R Observatory: Metrics for mispitools version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mispitools

2.0.1Package record

Missing Person Identification Tools

0packages depend

5.8Kdownloads / year

64.0%test coverage

13/13flavors OK

Overview

About

Maintained by Franco MarsicoCRAN page ↗GitHub ↗Issues ↗

A comprehensive toolkit for missing person identification combining genetic and non-genetic evidence within a Bayesian framework. Computes likelihood ratios (LRs) for DNA profiles, biological sex, age, hair color, and birthdate evidence. Provides decision analysis tools including optimal LR thresholds, error rate calculations, and ROC curve visualization. Includes interactive Shiny applications for exploring evidence combinations. For methodological details see Marsico et al. (2023) doi:10.1016/j.fsigen.2023.102891 and Marsico, Vigeland et al. (2021) doi:10.1016/j.fsigen.2021.102519.

Changes in 2.0.1

Fixes a test failure reported by CRAN on macOS arm64 (r-release and

r-oldrel) and on the M1mac additional check, and with it a genuine

platform dependence in the size of the exact LR support.

Atoms of the LR distribution

A log10 LR atom is a real number that the C++ engine and the R reference

implementation reach by different arithmetic routes. On a platform whose

compiler contracts a * b + c into a fused multiply-add, which is the

default on aarch64, one route rounds once where the other rounds twice, and

two mathematically equal atoms end up differing in the last bits. Grouping

them by IEEE equality, as 2.0.0 did, then split one atom into two, so the

number of support points of lr_distribution() depended on the platform and

the cross-check against the reference failed on arm64 while passing on x86.

Show all changes in 2.0.1Hide the rest of the changes in 2.0.1

lr_distribution(), per_marker_lr_dist() and the evidence combination kernel now close an atom group by a relative tolerance (kAtomRelTol, 1e-12) rather than by exact equality. The measured separation justifies the constant: consecutive keys are either within one unit in the last place of each other or more than 1e-8 apart in relative terms, with nothing in between.
The R reference aggregate_lr_dist() applies the same rule, so the two engines agree on the size of the support on every platform.
The composed distribution is unchanged as a distribution. Its support is smaller because the duplicates that rounding had split are now merged: composing two nine-allele markers on a trio gives 98 415 atoms instead of 602 991, with the same total mass and an expected weight of evidence identical to twelve decimal places. Exact composition of two markers of 10 and 12 alleles drops from about 1.9 million support points to about 317 000, so it is correspondingly cheaper in time and memory.

Documentation

The README opens the 2.0 section by carrying the tutorial case of Steps 1 to 6 through the four entry points of the exact engine, with the marker set and the frequency database used there.

From NEWS.md in the release

Install

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

install.packages("mispitools", 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("MarsicoFL/mispitools")

Development version from MarsicoFL/mispitools. 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-mispitools

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-mispitools

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-mispitools

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: 7.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-27
ERROR11 OK, 2 ERROR2026-08-26
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.1

READMEYes · 3,076 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 2.0.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 60 (1 internal)includes a package overview page
Examples that run: 98%55 run in a plain check (5 of them under a condition) · 1 never run
Exported functions with examples: 98%
Documented parameters: 99%
Return-value docs: 98%
Help pages citing references: 75%

Vignettes (3)

How these are measured

Downloads

5.8K

CRAN downloads in the past year

Rank #7,010 · ~16/day · ~482/mo

Releases R versions

Daily download trend is not available in this view yet.

40230 days

1.2K90 days

5.8K1 year

Compare downloads with other packages →

Also on125 r2u3 autocran

How downloads are counted

Repository

marsicofl/mispitools ↗Account: MarsicoFL

38Stars

14Forks

7Open issues

0Open PRs

13Releases

543Commits

14Commit identities

bayesian-inferencekinship

License file reads as GPL-3.0 · 543 commits · Last activity 2026-10-20 · +2.7% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-17 · 372026-10-16 · 38

How these are measured

PracticesBeta

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

Checks run against github.com/marsicofl/mispitools on 2026-10-22.

