R Observatory: Metrics for secr version 5.5.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

secr

5.5.1Package record

Spatially Explicit Capture-Recapture

5packages dependsuggested by 1

22.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Murray EffordCRAN page ↗GitHub ↗Website ↗

Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.

Changes in 5.5.1

New features or changed behaviour of old functions

improved telemetry-calibrated cue count model (telemetrytype 'marking'), developed with assistance from Claude (Anthropic); uses Tu unmarked counts only, models unidentified marked sightings Tm (pID estimated), and allows a density model and finite-mixture models with known classes (hcov)
derived() returns Dcw, the cue-weighted mean density
capthist attribute 'marked' has individual telemetry availability per occasion (new functions marked(), marked<-)
details$telemetryint = "GH" uses Gauss-Hermite quadrature for activity centres
addTelemetry() help page describes telemetry type 'marking'
details$chatmethod = "analytic" option for overdispersion of unmarked sightings
details safeLL and uselog now default to TRUE when the capthist includes telemetry

Show all changes in 5.5.1Hide the rest of the changes in 5.5.1

Bugs fixed

specifying fixed 'pmix' parameter of h2 finite mixture model applied one value to both classes, i.e. (p,p), now (1-p,p)
mixture models failed or gave wrong class weights when detector 1 was not in use on occasion 1

Other

tests for telemetrytype 'marking'
faster compilation: specific Boost distribution headers

From NEWS in the release

Install

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

install.packages("secr", 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("MurrayEfford/secr")

Development version from MurrayEfford/secr. 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-secr

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-secr

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-secr

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: 22.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-14
NOTE12 OK, 1 NOTE2026-07-11
OK13 OK2026-05-20
ERROR12 OK, 1 ERROR2026-05-19
OK12 OK2026-04-25

Show 2 earlier changesHide 2 earlier changes

ERROR11 OK, 2 NOTE, 1 ERROR2026-03-30
WARNING10 OK, 3 NOTE, 1 WARNING2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 5.5.1

README· In the repository, left out of the releaseVignettesYes · 2 · dynamicNEWSYes · 67% structured · mentions 5.5.1Citation fileYes · computed when R runs itWebsiteYes

Help pages: 176includes a package overview page
Examples that run: 72%114 run in a plain check (2 of them under a condition) · 5 only when donttest examples are enabled (R CMD check --as-cran) · 38 never run · 2 hold no code
Exported functions with examples: 93%
Documented parameters: 97%
Return-value docs: 97%
Help pages citing references: 46%

Vignettes (2)

How these are measured

Downloads

22.1K

CRAN downloads in the past year

Rank #2,875 · ~61/day · ~1.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.3K30 days

5K90 days

22.1K1 year

Compare downloads with other packages →

Also on597 r2u5 autocran239 c2d4u

How downloads are counted

Repository

murrayefford/secr ↗Account: MurrayEfford

7Stars

2Forks

6Open issues

0Open PRs

0Releases

1,057Commits

2Commit identities

1,057 commits · Last activity 2026-10-19 · 0% stars, 30d · Default branch at 5.5.2, ahead of CRAN 5.5.1 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-08-12 · 52026-08-14 · 7

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 1 family in the upstream repository

Checks run against github.com/murrayefford/secr on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

How this is detected·Detection ruleset v3 (2026-09-26)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-06-23
Named in .Rbuildignore: .claude
Commits: at least 23 crediting it in the message

Models named in its commits

Claude Sonnet 5.523 commits · Oct 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Installing secr adds 27 packages (22 with compiled code, 55 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, sf 9.3 MB.

Depends (2)

R >= 3.5.0methods

Imports (18)

secrfunc abindgraphicsgrDevicesMASSmgcvmvtnormnlmeparallelraster Rcpp RcppParallel sfstatsstringr terratoolsutils

LinkingTo (3)

BH Rcpp RcppParallel

Suggests (12)

gdistance igraph knitr readxl rmarkdown sp spatstat (>= 3.3-3)spatstat.geom spatstat.random spcosa spsurvey (>= 5.3.0)testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

5direct

0indirect

Depends 4 · Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

camtrapR openCR secrdesign secrlinear ipsecr

Suggests, most downloaded first

ScatterDensity

How these are counted

Code & Tests

Datasets

People & History

People (4)

Murray Efford

Author, Maintainer since 1.3.0 (2010)

Yan Ru Choo

Contributor · added in 5.0.0

goodness-of-fit

David Fletcher

Contributor · added in 4.6.1

overdispersion

Philipp Jund

Contributor · added in 4.6.0

faster transect search and spacing

Releases (88)

Pick two releases to compare their code metrics.

