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corHMM

Hidden Markov Models of Character Evolution

v2.8 · Jun 13, 2022 · GPL (>= 2)

Description

Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.

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CRAN Check Status

13 OK
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Flavor Status
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-windows-x86_64 OK
r-oldrel-macos-arm64 OK
r-oldrel-macos-x86_64 OK
r-oldrel-windows-x86_64 OK
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 History

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026
ERROR r-devel-linux-x86_64-debian-gcc

re-building of vignette outputs

Error(s) in re-building vignettes:
  ...
Fatal error: cannot create 'R_TempDir'
OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 25, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 30, 2026
ERROR r-oldrel-windows-x86_64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building 'corHMMv2.1-vignette.Rmd' using rmarkdown
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error : The formatR package is required by the chunk option tidy = TR
...[truncated]...
ebugging for debugging tips. See corHMMv2.1-vignette.log for more info.
--- failed re-building 'corHMMv2.1-vignette.Rmd'

SUMMARY: processing the following file failed:
  'corHMMv2.1-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

Reverse Dependencies (2)

imports

suggests

Dependency Network

Dependencies Reverse dependencies ape nloptr GenSA expm numDeriv corpcor MASS nnet phangorn viridis Rmpfr igraph phytools hisse DAISIEprep corHMM

Version History

21 tracked
new 2.8 Mar 10, 2026
updated 2.8 ← 2.7 diff Jun 13, 2022
updated 2.7 ← 2.6 diff May 13, 2021
updated 2.6 ← 2.5 diff Jan 5, 2021
updated 2.5 ← 2.4 diff Nov 23, 2020
updated 2.4 ← 2.3 diff Sep 30, 2020
updated 2.3 ← 2.2 diff Aug 4, 2020
updated 2.2 ← 2.1 diff Jul 8, 2020
updated 2.1 ← 1.22 diff Jul 7, 2020
updated 1.22 ← 1.20 diff Jul 19, 2017
updated 1.20 ← 1.19 diff Sep 26, 2016
updated 1.19 ← 1.18 diff Jun 8, 2016
updated 1.18 ← 1.17 diff Jan 6, 2016
updated 1.17 ← 1.16 diff Oct 29, 2015
updated 1.16 ← 1.15 diff Apr 7, 2015