Caetanods/ratematrix issues and pull requests

#52 - missing data?

Issue - State: open - Opened by jakeberv about 3 years ago - 1 comment

#51 - Correlations between on trait vector and 100 other vectors

Issue - State: open - Opened by bioinfowheat almost 4 years ago - 1 comment

#50 - Wrong species count -> handle summary single rate model

Issue - State: closed - Opened by Caetanods over 5 years ago - 2 comments

#49 - mergeMCMC does not work with single rate fit

Issue - State: closed - Opened by acope3 almost 6 years ago - 1 comment

#48 - typo

Pull Request - State: closed - Opened by josephwb almost 7 years ago - 1 comment

#47 - plotRatematrix does not match 'colors' when 'p' is rearranged

Issue - State: closed - Opened by Caetanods about 7 years ago - 1 comment
Labels: bug, interface bug

#46 - The wish list of enhancements for the package

Issue - State: open - Opened by Caetanods about 7 years ago - 4 comments
Labels: enhancement

#45 - If prior is very restrictive the MCMC can fail to start

Issue - State: closed - Opened by Caetanods about 7 years ago - 3 comments
Labels: bug, implementation bug

#44 - PlotRatematrix does not show scale when rates are very low

Issue - State: open - Opened by Caetanods about 7 years ago - 1 comment
Labels: bug, interface bug

#43 - apply 'checkConvergence' and 'mergePosterior' over lists

Issue - State: closed - Opened by Caetanods about 7 years ago - 1 comment
Labels: enhancement

#42 - Try to 'tar' the MCMC files

Issue - State: closed - Opened by Caetanods about 7 years ago - 1 comment
Labels: enhancement

#41 - makePropMultiSigma

Issue - State: closed - Opened by grahamjslater over 7 years ago - 3 comments
Labels: bug

#40 - Enhance output from 'checkConvergence' when using a single chain

Issue - State: closed - Opened by Caetanods over 7 years ago - 1 comment
Labels: enhancement

#39 - Bug when 'hpd' argument on 'plotRatematrix' is used

Issue - State: closed - Opened by Caetanods over 7 years ago - 1 comment
Labels: bug

#38 - Return error if data has no rownames

Issue - State: closed - Opened by Caetanods over 7 years ago - 1 comment
Labels: enhancement

#37 - Option 'singleregime=TRUE' in 'ratematrixMCMC' do not work

Issue - State: closed - Opened by Caetanods over 7 years ago - 2 comments
Labels: bug, wontfix

#36 - No print method for prior samples when 'rebuild.R=TRUE'

Issue - State: closed - Opened by Caetanods over 7 years ago - 1 comment
Labels: enhancement

#35 - Error in ratematrixMCMC

Issue - State: closed - Opened by drossoni almost 8 years ago - 2 comments
Labels: bug, enhancement

#34 - Some runs fail when using "mclapply" to launch many MCMC chains

Issue - State: closed - Opened by Caetanods almost 8 years ago - 2 comments
Labels: question

#33 - Unable to change the 'cex' argument for 'plotRootValue'

Issue - State: open - Opened by Caetanods almost 8 years ago
Labels: bug, interface bug

#32 - Silence 'mvMORPH' print to screen when starting from the MLE

Issue - State: closed - Opened by Caetanods almost 8 years ago - 1 comment
Labels: bug

#31 - Default colors of 'plotRatematrix' need to have names

Issue - State: closed - Opened by Caetanods almost 8 years ago - 1 comment
Labels: enhancement

#30 - Lose regime names with 'mergePosterior'

Issue - State: closed - Opened by Caetanods almost 8 years ago - 1 comment
Labels: bug

#29 - Allow for inverse-Gamma and half-Cauchy priors

Issue - State: closed - Opened by Caetanods almost 8 years ago - 1 comment
Labels: enhancement

#28 - Compute the contrasts only once

Issue - State: closed - Opened by Caetanods almost 8 years ago - 1 comment
Labels: enhancement

#27 - Need function to plot the prior for the root.

Issue - State: closed - Opened by Caetanods almost 8 years ago - 1 comment
Labels: enhancement

#26 - Starting point used by 'ratematrixMCMC' is not the same as provided

Issue - State: closed - Opened by Caetanods almost 8 years ago - 1 comment
Labels: bug, implementation bug

#25 - plotRootValue not showing the trait names

Issue - State: closed - Opened by Caetanods almost 8 years ago - 1 comment
Labels: bug

#24 - Ellipses in plot function do not respond to "hpd" argument.

Issue - State: closed - Opened by Caetanods almost 8 years ago - 1 comment
Labels: bug

#23 - 'plotRatematrix' gives error when sample is too small

Issue - State: closed - Opened by Caetanods almost 8 years ago - 1 comment
Labels: bug

#22 - Implement an adaptive MCMC cycle

Issue - State: closed - Opened by Caetanods almost 8 years ago - 1 comment
Labels: enhancement

#21 - Drop 'chain' argument from 'logLikSingleRegime'

Issue - State: closed - Opened by Caetanods almost 8 years ago - 1 comment
Labels: enhancement

#20 - First step phylo when start is MLE

Issue - State: closed - Opened by Caetanods almost 8 years ago - 1 comment
Labels: question

#19 - Fix calculation of 'chunk' in the MCMC

Issue - State: closed - Opened by Caetanods almost 8 years ago - 2 comments
Labels: bug

#18 - Extend 'plotPrior'

Issue - State: closed - Opened by Caetanods almost 8 years ago - 2 comments
Labels: enhancement

#17 - 'ratematrixMCMC' breaks with bad starting point

Issue - State: closed - Opened by Caetanods almost 8 years ago - 1 comment
Labels: bug

#16 - Bugs on 'plotRatematrix'

Issue - State: closed - Opened by Caetanods almost 8 years ago - 2 comments
Labels: bug

#15 - List of possible minor improvements:

Issue - State: closed - Opened by Caetanods almost 8 years ago

#14 - measurement error

Issue - State: closed - Opened by Caetanods about 8 years ago - 1 comment
Labels: enhancement

#13 - Plot function is terrible!

Issue - State: closed - Opened by Caetanods over 8 years ago - 2 comments

#12 - Export general tools (functions)

Issue - State: closed - Opened by Caetanods over 8 years ago - 1 comment
Labels: enhancement, wontfix

#11 - effective dependence and variance need to be stand alone functions.

Issue - State: closed - Opened by Caetanods over 8 years ago - 1 comment
Labels: enhancement

#10 - Let user continue unfinished chain.

Issue - State: closed - Opened by Caetanods over 8 years ago - 1 comment
Labels: enhancement

#9 - Bug in open file connections.

Issue - State: closed - Opened by Caetanods over 8 years ago - 1 comment
Labels: bug

GitHub / Caetanods/ratematrix issues and pull requests