5.5.1Latest
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2026-10-11 · current release · diff ↗ ·
added 2 exports
marked, marked<-
5.4.3
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2026-05-27 · diff ↗ ·
added 1 export
fillNA
R
R 4.6.0 released · 2026-04-24
5.4.2
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2026-02-24 · diff ↗
5.4.1
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2026-01-11 · diff ↗
5.3.0
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2025-09-27 · diff ↗ ·
added 5 exports
t2r2, simOU, simOU.capthist, derivedDfit, bufferBiasCheck
5.2.4
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2025-06-13 · diff ↗ ·
added 1 export
chat.nj
R
R 4.5.0 released · 2025-04-11
5.2.1
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2025-03-18 · diff ↗ ·
added 1 export
secr.refit
5.2.0
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2025-01-24 · diff ↗ ·
added 2 exports
derivedDcoef, derivedDsurface
5.1.0
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2024-11-04 · diff ↗ ·
added 1 export
fxi.secr
5.0.0
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2024-10-02 · diff ↗ ·
removed 3 exports
derivedSystematic, esa.plot.secr, fxi.secr

added 11 exports
MCgof, masksize, fxi, fxTotal, fxiContour, fxiMode, pdotContour, bufferContour, esaPlot, boundarytoSF, Dfn2
4.6.10
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2024-08-22 · diff ↗
4.6.9
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2024-06-29 · diff ↗
4.6.7
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2024-06-05 · diff ↗ ·
added 3 exports
make.spcosa, append.capthist, rlnormCV
R
R 4.4.0 released · 2024-04-24

Show 92 earlier eventsHide 92 earlier events

4.6.6
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2024-02-29 · diff ↗ ·
added 1 export
list.secr.fit
4.6.5
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2024-02-17 · diff ↗ ·
added 2 exports
binCovariate, ip.secr
4.6.4
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2023-10-18 · diff ↗ ·
added 4 exports
randomDensity, as.popn, kfn, predictDlambda
4.6.1
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2023-07-11 · diff ↗
4.6.0
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2023-05-23 · diff ↗ ·
added 2 exports
Fletcher.chat, nk
R
R 4.3.0 released · 2023-04-21
4.5.10
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2023-03-10 · diff ↗ ·
removed 2 exports
ip.secr, pfn
4.5.8
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2022-11-29 · diff ↗ ·
added 4 exports
trapsPerAnimal, adjustVarD, chat.nk, Enk
4.5.7
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2022-10-08 · diff ↗ ·
added 2 exports
nontarget, nontarget<-
4.5.6
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2022-08-15 · diff ↗
4.5.5
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2022-05-31 · diff ↗ ·
added 1 export
gridCells
4.5.4
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2022-04-22 · diff ↗ ·
added 1 export
makeStart
R
R 4.2.0 released · 2022-04-22
4.5.3
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2022-02-14 · diff ↗
4.5.1
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2022-01-18 · diff ↗
4.5.0
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2022-01-06 · diff ↗ ·
added 1 export
modelAverage
4.4.8
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2021-11-09 · diff ↗
4.4.7
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2021-10-18 · diff ↗
4.4.5
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2021-07-12 · diff ↗ ·
added 1 export
extractMoves
4.4.4
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2021-06-01 · diff ↗ ·
removed 1 export
make.newdata

added 1 export
makeNewData
R
R 4.1.0 released · 2021-05-18
4.4.1
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2021-04-30 · diff ↗ ·
removed 1 export
secr.make.newdata

added 1 export
make.newdata
4.3.3
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2020-12-11 · diff ↗
4.3.1
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2020-09-01 · diff ↗ ·
added 2 exports
ORL, centroids
4.3.0
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2020-07-14 · diff ↗
R
R 4.0.0 released · 2020-04-24
4.2.2
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2020-04-09 · diff ↗
4.2.0
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2020-02-22 · diff ↗ ·
added 2 exports
make.lacework, setNumThreads
4.1.0
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2019-12-17 · diff ↗ ·
added 1 export
AICcompatible
4.0.2
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2019-11-11 · diff ↗ ·
removed 2 exports
read.SPACECAP, write.SPACECAP

added 2 exports
write.mask, RSE
3.2.1
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2019-06-03 · diff ↗
R
R 3.6.0 released · 2019-04-26
3.2.0
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2019-01-25 · diff ↗ ·
added 1 export
derivedSystematic
3.1.8
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2018-11-19 · diff ↗
3.1.7
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2018-10-04 · diff ↗
3.1.6
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2018-05-14 · diff ↗ ·
added 1 export
CVpdot
R
R 3.5.0 released · 2018-04-23
3.1.5
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2018-02-25 · diff ↗ ·
removed 1 export
LLsurface.secr

added 6 exports
insertdim, LLsurface, intervals, intervals<-, sessionlabels, sessionlabels<-
3.1.3
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2017-12-03 · diff ↗ ·
removed 5 exports
derived.cluster, derived.session, derived.mash, derived.external, derived.nj

