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ratematrix

Bayesian Estimation of the Evolutionary Rate Matrix

v1.2.5 · Dec 6, 2025 · GPL (>= 2.0)
CRAN GitHub Mirror

Description

The Evolutionary Rate Matrix is a variance-covariance matrix which describes both the rates of trait evolution and the evolutionary correlation among multiple traits. This package has functions to estimate these parameters using Bayesian MCMC. It is possible to test if the pattern of evolutionary correlations among traits has changed between predictive regimes painted along the branches of the phylogenetic tree. Regimes can be created a priori or estimated as part of the MCMC under a joint estimation approach. The package has functions to run MCMC chains, plot results, evaluate convergence, and summarize posterior distributions.

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CRAN Check Status

1 ERROR
2 NOTE
11 OK
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r-devel-linux-x86_64-debian-clang OK
r-devel-linux-x86_64-debian-gcc OK
r-devel-linux-x86_64-fedora-clang OK
r-devel-linux-x86_64-fedora-gcc OK
r-devel-macos-arm64 OK
r-devel-windows-x86_64 OK
r-oldrel-macos-arm64 NOTE
r-oldrel-macos-x86_64 NOTE
r-oldrel-windows-x86_64 ERROR
r-patched-linux-x86_64 OK
r-release-linux-x86_64 OK
r-release-macos-arm64 OK
r-release-macos-x86_64 OK
r-release-windows-x86_64 OK
Check details (3 non-OK)
NOTE r-oldrel-macos-arm64

installed package size

installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
NOTE r-oldrel-macos-x86_64

installed package size

installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
ERROR r-oldrel-windows-x86_64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building 'Intro_on_the_package.Rmd' using rmarkdown
! Package pdftex.def Error: File `f769fce833cde68c6f69e009d7b5be0128e24963.pdf'
 not found: using draft setting.

Error: processing vignette 'Intro_on_the_package.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/ratematrix.Rcheck/vign_test/ratematrix/vignettes/Intro_on_the_package.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Intro_on_the_package.log for more info.
--- failed re-building 'Intro_on_the_package.Rmd'

--- re-building 'Making_prior_on_ratematrix.Rmd' using rmarkdown
! Package pdftex.def Error: File `649f71c257e82c9ffa90653fd8c25fb5087de12c.pdf'
 not found: using draft setting.

Error: processing vignette 'Making_prior_on_ratematrix.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/ratematrix.Rcheck/vign_test/ratematrix/vignettes/Making_prior_on_ratematrix.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Making_prior_on_ratematrix.log for more info.
--- failed re-building 'Making_prior_on_ratematrix.Rmd'

--- re-building 'Set_custom_starting_point.Rmd' using rmarkdown
! Package pdftex.def Error: File `231a4d08e13bba0753a58031d639ee059a0111ae.pdf'
 not found: using draft setting.

Error: processing vignette 'Set_custom_starting_point.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/ratematrix.Rcheck/vign_test/ratematrix/vignettes/Set_custom_starting_point.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Set_custom_starting_point.log for more info.
--- failed re-building 'Set_custom_starting_point.Rmd'

SUMMARY: processing the following files failed:
  'Intro_on_the_package.Rmd' 'Making_prior_on_ratematrix.Rmd'
  'Set_custom_starting_point.Rmd'

Error: Vignette re-building failed.
Execution halted

Check History

ERROR 11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 30, 2026
NOTE r-oldrel-macos-arm64

installed package size

installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
NOTE r-oldrel-macos-x86_64

installed package size

installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
ERROR r-oldrel-windows-x86_64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building 'Intro_on_the_package.Rmd' using rmarkdown
! Package pdftex.def Error: File `f769fce833cde68c6f69e009d7b5be0128e24963.pdf'
 not found: using draft setting.

Error: processing vignette 'Intro_on_the_p
...[truncated]...
 failed re-building 'Set_custom_starting_point.Rmd'

SUMMARY: processing the following files failed:
  'Intro_on_the_package.Rmd' 'Making_prior_on_ratematrix.Rmd'
  'Set_custom_starting_point.Rmd'

Error: Vignette re-building failed.
Execution halted
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
NOTE r-oldrel-macos-arm64

installed package size

installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
NOTE r-oldrel-macos-x86_64

installed package size

installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb

Reverse Dependencies (1)

imports

do3PCA

Dependency Network

Dependencies Reverse dependencies ape geiger coda corpcor MASS phylolm readr mvMORPH Rcpp ellipse do3PCA ratematrix

Version History

new 1.2.5 Mar 10, 2026
updated 1.2.5 ← 1.2.4 diff Dec 5, 2025
updated 1.2.4 ← 1.2.3 diff Jun 2, 2022
updated 1.2.3 ← 1.2.2 diff Feb 23, 2021
updated 1.2.2 ← 1.2.1 diff Feb 25, 2020
updated 1.2.1 ← 1.2 diff May 14, 2019
updated 1.2 ← 1.1 diff May 5, 2019
updated 1.1 ← 1.0 diff Oct 29, 2018
new 1.0 Jun 9, 2018