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- updating RScore subtree and set it on track to RScore repo - rm unnecessary GUI related functions, which were deleted in the current RScore repo - fixed issue with crashing R when raster files have decimal digits as cellsize (resulting from saving files with terra package)
# resolved conflicts: # RangeShiftR/src/Rinterface.cpp
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…_new_genetics_merge
ColonisationStats() checks whether patch maps are Raster Layers or Raster Stack objects from raster package and transform these to SpatRaster objects fixed a bug for extracting the number of layers for a stacked raster file
ColonisationStats() checks whether patch maps are Raster Layers or Raster Stack objects from raster package and transform these to SpatRaster objects fixed a bug for extracting the number of layers for a stacked raster file
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…_new_genetics_merge
…_new_genetics_merge
…_new_genetics_merge
…cs but haven't been changed yet in case of NOT RSDEBUG or RSRCPP For Rinterface.cpp: updated variable names, which changed in new_genetics For class_GeneticsParams.R and class_RSparams.R: introduced new genetic input structure and added all checks for inputs
…_new_genetics_merge
- Simulation() does not account for genetic output. This is shifted to the Genetic() function - completely new structure of Genetics(): Is now in line with Genetics.txt file needed for the batch interface - new function Traits() which includes parameter settings for NeutralTraits(), GeneticLoad, and all dispersal Traits - help files generated for all new functions - only for neutral genetics, the R input is passed to the c++ code. - already updated the version number to 3.0 - no additional changes to the RScore code, but there might need some adaptations for the R interface, as some error messages are specific to the batch interface input
still debugging
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New structure of Genetics() New function Traits() for all trait settings New function NeutralTraits() for setting up neutral trait New function GeneticLoadTraits() for setting up genetic load traits New function EmigrationTraits() for setting up emigration traits New function KernelTraits() for setting up dispersal kernel traits New function CorrRWTraits() for setting up correlated random walk traits New function SMSTraits() for setting up SMS traits New function SettlementTraits() for setting up settlement traits Adapted Emigration(), DispersalKernel(), CorrRW(), SMS(), Settlement() and check of RSparams because evolving dispersal traits shifted to new functions
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Dimension does not need to be checked if IndVar=T
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Included genetic output descriptions in functions
…/RScore - manually applying changes done by RoslynHenry in commits 242b90a26838915bb68b7399968ce57a11acbf96, 285ee1b867e6638e625ad7e7edbd44a8b91c72dd, 1b7da0fe59d4147e114b167227894ac3b7aef333
however, I am not sure whether unit tests will be successfull as changes in pairwise Fst were made
solved conflicts; compiling successfull on Win11
now returning spatial rasters (for cell-based models) or a data.frame (for patch based models) for total abundances per cell or specific (user defined) stages
- added new output option (returning spatial raster (cell-based) or dataframe (patch-based) for overall abundance and user defined stages - updated helpfiles - generating parameter table for documentation purposes
- version number - improved git subtree documentation
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The develop branch includes:
the new genetics module from RScore/new_genetics
spatial demography
translocation feature:
Additional changes:
the R-pkg version now allows all spatial inputs to be parsed as R matrices. This function is specifically suited for bayesian calibration
for the batch interface, reproduction and transfer can run in parallel to speed up running time
As the changes are major and complex. The merge will be done locally and not via GitHub. This pull request is aimed for providing an overview of all changes.
The RScore subtree repository was already merged at this point in time.
Next step is to run a
git subtree pull --prefix RangeShiftR/src/RScore RScore mainbefore running thegit merge developcommand'After the merge, a new release should be made with version number 3.0.0 and the prepared release note.