Johannes Radinger and Christian Wolter. 2015. Disentangling the effects of habitat suitability, dispersal, and fragmentation on the distribution of river fishes. Ecological Applications 25:914927. http://dx.doi.org/10.1890/14-0422.1


Supplement

GRASS-Python script to run FIDIMO for several species; derived data set and corresponding R code to calculate GLMMs and create interaction plots.
Ecological Archives A025-055-S1.

Copyright


Authors
File list (downloads)
Description


Author(s)

Johannes Radinger
Leibniz-Institute of Freshwater Ecology and Inland Fisheries
Müggelseedamm 310
12587 Berlin
Germany
E-mail: jradinger@igb-berlin.de

Christian Wolter
Leibniz-Institute of Freshwater Ecology and Inland Fisheries
Müggelseedamm 310
12587 Berlin
Germany


File list

01_GRASS_FIDIMO_analysis.py (MD5: 9beacd30eddc5c18906c26337a69ee0e)

02_habitat_dispersal_barriers_raw_data.csv (MD5: 6b9d8d5a7724f4dcea462279bfda36c3)

03_GLMM_habitat_dispersal_barriers.R (MD5: cbbde806275b0ae2b39c4843aa117253)

04_Plots_GLMM_interactions.R (MD5: 4da402149c5a3473b4295b574f021da9)

Description

01_GRASS_FIDIMO_analysis.py Commented Python code to run the dispersal model FIDIMO within a GRASS session. The script provides a FIDIMO calculation in loops for (i) 17 species, (ii) nine time intervals (1-9 years) and (iii) inclusive/exclusive barriers. The species-specific parameters for the model internal calculation of the dispersal distances are included in the script. Species' presence points (site name, catch per unit effort, site ID, X, Y) are used as FIDIMO input file (ascii point file).

02_habitat_dispersal_barriers_raw_data.csv – Derived data set including all information used for running the generalized linear mixed models (GLMM).

Columns are as follows:

row number (numeric; 1:20672)
SiteID        Site specific ID (numeric)
species       Species Code (character, species code)
presabs      Presence of a species (0: Absence, 1: Presence)
L                Species-specific common length  [mm] (numeric)     
AR             Aspect ratio of the caudal fin [-] (numeric)
variable     Variable name (MaxEnt output, Disperal probability, Barrier effects), e.g. "point_fidimo_corrected_9y" (character)
value          value of the corresponding variable

03_GLMM_habitat_dispersal_barriers.R – R code for running generalized linear mixed models using 02_habitat_dispersal_barriers_raw_data.csv as input data set.

04_Plots_GLMM_interactions.R – R code for plotting interaction effects of the output of the GLMM.