paleotree
Paleontological and Phylogenetic Analyses of Evolution
Description
Provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages. In particular, most users are interested in the functions timePaleoPhy, bin_timePaleoPhy, cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of fossil taxa using stratigraphic data. This package also contains a large number of likelihood functions for estimating sampling and diversification rates from different types of data available from the fossil record (e.g. range data, occurrence data, etc). paleotree users can also simulate diversification and sampling in the fossil record using the function simFossilRecord, which is a detailed simulator for branching birth-death-sampling processes composed of discrete taxonomic units arranged in ancestor-descendant relationships. Users can use simFossilRecord to simulate diversification in incompletely sampled fossil records, under various models of morphological differentiation (i.e. the various patterns by which morphotaxa originate from one another), and with time-dependent, longevity-dependent and/or diversity-dependent rates of diversification, extinction and sampling. Additional functions allow users to translate simulated ancestor-descendant data from simFossilRecord into standard time-scaled phylogenies or unscaled cladograms that reflect the relationships among taxon units.
Downloads
1.1K
Last 30 days
3525th
2.9K
Last 90 days
24K
Last year
Trend: +6.2% (30d vs prior 30d)
1
Last 30 days
27
Last 90 days
131
Last year
Trend: -90.9% (30d vs prior 30d)
9
Last 7 days
19
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: ‘David W. Bapst <dwbapst@gmail.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = c("David", "W."),
family = "Bapst",
role = c("aut", "cre"),
email = "dwbapst@gmail.com"),
person(given = c("Peter", "J."),
family = "Wagner",
role = "aut"))
as necessary.
CRAN incoming feasibility
Maintainer: ‘David W. Bapst <dwbapst@gmail.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = c("David", "W."),
family = "Bapst",
role = c("aut", "cre"),
email = "dwbapst@gmail.com"),
person(given = c("Peter", "J."),
family = "Wagner",
role = "aut"))
as necessary.
Check History
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
CRAN incoming feasibility
Maintainer: ‘David W. Bapst <dwbapst@gmail.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = c("David", "W."),
family = "Bapst",
role = c("aut", "cre"),
email = "dwbapst@gmail.com"),
person(given = c("Peter", "J."),
family = "Wagner",
role = "aut"))
as necessary.
CRAN incoming feasibility
Maintainer: ‘David W. Bapst <dwbapst@gmail.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = c("David", "W."),
family = "Bapst",
role = c("aut", "cre"),
email = "dwbapst@gmail.com"),
person(given = c("Peter", "J."),
family = "Wagner",
role = "aut"))
as necessary.
Code & tests
Open call graph →Code intelligence has not been computed for this package yet.
Code
Structure
Lines of code
46,297
Files
206
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
109
Internal functions
131
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
98.5%
\dontrun example ratio
14.5%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
No
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
27.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
CC0
License flags
SPDX valid, not OSI
History
Versions
28
First release
2012-01-17
Latest release
2024-07-06
Avg cadence
105 days
Cold removal rate
100%
Dep drift
12
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.