R Observatory: Metrics for RMark version 3.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

RMark

3.1.0Package record

R Code for Mark Analysis

3packages dependsuggested by 1

77.5Kdownloads / year

–test coverage

7/13flavors OK

Overview

About

Maintained by Simon BonnerCRAN page ↗GitHub ↗Issues ↗

An interface to the software package MARK that constructs input files for MARK and extracts the output. MARK was developed by Gary White and is freely available at http://www.phidot.org/software/mark/downloads/ but is not open source.

Changes in 3.1.0

CHANGE

Check was added to release.gof which will stop if number of occasions is 3 or less.
Locations of documentation were added and changed that are given when package is loaded with library function.
if invisible==TRUE as run option, then batch is added to mark.exe execution and output window is not opened and output set to FALSE.
Maintainer for RMark has been changed from Jeff Laake (jefflaake@gmail.com) to Simon Bonner(simon.bonner@uwo.ca) and URL and BugReports are set to his RMark repository on GitHub.

From NEWS in the release

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("sjbonner/RMark")

Development version from sjbonner/RMark. Installs pak first if it is not already available.

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-rmark

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-RMark

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-RMark

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

4ERROR2NOTE7OK

Check messages

ERRORexamplesr-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-release-macos-arm64, r-release-macos-x86_64

Running examples in ‘RMark-Ex.R’ failed
The error most likely occurred in:

> ### Name: Blackduck
> ### Title: Black duck known fate data
> ### Aliases: Blackduck
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(Blackduck)
> # Change BirdAge to numeric; starting with version 1.6.3 factor variables are
> # no longer allowed.  They can work as in this example but they can be misleading
> # and fail if the levels are non-numeric.  The real parameters will remain 
> # unchanged but the betas will be different.
> Blackduck$BirdAge=as.numeric(Blackduck$BirdAge)-1
> run.Blackduck=function()
+ {
+ #
+ # Process data
+ #
+ bduck.processed=process.data(Blackduck,model="Known")
+ #
+ # Create default design data
+ #
+ bduck.ddl=make.design.data(bduck.processed)
+ #
+ #  Add occasion specific data min < 0; I have no idea what it is
+ #
+ bduck.ddl$S$min=c(4,6,7,7,7,6,5,5)
+ #
+ #  Define range of models for S
+ #
+ S.dot=list(formula=~1)
+ S.time=list(formula=~time)
+ S.min=list(formula=
...[truncated]...
able to find or run mark.exe


S.dot

sh: mark: command not found
Warning in system(paste("mark i=", inputfile, " o=", outfile, " v=", vcvfile,  :
  error in running command
Error in run.mark.model(model, invisible = invisible, adjust = adjust,  : 
  
Output file does not exist. Unable to find or run mark.exe


S.min

sh: mark: command not found
Warning in system(paste("mark i=", inputfile, " o=", outfile, " v=", vcvfile,  :
  error in running command
Error in run.mark.model(model, invisible = invisible, adjust = adjust,  : 
  
Output file does not exist. Unable to find or run mark.exe


S.time

sh: mark: command not found
Warning in system(paste("mark i=", inputfile, " o=", outfile, " v=", vcvfile,  :
  error in running command
Error in run.mark.model(model, invisible = invisible, adjust = adjust,  : 
  
Output file does not exist. Unable to find or run mark.exe


No mark models found

Error in collect.models() : 
Calls: run.Blackduck -> mark.wrapper -> collect.models
Execution halted

NOTEfor non-standard things in the check directoryr-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Found the following files/directories:
  ‘mark001.resbatch’

CRAN check page ↗

Slowest check: 5.1 min · r-oldrel-macos-x86_64

Status changes

ERROR7 OK, 2 NOTE, 4 ERRORNow
ERROR9 OK, 5 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.1.0

READMENoVignettesNoNEWSYes · 33% structured · mentions 3.1.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 104
Examples that run: 17%13 run in a plain check · 55 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run · 7 hold no code
Exported functions with examples: 75%
Documented parameters: 100%
Return-value docs: 95%
Help pages citing references: 13%

How these are measured

Downloads

77.5K

CRAN downloads in the past year

Rank #3,040 · ~212/day · ~6.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.1K30 days

4.4K90 days

77.5K1 year

Compare downloads with other packages →

Also on173 r2u3 autocran

How downloads are counted

Repository

sjbonner/rmark ↗Account: sjbonnerFork of jlaake/RMark

0Stars

0Forks

2Open issues

0Open PRs

0Releases

Last activity 2026-10-08

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2024-08-15 · 202026-07-28 · 0

How these are measured

PracticesBeta

Checks run against github.com/sjbonner/rmark on 2026-10-21.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing RMark adds 16 packages (10 with compiled code, 6.3 MB of source tarballs). Heaviest: mvtnorm 1.0 MB, vctrs 1.0 MB, msm 972 KB.

Depends (1)

R >= 2.13.0

Imports (4)

parallelmatrixcalc msm coda

LinkingTo (0)

none

Suggests (4)

latticesplinesnlmeplotrix

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

Imports 3

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

multimark R2ucare MigConnectivity

Suggests, most downloaded first

openCR

How these are counted

Code & Tests

Datasets

People & History

People (14)

Simon Bonner

Maintainer since 3.1.0 (2026) · added in 3.1.0

Jeff Laake

Author

Ben Augustine

Contributor · added in 2.15.3

Bret Collier

Contributor · added in 2.14.1

Jim Hines

Contributor · added in 3.0.0

Jake Ivan

Contributor · added in 2.2.7

Brett McClintock

Contributor · added in 2.2.5

Andrew Paul

Contributor · added in 2.14.1

David Pavlacky

Contributor · added in 2.1.7

Luke Eberhart- Phillips

Contributor · added in 2.2.6

Show 4 more contributorsHide 4 contributors

Eldar Rakhimberdiev

Contributor · added in 2.1.1

Jay Rotella

Contributor · added in 2.14.1

Daniel Turek

Contributor · added in 2.1.5

Connor Wood.

