doc/B_run-script-demo.R

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

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


## ----setup--------------------------------------------------------------------
library(NMFSReports)

## ---- eval=FALSE--------------------------------------------------------------
#  
#  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
#  )

## ---- eval=FALSE--------------------------------------------------------------
#  source("./code/run.R")

## ---- eval=FALSE--------------------------------------------------------------
#  #' ---
#  #' 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 log
#