markophylo
Markov Chain Models for Phylogenetic Trees
Description
Allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data. Examples of such discrete character data include restriction sites, gene family presence/absence, intron presence/absence, and gene family size data. Hypothesis-driven user- specified substitution rate matrices can be estimated. Allows for biologically realistic models combining constrained substitution rate matrices, site rate variation, site partitioning, branch-specific rates, allowing for non-stationary prior root probabilities, correcting for sampling bias, etc. See Dang and Golding (2016) <doi:10.1093/bioinformatics/btv541> for more details.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | NOTE |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| 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 | 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 details (14 non-OK)
CRAN incoming feasibility
Maintainer: ‘Utkarsh J. Dang <utkarshdang@cunet.carleton.ca>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = c("Utkarsh", "J."),
family = "Dang",
role = c("aut", "cre"),
email = "utkarshdang@cunet.carleton.ca"),
person(given = c("G.", "Brian"),
family = "Golding",
role = "aut"))
as necessary.
CRAN incoming feasibility
Maintainer: ‘Utkarsh J. Dang <utkarshdang@cunet.carleton.ca>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = c("Utkarsh", "J."),
family = "Dang",
role = c("aut", "cre"),
email = "utkarshdang@cunet.carleton.ca"),
person(given = c("G.", "Brian"),
family = "Golding",
role = "aut"))
as necessary.
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Check History
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026
CRAN incoming feasibility
Maintainer: ‘Utkarsh J. Dang <utkarshdang@cunet.carleton.ca>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = c("Utkarsh", "J."),
family = "Dang",
role = c("aut", "cre"),
email = "utkarshdang@cunet.carleton.ca"),
person(given = c("G.", "Brian"),
family = "Golding",
role = "aut"))
as necessary.
CRAN incoming feasibility
Maintainer: ‘Utkarsh J. Dang <utkarshdang@cunet.carleton.ca>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = c("Utkarsh", "J."),
family = "Dang",
role = c("aut", "cre"),
email = "utkarshdang@cunet.carleton.ca"),
person(given = c("G.", "Brian"),
family = "Golding",
role = "aut"))
as necessary.