Contributor · added in 2.2.7

Previously maintained by Jeff Laake (2.0.2 to 3.0.8).

Listed in earlier versions (10)

Show 8 of 10 peopleHide 8 people

Eldar Rakimberdiev

no longer listed · 2.14.1 to 2.1.0

analysis from Bret Collier

no longer listed · 2.15.3 to 3.0.0

Jeff Laake with code contributions from Eldar Rakhimberdiev

no longer listed · 2.15.3 to 3.0.0

example data

no longer listed · 2.15.3 to 3.0.0

Andrew Paul.

no longer listed · 2.1.5 to 2.1.13

Luke Eberhart-Phillips.

no longer listed · 2.1.14

Luke Eberhart- Phillips.

no longer listed · 2.2.0 to 2.2.5

Jake Ivan.

no longer listed · 2.2.6

Releases (40)

Pick two releases to compare their code metrics.

3.1.0Latest
record
2026-07-27 · current release · diff ↗
3.0.8
record
2026-06-14 · diff ↗
R
R 4.6.0 released · 2026-04-24
3.0.7
record
2026-01-31 · diff ↗
3.0.6
record
2026-01-14 · diff ↗
R
R 4.5.0 released · 2025-04-11
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
R
R 4.0.0 released · 2020-04-24
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
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16

Show 41 earlier eventsHide 41 earlier events

R
R 3.1.0 released · 2014-04-10
3.0.3
record
2013-12-15 · diff ↗
3.0.2
record
2013-08-20 · diff ↗
3.0.0
record
2022-08-14 · diff ↗ ·
added 1 export
readMarkVcv
R
R 3.0.0 released · 2013-04-03
2.15.3
record
2012-12-11 · diff ↗
2.15.1
record
2012-06-18 · diff ↗ ·
added 5 exports
collapseCH, create.mark.mcmc, find.possible.transitions, splitCH, transition.pairs
R
R 2.15.0 released · 2012-03-30
2.14.2
record
2012-01-27 · diff ↗
2.14.1
record
2011-12-01 · diff ↗ ·
added 1 export
mark.wrapper.parallel
R
R 2.14.0 released · 2011-10-31
2.14.0
record
2011-10-17 · diff ↗ ·
added 53 exports
add.design.data, adjust.chat, adjust.parameter.count, adjust.value, cleanup, coef.mark, collect.models, compute.real, compute.Sn, convert.inp, covariate.predictions, create.model.list, deltamethod.special, export.chdata, export.MARK, export.model, extract.indices, fill.covariates, find.covariates, get.real, import.chdata, logitCI, make.design.data, make.mark.model, make.time.factor, mark, mark.wrapper, merge.mark, merge_design.covariates, model.average and 23 more
2.13.2
record
2011-08-25 · diff ↗
2.13.1
record
2011-07-01 · diff ↗
2.2.7
record
2019-11-06 · diff ↗
2.2.6
record
2019-02-04 · diff ↗
2.2.5
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2018-07-13 · diff ↗
2.2.4
record
2017-08-08 · diff ↗
2.2.2
record
2016-12-02 · diff ↗
2.2.0
record
2016-06-23 · diff ↗ ·
added 1 export
predict_real
2.1.14
record
2015-12-15 · diff ↗
2.1.13
record
2015-06-05 · diff ↗ ·
added 3 exports
MStruncate, process.ch, restore
2.1.12
record
2015-03-15 · diff ↗ ·
removed 3 exports
model.average.list, model.average.marklist, print.mark

added 1 export
MS_popan
2.1.9
record
2014-10-06 · diff ↗
2.1.8
record
2014-06-26 · diff ↗ ·
added 2 exports
model.average.list, model.average.marklist
2.1.7
record
2013-12-15 · diff ↗
2.1.6-1
record
2013-08-21 · diff ↗
2.1.5
record
2013-04-03 · diff ↗ ·
added 1 export
mata.wald
2.1.4
record
2012-12-12 · diff ↗
2.1.3
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2012-06-19 · diff ↗
2.1.1
record
2012-05-05 · diff ↗ ·
added 1 export
collect.model.names
2.1.0
record
2012-01-28 · diff ↗
2.0.9
record
2011-12-06 · diff ↗
2.0.8
record
2011-10-19 · diff ↗
2.0.7
record
2011-08-25 · diff ↗
2.0.6
record
2011-07-02 · diff ↗
2.0.5
record
2011-06-30 · diff ↗
2.0.4
record
2011-06-02 · diff ↗
2.0.3
record
2011-05-19 · diff ↗
2.0.2
record
2011-05-17
R
R 2.13.0 released · 2011-04-13

Package metadata

First published: 2011-05-17
Total releases: 40 / 15 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.13.0
Bundled data: 150 KB / 29 files
Download size: 899 KB

Appears in task views

Analysis of Ecological and Environmental Data

Cite

Cite this package

Run in R for the authors' entry:

citation("RMark")

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

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 RMark version 3.1.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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