R Observatory: Metrics for nimbleSCR version 0.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

nimbleSCR

0.2.1Package record

Spatial Capture-Recapture (SCR) Methods Using 'nimble'

0packages depend

3.4Kdownloads / year

58.6%test coverage

0/13flavors OK

Overview

About

Maintained by Daniel TurekCRAN page ↗

Provides utility functions, distributions, and fitting methods for Bayesian Spatial Capture-Recapture (SCR) and Open Population Spatial Capture-Recapture (OPSCR) modelling using the nimble package (de Valpine et al. 2017 <doi:10.1080/10618600.2016.1172487 >). Development of the package was motivated primarily by the need for flexible and efficient analysis of large-scale SCR data (Bischof et al. 2020 <doi:10.1073/pnas.2011383117 >). Computational methods and techniques implemented in nimbleSCR include those discussed in Turek et al. 2021 doi:10.1002/ecs2.3385; among others. For a recent application of nimbleSCR, see Milleret et al. (2021) doi:10.1098/rsbl.2021.0128.

Changes in 0.2.1

-- Add dcatState1Alive1Dead(), dcatState1Alive2Dead(), and dcatState2Alive2Dead() to sample state transition based on spatial probabilities.

-- Add sampler_categorical_general() to allow the addition of categorical samplers

-- Add calculateDensity() to calculate the density of individual in each habitat cell.

-- fix bug in the registration of dbernppDetection_normal().

From inst/NEWS in the release

Install

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

install.packages("nimbleSCR", 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-nimblescr

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-nimbleSCR

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-nimbleSCR

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probabil
...[truncated]...
ng for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘methods’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 9.3 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTENow
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.1

READMENoVignettesYes · 5 · dynamicNEWSYes · 100% structured · mentions 0.2.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 42 (2 internal)
Examples that run: 90%37 run in a plain check · 4 never run
Exported functions with examples: 98%
Documented parameters: 85%
Return-value docs: 88%
Help pages citing references: 45%

Vignettes (5)

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #10,798 · ~9/day · ~280/mo

Releases R versions

Daily download trend is not available in this view yet.

46730 days

96990 days

3.4K1 year

Compare downloads with other packages →

Also on123 r2u6 autocran

How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing nimbleSCR adds 14 packages (7 with compiled code, 12 MB of source tarballs). Heaviest: igraph 4.8 MB, nimble 3.2 MB, vctrs 1.0 MB.

Depends (2)

R >= 3.5.0nimble

Imports (1)

methods

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown testthat coda basicMCMCplots

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 (8)

Daniel Turek

Author, Maintainer since 0.1.0 (2020)

Richard Bischof

Author

Soumen Dey

Author · added in 0.1.2

Author

Author

Author

Author · added in 0.1.3

Perry de Valpine

Author

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
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.2.1Latest
record
2022-11-30 · current release · diff ↗ ·
added 8 exports
calculateDensity, dcatState1Alive1Dead, dcatState1Alive2Dead, dcatState2Alive2Dead, rcatState1Alive1Dead, rcatState1Alive2Dead, rcatState2Alive2Dead, sampler_categorical_general
0.2.0
record
2022-09-02 · diff ↗ ·
removed 3 exports
dbinom_sparseLocalSCR, getLocalTraps, rbinom_sparseLocalSCR

added 7 exports
dbinomLocal_exp, dbinomLocal_normalPlateau, dmultiLocal_normal, getHomeRangeArea, rbinomLocal_exp, rbinomLocal_normalPlateau, rmultiLocal_normal
R
R 4.2.0 released · 2022-04-22
0.1.3
record
2021-10-25 · diff ↗ ·
added 35 exports
calcWindowSizes, dbernppAC, dbernppACmovement_exp, dbernppACmovement_normal, dbernppDetection_normal, dbernppLocalACmovement_exp, dbernppLocalACmovement_normal, dbernppLocalDetection_normal, dnormalizer, dpoisppAC, dpoisppDetection_normal, dpoisppLocalDetection_normal, getMidPointNodes, getWindowCoords, getWindowIndex, integrateIntensityLocal_exp, integrateIntensityLocal_normal, integrateIntensity_exp, integrateIntensity_normal, makeConstantNimbleFunction, marginalVoidProbIntegrand, marginalVoidProbNumIntegration, rbernppAC, rbernppACmovement_exp, rbernppACmovement_normal, rbernppDetection_normal, rbernppLocalACmovement_exp, rbernppLocalACmovement_normal, rbernppLocalDetection_normal, rnormalizer and 5 more
0.1.2
record
2021-07-01 · diff ↗ ·
added 2 exports
dpoisLocal_normal, rpoisLocal_normal
R
R 4.1.0 released · 2021-05-18
0.1.1
record
2021-01-07 · diff ↗ ·
added 4 exports
dbinomLocal_normal, getLocalObjects, rbinomLocal_normal, scaleCoordsToHabitatGrid
0.1.0
record
2020-08-20
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-08-20
Total releases: 6 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 4.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("nimbleSCR")

Format

Turek, D., Bischof, R., Dey, S., Dupont, P., Ergon, T., Milleret, C., Zhang, W., & de Valpine, P. (2022). nimbleSCR: Spatial Capture-Recapture (SCR) Methods Using 'nimble' (Version 0.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.nimbleSCR

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 nimbleSCR version 0.2.1 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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