Species indicator list optimization using multiple criteria

Summary

The silo R-package is a multi-criteria optimization tool intended for selection of species for monitoring or indicator assessment with an emphasis on representativeness of the selected species list. The methodology is quite general and should be easily applicable outside of the field of biological and genetic diversity.

Documentation

The package is documented in its help files and vignettes. Additionally an upcoming publication will describe overall methodology more generally.

Installation

To install the development version of this package you have two options:

1. Use the devtools R-package. In an R session run the command devtools::install_github("sykefi/r-silo", subdir = "silo").

2. Clone the repository and install locally. Run git clone https://github.com/sykefi/r-silo.git on the command line, enter the repository cd r-silo/silo and run the commands R CMD build silo. Alternatively run the command make install if Make is available in the r-silo/ directory. Installation on Windows will require Rtools.

Development

The root directory of the repository contains a Makefile that can help with development of the package. It has the following targets.

• check: Run the R CMD check in CRAN mode.
• clean: Remove all generated files ignored by the git from the repository.
• format: Reformat C++ and R code in the repository.
• install: Install the package locally.
• rcpp: Create the Rcpp interface files, run automatically by targets requiring it.
• test: Run the tinytest test suite.
• data: Recreate the test and demonstration data used by the package.

To reattach the package in a running R-session after installing a new version, run

detach("package:silo", unload = TRUE); library("silo")

The test data set is generated from the Finnish Biodiversity Information Facility species checklist and the Red List of Finnish Species.