R Observatory: Metrics for SemNetCleaner version 2.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SemNetCleaner

2.0.0Package record

An Automated Cleaning Tool for Semantic and Linguistic Data

0packages depend

8.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

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

Implements several functions that automates the cleaning and spell-checking of text data. Also converges, finalizes, removes plurals and continuous strings, and puts text data in binary format for semantic network analysis. Uses the 'SemNetDictionaries' package to make the cleaning process more accurate, efficient, and reproducible.

Changes in 2.0.0

UPDATE: package rebuilt from the ground up: one file per function, input checks up front, the fluency and free association code paths merged, and a testthat suite (there were no tests before)
ADD: bad_response, best_guess, binary_to_responses, qwerty_distance, read_data, and responses_to_binary replace bad.response, best.guess, bin2resp, qwerty.dist, read.data, and resp2bin; the dotted names still work
REMOVE: lowercase argument of textcleaner; responses are always lowercased because capitalization does not change the word (a capital counted as a spelling error and Cat could be corrected to gnat). Calls that pass lowercase now fail with "unused argument"
ADD: keepRepeats argument in textcleaner (fluency only) keeps repeated responses in $responses$clean (GitHub Issue #17); $responses$binary and $behavioral$Perseverations are unchanged
ADD: $dictionary (the whole dictionary, reusable as dictionary = result$dictionary) and $added_words (only the words added in the session) in the textcleaner output when the dictionary is saved "In my results"
ADD: the manual spell-check help opens in a separate browser window when the manual spell-check starts (and again with H); options(SemNetCleaner.help_window = FALSE) keeps the help in the console
ADD: the instructions for reviewing the automated corrections (shown after the manual spell-check) open in a separate browser window too, followed by one ENTER prompt, instead of three screens of text in the console; options(SemNetCleaner.help_window = FALSE) keeps the console instructions
UPDATE: requires SemNetDictionaries (>= 0.3.0) (new category dictionaries and monikers, and a classed warning for a dictionary that cannot be found); a missing dictionary still stops with the textcleaner message when none loads, and gives one warning naming it when only some are missing
FIX: saving the dictionary at the end of the manual spell-check under a name that already exists kept the old file and lost the words added in that session
FIX: a cell that holds only spaces in the review of the automated corrections is now treated as missing (a space typed to clear to_2 left a blank response in the cleaned data)
FIX: the review app for the automated corrections (automated_edit) redrew the whole table after every edit, so the user lost their place; the table is now processed in the browser and an edit no longer redraws it
UPDATE: the review of the automated corrections shows only the responses the automated spell-check changed ($spellcheck$automated, as documented); responses that were already correct are no longer listed, and the review is skipped when nothing changed (open.animals: 462 rows instead of 793)

Show all changes in 2.0.0Hide the rest of the changes in 2.0.0

ADD: options(SemNetCleaner.pause = FALSE) turns off the deliberate pauses in the console wizard
UPDATE: parallel_process (used by textcleaner) no longer changes the global random seed
ADD: best_guess uses a phonetic (Metaphone) match alongside the QWERTY keyboard distance ("graple" is now corrected); when the two disagree the response goes to manual review
UPDATE: keepStrings = TRUE (fluency) splits a string of dictionary words unless the whole string is a dictionary entry ("sea slug" stays, "marmoset otter" becomes "marmoset" and "otter", "sea slug dog" becomes "sea slug" and "dog"); with keepStrings = FALSE a dictionary entry inside a longer string is kept whole
UPDATE: with keepStrings = FALSE, a multi-word string that cannot be split automatically is asked about word by word, and strings are separated unless they are dictionary entries
UPDATE: BAD WORD with keepStrings = TRUE drops only the bad word and keeps the rest of the string (one NA is kept for the intrusion count); BAD STRING still drops the whole string
UPDATE: ID columns are only inferred when they look like IDs (numeric, or every value contains a digit); the names Participants, IDs, Subjects, etc. are recognized; explicit row names are used as IDs when there is no ID column (also for partBY = "col")
UPDATE: task type is detected from the presence of Cue and Response columns rather than ncol(data) > 3
UPDATE: duplicated or missing participant IDs are an error naming the values and rows (they were silently renamed)
UPDATE: unusable input (NULL, no rows or columns, all responses missing, a failed preparation step) stops with a plain-language error instead of printing a bug report and returning NULL
UPDATE: correct_changes (through textcleaner) opens the Shiny/DT review app on every operating system (Linux used edit); pass edit_fn = edit for no extra packages. A review table with extra to_ columns is accepted
UPDATE: separators written without spaces (cow/pig, fish,bird) separate words, digits inside words are kept for the spell-check, accented characters are transliterated ("cafe"), and runs of spaces are collapsed
UPDATE: words typed in the manual spell-check receive the same cleaning as every other response
UPDATE: typing x or pressing ENTER at "Please enter a new selection:" exits; GO BACK across responses is announced and documented
UPDATE: dependencies: hunspell and phonics are now Imports; pbapply, parallel, and easycsv are dropped; shiny, DT, promises, tcltk, and rstudioapi are Suggests only, and so are foreign, readxl, and R.matlab, which read_data needs only for .sav, .xls/.xlsx, and .mat files (it names the package to install); requires R (>= 4.0.1) and SemNetDictionaries (>= 0.2.1)
UPDATE: parallel processing uses future, future.apply, and progressr; the worker plan is always restored. Workers load the installed package, so cores > 1 needs the package installed
REMOVE: the vignettes (and the knitr, rmarkdown, markdown, and htmlTable suggestions); the tutorial is Christensen and Kenett (2021, https://doi.org/10.1037/met0000463)
UPDATE: faster spell-checking against very large dictionaries such as "general" (370,000 words)
MOVE: textcleaner_shiny (point-and-click wizard) and the functions that support it are internal while the app is developed
FIX: correct_data perseverations were always 0 for a participant with no "NA" response (3 instead of 116 in open.animals); the same empty-which() negative index also emptied other vectors, matrix columns, and lists
FIX: a manual edit made while reviewing automated corrections was discarded for fluency data
FIX: textcleaner crashed with the default partBY ("the condition has length > 1")
FIX: keepLength filtered nothing for keepLength >= 2 and everything for keepLength <= 1
FIX: GO BACK in the manual spell-check could discard every other recorded change; after a mistyped answer GO BACK and HELP replaced the word with NA; with keepStrings = TRUE and no suggestions GO BACK acted as BAD STRING
FIX: menus crashed on narrow consoles (object 'def' not found) and printed 1: SKIP twice on consoles of 132 or more columns (GitHub Issues #20, #22, #26, #28)
FIX: data with one response column after the ID column failed (attempt to set 'rownames' on an object with no dimensions) (GitHub Issue #16); data with three or fewer columns was treated as free association (GitHub Issue #18)
FIX: a single column of whole word lists stops with a message explaining the one-response-per-column format (GitHub Issue #25)
FIX: correct_data overflowed when a response was corrected into three or more words (GitHub Issue #23)
FIX: errors in the corrections review were hidden behind a dump of the results object (GitHub Issues #27, #29)
FIX: a dictionary that cannot be found stops immediately, explaining that custom dictionaries are saved as <name>.dictionary.rds; auto_spellcheck crashed with keepStrings = FALSE when no multi-word response could be corrected (GitHub Issues #21, #24)
FIX: saving a dictionary with "choose the directory" falls back to the working directory when tcltk cannot load (GitHub Issue #24); add.path = "choose" is resolved once, up front
FIX: a dictionary name that is not a valid file name, or a failed save, no longer loses the manual session; names are validated and a failed save keeps the dictionary in $dictionary
FIX: participant IDs came back space-padded when the ID column was numeric
FIX: pressing ENTER at "TYPE MY OWN WORD" or "TYPE MY OWN STRING" crashed; menu answers with stray whitespace were rejected
FIX: the HELP screen and the walkthrough described the wrong option numbers and wording under keepStrings = TRUE
FIX: allowNumbers = TRUE and capital letters crashed the automated spell-check (qwerty_distance now lowercases and has digits on the keyboard); allowPunctuations = "" crashed
FIX: a single participant failed; continue = a finished result failed with argument is of length zero and now explains what can be continued
FIX: resuming after exiting at a single-word decision could fail with input 'word' has length 0
FIX: a response that repeats an unknown word ("teh cat teh dog") stopped the run; the word is now asked about once for all occurrences
FIX: "pollar bear" became "polar bear bear", "tardigrade goose" lost "goose", "sea sponge" became "seal sponge", and "english cocker spaniel" repeated "spaniel"; "sting" in "sting ray" was asked about although "sting ray" is a dictionary entry
FIX: free association: KEEP ORIGINAL and a one-word TYPE MY OWN STRING garbled the response; a response reduced to nothing (all stop words) aborted the final cleaning; the moniker lists returned capitalized proper nouns ("I do know")
FIX: convert2snafu with a single dataset wrote an empty file
FIX: qwerty_distance and singularize were never exported; bad.response was defined twice and the unreviewed copy won at load time
FIX: several 1:length(), 1:nrow(), and 1:ncol() ranges ran backwards on empty or one-row input

From NEWS in the release

Install

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

install.packages("SemNetCleaner", 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/SemNetCleaner")

Development version from AlexChristensen/SemNetCleaner. 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-semnetcleaner

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-SemNetCleaner

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-SemNetCleaner

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: 1.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-21
NOTE11 OK, 2 NOTE2026-07-16
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.0

README· In the repository, left out of the releaseVignettesNoNEWSYes · 67% structured · mentions 2.0.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 26 (11 internal)includes a package overview page
Examples that run: 100%14 run in a plain check (2 of them under a condition)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 27%

How these are measured

Downloads

8.1K

CRAN downloads in the past year

Rank #6,123 · ~22/day · ~675/mo

Releases R versions

Daily download trend is not available in this view yet.

57130 days

1.4K90 days

8.1K1 year

Compare downloads with other packages →

Also on77 r2u4 autocran1.2K conda_forge88 c2d4u

How downloads are counted

Repository

alexchristensen/semnetcleaner ↗Account: AlexChristensen

10Stars

0Forks

14Open issues

0Open PRs

6Releases

288Commits

2Commit identities

rsemantic-network-analysispreprocessing

License file reads as GPL-3.0 · 288 commits · Last activity 2026-10-15

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 8
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-02-04 · 102026-07-07 · 10

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/semnetcleaner 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 2026-09-12
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

17 external dependencies (excludes base and recommended)

Installing SemNetCleaner adds 15 packages (8 with compiled code, 27 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, hunspell 3.1 MB.

Depends (2)

R >= 4.0.1SemNetDictionaries

Imports (8)

future future.apply hunspell phonics progressr searcher stringi stringdist

LinkingTo (0)

none

Suggests (10)

DTforeignpromises R.matlab readxl rstudioapi shinytcltktestthat withr

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 (1)

Alexander P. Christensen

Author, Maintainer · added in 0.9.9

Maintainer since 0.1.1 (2018)

Listed in earlier versions (1)

Alexander Christensen

no longer listed · 0.1.1

Releases (16)

Pick two releases to compare their code metrics.

2.0.0Latest
record
2026-10-16 · current release · diff ↗ ·
added 6 exports
bad_response, best_guess, binary_to_responses, qwerty_distance, read_data, responses_to_binary
·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-16 12:54 UTC, so it stayed less than the time between readings.
R
R 4.6.0 released · 2026-04-24
1.3.7
record
2025-05-08 · diff ↗ ·
removed 1 export
correct.changes
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
R
R 4.2.0 released · 2022-04-22
1.3.4
record
2021-09-16 · diff ↗
1.3.3
record
2021-08-16 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.3.1
record
2020-12-04 · diff ↗ ·
added 1 export
bad.response
1.3.0
record
2020-09-24 · diff ↗ ·
added 1 export
convert2snafu
1.2.0
record
2020-06-09 · diff ↗ ·
removed 16 exports
bad.response, combine.responses, converge, destr, dup.match, equate, finalize, full.match, is.letter, moniker, multi.word.check, rm.lead.space, spell.check.dictionary, splitstr.check, starting.letter, word.check.wrapper

added 1 export
resp2bin
R
R 4.0.0 released · 2020-04-24
1.1.5
record
2020-03-22 · diff ↗
1.1.4
record
2020-02-17 · diff ↗

Show 9 earlier eventsHide 9 earlier events

1.1.3
record
2019-12-02 · diff ↗
1.1.2
record
2019-10-28 · diff ↗
1.1.1
record
2019-09-27 · diff ↗ ·
removed 4 exports
autoConverge, autoDestr, corr.chn, equate.multi

added 2 exports
correct.changes, read.data
1.1.0
record
2019-08-06 · diff ↗ ·
removed 5 exports
add.let, chn.let, misnomer, miss.let, spell.opt

added 2 exports
dup.match, moniker
1.0.0
record
2019-07-01 · diff ↗ ·
removed 2 exports
normalize, spell.check.database

added 13 exports
bad.response, combine.responses, corr.chn, equate.multi, full.match, is.letter, multi.word.check, pluralize, qwerty.dist, rm.lead.space, spell.check.dictionary, starting.letter, word.check.wrapper
R
R 3.6.0 released · 2019-04-26
0.9.9
record
2018-07-28 · diff ↗ ·
removed 9 exports
autoDeStr, convert2cytoscape, cosine, org.plot, partboot, partboot.plot, partboot.test, semnetcleaner, semnetmeas

added 13 exports
add.let, autoDestr, best.guess, bin2resp, chn.let, misnomer, miss.let, normalize, singularize, spell.check.database, spell.opt, splitstr.check, textcleaner
0.1.1
record
2018-05-16
R
R 3.5.0 released · 2018-04-23

Across CRAN, the median accepted release of the past year spent 26 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2018-05-16
Total releases: 16 / 8 yrs
License: GPL (>= 3.0)
Minimum R: ≥ 4.0.1
Bundled data: 134 KB / 4 files
Download size: 262 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("SemNetCleaner")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1037/met0000463.

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 SemNetCleaner version 2.0.0 [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.

Report a problem with this page →