R Observatory: Metrics for surface version 0.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

surface

0.6Package record

Fitting Hansen Models to Investigate Convergent Evolution

0packages depend

3.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Travis IngramCRAN page ↗Website ↗

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 5.3 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.6

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsiteYes

Help pages: 16includes a package overview page
Examples that run: 63%10 run in a plain check · 5 never run · 1 hold no code
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 100%

Vignettes (1)

Introduction to surface PDF

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #13,872 · ~9/day · ~286/mo

Releases R versions

Daily download trend is not available in this view yet.

29630 days

85590 days

3.4K1 year

Compare downloads with other packages →

Also on81 r2u6 autocran134 c2d4u

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing surface adds 37 packages (22 with compiled code, 32 MB of source tarballs). Heaviest: ncbit 9.4 MB, igraph 4.8 MB, maps 2.2 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Travis Ingram

Author, Maintainer since 0.2 (2012)

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
unarchivedReturned to CRAN
2024-08-19
archivedRemoved from CRAN
2024-08-19
issues were not corrected despite reminders
0.6Latest
record
2024-08-19 · current release · diff ↗
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
unarchivedReturned to CRAN
2020-12-18
0.5
record
2020-12-18 · diff ↗
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 eventsHide 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
record
2014-02-14 · diff ↗
0.4
record
2013-11-01 · diff ↗ ·
removed 1 export
pmcSurface
R
R 3.0.0 released · 2013-04-03
0.3
record
2013-02-21 · diff ↗ ·
added 1 export
surfaceAICMultiPlot
0.2
record
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

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' entry:

citation("surface")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1111/2041-210x.12034.

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 v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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