R Observatory: Metrics for surface version 0.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

surface

0.6

Fitting Hansen Models to Investigate Convergent Evolution

0packages depend

3.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Travis IngramFirst published 2013-01-046 releasesCRAN page ↗

This data-driven phylogenetic comparative method fits stabilizing selection models to continuous trait data, building on the 'ouch' methodology of Butler and King (2004) doi:10.1086/426002. The main functions fit a series of Hansen models using stepwise AIC, then identify cases of convergent evolution where multiple lineages have shifted to the same adaptive peak. For more information see Ingram and Mahler (2013) doi:10.1111/2041-210X.12034.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("surface", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-surface

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-surface

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-surface

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 5.0 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

6

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 69%
Documented parameters: 100%
Return-value docs: 100%
References docs: 100%

Downloads

3.6K

CRAN downloads in the past year

Rank #11,345 · ~10/day · ~303/mo

Releases R versions

Daily download trend is not available in this view yet.

24030 days

87990 days

3.6K1 year

Compare downloads with other packages →

Also on99 r2u24 autocran87 c2d4u

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (5)

R >= 2.6ape ouchMASSgeiger

Imports (2)

methodsphytools

LinkingTo (0)

none

Suggests (1)

igraph

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Travis Ingram

Author, Maintainer

Authors (1)

Travis Ingram

Author, Maintainer

Package Timeline

6 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.6Latest
2024-08-19 · current release · diff ↗
unarchivedReturned to CRAN
2024-08-19
archivedRemoved from CRAN
2024-08-19
issues were not corrected despite reminders
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.5
2020-12-18 · diff ↗
unarchivedReturned to CRAN
2020-12-18
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-02-19
check problems were not corrected despite reminders
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21

Show 9 earlier events

R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
0.4-1
2014-02-14 · diff ↗
0.4
2013-11-01 · diff ↗
R
R 3.0.0 released · 2013-04-03
0.3
2013-02-21 · diff ↗
0.2
2013-01-04
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2013-01-04
Total releases: 6 / 13 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.6
Bundled data: 4.9 KB / 1 file
Download size: 222 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("surface")

Format

Ingram, T. (2024). surface: Fitting Hansen Models to Investigate Convergent Evolution (Version 0.6) [Computer software]. https://doi.org/10.32614/CRAN.package.surface

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for surface version 0.6 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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