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umx

Making Structural Equation Modeling (SEM) in R quick & powerful

https://github.com/tbates/umx

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 7 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.2%) to scientific vocabulary

Keywords

behavior-genetics cran genetics openmx psychology r sem statistics structural-equation-modeling tutorials twin-models umx

Keywords from Contributors

estimation graphical-models growth-curves item-response-theory multilevel-models standardization report
Last synced: 6 months ago · JSON representation

Repository

Making Structural Equation Modeling (SEM) in R quick & powerful

Basic Info
Statistics
  • Stars: 47
  • Watchers: 7
  • Forks: 17
  • Open Issues: 21
  • Releases: 34
Topics
behavior-genetics cran genetics openmx psychology r sem statistics structural-equation-modeling tutorials twin-models umx
Created over 13 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog

README.md

umx

Codecov test coverage Github commits cran version Monthly Downloads Total Downloads Rdoc DOI License

Road map, and Tutorials (let me know what you'd like, or perhaps a book?)

umx is a package designed to make structural equation modeling easier, from building, to modifying and reporting.

citation("umx")

You should cite: Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. DOI:10.1017/thg.2019.2

umx includes high-level functions for complex models such as multi-group twin models, as well as graphical model output.

Install it from CRAN:

splus install.packages("umx") library(umx) ?umx

Most functions have extensive and practical examples (even figures for the twin models): so USE THE HELP :-).

See what is on offer with '?umx'. There are online tutorials at tbates.github.io.

umx stands for "user" OpenMx functions. It provides over 100 functions, but most importantly:

  1. umxRAM that makes path-based SEM in R straightforward, with umxSummary and plot for table and graphical display of your models. It can also interpret basic lavaan if you get a script in that language.
  2. A suite of twin modelling functions, such as umxACE.

These are supported by many low-level functions automating activities such as parameter labels, start values etc., as well as helping with data-wrangling, journal-ready presentation (try umxAPA() among other tasks.

Some highlights include:

  1. Building Path Models
    • umxRAM() # Take umxPaths + data data = run and return a model, along with a plot and umxSummary
    • umxPath() # write paths with human-readable language like var = , mean = cov =, fixedAt=. Quickly define a variance and mean ('v.m. = ') and more.
  2. Reporting output
    • umxSummary(model) # Nice summary table, in markdown or browser. Designed for journal reporting (Χ², p, CFI, TLI, & RMSEA). Optionally show path loadings
    • plot(model, std=TRUE, digits = 3, ...) # Graphical model in your browser! or edit in programs like OmniGraffle
    • parameters(m1, "below", .1, pattern="_to_")) # A powerful assistant to get labels and values from a model (e.g. all 'to' params, below .1 in value)
    • residuals(m1, supp=.1) # Show residual covariances filtered for magnitude
  3. Modify models
    • umxModify(model, update = ) *# Modify and re-run a model. You can add objects, drop or add paths, including by wildcard label matching), re-name the model, and even return the comparison. All in 1 line *
  4. Twin modeling!
    • umxACE # Twin ACE modeling with aplomb paths are labeled! Works with plot() and umxSummary!
    • umxCP, umxIP, umxGxE, umxCP, umxGxEbiv, umxSexLim
    • umxACE
  5. Easy-to-remember options
    • umx_set_cores()
    • umx_set_optimizer()
  6. Many more miscellaneous helpers e.g.
    • umx_time(model1, model2) reports and compares run times in a compact programmable format (also "start" and "stop" a timer)
    • umxHetcor(data, use = "pairwise.complete.obs") # Compute appropriate pair-wise correlations for mixed data types.
    • Dozens more: Check out the "family links" in ?umx and in any help file!