added 5 exports
derivedCluster, derivedSession, derivedMash, derivedExternal, derivednj
3.1.0
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2017-09-20 · diff ↗ ·
removed 2 exports
rbind.capthist, rbind.popn
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
3.0.3
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2013-10-30 · diff ↗
3.0.2
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2013-06-28 · diff ↗
3.0.1
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2017-05-03 · diff ↗ ·
added 10 exports
as.mask, telemetrytype, Tn, sightingPlot, occasionKey, telemetrytype<-, Tn<-, telemetryxy<-, updateCH, shareFactorLevels
R
R 3.0.0 released · 2013-04-03
2.15.3
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2013-01-24 · diff ↗
2.15.1
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2012-05-15 · diff ↗
R
R 2.15.0 released · 2012-03-30
2.14.1
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2011-12-16 · diff ↗ ·
added 3 exports
join, unjoin, RMarkInput
R
R 2.14.0 released · 2011-10-31
2.14.0
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2011-10-01 · diff ↗ ·
removed 2 exports
unmarked, unmarked<-
2.13.1
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2011-06-17 · diff ↗
R
R 2.13.0 released · 2011-04-13
2.12.2
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2011-02-21 · diff ↗
2.12.1
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2010-12-02 · diff ↗ ·
removed 1 export
searcharea<-

added 12 exports
esa.plot, esa.plot.secr, suggest.buffer, bias.D, mask.check, polyarea, pdot.contour, buffer.contour, detectpar, ms, spacing, spacing<-
R
R 2.12.0 released · 2010-10-15
2.12.0
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2010-08-29 · diff ↗ ·
added 4 exports
make.tri, clip.hex, moves, empirical.varD
2.11.1
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2010-05-07 · diff ↗
R
R 2.11.0 released · 2010-04-22
2.11.0
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2010-03-11 · diff ↗
2.10.4
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2016-12-04 · diff ↗
2.10.3
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2016-05-13 · diff ↗ ·
added 1 export
plotMaskEdge
2.10.2
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2016-01-09 · diff ↗
2.10.0
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2015-12-07 · diff ↗ ·
added 10 exports
addSightings, markocc, Tu, Tm, sighting, discretize, markocc<-, Tu<-, Tm<-, pmixProfileLL
2.9.5
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2015-06-16 · diff ↗
2.9.4
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2015-03-25 · diff ↗ ·
added 2 exports
nedist, deleteMaskPoints
2.9.3
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2015-01-11 · diff ↗
2.9.2
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2014-11-26 · diff ↗
2.9.1
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2014-11-18 · diff ↗ ·
added 1 export
edist
2.9.0
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2014-09-22 · diff ↗ ·
added 7 exports
fx.total, strip.legend, sim.detect, secr.test, getMeanSD, maskarea, masklength
2.8.2
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2014-04-30 · diff ↗
2.8.1
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2014-04-03 · diff ↗
2.8.0
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2014-03-31 · diff ↗ ·
added 14 exports
par.secr.fit, par.derived, par.region.N, ellipse.bvn, clone, telemetryxy, telemetered, PG, Rsurface, CV, CVa, CVa0, plotMCP, xy2CH
2.7.0
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2013-10-30 · diff ↗
2.6.1
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2013-06-28 · diff ↗ ·
added 1 export
read.telemetry
2.6.0
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2013-06-12 · diff ↗
2.5.0
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2013-01-23 · diff ↗ ·
added 4 exports
secrlist, make.lookup, usagePlot, snip
2.4.0
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2012-11-05 · diff ↗ ·
added 7 exports
addTelemetry, make.telemetry, timevaryingcov, signalframe, signalmatrix, timevaryingcov<-, signalframe<-
2.3.2
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2012-05-15 · diff ↗ ·
added 4 exports
unRMarkInput, randomHabitat, noise, noise<-
2.3.1
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2011-12-20 · diff ↗
2.3.0
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2011-11-20 · diff ↗ ·
added 6 exports
tile, addCovariates, pointsInPolygon, predictDsurface, rectangularMask, spotHeight
2.2.0
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2011-10-02 · diff ↗
2.1.0
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2011-06-17 · diff ↗ ·
removed 1 export
empirical.varD

added 22 exports
region.N, expected.n, trap.builder, make.systematic, writeGPS, mash, cluster.counts, cluster.centres, circular.r, circular.p, derived.cluster, derived.session, derived.mash, derived.external, derived.nj, clusterID, clustertrap, alongtransect, unmarked, clusterID<-, clustertrap<-, unmarked<-
2.0.0
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2011-02-21 · diff ↗ ·
added 6 exports
read.DA, write.DA, fxi.secr, fxi.contour, fxi.mode, alive
1.5.1
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2010-12-03 · diff ↗
1.4.1
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2010-08-30 · diff ↗
1.4.0
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2010-05-07 · diff ↗ ·
removed 1 export
read.captures

added 9 exports
read.capthist, MMDM, ARL, write.captures, closure.test, closedN, read.SPACECAP, write.SPACECAP, logmultinom
1.3.0
record
2010-03-11
R
R 2.10.0 released · 2009-10-26

Package metadata

First published: 2010-03-11
Total releases: 88 / 16 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 126 KB / 11 files
Download size: 1.2 MB

Appears in task views

Analysis of Ecological and Environmental Data

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("secr")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 secr version 5.5.1 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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