When I perform the modeling of species for the present and the future in various scenarios, I want to calculate the loss or gain in certain areas and in certain pixel values, how do I do this?...
In QGIS, check the add-on menu> manage and install add-on. Search for the semi-automatic classification plugin: https://fromgistors.blogspot.com/p/semi-automatic-classification-plugin.html
Analyze if he tends to you.
There are other plugins in qgis, search for keywords.
My first idea would be to simply subtract the future model raster from the the present model raster using the continuous model ouputs. This would indicate the cell based change in suitability/occupancy (or whatever it is you are modelling).
Also I could imagine to simply count the number of presence cells as predicted by both models using the thresholded model outputs. If the cell area is equal across the raster (e.g. if you use an equal area coordinate reference system, such as epsg6933) then computing the change in area is straightforward. All jobs can be easily done in for example, R or QGIS.
If in QGIS there is a function of the principal component, then you can take in chronological order the composit of the rasters to calculate the PC and starting from the second component there will be find changes.