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.
Downloads
360
Last 30 days
12185th
735
Last 90 days
2.8K
Last year
Trend: +103.4% (30d vs prior 30d)
24
Last 30 days
114
Last 90 days
406
Last year
Trend: -40% (30d vs prior 30d)
2
Last 7 days
12
Last 30 days
0
All-time
autoCRAN-only: this name is served only by autoCRAN, so the count is exact.
CRAN Check Status
Show all 13 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-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 (2 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.
Check History
NOTE 11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 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.
ERROR 11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 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.
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 22, 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.
ERROR 11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 18, 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.
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.6/markophylo.Rcheck/00install.out' for details.
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 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.
Code
Structure
Lines of code
2,573
Files
31
Compiled share
7.1%
Has compiled src
Yes
Language breakdown
API
Exported functions
5
Internal functions
6
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.22
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
100%
\dontrun example ratio
0%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
Yes
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
80%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.10
System requirements
–
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2015-07-07
Latest release
2023-09-19
Avg cadence
416 days
Cold removal rate
100%
Dep drift
6
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.