R Observatory: Metrics for Nestimate version 0.9.24

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Nestimate

0.9.24Package record

Dynamic, Probabilistic, and Higher-Order Network Analysis

1packages dependsuggested by 4

3.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Mohammed SaqrCRAN page ↗GitHub ↗Website ↗Issues ↗

Estimate, compare, and analyze dynamic and psychological networks using a unified interface. Provides transition network analysis estimation (transition, frequency, co-occurrence, attention-weighted) Saqr et al. (2025) doi:10.1145/3706468.3706513, psychological network methods (correlation, partial correlation, 'graphical lasso', 'Ising') Saqr, Beck, and Lopez-Pernas (2024) doi:10.1007/978-3-031-54464-4_19, and higher-order network methods including higher-order networks, higher-order network embedding, hyper-path anomaly, and multi-order generative model. Supports bootstrap inference, permutation testing, split-half reliability, centrality stability analysis, mixed Markov models, multi-cluster multi-layer networks and clustering.

Changes in 0.9.24

Documentation

Fixes to the 0.9.23 help-page merge, found in review:
Pages are named after their function again: build_mcml and plot_state_frequencies had been named after a print() method, and their usage now lists the function before its methods.
The descriptions of 51 methods (what a plot draws, what a print shows) are restored, as a "Methods" section on each function's page.
Each page's ... entry states what each method does with extra arguments: methods that reject them say so, plot.net_bayes() names cograph::splot(), and the rest say they are ignored.
compare_networks: the ... and labels entries no longer repeat; net_edge_betweenness and net_pruning_details no longer list a non-existent class.

Show all changes in 0.9.24Hide the rest of the changes in 0.9.24

Every S3 method has a documented return value.

Behaviour notes

The mgm estimator rejects scale = FALSE with a classed error (nestimate_mgm_unscaled); this started in 0.9.23 and was not listed there. Missing values are handled pairwise, now passed explicitly.

Tests

Two more reference-implementation tests (a hand-written linear solve for passage_time(), a manual multinom re-computation) and unused reference helpers moved to the local suite; section headers that claimed equivalence tests are renamed. New tests: mgm on data with missing values, and the scale = FALSE error.

From NEWS.md in the release

Install

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

install.packages("Nestimate", 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("mohsaqr/Nestimate")

Development version from mohsaqr/Nestimate. 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-nestimate

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-Nestimate

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-Nestimate

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: 9.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-19

Show 3 earlier changesHide 3 earlier changes

WARNING11 OK, 2 WARNING2026-07-08
OK12 OK2026-04-26
ERROR5 OK, 1 ERROR2026-04-09

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.9.24

READMEYes · 1,140 wordsVignettesYes · 6 · evaluation depends on the environmentNEWSYes · 67% structured · mentions 0.9.24Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 139 (2 internal)includes a package overview page
Examples that run: 99%136 run in a plain check (5 of them under a condition) · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 99%
Documented parameters: 96%
Return-value docs: 100%
Help pages citing references: 29%

Vignettes (6)

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #8,753 · ~9/day · ~262/mo

Releases R versions

Daily download trend is not available in this view yet.

40130 days

1.1K90 days

3.1K1 year

Compare downloads with other packages →

Also on108 r2u2 autocran

How downloads are counted

Repository

mohsaqr/nestimate ↗Account: mohsaqr

3Stars

1Forks

0Open issues

1Open PRs

0Releases

291Commits

2Commit identities

291 commits · Last activity 2026-10-12 · 0% stars, 30d · Default branch at 0.9.26, ahead of CRAN 0.9.24 (checked 2026-10-21)

Responsiveness

not measured

Stars over time

2026-05-03 · 12026-08-09 · 3

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/mohsaqr/nestimate on 2026-10-21.

