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Create an Rmarkdown Report to Explore User Data

Source: R/fb_make_report.R
fb_make_report.Rd

Creates an R Markdown (.Rmd) report from a template to explore and summarize user data. User can modify this report and use the function rmarkdown::render() (or click the Render of the RStudio IDE) to convert this .Rmd in different formats:

  • HTML document (output_format = "bookdown::html_document2");

  • PDF document (output_format = "bookdown::pdf_document2");

  • Word document (output_format = "bookdown::word_document2");

  • HTML, PDF and Word documents (output_format = "all").

Usage

fb_make_report(
  path = ".",
  filename = NULL,
  title = NULL,
  author = NULL,
  species_traits,
  site_species,
  site_locations,
  species_categories = NULL,
  overwrite = FALSE,
  open = TRUE,
  interactive = TRUE
)

Arguments

path

a character of length 1. The directory in which the .Rmd and .rds files will be created. This directory must exist. Note that subdirectories funbiogeo/ and funbiogeo/data/ will be created. Default is the current directory.

filename

a character of length 1. The name of the .Rmd file to be created. If NULL (default) the .Rmd file will be named from the title (if provided) or funbiogeo_report.Rmd otherwise.

title

a character of length 1. The title of the report. If NULL (default) the title will be named from the title (if provided) or funbiogeo Report otherwise.

author

a character of length 1. The author(s) of the report. If NULL (default) no author will be added.

species_traits

a data.frame with species in rows and traits as columns. NOTE: The first column should be named "species" and contain species names. The other columns should be named according to trait names.

site_species

a data.frame with sites in rows and species in columns. NOTE: the first column should be named "site" and indicate site names. The other columns should be named according to species names.

site_locations

an sf object with the spatial geometries of sites. NOTE: the first column should be named "site" and indicate site names.

species_categories

(default = NULL) 2-columns data.frame giving species categories, with the first column describing the species name, and the second column giving their corresponding categories

overwrite

a logical. If the .Rmd file (or any .rds dataset) is already present and overwrite = TRUE, the .Rmd file (and all .rds files) will be replaced. Default is FALSE.

open

a logical. If TRUE (default), the .Rmd file will be opened in the text editor.

interactive

a logical. If TRUE (default), the function will ask user to accept the copy of datasets.

Value

No return value.

Details

Note that a copy of user data will be saved as .rds files in path/funbiogeo/data/ (where path is the directory defined by the user).

Examples

if (FALSE) { # \dontrun{
# Create temporary folder (optional) ----
temp_path <- tempdir()

# Create report ----
fb_make_report(
  path           = temp_path, 
  author         = "Casajus N. and Grenié M.",
  species_traits = woodiv_traits,
  site_species   = woodiv_site_species,
  site_locations = woodiv_locations,
  open           = FALSE
)

# Open Rmd file ----
utils::file.edit(file.path(temp_path, "funbiogeo", "funbiogeo_report.Rmd"))

# Render Rmd file ----
rmarkdown::render(
  input         = file.path(temp_path, "funbiogeo", "funbiogeo_report.Rmd"),
  output_format = "all"
)
} # }