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Codexfirst seen 2025-12-30
Pull request it wrote: opened by a project member
Claude Codefirst seen 2026-01-08
Named in .Rbuildignore: .claude

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing mispitools adds 66 packages (37 with compiled code, 58 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

Depends (1)

R >= 3.5.0

Imports (11)

pedtools dplyr tidyrstatsreshape2 patchworkgraphicsggplot2 shiny Rcpp RcppArmadillo

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (10)

forrel Familias pedprobr pedmut fbnet DirichletReg shinythemes knitr rmarkdown testthat

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 (2)

Franco Marsico

Author, Maintainer since 0.1.0 (2021)

Suisei Nakagawa

Author · added in 2.0.0

Releases (15)

Pick two releases to compare their code metrics.

2.0.1Latest
record
2026-08-26 · current release · diff ↗
2.0.0
record
2026-08-25 · diff ↗ ·
removed 10 exports
bidirectionalKL, klPIE, kl_bidirectional, kl_multi, kl_pie, makePOIgen, multi_kl_divergence, postSim, sim_poi_genetic, sim_posterior

added 19 exports
as_lr_dist, belief_trajectory, binary_belief_trajectory, calibrate_concentration_cutoff, concentration_index, concentration_index_positive, entropy_log10, familias_trajectory, fragility_report, herfindahl_index, kl_divergence_log10, leave_one_out, lr_distribution, marker_model, nongenetic_feature, per_marker_kl, per_marker_kl_profile, shannon_concentration, trajectory_metrics
R
R 4.6.0 released · 2026-04-24
1.4.0
record
2026-01-09 · diff ↗ ·
added 34 exports
app_lr_comparison, app_mispitools, compute_conditioned_prop, compute_reference_prop, cpt_missing_person, cpt_population, decision_threshold, error_matrix_hair, get_allele_freqs, kl_bidirectional, kl_multi, kl_pie, lrComparisonApp, lr_age, lr_birthdate, lr_combine, lr_compute_pigmentation, lr_hair_color, lr_pigmentation, lr_sensitivity, lr_sex, lr_to_dataframe, mispitools_app, plot_cpt, plot_decision_curve, plot_lr_distribution, sim_lr_genetic, sim_lr_prelim, sim_mp_prelim, sim_poi_genetic and 4 more
R
R 4.5.0 released · 2025-04-11
1.2.0
record
2024-08-17 · diff ↗ ·
added 7 exports
LRcolors, compute_LRs_colors, conditionedProp, klPIE, refProp, simLR2dataframe, simRef
1.1.0
record
2024-07-08 · diff ↗ ·
added 2 exports
bidirectionalKL, multi_kl_divergence
R
R 4.4.0 released · 2024-04-24
1.0.0
record
2023-09-05 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.4.0
record
2023-04-06 · diff ↗ ·
removed 1 export
LRprelim

added 10 exports
CPT_MP, CPT_POP, Cmodel, CondPlot, LRage, LRcol, LRdate, LRsex, mispiApp, postSim
0.3.0
record
2023-02-27 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.2.1
record
2022-03-29 · diff ↗
0.2.0
record
2022-03-26 · diff ↗ ·
removed 3 exports
DTsim, makeLRsims, makePrelim

added 6 exports
DeT, combLR, makeMPprelim, makePOIprelim, simLRgen, simLRprelim
0.1.9
record
2022-02-18 · diff ↗ ·
removed 2 exports
makeMPprelim, makePOIprelim

added 2 exports
makePOIgen, makePrelim

Show 5 earlier eventsHide 5 earlier events

0.1.5
record
2022-01-04 · diff ↗ ·
removed 1 export
makePrelim

added 3 exports
getfreqs, makeMPprelim, makePOIprelim
0.1.3
record
2021-12-20 · diff ↗ ·
added 1 export
LRprelim
0.1.1
record
2021-12-10 · diff ↗ ·
added 1 export
makePrelim
0.1.0
record
2021-12-03
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-12-03
Total releases: 15 / 5 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Bundled data: 22 KB / 8 files
Download size: 1.8 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("mispitools")

Format

Marsico, F., & Nakagawa, S. (2026). mispitools: Missing Person Identification Tools (Version 2.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.mispitools

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 mispitools version 2.0.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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