In EmilyMarkowitz-NOAA/NMFSReports: Easily write NOAA reports and Tech Memos in R Markdown!

knitr::opts_chunk$set(
  message = FALSE, echo = TRUE, warning = FALSE, 
  comment = FALSE, collapse = TRUE,
  comment = "#>"
)
options(rmarkdown.html_vignette.check_title = FALSE)

library(NMFSReports)

Quick! Get started!

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!

Step by Step: Create initial structure of report

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:

buildReport(report_title = ...)

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!"

buildReport(report_authors = ...)

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"

buildReport(sections = ...)

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. 
) 

buildReport(styles_reference_docx = ...)

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:

refdoc_noaa_tech_memo

refdoc_fisheries_economics_of_the_us

buildReport(styles_reference_pptx = ...)

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:

refpptx_nmfs

buildReport(csl = ...)

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)

buildReport(bibliography.bib = ...)

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

Create Report Outline

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
)

Alternative report structures:

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
)

EmilyMarkowitz-NOAA/NMFSReports documentation built on March 26, 2023, 1:08 a.m.