RangeShifter 3.0 merge (develop into main) - #90

Merged

JetteReeg merged 489 commits into

mainfrom

Mar 24, 2026

This pull request is big! We're only showing the most recent 250 commits

Commits on Aug 16, 2024

Commits on Aug 17, 2024

readGenetics, readTraitsFile now reads the correct nb of lines for each simulation
TheoPannetier
committed
3cc291e

Commits on Aug 20, 2024

output dominance coefficients, solve #60
TheoPannetier
committed
23cda73
enable selecting which traits are output, solve #53
TheoPannetier
committed
da35269

Commits on Aug 26, 2024

Commits on Aug 27, 2024

fix incorrect initiation of rows and columns in PatchMatrix
TheoPannetier
committed
5d5da87
Fst for monomorphic pops is correct, fix #44
TheoPannetier
committed
ae5ae91
fst is zero when it cannot be computed, fix #46
TheoPannetier
committed
1490006
fix incorrect sample size
TheoPannetier
committed
c98221b
calculation fits weir and cockerham expectation, fix #41
TheoPannetier
committed
2b6263a
solution for test var within vs between, fix #68 #69
TheoPannetier
committed
0d6a0dc
test all heterozygotes case, fix #71 #68
TheoPannetier
committed
54c2330
assert correct nb of individuals is sampled, fix #53
TheoPannetier
committed
e9dbab2

Commits on Aug 28, 2024

Commits on Aug 29, 2024

traitsFile is indicated in ControlFile instead of GeneticsFile
TheoPannetier
committed
c497680

Commits on Aug 30, 2024

a large populations confroms to hardy-weinberg expectations, fix #57
TheoPannetier
committed
b394cd1

Commits on Sep 2, 2024

haploid fst matches equivalent diploid fst, fix #75
TheoPannetier
committed
3409068
weir and cockerham, weir & hill converge, fix #73
TheoPannetier
committed
43da58f
Weir & Cockerham > Weir&Hill if heterozygotes present
TheoPannetier
committed
6eb36c0
population-specific estimates average to weri & hill, fix #76
TheoPannetier
committed
739beeb
nb of offspring dying matches HW expectations, fix #56
TheoPannetier
committed
f76c10e
higher tolerance
TheoPannetier
committed
b306fb1
merge rscore tests
TheoPannetier
committed
04484af
reorganise neutral genetics output
TheoPannetier
committed
1cfb768
rm unused function
TheoPannetier
committed
62a7d5c

Commits on Sep 3, 2024

doc update
TheoPannetier
committed
e6c977f
per locus fst are computed separately, fix #72
TheoPannetier
committed
9fabc91

Commits on Sep 4, 2024

Merge remote-tracking branch 'origin/new_genetics' into transloc_new_genetics_merge
JetteReeg
committed
b29bee6
bugfix for github check renamed trfrRules to transferRules
JetteReeg
committed
1317d2f
added unit_tests in CMakeLists.txt
JetteReeg
committed
4ec1690
bring last changes from RScore to batch
TheoPannetier
committed
52cf90b
fix list reading
TheoPannetier
committed
3dcd269
fix patch headers for perLocusNeutralGenetics
TheoPannetier
committed
1710790

Commits on Sep 5, 2024

Commits on Sep 6, 2024

why force setting move process to true??
TheoPannetier
committed
bdab3ff
only set goal bias if enabled
TheoPannetier
committed
9035771

Commits on Sep 10, 2024

unnecessary arrays
TheoPannetier
committed
6312d4a
trying out smart pointers
TheoPannetier
committed
fe428f1
replace RSDEBUG with standard NDEBUG
TheoPannetier
committed
807eff0
fix missed renaming in release mode
TheoPannetier
committed
05e8a42
rm last mentions of RSDEBUG
TheoPannetier
committed
390765d

Commits on Sep 11, 2024

don't output gene values if genetics disabled
TheoPannetier
committed
d7306c0
are these macro conditions necessary?
TheoPannetier
committed
5b60607
drop RSWIN64, except inside RCPP
TheoPannetier
committed
6305931

Commits on Sep 12, 2024

wrong default value
TheoPannetier
committed
209ad5e

Commits on Sep 18, 2024

Merge pull request #72 from RangeShifter/release
TheoPannetier
authored
3e2e6e2

Commits on Sep 19, 2024

fix possible division by zero
TheoPannetier
committed
84fa7c6

Commits on Sep 23, 2024

fix misleading variable names
TheoPannetier
committed
64177e2
output the right number of sexes for genetic load
TheoPannetier
committed
e50907c

Commits on Sep 25, 2024

why
TheoPannetier
committed
0742a3b
if default repro is asexual then propmales should be zero
TheoPannetier
committed
f72765a

