This directory contains the R (https://www.r-project.org/) code for transforming raw animal trait observations into a standardised form, plus some functions for reporting on and plotting the results. Raw observations are recorded in CSV files with a predefined set of columns. Observations are read in, checked for errors, converted to standard units, and written to a CSV file and a spreadsheet.
To run the conversion, execute the R script analysis.R.
The list of traits and units to be written to the output file is
defined in standardisation/traits-config.R. It also contains
conversion parameters, eg. O2 consumption to Joules. You can edit the file if you wish to re-generate the database with different units or conversion parameters. For example, to generate the database with brain sizes in grams, edit standardisation/traits-config.R and change list("brain size", units = "kg" to list("brain size", units = "g", then execute analysis.R. Read the comments in the script for further information.
To generate the figures for the publication, execute figures-and-stats.R.
R files for performing the standardisation are in the sub-directory standardisation.
Input and output directory and file names are defined in standardisation/constants.R.
The file AnimalTraits.Rproj is an Rstudio project file.
The scripts use a number of external packages. Most can be installed from The Comprehensive R Archive Network (CRAN). The JUtils package is only available from GitHub; refer to its README for installation instructions.
The file AT-functions.R contains 2 functions that may be useful to users of the database who are using R. Feel free to download the script to include in your own projects. The functions are:
| Function | Description |
|---|---|
ReadStandardisedObservations |
Reads the observations database from a CSV file. Enforces the correct encoding. |
SpeciesTraitsFromObservations |
Given a dataframe of observations, aggregates them into species-level traits. |
Both functions are documented within the source file.