opp_render_report: Render KBA report for a given species

In popovs/OPPtools: This package contains tools and templates to analyze seabird tracking data

Render KBA report for a given species

Description

This function will generate a KBA report using the 'opp-kba-report' RMarkdown template in OPPtools, with options to save the generated report as an .Rmd file in addition to the output PDF.

Usage

opp_render_report(
  params,
  iterations = 5,
  level_ud = 95,
  save_rmd = FALSE,
  save_shp = TRUE,
  save_pts = TRUE,
  output_dir = "temp",
  out_format = "pdf_document",
  ...
)

Arguments

params	List of 19 parameter values used to generate report.
iterations	Numeric. Number of iterations to perform for track2KBA::repAssess. More iterations will result in a more accurate assessment, but take longer to run. Default 5.
level_ud	Numeric, from 0 to 100. Utilization distribution volume to extract from kernel densities. Defaults to 95.
save_rmd	Logical (T/F). Should the .Rmd file used to generate the PDF report be saved as well?
save_shp	Logical (T/F). Should the final OPP key area polygon be saved as a shapefile?
save_pts	Logical (T/F). Should the raw downloaded Movebank points be saved as a shapefile?
output_dir	Output directory for generated files, relative to your working directory. Defaults to 'temp'. If the directory does not exist, the script will create the directory.
out_format	Output file format for the knitted document. Defaults to 'pdf_document'.

Details

The analysis run using the Rmarkdown template expects reporting parameters available in cpf_report_params. See the help for this dataset for a description of each parameter. If you would like to permanently modify or add to these parameters within the package, open an issue or make a pull request to the Github repo at: https://github.com/popovs/OPPtools

Saving shapefiles from this template may only work when run within an R Project. If you are getting errors using save_shp == TRUE or save_pts == TRUE, try working from an R project. Within RStudio go to File>>NewProject or use OPPtools::CreateProject() to create a new project.

Examples

## Not run: 
for (i in 1:nrow(cpf_report_params)) {
  opp_render_report(params = cpf_report_params[i,],
                    kernel_smoother = cpf_report_params$smoother[i],
                    iterations = 10,
                    level_ud = 95,
                    save_rmd = FALSE,
                    save_pts = TRUE,
                    output_dir = 'temp',
                    out_format = 'pdf_document')
                    }

## End(Not run)

popovs/OPPtools documentation built on July 8, 2023, 2:29 a.m.