Source code supplement for article Louca et al. - Detecting cyclicity in ecological time series.

This supplement comprises the R script used for our statistical analysis of the Global Population Dynamics Database (GPDD) ("GPDD_main.R"). The script was tested using R 3.1.1 on Mac OS 10.6. A more elaborate documentation of the script can be found as comments therein.

What you need to analyze the GPDD:
Due to licensing issues, we do not include the GPDD with this supplement. The entire database can be downloaded for free from the Imperial College website: http://www3.imperial.ac.uk/cpb/databases/gpdd
You will need to create an account first before you can download the database.
You also need to install the 'peacots' package from CRAN.

What format should the GPDD be in:
The original GPDD can only be downloaded in Microsoft Access format. Our code can not handle this format, so each time series must be saved in a separate file with the name prefix "GPDD_". Each time series file must only contain two data columns separated by a comma, one for the time value (e.g. decimal year) and one for the population density. All time series files must be stored in the directory GPDD. If you wish to reproduce our results, you need to have all time series values in a linear scale (e.g. exponentiate logarithmically transformed densities first).

How to execute the GPDD script:
Type source("GPDD_main.R") in your R console. The execution might take several minutes. If you want to change the analysis parameters you need to modify the first few lines of the source file GPDD_main.R.

Disclaimer
This code is provided as is. Use at your own risk and discretion. The authors of this code can not be held responsible for any damage or costs resulting from the use of this code.

Stilianos Louca
October 30, 2014