Commits on Sep 26, 2024

Commits on Sep 27, 2024

rm empty filestreams
TheoPannetier
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cd4d91f
more concise main
TheoPannetier
committed
bd59315
check dir hidden from main
TheoPannetier
committed
dce4836
set batchnum out of main
TheoPannetier
committed
f1f6d98
clean readParameters
TheoPannetier
committed
97f09b2

Commits on Sep 29, 2024

default arg to let rscore run
TheoPannetier
committed
df1233e

Commits on Oct 3, 2024

only clear if closing file
TheoPannetier
committed
5da938b
resolve merge conflict
TheoPannetier
committed
43727fb

Commits on Oct 8, 2024

Commits on Oct 18, 2024

allow negative values for settlement and emigration alphas
TheoPannetier
committed
73a674b
small cleanup
TheoPannetier
committed
03681a8

Commits on Oct 23, 2024

expression should be half both allele if all dom coeffs are 0
TheoPannetier
committed
0c450bc

Commits on Oct 24, 2024

Commits on Nov 4, 2024

bit of cleaning of survival
TheoPannetier
committed
02adc82

Commits on Nov 14, 2024

Commits on Nov 15, 2024

changed gNameCostfile to name_costfile
JetteReeg
committed
6d08f65

Commits on Nov 19, 2024

initialise genetic load with non-zero sel + dom coeffs #75
TheoPannetier
committed
139387b

Commits on Nov 20, 2024

oops bugs in #75
TheoPannetier
committed
edf9cf8
update tests to non-zero initial dominance coeffs
TheoPannetier
committed
e2834e7

Commits on Jan 30, 2025

improve readability of readDynLand
TheoPannetier
committed
52becba

Commits on Feb 4, 2025

drop unused map and views features
TheoPannetier
committed
187d9bd

Commits on Feb 12, 2025

integrated spatial_demography branch
JetteReeg
committed
3c94049

Commits on Mar 18, 2025

Commits on Mar 19, 2025

Commits on Mar 20, 2025

Commits on Mar 24, 2025

Merge pull request #82 from RangeShifter/avoid_memory_copies
TheoPannetier
authored
baefdac
Merge branch 'develop' into memory_usage
nboullis
committed
8218cf3

Commits on Mar 27, 2025

Add a full() method to the new MemoryQueue class for a cleaner design.
nboullis
committed
6e2aefe

Commits on Mar 28, 2025

Merge pull request #83 from RangeShifter/memory_usage
TheoPannetier
authored
870ad76

Commits on Mar 31, 2025

Commits on Apr 8, 2025

added RS_RCPP macro for R specific landscape inputs
JetteReeg
committed
47e06af
compared to RangeShifter_batch/new_genetics; now in line
JetteReeg
committed
ced9044

Commits on Apr 22, 2025

rm duplicated batch name
TheoPannetier
committed
365d736

Commits on Apr 25, 2025

refactor trait summaries
TheoPannetier
committed
b0df20d
settlement and genetic load per cell trait refactor
TheoPannetier
committed
3b010f7
refactor transfer
TheoPannetier
committed
ea64bb5

Commits on Apr 28, 2025

Commits on Apr 29, 2025

can initialise only a subset of positions
TheoPannetier
committed
34b3414
initial individuals do not suffer genetic load
TheoPannetier
committed
e816843
Merge pull request #85 from RangeShifter/no_intptr
TheoPannetier
authored
a1a4d7c

Commits on Apr 30, 2025

Commits on May 1, 2025

Commits on May 5, 2025

Commits on May 6, 2025

Split the survival functions.
nboullis
committed
e0cd7dd

Commits on May 7, 2025

added debug output for translocations
JetteReeg
committed
b7f2d60

Commits on May 9, 2025

Commits on May 12, 2025

Split the functions to open/close the genetics files.
nboullis
committed
7c72197
Split the functions to open/close the occupancy files.
nboullis
committed
f3b71b7
Split the functions to open/close the connect and paths files.
nboullis
committed
0dac7fb

Commits on May 14, 2025

Commits on May 22, 2025

Relax the thread synchronization in the Community::transfer method.
nboullis
committed
6655955

Commits on May 26, 2025

Replace the custom split_barrier class by standard std::barrier (and std::optional) when available.
nboullis
committed
2275c4a

Commits on May 28, 2025

Merge branch 'new_genetics' into transloc_new_genetics_spatial_demog_merge
JetteReeg
committed
fa61fa6

Commits on Jun 1, 2025

Merge pull request #86 from RangeShifter/split_functions
TheoPannetier
authored
2dfe022

Commits on Jun 2, 2025

Merge branch 'develop' into refactor_transfer_parallelization
nboullis
committed
a4b3e85

