This repository shares the code and details on the Spatial Individual Specialization Index (SpatIS) and the Spatis Individual Complementary Specialization Index (SpatICS). Those two indices were developed and first presented in Kerches-Rogeri et al (2020, see reference below).
For more information on how to run it for your data please look at the SpatIS website: https://leeclab.github.io/SpatIS/. You will also find further information in the main article and supplementary information of the reference below (Kerches-Rogeri et al. 2020).
We present here the source code for running SpatIS and SpatICS using movement data of individuals. We also show VHF movement data for the yellow–shouldered bats Sturnira lilium in Southeastern Brazil, an R script for analyzing this data using SpatIS and SpatICS, and other scripts and data used in Kerches-Rogeri et al (2020).
The scripts in this repository are the following (look at the folder code):
- spatis_source_code_v1_0.R: source code with SpatIS and SpatIS_randomize R functions (details within the script); this is the main file for running SpatIS and SpatICS;
- individual_specialization_space_use.R: script for spatial and individual specialization analyses from Kerches-Rogeri et al. (*2020);
- test_for_body_size_and_sex.R: script for testing for body size and sex effects on individual use of space through binomial GLMs;
- use_foraging_areas_fruit_density.R: script for testing the effects of fruit density on the use of foraging areas y each individual;
- spatis_tutorial (in pdf and Rmarkdown formats): Tutorial for applying SpatIS for other data sets. It may also be found here.
- scripts and pdf for the other supplementary material from Kerches-Rogeri et al (2020).
We present here all the data used for analysis by Kerches-Rogeri et al (2020):
- spatis_paper_bat_positions.csv: telemetry fixes for 11 individual bats monitored in Sao Carlos, SP, Brazil.
- spatis_paper_individual_bat_info.csv: individual information for the tracked bats.
- proportion_use_landcover_polygons.csv: proportion of use of land cover polygons in the landscape by each individual.
- proportion_use_foraging_sites.csv: proportion of use of foraging sites by each individual.
- use_foraging_areas_density_fruits.csv: density of the main fruit genera consumed by bats in each foraging area.
If you use SpatIS, please refer to
Kerches-Rogeri, P.; Niebuhr, B. B.; Muylaert, R. L., Mello, M. A. R. 2020. Individual specialization in the use of space of frugivorous bats. Journal of Animal Ecology. DOI: 10.1111/1365-2656.13339.
You can also cite this repository, which contains both the code and data used in the publication:
Niebuhr, B. B.; Kerches-Rogeri P.; Muylaert, R. L., Mello, M. A. R. (2020). SpatIS: Spatial Individual Specialization Indices (Version v1.0). Zenodo.
The movement data of bats presented here may also be found and downloaded from MoveBank, in the study "Individual specialization in the use of space by frugivorous bats".
In Portuguese:
Novo artigo sobre a relação entre dieta e o movimento de morcegos
Mesma espécie de morcegos, gosto diferente para comida: como isso pode impactar o ambiente?
If you have questions or suggestions, do not hesitate to contact us (or open an issue here):
- Patricia Kerches-Rogeri <parogeri@gmail.com>
- Bernardo Brandão Niebuhr <bernardo_brandaum@yahoo.com.br>
- Renata L. Muylaert <renatamuy@gmail.com>
- Marco A. R. Mello <marmello@usp.br>