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rmcminds
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stan_models
collection of models written in Stan, with data wrangling code to run the models on real data
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merge latest changes
#36
rmcminds
closed
1 year ago
0
in BGFA_pipeline.r, collect similar data structures into lists
#35
rmcminds
opened
3 years ago
0
clean up continuous indexing code in BGPFA
#34
rmcminds
closed
3 years ago
1
implement stan 2.19's glm functions
#33
rmcminds
opened
5 years ago
1
gather code blocks into functions and annotate code
#32
rmcminds
opened
5 years ago
0
identify microbeScales etc.
#31
rmcminds
opened
5 years ago
1
incorporate within-sample information
#30
rmcminds
opened
5 years ago
3
log crossprodexp
#29
rmcminds
opened
5 years ago
1
implement QR
#28
rmcminds
opened
5 years ago
2
Distinguish between general increase in evolution vs codiv
#27
rmcminds
opened
5 years ago
5
change OU prior so that it is flat on the proportion of variance explained
#26
rmcminds
opened
5 years ago
1
allow OU parameter to vary for different interactions
#25
rmcminds
opened
5 years ago
3
implement Bridge Sampling for across-tree comparisons
#24
rmcminds
opened
5 years ago
1
formalize links between location effects and changes in variance
#23
rmcminds
opened
5 years ago
0
incorporate non-biological samples
#22
rmcminds
opened
5 years ago
1
incorporate OU process evolution
#21
rmcminds
opened
5 years ago
0
allow separate priors for each tree's branch length modifiers
#20
rmcminds
opened
5 years ago
2
improve model for phylo variance modifers if interpreting as codiv
#19
rmcminds
opened
5 years ago
0
distinguish between ancestral states and shared effects
#18
rmcminds
closed
5 years ago
1
implement symmetric priors on effect-coded variables
#17
rmcminds
closed
5 years ago
2
allow a model matrix on sequence variants in addition to the samplewise model matrix
#16
rmcminds
opened
6 years ago
0
incorporate rate of molecular evolution into variance estimates
#15
rmcminds
opened
6 years ago
1
more consistent phylogenetic variance modifiers
#14
rmcminds
opened
6 years ago
0
simplify log-scale sparse matrix multiplications
#13
rmcminds
closed
6 years ago
1
implement sparse matrix multiplication on log scale
#12
rmcminds
closed
6 years ago
1
add ultrametric-sustaining node modifications
#11
rmcminds
closed
5 years ago
1
combination of branch length modifiers and time bins is difficult to interpret
#10
rmcminds
closed
5 years ago
2
estimation of branch lengths leads to divergences
#9
rmcminds
closed
6 years ago
4
create data simulation methods
#8
rmcminds
opened
6 years ago
0
merge marginalization of host tree into cophylogeny project
#7
rmcminds
closed
6 years ago
0
implement clade-by-clade variance modifiers for codivergence estimation
#6
rmcminds
closed
6 years ago
1
Alternate pre-existing models
#5
rmcminds
opened
6 years ago
1
adding treatment effects to source mixture model
#4
rmcminds
closed
6 years ago
1
source mixtures does not converge; has divergent transitions
#3
rmcminds
opened
6 years ago
2
implement something similar to Hadfield 2012 for cophylogeny
#2
rmcminds
opened
6 years ago
0
splinephy using min() for positive definiteness
#1
rmcminds
closed
6 years ago
2