Commits on Jun 12, 2025

patchnums not used anywhere so dropped them
TheoPannetier
committed
d8e5256
ensure patch heterogeneity is written in the correct order
TheoPannetier
committed
e0e40bc

Commits on Jun 19, 2025

cleanup readLandscape
TheoPannetier
committed
dc2d350

Commits on Jul 17, 2025

bug in calculation of Ho: heterogeneity shouldn't be an integer
TheoPannetier
committed
114c909

Commits on Jul 21, 2025

merge conflict develop - new_genetics first attempt
TheoPannetier
committed
c142585

Commits on Jul 22, 2025

fixing git merge mistakes
TheoPannetier
committed
f350ce7
resolving more merge mistakes
TheoPannetier
committed
091ebe4
solved linker issues raised by develop merge
TheoPannetier
committed
5f25433

Commits on Jul 23, 2025

bring omp generalisation of the RNG to the RCPP version
TheoPannetier
committed
68c87ef
merge conflict
TheoPannetier
committed
57c20b8

Commits on Jul 25, 2025

Integrated option for file inputs for spatial demographic scaling
JetteReeg
committed
5aea418

Commits on Sep 8, 2025

Commits on Sep 12, 2025

Commits on Sep 15, 2025

Unit_test:
JetteReeg
committed
4c70c77
updated Individual() constructor in unit_tests/testIndividual.cpp
JetteReeg
committed
a7cf75e

Commits on Sep 17, 2025

fix argument errors in unit tests
TheoPannetier
committed
fc73cc5

Commits on Sep 18, 2025

bugfix missing increment of total steps
TheoPannetier
committed
0b9b20e

Commits on Sep 23, 2025

updated unit tests according to RScore/new_genetics
JetteReeg
committed
f01ac87
adapted unit tests
JetteReeg
committed
f19dbdd

Commits on Sep 26, 2025

fix test by shuffling individuals
TheoPannetier
committed
371e891
shuffle individuals before reproduction
TheoPannetier
committed
e120416

Commits on Sep 29, 2025

fix unreliable kernel tests
TheoPannetier
committed
39d5a68
separate unit tests from NDEBUG macro
TheoPannetier
committed
d996e37

Commits on Sep 30, 2025

higher tolerance
TheoPannetier
committed
f393706
small merge conflict
TheoPannetier
committed
6d2b2da
resolve merge conflict develop into new_genetics
TheoPannetier
committed
24626b2

Commits on Oct 2, 2025

bug fix on single-locus genes?
TheoPannetier
committed
4584169

Commits on Oct 20, 2025

Commits on Nov 13, 2025

Commits on Nov 14, 2025

Manually merged changes from new_genetics
JetteReeg
committed
81212f0

Commits on Nov 17, 2025

fixing minor bugs for RCPP flag
JetteReeg
committed
9516aa1

Commits on Nov 21, 2025

bugfix for dynamic landscapes:
JetteReeg
committed
8c990d2

Commits on Nov 27, 2025

Commits on Dec 3, 2025

Potential fix for pairwise fst calculation. Charlotte to test.
RoslynHenry
committed
f751f01

Commits on Dec 11, 2025

Corrected pairwise fst calculation using weir and cockerham
RoslynHenry
committed
c52063c

Commits on Dec 16, 2025

Merge remote-tracking branch 'origin/transloc_new_genetics_spatial_demog_merge' into develop see also PR #89 https://github.com/RangeShifter/RScore/pull/89
JetteReeg
committed
dbc2a1a

Commits on Jan 12, 2026

Changes to outputPairwiseFst rather than outputWeirHill
RoslynHenry
committed
e2a2a46

Commits on Jan 13, 2026

Commits on Jan 22, 2026

Changes to decouple genetic output
RoslynHenry
committed
a64666d

Commits on Jan 26, 2026

bug fixes for outputting genetics interval
RoslynHenry
committed
097599d

Commits on Feb 5, 2026

Bug fix for genetic output
RoslynHenry
committed
1d82072

Commits on Feb 19, 2026

Merge remote-tracking branch 'origin/new_genetics' into develop
JetteReeg
committed
ce62662

Commits on Feb 20, 2026

Changed output for R interface:
JetteReeg
committed
cfceeb4

Commits on Mar 19, 2026

Minor changes for R output option of the R package interface
JetteReeg
committed
957e2ce

Commits on Mar 20, 2026

Updated README.md
JetteReeg
committed
09e171e
Updated Copyright section on each file
JetteReeg
committed
1d1532d

Commits on Mar 22, 2026

theo is no longer a maintainer 🥲
TheoPannetier
authored
4c7364f

Commits on Mar 24, 2026

Clean-up
JetteReeg
committed
072d3af