thej022214 corHMM issues

thej022214 / 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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issues

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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