How to use the run.R file to be the skeleton of your report
July 03 2022
Source:vignettes/B_run-script-demo.Rmd
B_run-script-demo.RmdFirst, run
NMFSReports::buildReport() to produce our basic report
outline. It should produce something like this:
library(NMFSReports)
# Input variables for buildReport()
sections = c("frontmatter", "abstract", "introduction", "methods", "results",
"discussion", "endmatter")
authors = "Me, Myself, and I"
title = "Awesome Report!"
styles_reference_pptx = "refppt_nmfs"
styles_reference_docx = "refdoc_noaa_tech_memo"
bibliography.bib = "bib_example"
csl = "bulletin-of-marine-science"
# Run buildReport() function
buildReport(
sections = sections,
report_authors = authors,
report_title = title,
styles_reference_pptx = styles_reference_pptx,
styles_reference_docx = styles_reference_docx,
bibliography.bib = bibliography.bib,
csl = csl
)We’ll navigate to the spine of this report, the run.R
file, in the code folder. This is where we run all of our files (.R,
.Rmd, etc.) from.
source("./code/run.R")run.R
#' ---
#' title: 'Awesome Report!'
#' author: 'Me, Myself, and I'
#' purpose: Run Scripts and R Markdown Files
#' start date: 2022-01-02
#' date modified: 2022-01-02 # CHANGE
#' Notes: # CHANGE
#' ---
# START ------------------------------------------------------------------------
# *** REPORT KNOWNS ------------------------------------------------------------
report_title <- 'Awesome Report!'
report_authors <- 'Me, Myself, and I'
report_yr <- substr(x = Sys.Date(), start = 1, stop = 4) # SUGGESTION
# *** OUTPUT TYPE --------------------------------------------------------------
#Is this for InDesign?
indesign_flowin <- FALSE
# *** SOURCE SUPPORT SCRIPTS ---------------------------------------------------
source('./code/directories.R')
source('./code/functions.R')
source('./code/dataDL.R')
source('./code/data.R')
# *** RENV: SAVE PACKAGES USED TO CREATE THIS REPORT ---------------------------
# renv::init()
# renv::snapshot()
# *** SIGN INTO GOOGLE DRIVE----------------------------------------------------
# googledrive::drive_deauth()
# googledrive::drive_auth()
# 1
# RUN FIGURES, TABLES, & EQUATIONS FOR REPORT ----------------------------------
if (FALSE) {
cnt_chapt_content<-"000"
filename0<-paste0(cnt_chapt, "_")
rmarkdown::render(paste0(dir_code, "/0_figtab.Rmd"),
output_dir = dir_out_ref,
output_file = paste0(filename0, cnt_chapt_content, ".docx"))
save(list_figures, file=paste0(dir_out_figures, "/report_figures.rdata"))
save(list_tables, file=paste0(dir_out_tables, "/report_tables.rdata"))
save(list_equations, file=paste0(dir_out_tables, "/report_equations.rdata"))
}
load(file = paste0(dir_out_figures, "/report_figures.rdata"))
load(file = paste0(dir_out_tables, "/report_tables.rdata"))
load(file = paste0(list_equations, "/report_equations.rdata"))
# RUN EACH REPORT SECTION ------------------------------------------------------
# *** RUN EACH REPORT SECTION --------------------------------------------------
# *** 0 - Example ------------------------
cnt_chapt<-auto_counter(cnt_chapt)
cnt_chapt_content<-"001"
filename0<-paste0(cnt_chapt, "_example_")
rmarkdown::render(paste0(dir_code, "/0_example.Rmd"),
output_dir = dir_out_chapters,
output_file = paste0(filename0, cnt_chapt_content, ".docx"))
# *** 1 - Frontmatter ------------------------
cnt_chapt<-auto_counter(cnt_chapt)
cnt_chapt_content<-"001"
filename0<-paste0(cnt_chapt, "_frontmatter_")
rmarkdown::render(paste0(dir_code, "/1_frontmatter.Rmd"),
output_dir = dir_out_chapters,
output_file = paste0(filename0, cnt_chapt_content, ".docx"))
# *** 2 - Abstract ------------------------
cnt_chapt<-auto_counter(cnt_chapt)
cnt_chapt_content<-"001"
filename0<-paste0(cnt_chapt, "_abstract_")
