R Observatory: Metrics for marked version 1.2.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

marked

1.2.8Package record

Mark-Recapture Analysis for Survival and Abundance Estimation

1packages depend

8.8Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Jeff LaakeCRAN page ↗

Functions for fitting various models to capture-recapture data including mixed-effects Cormack-Jolly-Seber(CJS) and multistate models and the multi-variate state model structure for survival estimation and POPAN structured Jolly-Seber models for abundance estimation. There are also Hidden Markov model (HMM) implementations of CJS and multistate models with and without state uncertainty and a simulation capability for HMM models.

Changes in 1.2.8

CHANGES

*Minor changes to function names, examples etc to fix warnings/notes on CRAN check.

From NEWS in the release

Install

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

install.packages("marked", 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-marked

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-marked

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-marked

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Jeff Laake <jefflaake@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jeff",
                      family = "Laake",
                      role = c("aut", "cre"),
                      email = "jefflaake@gmail.com"),
               person(given = "Devin",
                      family = "Johnson",
                      role = "aut",
                      email = "devin.johnson@noaa.gov"),
               person(given = "Paul",
                      family = "Conn",
                      role = "aut",
                      email = "paul.conn@noaa.gov"),
               person(given = c("example", "for", "simHMM", "from", "Jay"),
                      family = "Rotella",
                      role = "aut"))
as necessary.

CRAN check page ↗

Slowest check: 5.8 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.8

READMENoVignettesYes · 1 · dynamicNEWSYes · 33% structured · mentions 1.2.8Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 73
Examples that run: 38%8 run in a plain check · 12 only when donttest examples are enabled (R CMD check --as-cran) · 1 hold no code
Exported functions with examples: 37%
Documented parameters: 100%
Return-value docs: 93%
Help pages citing references: 26%

Also includes 1 demo script (run with demo())

Vignettes (1)

"marked Package Vignette"

How these are measured

Downloads

8.8K

CRAN downloads in the past year

Rank #4,298 · ~24/day · ~732/mo

Releases R versions

Daily download trend is not available in this view yet.

90130 days

2K90 days

8.8K1 year

Compare downloads with other packages →

Also on378 r2u7 autocran166 c2d4u

How downloads are counted

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing marked adds 60 packages (33 with compiled code, 58 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, bslib 5.6 MB.

Depends (4)

R >= 3.5.0lme4methodsparallel

Imports (16)

graphicsstatsutilsR2admb truncnorm codaMatrixnumDeriv expm Rcpp TMB optimx data.table knitr kableExtra bookdown

LinkingTo (1)

Rcpp

Suggests (1)

ggplot2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

RWildbook

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (4)

Jeff Laake

Devin Johnson

Paul Conn

example for simHMM from Jay Rotella

· added in 1.2.1

Maintainer since 1.0.9 (2013)

Releases (15)

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
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
R
R 3.1.0 released · 2014-04-10
3.0.3Latest
record
2013-11-22 · current release · diff ↗ ·
added 11 exports
cjs_delta, cjs_dmat, cjs_gamma, hmmDemo, ms2_gamma, ms_dmat, ms_gamma, probitMsCJS, simHMM, ums2_dmat, ums_dmat
3.0.2
record
2013-08-14 · diff ↗
R
R 3.0.0 released · 2013-04-03

Show 14 earlier eventsHide 14 earlier events

2.15.3
record
2013-01-24 · diff ↗ ·
added 31 exports
accumulate_data, cjs.hessian, collapseCH, compute.real, create.model.list, crm, crm.wrapper, fix.parameters, function.wrapper, fx.aic, fx.par.count, js.hessian, load.model, make.design.data, mcmc_mode, merge_design.covariates, model.table, naive.survival, p.boxplot, p.mean, Phi.boxplot, Phi.mean, predict.crm, print.crm, probitCJS, process.ch, process.data, resight.matrix, setup.model, setup.parameters and 1 more
1.2.8
record
2023-10-19 · diff ↗ ·
added 1 export
smsld_tmb
1.2.6
record
2019-12-09 · diff ↗ ·
removed 1 export
compute.real

added 3 exports
compute_real, msld_tmb, mvmscjs_tmb
1.2.1
record
2018-03-30 · diff ↗ ·
added 1 export
mscjs_tmb
1.1.13
record
2016-12-06 · diff ↗ ·
added 8 exports
dmat_hsmm2hmm, hsmm2hmm, initiate_pi, mscjs, mvmscjs, mvmscjs_delta, setup_admb, setup_tmb
1.1.11
record
2016-03-07 · diff ↗
1.1.10
record
2015-08-20 · diff ↗
1.1.9
record
2015-08-20 · diff ↗
1.1.8
record
2015-03-17 · diff ↗ ·
removed 1 export
print.crm

added 9 exports
R_HMMLikelihood, backward_prob, crmlist_fromfiles, global_decode, local_decode, loglikelihood, mvms_design_data, mvms_dmat, rerun_crm
1.1.6
record
2014-06-17 · diff ↗ ·
removed 2 exports
predict.crm, probitMsCJS

added 3 exports
compute_matrices, omega, set_mvms
1.1.3
record
2013-11-23 · diff ↗
1.1.2
record
2013-08-16 · diff ↗
1.0.9
record
2013-01-25
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2013-01-24
Total releases: 15 / 13 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 24 KB / 6 files
Download size: 346 KB

Appears in task views

Analysis of Ecological and Environmental Data

Cite

Cite this package

Run in R for the authors' entry:

citation("marked")

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 marked version 1.2.8 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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