Caetanods ratematrix issues

Caetanods / ratematrix

Bayesian estimation of the evolutionary rate matrix.

9 stars 3 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

missing data?

#52 jakeberv opened 3 years ago
1
Correlations between on trait vector and 100 other vectors

#51 bioinfowheat opened 3 years ago
1
Wrong species count -> handle summary single rate model

#50 Caetanods closed 3 years ago
2
mergeMCMC does not work with single rate fit

#49 acope3 closed 5 years ago
1
typo

#48 josephwb closed 6 years ago
1
plotRatematrix does not match 'colors' when 'p' is rearranged

#47 Caetanods closed 3 years ago
1
The wish list of enhancements for the package

#46 Caetanods opened 7 years ago
4
If prior is very restrictive the MCMC can fail to start

#45 Caetanods closed 6 years ago
3
PlotRatematrix does not show scale when rates are very low

#44 Caetanods opened 7 years ago
1
apply 'checkConvergence' and 'mergePosterior' over lists

#43 Caetanods closed 7 years ago
1
Try to 'tar' the MCMC files

#42 Caetanods closed 7 years ago
1
makePropMultiSigma

#41 grahamjslater closed 7 years ago
3
Enhance output from 'checkConvergence' when using a single chain

#40 Caetanods closed 7 years ago
1
Bug when 'hpd' argument on 'plotRatematrix' is used

#39 Caetanods closed 7 years ago
1
Return error if data has no rownames

#38 Caetanods closed 7 years ago
1
Option 'singleregime=TRUE' in 'ratematrixMCMC' do not work

#37 Caetanods closed 7 years ago
2
No print method for prior samples when 'rebuild.R=TRUE'

#36 Caetanods closed 7 years ago
1
Error in ratematrixMCMC

#35 drossoni closed 7 years ago
2
Some runs fail when using "mclapply" to launch many MCMC chains

#34 Caetanods closed 7 years ago
2
Unable to change the 'cex' argument for 'plotRootValue'

#33 Caetanods opened 7 years ago
0
Silence 'mvMORPH' print to screen when starting from the MLE

#32 Caetanods closed 7 years ago
1
Default colors of 'plotRatematrix' need to have names

#31 Caetanods closed 7 years ago
1
Lose regime names with 'mergePosterior'

#30 Caetanods closed 7 years ago
1
Allow for inverse-Gamma and half-Cauchy priors

#29 Caetanods closed 7 years ago
1
Compute the contrasts only once

#28 Caetanods closed 7 years ago
1
Need function to plot the prior for the root.

#27 Caetanods closed 7 years ago
1
Starting point used by 'ratematrixMCMC' is not the same as provided

#26 Caetanods closed 6 years ago
1
plotRootValue not showing the trait names

#25 Caetanods closed 7 years ago
1
Ellipses in plot function do not respond to "hpd" argument.

#24 Caetanods closed 7 years ago
1
'plotRatematrix' gives error when sample is too small

#23 Caetanods closed 7 years ago
1
Implement an adaptive MCMC cycle

#22 Caetanods closed 7 years ago
1
Drop 'chain' argument from 'logLikSingleRegime'

#21 Caetanods closed 7 years ago
1
First step phylo when start is MLE

#20 Caetanods closed 7 years ago
1
Fix calculation of 'chunk' in the MCMC

#19 Caetanods closed 7 years ago
2
Extend 'plotPrior'

#18 Caetanods closed 7 years ago
2
'ratematrixMCMC' breaks with bad starting point

#17 Caetanods closed 7 years ago
1
Bugs on 'plotRatematrix'

#16 Caetanods closed 7 years ago
2
List of possible minor improvements:

#15 Caetanods closed 7 years ago
0
measurement error

#14 Caetanods closed 7 years ago
1
Plot function is terrible!

#13 Caetanods closed 8 years ago
2
Export general tools (functions)

#12 Caetanods closed 7 years ago
1
effective dependence and variance need to be stand alone functions.

#11 Caetanods closed 7 years ago
1
Let user continue unfinished chain.

#10 Caetanods closed 7 years ago
1
Bug in open file connections.

#9 Caetanods closed 7 years ago
1
Make prior functions more flexible.

#8 Caetanods closed 8 years ago
2
Workflow need to be more intuitive

#7 Caetanods closed 8 years ago
1
Remake lik functions...

#6 Caetanods closed 8 years ago
1
Force data to 'matrix'

#5 Caetanods closed 8 years ago
1
single.R.iwish.mcmc needs 'simmap' format

#4 Caetanods closed 8 years ago
1
Create a tutorial

#3 Caetanods closed 7 years ago
0