LSCorridorsDescription

Brief description

The package

LandScape Corridors (LSCorridors) is a free and open source package developed in Python that simulates multiple functional ecological corridors.

The input to run LSCorridors is a resistance surface map and a raster map of possible source-target patches, a set of regions that will be connected by the simulated corridors. LSCorridors uses these maps and a least-cost path algorithm to generate multiple ecological corridors.

There are three main components that are gathered with the algorithm to generate ecological corridors:

• Biological species information: this information is included in simulations by (i) defining the resistance map, i.e., classifying the landscape in the species' view, and (ii) defining the scale at which the landscape elements affect the species (this works only for methods MLmin, MLavg, and MLmax, take a look in the parameters section).
• Stochasticity: it is included in the model in two ways. First, there is variability in the initial (source) and final (target) positions of the corridors. The larger the size of source-target patches, the greater the variability in initial and final locations. Second, local resistance values are subject to random variation in each corridor simulation. Local variability in landscape resistance may be set by the user (parameter 'Variability').
• Influence of the landscape: there are three methods for including landscape influence on local resistance (MLmin, MLavg, and MLmax), so that landscape composition in the surroundings of a corridor matters for its outline.

For more information on the package details, look at the publication:

Ribeiro, J. W.; Santos, J. S.; Dodonov, P.; Martello, F.; Niebuhr, B. B. S.; Ribeiro, M. C. LandScape Corridors (LSCorridors): a new package for modeling ecological corridors based on landscape patterns and species requirements. Methods in Ecology and Evolution. doi: 10.1111/2041-210X.12750.

The repository

This repository is organized in 5 folders:

• _LS_Corridors_v1_0_0_stable: Here the main pieces of the LSCorridors stable code are located:
  1. LS_corridors_v1_0_0.py: main script.
  2. test_LS_corridors.py: testing script.
  3. script_calculate_connectivity_index.R: an R script for calculating the connectivity index of landscapes based on the corridors simulated on them, using LSCorridors.
  4. gathering_LSCorridors_output.R: an R script for gathering LSCorridors output in a single data frame (outdated, used in old versions of the package; now all the simulated corridors information is saved in a single file).
• old_versions: Old versions of the code (before package release).
• DB_demo: raster maps for testing and tutorials. This includes:
  1. Resistance_map1.img: A resistance map in Rio de Janeiro state, Brazil, inside the Golden Lion Tamarin (GLT) occurrence region. The map was classified based on LANDSAT 7 satellite images; resistance values were defined using expert knowledge on GLT mobility for each land use class.
  2. ST_map1.img and ST_list1.txt: A raster of source-target patches inside the area of Resistance_map1 and list of three possible source-target combinations.

• GIS_DB_Demo_location: GRASS GIS project location for demonstration and testing. The geographic information settings agree with Resistance_map1.img.
• images: images for LSCorridors wiki.