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thej022214
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corHMM
Fits a generalized form of the covarion model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as “hidden” states in a Markov process.
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making a density map from makeSimmap output?
#63
GinaMCalabrese
opened
2 weeks ago
0
Understanding columns in tip.states from corhmm output
#62
alrichardbollans
closed
3 weeks ago
2
Add gh links to DESCRIPTION
#61
olivroy
opened
8 months ago
0
Is this state distribution in data correct? And an error message
#60
jamie-thompson
opened
1 year ago
4
How to estimate memory usage with large data size
#59
ajdemery93
opened
1 year ago
0
Move utility match.tree.data to separate file
#58
jcoliver
opened
1 year ago
0
Make rayDISC a wrapper for corHMM
#57
jcoliver
opened
1 year ago
0
Tip states argument
#56
HedvigS
opened
1 year ago
0
make it possible to remove margins
#55
HedvigS
opened
1 year ago
0
Update plotRECON.R
#54
HedvigS
opened
1 year ago
0
plotRECON legend specs
#53
HedvigS
opened
1 year ago
2
plot issue on function plotRECON
#52
RisenL
opened
1 year ago
0
Fix bug when collapse=FALSE
#51
Caetanods
closed
1 year ago
0
fixed small mistakes and clarified rate.mat and p
#50
oschwery
closed
1 year ago
0
Are transition rates "significantly" different?
#49
AlesBucek
opened
1 year ago
1
corHMM_2.8: "Description: Estimates hidden rates underlying the evolution of a BINARY character"
#48
AlesBucek
opened
2 years ago
1
Error when specifying rate matrix for `corHMM` with polymorphic or missing data
#47
rubysaltbush
closed
2 years ago
2
`print.corhmm` returns error with missing or polymorphic data
#46
rubysaltbush
closed
2 years ago
2
Allow fixing more than one node in stochastic character map makeSimmap
#45
SimonGreenhill
closed
2 years ago
2
makeSimmap could return state labels rather than state integers
#44
SimonGreenhill
closed
2 years ago
3
Showing tip states for PlotRECON?
#43
ymilesz
closed
2 years ago
4
Stochastic character mapping with precursor model
#42
eliotmiller
closed
2 years ago
2
Precursor model no longer running
#41
eliotmiller
closed
2 years ago
2
Fix probabilities at a non-root node?
#40
HeatherKates
closed
2 years ago
0
Suggestion: function "makeSimmap" return class "multiSimmap"
#39
Caetanods
closed
2 years ago
2
Unclear functionality of get.tip.states in corHMM
#38
jcoliver
opened
2 years ago
3
Correlation between missing data and rate
#37
NataliiaHue
closed
2 years ago
4
corHMM giving warning instead of error when there is only one tip state :)?
#36
HedvigS
closed
2 years ago
2
Confirming node numbering scheme for compatibility with ggtree plotting
#35
HeatherKates
closed
2 years ago
1
corHMM producing error
#34
dasyuridae
closed
2 years ago
2
length of 'dimnames' [1] not equal to array extent
#33
Victaphanta
closed
2 years ago
2
dropStateMatPars bug
#32
Victaphanta
closed
2 years ago
1
Is choosing the ML solution from across independent runs different from nstarts?
#31
HeatherKates
closed
2 years ago
13
Using ancRECON with transition rates from corHMM
#30
HeatherKates
closed
2 years ago
10
State distribution printout is "1&2" for missing data
#29
HeatherKates
closed
3 years ago
2
functions not found
#28
Victaphanta
closed
2 years ago
5
warning when encountering 0 branch lengths?
#27
HedvigS
opened
3 years ago
6
error when combining ambiguities and a custom rate matrix
#26
santiagombv
closed
3 years ago
3
Super fast run and super high AIC/low likelihood sometimes
#25
HeatherKates
closed
2 years ago
4
Default rate matrices are not "ARD"
#24
HeatherKates
closed
3 years ago
4
various small tweaks.
#23
jboyko
closed
3 years ago
0
root state probabilities with hidden rates
#22
HeatherKates
closed
3 years ago
2
Errors when NA's are present in character data
#21
HeatherKates
closed
3 years ago
3
makeSimmap returns vector size error
#20
vficarrotta
closed
3 years ago
3
In rayDISC() returned object, add column names to tip.states matrix
#19
jcoliver
opened
3 years ago
1
Cases where removing dual transitions leaves no way to transition between all states.
#18
jboyko
opened
4 years ago
3
Primates file format
#17
GhadeerB
closed
4 years ago
3
Traits dataframe that has more than 20 traits causes an error
#16
shamsbhuiyan
closed
4 years ago
3
new plotMK function and passing cor checks
#15
jboyko
closed
4 years ago
0
cleaner cor code
#14
jboyko
closed
4 years ago
0
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