rmarkdown::render(paste0(dir_code, "/2_abstract.Rmd"),
output_dir = dir_out_chapters,
output_file = paste0(filename0, cnt_chapt_content, ".docx"))
# *** 3 - Introduction ------------------------
cnt_chapt<-auto_counter(cnt_chapt)
cnt_chapt_content<-"001"
filename0<-paste0(cnt_chapt, "_introduction_")
rmarkdown::render(paste0(dir_code, "/3_introduction.Rmd"),
output_dir = dir_out_chapters,
output_file = paste0(filename0, cnt_chapt_content, ".docx"))
# *** 4 - Methods ------------------------
cnt_chapt<-auto_counter(cnt_chapt)
cnt_chapt_content<-"001"
filename0<-paste0(cnt_chapt, "_methods_")
rmarkdown::render(paste0(dir_code, "/4_methods.Rmd"),
output_dir = dir_out_chapters,
output_file = paste0(filename0, cnt_chapt_content, ".docx"))
# *** 5 - Results ------------------------
cnt_chapt<-auto_counter(cnt_chapt)
cnt_chapt_content<-"001"
filename0<-paste0(cnt_chapt, "_results_")
rmarkdown::render(paste0(dir_code, "/5_results.Rmd"),
output_dir = dir_out_chapters,
output_file = paste0(filename0, cnt_chapt_content, ".docx"))
# *** 6 - Discussion ------------------------
cnt_chapt<-auto_counter(cnt_chapt)
cnt_chapt_content<-"001"
filename0<-paste0(cnt_chapt, "_discussion_")
rmarkdown::render(paste0(dir_code, "/6_discussion.Rmd"),
output_dir = dir_out_chapters,
output_file = paste0(filename0, cnt_chapt_content, ".docx"))
# *** 7 - Endmatter ------------------------
cnt_chapt<-auto_counter(cnt_chapt)
cnt_chapt_content<-"001"
filename0<-paste0(cnt_chapt, "_endmatter_")
rmarkdown::render(paste0(dir_code, "/7_endmatter.Rmd"),
output_dir = dir_out_chapters,
output_file = paste0(filename0, cnt_chapt_content, ".docx"))
# *** 8 - Presentation ------------------------
cnt_chapt<-auto_counter(cnt_chapt)
cnt_chapt_content<-"001"
filename0<-paste0(cnt_chapt, "_presentation_")
rmarkdown::render(paste0(dir_code, "/8_presentation.Rmd"),
output_dir = dir_out_chapters,
output_file = paste0(filename0, cnt_chapt_content, ".pptx"))
# MAKE MASTER DOCX -------------------------------------------------------------
#USE GUIDENCE FROM THIS LINK
#https://support.microsoft.com/en-us/help/2665750/how-to-merge-multiple-word-documents-into-one
# SAVE METADATA ----------------------------------------------------------------
con <- file(paste0(dir_out_todaysrun, "metadata.log"))
sink(con, append=TRUE)
sessionInfo()
sink() # Restore output to console
# cat(readLines("notes.log"), sep="\n") # Look at the logWhat this file produces:
When we run the above run.R file (completely
unaltered/fresh from NMFSReports::buildReport()), it produces the below
content in our ./output/[YYY-MM-DD]/ folder.
This is useful because your progress is saved each day that you work on this project and you can easily find your outputs to make sure they look like you want them too!
Output folder post running the run.R script
Notes:
Support Scripts
To make sure we nice and neatly compartmentalize our work, the below supporting .R scripts are going to be created and will source into the ‘run’ file:
*note a ‘run’ file is automatically created. Think of this as the spine of your document.
functions: Where we will save all report-specific functions.
directories: Where we will systematically create and save objects describing all of our directories. I’ve found that it can be helpful to have these as objects to cut down on verboseness.
dataDL: Where we will download the data (e.g., from Oracle or an API). You may only want to run this every so often or regularly, up to you.
data: Where we will load that data kept locally that was either downloaded in “dataDL” or created locally.
Things to change
Now that you have your initial run, you can start to modify and add to the structure with content specific to your project. Here are a few things to change: