R Observatory: Metrics for SemNeT version 2.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SemNeT

2.1.0Package record

Methods and Measures for Semantic Network Analysis

0packages depend

4.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Alexander P. ChristensenCRAN page ↗GitHub ↗Issues ↗

Implements several functions for the analysis of semantic networks including different network estimation algorithms, partial node bootstrapping (Kenett, Anaki, & Faust, 2014 doi:10.3389/fnhum.2014.00407), random walk simulation, and a function to compute global network measures. Significance tests, including permutation testing, and plotting features are also implemented.

Changes in 2.1.0

FIX: group tests in bootstrap_test_SemNeT and test.bootSemNeT inflated statistics by sqrt(iter) (Tu, Chodorow, Brooks, Ezrina, & Valian, under review); recompute any results
UPDATE: bootstrap_test_SemNeT now returns bootstrap intervals of within-iteration group contrasts (ci_level, adjust, ci_type, power, legacy arguments)
UPDATE: bootstrap_test_SemNeT node bootstraps are summarized descriptively (no interval or p-value)
UPDATE: bootstrap_test_SemNeT legacy parametric tests need legacy = TRUE and always warn
UPDATE: bootstrap_SemNeT $summary standard error is no longer divided by sqrt(iter); observed (full-data) statistics are stored in $observed
ADD: bootstrap_test_SemNeT Wald z, p_value, and minimal detectable effect mde for normal intervals (the default)
ADD: bootstrap_test_SemNeT bias_se (|bias| / se; above about 0.25 the bootstrap is off-centre from the observed difference), printed as bias/se
ADD: bootstrap_test_SemNeT and permutation_SemNeT print a note under their summary tables that they should always be run together
FIX: cn alpha had no effect
FIX: cn counted co-occurrences on uncleaned responses, so placeholders (" ", "NA") emptied the network
FIX: nrw counted every adjacent pair twice per participant; pairs are now counted once (counts are numbers of participants)
FIX: pf dropped zero-distance pairs, leaving identical responses unlinked

Show all changes in 2.1.0Hide the rest of the changes in 2.1.0

FIX: binary2responses ignored response order in an ordered numeric matrix
FIX: permutation_SemNeT computed q on the weighted network; all measures are now unweighted
FIX: aspl per-node averages use distances to the other nodes; weighted aspl rejects negative weights
FIX: similarity method "euclid" returned a distance, which tmfg treated as a similarity; it now returns 1 / (1 + d)
FIX: tmfg stops on undefined similarities and on asymmetric input without depend = TRUE
FIX: equate rejects raw responses and duplicated response names
FIX: forward_flow treats "", " ", and "NA" as missing and requires min_response of at least 2
FIX: q with signed = TRUE weighted the negative term by N / (P - N) instead of N / (P + N) (Gomez et al., 2009); also fixed in {EGAnet}
FIX: cohens_d pools standard deviations by degrees of freedom (agrees with the equal-variance t-test) and handles groups of one
FIX: random_walk 5-unique-node statistic depended on the other network's walk; isolated start nodes and zero variation handled
FIX: random_network_test summed weights for edge counts; networks are binarized, p-values are Monte Carlo, and a degree-preserving null is added
UPDATE: cn gains cutoff for enrich = TRUE (default 0.50, was a hardcoded 0.35) and warns that there is no established value
UPDATE: pf now uses the response-order distance of Paulsen et al. (1996) and needs response order (raw or ordered responses, not 0/1 data)
UPDATE: semantic_network_measures defaults to weighted = FALSE (as documented) and gains na.rm, signed, and type (passed to cc, q, and aspl)
UPDATE: cc gains na.rm and no longer rounds per-node values; weighted cc divides weights by the largest absolute weight
UPDATE: similarity stops on missing or infinite values (and non-0/1 data for "angular", "faith", "jaccard", "rr"); finalize stops on missing values and non-whole minimum_cases
UPDATE: q requires a symmetric network and returns NaN for a network without edges
UPDATE: seed = 0 means random results, like NULL
UPDATE: response_analysis returns vocabulary (Jaccard overlap and rarefied richness) and ignores never-given responses in binary input
UPDATE: random_walk no longer reports p-values (they only reflect iter); differences, Monte Carlo intervals, and Cohen's d are given instead
UPDATE: bootstrap_SemNeT node bootstrap drops the same nodes from every group in an iteration
UPDATE: bootstrap_SemNeT retries draws only for correlation similarities ("cor", "phi"); plot shows the full-data value
UPDATE: permutation_SemNeT tests several measures at once and returns mde and diagnostics
UPDATE: permutation_SemNeT gains two-sided options "two_tailed_centered" and "two_tailed_doubled", tolerates floating-point ties, and aligns samples of different widths or vocabularies
UPDATE: Shiny Bootstrap tab shows intervals instead of t-test/ANOVA/ANCOVA; labels and captions updated
ADD: aspl type argument ("arithmetic", the default and previous behavior, or "harmonic")
ADD: seed for bootstrap_SemNeT and permutation_SemNeT; each resample gets its own seed, so results do not depend on cores or set.seed
ADD: random_network_test seed argument
ADD: print methods for bootstrap_test_SemNeT and permutation_SemNeT

