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Stairwayplot method #460

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Stairwayplot method #460

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hoehna
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@hoehna hoehna commented Apr 26, 2024

Here I added two main new features:

  1. The stairway plot approach (https://www.nature.com/articles/ng.3254)
  2. Leave one out cross validation (https://academic.oup.com/sysbio/article/72/3/616/7050004)

hoehna and others added 30 commits May 25, 2022 08:58
@hoehna
Adding the StairwayPlot method
f37b433
@hoehna
fixing issue with member functions not updating
58a47a5
@hoehna
clean up
a30500e
@hoehna
fixing stairway plot issues
6fff3d6
@hoehna
adding rev for vector of probs
cbf598b
@hoehna
Adding probability of monomorphic sites
58dc1ad
@hoehna
new coalescent SFS simulator
e229990
@hoehna
Adding new simulator to Rev
4729198
@hoehna
quick fix
8fb0095
@hoehna
fixing issue in simulator
444dcc7
@hoehna
Merge branch 'dev_stairwayplot' of https://github.com/revbayes/revbayes…
b172fb3 
… into dev_stairwayplot
@hoehna
testing
185ab7b
@hoehna
correcting
5493e91
@hoehna
ploidy
9fa5800
@hoehna
changing stairwayplot to be of type real pos
a22e0c0
@hoehna
not running default script
853ee54
@hoehna
new BSP interval function
f2026ef
@hoehna
new move
996a218
@hoehna
testing
270945c
@hoehna
fix new move
1079e0d
@hoehna
using demographic functions
050c5aa
@hoehna
fixing
abe4d9b
@hoehna
MPI
fb0a1ec
@hoehna
working on ascertainment bias correction
0aacc69
@hoehna
fixing issue with folded data
6a1ab6e
@hoehna
more stable assert
1126b08
@hoehna
cleanup
0b3dc05
@hoehna
proper rounding
087e438
@hoehna
correcting number of bins
650257d
@hoehna
adding method to extract the expected SFS
2ca3405
hoehna and others added 29 commits September 12, 2022 15:08
@hoehna
CPO
3fde971
@hoehna
fixing stairwayplot for folded
97400ee
@hoehna
implementing CPO
0da989c
@hoehna
fix tree length
3b904e7
@hoehna
cleaning
44377ce
@hoehna
Merge commit '6c5f1c70d8614c8ba3c1cf6ed9c34c18b87a3000' into dev_stai…
e56599e 
…rwayplot
@hoehna
fixing merge issue with file manager
d3167b2
@hoehna
updating tests
2f5c94a
@hoehna
Merge commit '04666defc0d528ce0fd1ce354f268b0414fb81a3' into dev_stai…
5baa11a 
…rwayplot

# Conflicts:
#	tests
@hoehna
fixing CPO for folded spectra
89594c7
@hoehna
fixing exp demography
8a0c2b9
@hoehna
new type of coalescent simulations
7165a42
@hoehna
coal sims
fa64491
@hoehna
fixing CPO
3956f3f
@hoehna
better handling of ploidy
41e82c0
@hoehna
Merge branch 'dev_stairwayplot' of github.com:revbayes/revbayes into …
96bcedf 
…dev_stairwayplot
@hoehna
fix exp demo
d29680f
@hoehna
cleanup
52a47b7
@hoehna
initial work on adaptive RJ move
bfb13b3
@hoehna
Merge branch 'dev_stairwayplot' of github.com:revbayes/revbayes into …
66299a8 
…dev_stairwayplot
@hoehna
fix exp demo
3faf1b5
@hoehna
fix compiler issue
7a18839
@hoehna
merge
df24a46
@hoehna
fix rv linear demo
6158585
@hoehna
working version of adaptive RJ move
32c62a5
@hoehna
cleaning up new adaptive RJ switch move
902daa4
@hoehna
cleaning up new adaptive RJ switch move
3798b5d
@hoehna
doh, forgot to divide the state space by 2 when folding
c075d76
@hoehna
Merge commit 'c7fd734339e5a762c29e0c63012e3a23be90d664' into dev_stai…
ef2e45f 
…rwayplot

# Conflicts:
#	tests~HEAD
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