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Rename transformed (Update for Measure terminology) #441

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c1cec60
use Tranformed prefix for all structs
Jun 30, 2023
9cbacf2
use Transformed prefix for all types
Jun 30, 2023
6cbe392
update deps
Jun 30, 2023
e32abca
add AdaptiveTransform
Jun 30, 2023
50c02ba
include transformed_mcmc
Jun 30, 2023
b0794f0
Revert "use Transformed prefix for all types"
Cornelius-G Jun 30, 2023
e1d7aba
chnage replace_type script
Cornelius-G Jun 30, 2023
66fa0ad
use Transformed prefix for all abstract types
Jun 30, 2023
6c39fee
new TransformedMCMCSampling and old MCMCSampling now both working
Cornelius-G Jun 30, 2023
f640fbc
move example
Cornelius-G Jul 3, 2023
d0ce010
use full matrix instead of lower cholesky in AdaptiveMHTuner
Cornelius-G Jul 3, 2023
972d967
use cholesky lower for AdaptiveMHTuning
Cornelius-G Jul 4, 2023
756827f
Merge commit 'c9d7fd98bf61d05fedc0be1643b41d7aabe43c98' into RenameTr…
oschulz Jul 6, 2023
9cb2625
Adapt transformed MCMC code to using BATContext
oschulz Jul 6, 2023
bb97b3a
FIx TransformedAdaptiveMHTuning and example
oschulz Jul 6, 2023
b2d5449
Merge branch 'main' into RenameTransformed
oschulz Jul 9, 2023
119c3fe
Fix Project.toml
oschulz Jul 9, 2023
7f45cee
Fix include order in transformed_mcmc
oschulz Jul 9, 2023
9457054
Fix transformed_check_convergence!
oschulz Jul 9, 2023
6552733
Fix transformed bat_sample_impl and mcmc_burnin!
oschulz Jul 9, 2023
8dc1ebf
Merge branch 'main' into trafo-merge
oschulz Jul 9, 2023
0a027e8
Adapt transformed example to API changes
oschulz Jul 9, 2023
85dc22a
RAMTuner properly persist stepno through multi_cycle_burnin
waldie11 Jul 11, 2023
9602973
Merge remote-tracking branch 'origin/main' into RenameTransformed
waldie11 Jul 11, 2023
f8f4b8d
Merge branch 'main' into RenameTransformed
waldie11 Jul 19, 2023
109a5c9
rewrite mcmc_init! for optimized overall runtime
waldie11 Jul 24, 2023
756d0e4
add infrastructure to ease continue of chains
waldie11 Jul 25, 2023
3647b6e
spaces in return of bat_sample_impl
waldie11 Jul 25, 2023
902257d
introduce _bat_sample_continue
waldie11 Jul 25, 2023
8cc015b
ProgressMeter for known infrastructure
waldie11 Jul 25, 2023
41b817d
ahmc evaluates params [NaN,...] in times
waldie11 Jul 25, 2023
0c4a703
clustered init suggestion
waldie11 Jul 27, 2023
d988a84
switch to median in cluster selection
waldie11 Jul 28, 2023
9909eed
forward best cluster
waldie11 Jul 28, 2023
fc93e18
_cluster_selection correct forward of chains&tuner
waldie11 Jul 28, 2023
3372df3
_cluster_selection proper fail criterion
waldie11 Jul 28, 2023
d6c01b3
viable_idxs corrected
waldie11 Aug 2, 2023
a27f521
Merge branch 'main' into RenameTransformed
Cornelius-G Sep 25, 2023
b6565c3
quick fixes
Cornelius-G Sep 25, 2023
921dc8b
Update to measure terminology, fix type inference, adjust compats
Micki-D Jun 3, 2024
427481f
Relax scale parameter in _cluster_selection() for chain pool init
Micki-D Jun 16, 2024
7fd0b91
Move proposaldist.jl to transformed version
Micki-D Jun 17, 2024
cb6e102
Move mcmc_stats.jl to transformed version
Micki-D Jun 20, 2024
17edf2f
Move mcmc_weighting.jl to transformed version
Micki-D Jun 20, 2024
eeed71f
Preliminary move of mcmc_sampleid.jl to transformed version
Micki-D Jun 20, 2024
2ea612b
Move mcmc_sampleid.jl to transformed version
Micki-D Jun 20, 2024
bfa008e
Move chain_pool_init.jl to transformed version
Micki-D Jun 20, 2024
5be3b3f
Merge mcmc_sample.jl and its transformed version
Micki-D Jun 20, 2024
1fa71cc
Merge mcmc_algorithm.jl and its transformed version
Micki-D Jun 20, 2024
924cfdf
Merge multi_cycle_burnin.jl and transformed version
Micki-D Jun 21, 2024
a1033f1
Move mcmc_noop_tuner.jl to transformed version
Micki-D Jun 21, 2024
189c285
Adjust mcmc.jl
Micki-D Jun 21, 2024
1e9ede9
Stash Changes
Micki-D Jul 19, 2024
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ahmc evaluates params [NaN,...] in times
waldie11 committed Jul 25, 2023
commit 41b817d64e3562595ede84175257603618791372
3 changes: 2 additions & 1 deletion ext/ahmc_impl/ahmc_sampler_impl.jl
Original file line number Diff line number Diff line change
@@ -78,7 +78,8 @@ function AHMCIterator(
throw(ErrorException("HamiltonianMC requires an ADSelector to be specified in the BAT context"))
end

f = checked_logdensityof(density)
# TODO AC ToDo!: discuss with @oschulz
f = logdensityof(density)
fg = valgrad_func(f, adsel)

init_hamiltonian = AdvancedHMC.Hamiltonian(metric, f, fg)