Continuous integration (1)

GitHub Actions

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-16 · The repository has a site deploy workflow

pkgdown site last built 2026-10-16

Reproducibility and dev environment (1)

data-raw/

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-03-17
Named in .Rbuildignore: .claude, CLAUDE.md
Named in .gitignore: CLAUDE.md
Commits: at least 109 crediting it in the message

Models named in its commits

Claude Opus 4.667 commits · Mar to Apr 2026
Claude Sonnet 4.619 commits · Mar to Apr 2026
Claude Opus 4.714 commits · May 2026

Some of these counts are a minimum, because the search stopped before the oldest commits.

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

19 external dependencies (excludes base and recommended)

Installing Nestimate adds 25 packages (11 with compiled code, 25 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, brglm2 2.3 MB.

Depends (1)

R >= 4.1.0

Imports (8)

ggplot2 data.tableclusterscales brglm2nnetidiographic psychnets

LinkingTo (0)

none

Suggests (14)

testthat igraph glmnet lavaan stringdist gridExtra lme4 corpcorMatrixcograph ggfittext knitr rmarkdown tna

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 4

Depends, Imports or LinkingTo, most downloaded first

htna

Suggests, most downloaded first

cograph cooccure transitiontrees lagdynamics

How these are counted

Code & Tests

Datasets

People & History

People (3)

Mohammed Saqr

Sonsoles López-Pernas

Author

Kamila Misiejuk

Author · added in 0.6.0

Releases (6)

Pick two releases to compare their code metrics.

0.9.24Latest
record
2026-10-07 · current release · diff ↗ ·
added 20 exports
state_colors<-, compare_networks, composites, edge_differences, effects_table, extract_pathways, global_differences, hypergraph_cluster, hypergraph_laplacian, hypergraph_transduction, item_loadings, macro_network, network_metrics, node_differences, outcome_model, permutation_diagnostics, session_ids, set_state_colors, simplicial_features, state_colors
0.8.5
record
2026-08-21 · diff ↗ ·
added 3 exports
entropy_bayes, entropy_network, entropy_trajectory
0.8.0
record
2026-07-10 · diff ↗ ·
added 18 exports
as_htna, as_netdifference, as_netobject, as_networks, bayes_compare, build_mcml_pc, certainty, loading_stability, mosaic_analysis, net_deprune, net_edge_betweenness, net_prune, net_pruning_details, net_reprune, subtract_networks, validate_netobject, vertex_bootstrap, vertex_compare
0.6.0
record
2026-05-31 · diff ↗ ·
added 25 exports
actor_endpoints, bipartite_groups, bottleneck_distance, build_hypergraph, casedrop_reliability, chain_structure, clique_expansion, cluster_choice, cluster_data, cluster_diagnostics, compare_model, hypergraph_centrality, hypergraph_measures, magnitude_difference, mark_first_state, mark_terminal_state, markov_order_test, mosaic_plot, path_dependence, persistence_landscape, plot_mosaic, plot_state_frequencies, rename_models, state_distribution, transition_entropy
R
R 4.6.0 released · 2026-04-24
0.4.3
record
2026-04-20 · diff ↗ ·
removed 9 exports
aggregate_weights, centrality, cluster_data, cluster_sequences, csum, permutation_test, prepare_data, reliability, wagg

added 23 exports
build_atna, build_clusters, build_cna, build_cor, build_ftna, build_glasso, build_ising, build_mlvar, build_pcor, build_tna, coefs, cooccurrence, distribution_plot, markov_stability, nct, net_aggregate_weights, net_centrality, network_reliability, passage_time, permutation, prepare, sequence_compare, sequence_plot
0.3.0
record
2026-04-08
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-04-08
Total releases: 6 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 149 KB / 7 files
Download size: 3.3 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Nestimate")

Format

Saqr, M., López-Pernas, S., & Misiejuk, K. (2026). Nestimate: Dynamic, Probabilistic, and Higher-Order Network Analysis (Version 0.9.24) [Computer software]. https://doi.org/10.32614/CRAN.package.Nestimate

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 Nestimate version 0.9.24 [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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