From NEWS in the release

Install

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

install.packages("SemNeT", 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("AlexChristensen/SemNeT")

Development version from AlexChristensen/SemNeT. 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-semnet

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-SemNeT

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-SemNeT

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: 4.9 min · r-patched-linux-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 OK2026-06-09

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 2.1.0

README· In the repository, left out of the releaseVignettesNoNEWSYes · 67% structured · mentions 2.1.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 47includes a package overview page
Examples that run: 100%37 run in a plain check (1 of them under a condition)
Exported functions with examples: 77%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 51%

How these are measured

Downloads

4.2K

CRAN downloads in the past year

Rank #6,071 · ~12/day · ~353/mo

Releases R versions

Daily download trend is not available in this view yet.

69030 days

1.4K90 days

4.2K1 year

Compare downloads with other packages →

Also on129 r2u1 autocran142 c2d4u

How downloads are counted

Repository

alexchristensen/semnet ↗Account: AlexChristensen

28Stars

5Forks

1Open issues

0Open PRs

8Releases

328Commits

1Commit identities

rsemantic-network-analysis

328 commits · Last activity 2026-10-21 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 68
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-01 · 232026-08-31 · 28

How these are measured

PracticesBeta

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

Checks run against github.com/alexchristensen/semnet on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (1)

Issue templates

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-09-07
Named in .Rbuildignore: .claude
Commits: at least 1 crediting it in the message

Models named in its commits

Claude Sonnet 51 commit · Sep 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

20 external dependencies (excludes base and recommended)

Installing SemNeT adds 117 packages (61 with compiled code, 98 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.6.0

Imports (12)

methodsutilsstatsgraphicsfuture future.apply progressr igraph qgraph car broom effects

LinkingTo (0)

none

Suggests (14)

testthat shiny shinyjs shinyalert DT promises spreadr shinyMatrix shinyBS readxlforeignR.matlabtoolsggplot2

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)

Alexander P. Christensen

Author, Maintainer since 1.0.0 (2019)

Yoed N. Kenett

Author, Contributor

Releases (14)

Pick two releases to compare their code metrics.

2.1.0Latest
record
2026-10-14 · current release · diff ↗ ·
removed 1 export
responses_to_binary

added 3 exports
binary2responses, find_textcleaner_objects, responses2binary
2.0.0
record
2026-09-12 · diff ↗ ·
added 19 exports
aspl, bootstrap_SemNeT, bootstrap_test_SemNeT, cc, cn, compare_networks, forward_flow, nrw, permutation_SemNeT, pf, q, random_network_test, random_walk, read_uploaded_file, response_analysis, responses_to_binary, semantic_network_measures, simulate_fluency, tmfg
R
R 4.6.0 released · 2026-04-24
1.4.5
record
2025-11-03 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2023-08-12
1.4.4
record
2023-08-12 · diff ↗
R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2023-03-27
issues were not corrected in time
R
R 4.2.0 released · 2022-04-22
1.4.3
record
2021-09-04 · diff ↗
1.4.2
record
2021-06-22 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.4.1
record
2020-12-04 · diff ↗ ·
added 1 export
response.analysis
1.4.0
record
2020-09-27 · diff ↗ ·
added 5 exports
ASPL, CC, Q, TMFG, convert2igraph

Show 8 earlier eventsHide 8 earlier events

1.3.0
record
2020-06-09 · diff ↗ ·
removed 3 exports
compare.nets, partboot, partboot.test

added 8 exports
CN, NRW, PF, bootSemNeT, compare_nets, equate, finalize, test.bootSemNeT
R
R 4.0.0 released · 2020-04-24
1.2.0
record
2020-03-22 · diff ↗ ·
removed 2 exports
org.plot, partboot.one.test

added 1 export
SemNeTShiny
1.1.3
record
2020-02-07 · diff ↗
1.1.2
record
2019-10-29 · diff ↗
1.1.1
record
2019-09-27 · diff ↗ ·
added 1 export
partboot.one.test
1.0.0
record
2019-08-05
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-08-05
Total releases: 14 / 7 yrs
License: GPL (>= 3.0)
Minimum R: ≥ 3.6.0
Bundled data: 544 KB / 9 files
Download size: 719 KB

Appears in task views

Psychometric Models and Methods

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SemNeT")

Format

Christensen, A. P., & Kenett, Y. N. (2026). SemNeT: Methods and Measures for Semantic Network Analysis (Version 2.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.SemNeT

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 SemNeT version 2.1.0 [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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