Inputs
LSCorridors needs two raster maps as input files: a resistance surface map and a map of the patches that will be connected (source-target map, or simply ST map). These maps may be prepared outside GRASS (using other GIS softwares, for example).
The former may be a result of a reclassification of a land use map using expert knowledge, a species distribution model output, or the result of the analysis of movement or gene flow for an organism, for instance. They can represent the difficulty of organisms to cross (or the mortality probability in) different habitats. More information on resistance maps may be found in this paper.
In the latter map, pixels of the same patch must be identified with a number that identifies that patch, without repetition. Although not necessary, another file that may be useful (and that may be imported into LSCorridors) is a list with the patches identification numbers (ID) that one wants to connect. Pixels not belonging to any patch must be assigned the NULL value.
The user may find a set of resistance and ST maps in the demonstration maps database folder of the repository, as well as a list of patches to be connected by corridors.
There are two ways to selected the resistance map before running simulations: 1) selecting it in a specific folder with the button Resistance Map and importing it using the button IMPORT FILES; 2) if the user has already imported the map to the GRASS database (look here and here to learn how to do that) the map can be selected in the “Resistance” field.
As an illustrative example, we will use the first option. Click in the select files button besides the Resistance Map and inside the folder DB_demo select the file Resistance_map1.img. In the LSCorridors display the selected map name will be shown.
Similar to the resistance map, there are two ways of selecting habitat patch map: 1) selecting the raster file in a specific folder with the Source-Target Map button and importing it using IMPORT FILES button; 2) if the user has already imported the map to the GRASS database it can be selected in the ST field.
As an illustrative example, we will use the first option. Click in the select files button besides the Source-Target Map and select the ST_map1.img inside the DB_demo folder. The selected map will also appear in the LSCorridors display.
After selected both Resistance and ST maps click in IMPORT FILES button: in the LSCorridors display it will appear the message “Importing rasters…”.
OBSERVATION: The definition of the ST map is one of the sources of variability in the corridors simulated by LSCorridors. If you define large patches or areas as sources and targets for corridor simulation, the initial and final locations will vary between simulations and be randomly selected inside these patches. Instead, if you want to keep initial and final locations fixed, you may create the ST map considering patches composed of only one pixel, so that this source of variability is removed.
The following step is to define which combinations of patches the user wants to connect through the ecological corridors to be simulated. There are also two ways to insert the list of Source-Target patches that will be connected: 1) manually, inserting the patch ID list in the Enter a list manually field; 2) selecting a .txt file with the READ LIST TXT button. In both cases, the patch IDs must be separate by comma and all patches must have a subsequent pair, which means that the list must have an even number of patches. For example, the list 1,2,5,7 will set LSCorridors to connect patches 1 and 2 first, and 5 and 7 after that.
As example, we will use the second option: click in READ LIST TXT' button and select the ST_list1.txt file in the [DB_demo`](https://github.com/LEEClab/LS_CORRIDORS/tree/master/DB_demo) folder. LSCorridors display shows the message “TXT Combinations” with the patch IDs.
Still, if the user wants to generate corridors between all fragmented present in the habitat patches (ST) map, it is necessary to click the COMBINE ALL button, but note that if the number of patches in the ST map is too extensive it may cause an excessive delay in the corridors processing.