Code and requests welcome via Github. Tell your friends! Publish good science :-)

For thrill-seekers and collaborators only: the bleeding-edge development version is here:

splus install.packages("devtools") library("devtools") install_github("tbates/umx") library("umx") ?umx

Owner

  • Name: Tim Bates
  • Login: tbates
  • Kind: user
  • Location: Edinburgh
  • Company: University of Edinburgh

Professor of individual differences. Often using behavior genetics. I largely study human attainment (ability, conscientiousness, optimism…)

GitHub Events

Total
  • Create event: 1
  • Release event: 1
  • Issues event: 18
  • Watch event: 5
  • Issue comment event: 26
  • Push event: 79
  • Pull request review event: 1
  • Pull request event: 10
  • Fork event: 3
Last Year
  • Create event: 1
  • Release event: 1
  • Issues event: 18
  • Watch event: 5
  • Issue comment event: 26
  • Push event: 79
  • Pull request review event: 1
  • Pull request event: 10
  • Fork event: 3

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 3,085
  • Total Committers: 7
  • Avg Commits per committer: 440.714
  • Development Distribution Score (DDS): 0.015
Past Year
  • Commits: 108
  • Committers: 3
  • Avg Commits per committer: 36.0
  • Development Distribution Score (DDS): 0.093
Top Committers
Name Email Commits
Timothy Bates t****s@g****m 3,039
lf-araujo l****o@u****u 27
Brenton M. Wiernik b****k 11
Joshua Nathaniel Pritikin j****n@p****m 5
Teun van den Brand t****d@g****m 1
Liang Zhang p****h@o****m 1
Kyle Husmann k****n@g****m 1
Committer Domains (Top 20 + Academic)
pobox.com: 1 unimelb.edu.au: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 121
  • Total pull requests: 28
  • Average time to close issues: 8 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 21
  • Total pull request authors: 5
  • Average comments per issue: 2.67
  • Average comments per pull request: 0.64
  • Merged pull requests: 23
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 9
  • Average time to close issues: 9 days
  • Average time to close pull requests: 9 days
  • Issue authors: 3
  • Pull request authors: 2
  • Average comments per issue: 1.4
  • Average comments per pull request: 0.78
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • tbates (66)
  • lf-araujo (27)
  • khusmann (6)
  • jpritikin (2)
  • salvatoj (2)
  • mcneale (2)
  • ukuvainik (1)
  • ldasey (1)
  • doge73 (1)
  • shenjean (1)
  • okeep (1)
  • rogercompte (1)
  • mariahkahwaji (1)
  • nathangillespie (1)
  • bwiernik (1)
Pull Request Authors
  • lf-araujo (27)
  • teunbrand (2)
  • psychelzh (1)
  • khusmann (1)
  • dmurdoch (1)
Top Labels
Issue Labels
enhancement (30) graphics/UI (16) top5 (11) Models (11) bug (4) tutorials/Rd (3) low (2) teaching function (2) Good first issue (1)
Pull Request Labels
enhancement (2)

Packages

  • Total packages: 2
  • Total downloads:
    • cran 2,575 last-month
  • Total dependent packages: 2
    (may contain duplicates)
  • Total dependent repositories: 6
    (may contain duplicates)
  • Total versions: 49
  • Total maintainers: 1
cran.r-project.org: umx

Structural Equation Modeling and Twin Modeling in R

  • Versions: 41
  • Dependent Packages: 2
  • Dependent Repositories: 6
  • Downloads: 2,575 Last month
Rankings
Forks count: 4.4%
Stargazers count: 8.0%
Downloads: 9.0%
Average: 9.4%
Dependent repos count: 12.1%
Dependent packages count: 13.3%
Maintainers (1)
timothy.c.bates@gmail.com
Last synced: 6 months ago
conda-forge.org: r-umx
  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Forks count: 36.1%
Average: 40.4%
Stargazers count: 40.5%
Dependent packages count: 51.2%
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • OpenMx >= 2.11.5 depends
  • R >= 3.5.0 depends
  • DiagrammeR * imports
  • DiagrammeRsvg * imports
  • MASS * imports
  • Matrix * imports
  • MuMIn * imports
  • R2HTML * imports
  • RCurl * imports
  • cowplot * imports
  • ggplot2 * imports
  • kableExtra * imports
  • knitr * imports
  • lavaan * imports
  • methods * imports
  • mvtnorm * imports
  • nlme * imports
  • polycor * imports
  • rsvg * imports
  • scales * imports
  • utils * imports
  • xtable * imports
  • cocor * suggests
  • devtools * suggests
  • gdata * suggests
  • gert * suggests
  • hrbrthemes * suggests
  • paran * suggests
  • psych * suggests
  • psychTools * suggests
  • pwr * suggests
  • rhub * suggests
  • rmarkdown * suggests
  • spelling * suggests
  • testthat * suggests