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Merging main into macros#13

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JetteReeg wants to merge 597 commits intomacrosfrom
main
Open

Merging main into macros#13
JetteReeg wants to merge 597 commits intomacrosfrom
main

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@JetteReeg
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@JetteReeg JetteReeg commented Sep 28, 2023

Everyting apart from Rinterface.cpp and Version.cpp/.h should be fine

TheoPannetier and others added 30 commits April 16, 2024 18:09
@TheoPannetier
output gene values, but linking issue
1dba7c4
@TheoPannetier
enable output of gene values
358cbd7
@TheoPannetier
fix genetic output filestream
854e4ab
@TheoPannetier
output gene values uses neutral genetics sampling feature
7a366c3
@TheoPannetier
add push instructions
c40aa22
@TheoPannetier
Merge pull request #26 from RangeShifter/TheoPannetier-patch-1
cc3b95e 
add push instructions
@TheoPannetier
fix merge conflict with develop
43c3046
@TheoPannetier
post merge fixes to README and RSrandom
d5c8623
@TheoPannetier
refactor adaptive trait and fitness into genetic load and p survival
ef7cf7e
@TheoPannetier
fix merge conflict with RScore
6c08cbf
@TheoPannetier
allele dominance is calculated on a locus basis
42e241a
@TheoPannetier
debug assert to try to catch a rare overflow
a29fcb1
@TheoPannetier
fix heterozygosity calls in haploid cases
3d468b3
@TheoPannetier
can catch exceptions
b94b5e7
@TheoPannetier
Merge pull request #25 from RangeShifter/develop
ca57ce8 
Bugfixes from Develop
@TheoPannetier
progress with genetics doc
3d7bc69
@TheoPannetier
doc genetic traits
8adce17
@TheoPannetier
progress with doc of neutral stats
9b73522
@TheoPannetier
doc neutral stats
96e0496
@TheoPannetier
removing some commented out lines
6a2547f
@TheoPannetier
keep trait values valid + ensure parameters correct
0abb3aa
@TheoPannetier
fix invalid input parameter values
ecdadb8
@TheoPannetier
forbid GenomeSize = 0; clarify recombination
e4fd089
@TheoPannetier
fix merge conf.
4a32b13
@TheoPannetier
rename GeneticFitness into GeneticLoad
6fd3c1e
@TheoPannetier
switch sampledInds to vector - sets really don't like to be empty
a4ab791
@TheoPannetier
bug fix; prevent the matrix from being sampled
31a3d8d
@TheoPannetier
adding option to randomly sample once per sim or once per gen
591ad94
@TheoPannetier
Merge branch 'new_genetics' into new_genetics_tmp
76fb158
@TheoPannetier
allow negative genetic loads
5c47e6a
TheoPannetier and others added 30 commits September 27, 2024 14:15
@TheoPannetier
clean readParameters
97f09b2
@TheoPannetier
default arg to let rscore run
df1233e
@TheoPannetier
only clear if closing file
5da938b
@TheoPannetier
resolve merge conflict
43727fb
@JetteReeg
Updated variable names, which changed in new_genetics but haven't bee…
cfd8f86 
…n changed yet if macro RSDEBUG was not active
@TheoPannetier
drop useless allele ID to save memory
902f089
@TheoPannetier
allow negative values for settlement and emigration alphas
73a674b
@TheoPannetier
small cleanup
03681a8
@TheoPannetier
expression should be half both allele if all dom coeffs are 0
0c450bc
@JetteReeg
Merge remote-tracking branch 'origin/new_genetics' into transloc_new_…
3c63422 
…genetics_merge

Edit confilcts in Cell.cpp, Individual.cpp, Landscape.cpp, Main.cpp, Model.cpp, Model.h, Parameters.h, Population.cpp
@JetteReeg
fixed compiling bug in Management.h
70ec1f6
@JetteReeg
fixed bug due to merging in Model.cpp
7509111
@TheoPannetier
fix scaled sd parameter not being passed from parent to offspring
3b81ba1
@TheoPannetier
bit of cleaning of survival
02adc82
@JetteReeg
Merge remote-tracking branch 'origin/new_genetics' into transloc_new_…
e31c278 
…genetics_merge

Edited conflicts in Model.cpp and Population.cpp manually (but there were actually no conflicts)
@JetteReeg
For now only commented out code for file reads that are not necessary…
e5a314b 
… anymore (still need to be tested for unix)

RS_random_seed not defined but needed for R package
@JetteReeg
changed gNameCostfile to name_costfile
6d08f65
@JetteReeg
switching subtree branch to transloc_new_genetics_spatial_demog
3e50c77
@JetteReeg
Add 'RangeShiftR/src/RScore/' from commit '6d08f6599a3a64fec8ceba50e9…
12739e5 
…8c7e2ff6254d50'

git-subtree-dir: RangeShiftR/src/RScore
git-subtree-mainline: 3e50c77
git-subtree-split: 6d08f65
@JetteReeg
switched within the wrong branch - redo everything
73ffec9
@JetteReeg
Add 'RangeShiftR/src/RScore/' from commit '56516758d795248c3b2c16f8cd…
d70f930 
…0561132933e923'

git-subtree-dir: RangeShiftR/src/RScore
git-subtree-mainline: 73ffec9
git-subtree-split: 5651675
@JetteReeg
Bugfix in SMS:
68bf5b6 
- issue: in some/rare cases individuals would jump to cell 0,0 during the SMS transfer process
- fix: initial values for the new location (newX and newY) now set to -9 (cell is out of boundary)
- additional: at the end of moveStep() function, the status is set to 2 for potential settlers; but this was also done for individuals dying during the current step (status==6 & dispersing == 0) -> added another condition
@JetteReeg @TheoPannetier
removed comment
6e86061 
Co-authored-by: Théo Pannetier <theo.pannetier@abdn.ac.uk>
@JetteReeg @TheoPannetier
removed comment
5cb14cf 
Co-authored-by: Théo Pannetier <theo.pannetier@abdn.ac.uk>
@JetteReeg
removed repeated line
97a5f06
@JetteReeg
Merge commit '5cb14cfbc36db691dde9804715324d338d8da597'
27ba723
@JetteReeg
Merge branch 'main' of https://github.com/RangeShifter/RangeShiftR-pkg
58267ce
@JetteReeg
Bugfix in ReadSettlementR():
1c90cad 
for stage structured models with repType > 0 and settlement not being stage or sex dependent, it would assign stage 0 + sex 1 the constant settlement parameters
@JetteReeg
Merge branch 'main' of https://github.com/RangeShifter/RangeShiftR-pkg
fc21abb
@JetteReeg
update version
cb8114d
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2 participants

@JetteReeg @TheoPannetier