This is a specific template for a 1 page coverpage "history", "studyimportance", "actions", "endmatter") # This is a specific template that will document all of your citations throughout the report, the R packages you used to create this report. I'm biased, but please give credit where credit is due! There are also spots here to list people's ORCID numbers and acknowlegements. report_authors = "Very important people" report_title = "Shorter Report!" styles_reference_pptx = "refpptx_nmfs" styles_reference_docx = "refdoc_fisheries_economics_of_the_us" bibliography.bib = "bib_example" # Find citation styles at: https://github.com/citation-style-language/styles csl0 <- read.delim(file = "https://raw.githubusercontent.com/citation-style-language/styles/master/american-fisheries-society.csl", header = FALSE, ) colnames(csl0)<-NULL rownames(csl0)<-NULL write.table(x = csl0, file = "csl.csl", quote = FALSE, row.names = FALSE, col.names = FALSE) csl = ("./csl.csl") head(csl0)
# Run buildReport() function NMFSReports::buildReport( sections = sections, report_authors = report_authors, report_title = report_title, styles_reference_pptx = styles_reference_pptx, styles_reference_docx = styles_reference_docx, bibliography.bib = bibliography.bib, csl = csl )
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