Merging translocation, new genetics and spatial demography

[JetteReeg]

The transloc_new_genetics_spatial_demog branch includes:

• all changes introduced in the new genetic module (regular merges of new_genetics into transloc_new_genetics_spatial_demog_merge)
• translocation feature:
  • introduces a new class for management features. So far it only holds translocation of individuals.
  • Individuals with given characteristics in a given cell or patch are randomly selected and translocated/added to a different given cell or patch
• spatial demography:
  • the three demographic rates fecundity, development and survival can vary spatially for models using habitat suitability maps.
  • in the transition matrix, the user sets the maximal rates.
  • in habitat maps, the user defines the factors for each cell, which are applied to the maximal demographic rates. (similar to the effect of habitat quality on the K_DensDep parameter)
  • there can be up to 3sexesstages additional maps/layers provided
  • each stage and sex is assigned a layer number, which are used for spatially varying rates. If a rate is not spatially varying, the user assigns -9 (batch) or NA (R-pkg).
  • this feature was first published in Malchow et al (2022), who developed it for the R-pkg and will be incorporated in the next release

Additional changes:

• the R-pkg version now allows all spatial inputs to be parsed as Rcpp matrices. This function is specifically suited for bayesian calibration

As the changes are major and quite complex, I will do the main work locally, avoiding automatic merges, but wanted to have an office pull request for documentation.