Data and code to reproduce "Effects of occupancy estimation on abundance-occupancy relationships"

This repository contains the code and data to reproduce the analyses in :

Ten Caten, C., Holian, L., Dallas, T. "Effects of occupancy estimation on abundance-occupancy relationships"

In the Data.rar file we provide the datasets needed to run the code. The file MammalsData.RData contains the exact NEON small-mammal data used in our analyses. Thus, instead of using the function loadByProduct to download the data (line 36) from the NEON database (might take some time), the user can run line 38 and skip that part.

The second chunk of code download occurrence data for the species found in the NEON dataset from GBIF database. That chunk of code might also take a while to run, so we provide the final product (MammalsOccNEON.txt) that can be imported in line 201 so that chunk doesn't need to be run. 

The third chunk of code create the spatial poligons for the species geographic range. We also provide these poligons (MammalsHull.RData) that can be loaded by running line 242 instead of running the entire code. Notice that if the poligons are imported, lines 207-213 in the third chunk will still needed to be run in order to name each poligon so that the rest of the code runs smoothly.