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semEff

Automatic Calculation of Effects for Piecewise Structural Equation Models

https://github.com/murphymv/semeff

Science Score: 57.0%

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    Found 6 DOI reference(s) in README
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Repository

Automatic Calculation of Effects for Piecewise Structural Equation Models

Basic Info
Statistics
  • Stars: 12
  • Watchers: 2
  • Forks: 0
  • Open Issues: 3
  • Releases: 9
Created almost 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License Citation

README.Rmd 

---
output: github_document
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# semEff



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Buy Me A Coffee



`semEff` provides functionality to automatically calculate direct, indirect, and total effects for 'piecewise' structural equation models, comprising lists of fitted models representing structured equations (Lefcheck, 2016; Shipley, 2000, 2009). Confidence intervals are provided via bootstrapping.

Currently supported model classes are `"lm"`, `"glm"`, `"lmerMod"`, `"glmerMod"`, `"lmerModLmerTest"`, `"gls"`, and `"betareg"`.

## Installation

You can install the released version of `semEff` from [CRAN](https://CRAN.R-project.org) with:

``` r
install.packages("semEff")
```

And the development version from [GitHub](https://github.com/) with:

``` r
devtools::install_github("murphymv/semEff@dev")
```

## Usage

The primary function is [`semEff()`](https://murphymv.github.io/semEff/reference/semEff.html), which returns an object of class `"semEff"` with associated `print()` and `summary()` methods. Everything can technically be accomplished in a single call to `semEff()`; however, since bootstrapping is employed to generate resamples for confidence intervals (via [`bootEff()`](https://murphymv.github.io/semEff/reference/bootEff.html)), it is usually preferable to save these estimates separately prior to calling `semEff()` -- allowing more flexibility and saving time if/when recalling the function.

## Examples

Package functions are well-documented and most include some short examples. In addition, see the following vignettes for some longer demonstrations:

-   [Analysing direct vs. indirect effects of landscape location on plant species richness](https://murphymv.github.io/semEff/articles/semEff.html)

-   [Predicting and plotting indirect effects of degree days to bud burst on tree growth](https://murphymv.github.io/semEff/articles/predicting-effects.html)

## References

Lefcheck, J. S. (2016). piecewiseSEM: Piecewise structural equation modelling in R for ecology, evolution, and systematics. *Methods in Ecology and Evolution*, *7*(5), 573--579. [doi:10/f8s8rb](https://doi.org/10.1111/2041-210X.12512)

Shipley, B. (2000). A New Inferential Test for Path Models Based on Directed Acyclic Graphs. *Structural Equation Modeling: A Multidisciplinary Journal*, *7*(2), 206--218. [doi:10/cqm32d](https://doi.org/10.1207/S15328007SEM0702_4)

Shipley, B. (2009). Confirmatory path analysis in a generalized multilevel context. *Ecology*, *90*(2), 363--368. [doi:10/bqd43d](https://doi.org/10.1890/08-1034.1)

Owner

  • Name: Mark Murphy
  • Login: murphymv
  • Kind: user
  • Location: UK

Data Analyst | PhD (Ecology) | Interested in research, data, stats, programming, AI.

Citation (CITATION.cff) 

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "semEff" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'semEff: Automatic Calculation of Effects for Piecewise Structural Equation
  Models'
version: 0.7.2
doi: 10.32614/CRAN.package.semEff
identifiers:
- type: url
  value: https://buymeacoffee.com/murphymv
abstract: Automatically calculate direct, indirect, and total effects for piecewise
  structural equation models, comprising lists of fitted models representing structured
  equations (Lefcheck, 2016 <https://doi.org/10/f8s8rb>). Confidence intervals are
  provided via bootstrapping.
authors:
- family-names: Murphy
  given-names: Mark V.
  email: murphymv@gmail.com
repository: https://CRAN.R-project.org/package=semEff
repository-code: https://github.com/murphymv/semEff
url: https://murphymv.github.io/semEff/
contact:
- family-names: Murphy
  given-names: Mark V.
  email: murphymv@gmail.com
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
  version: '>= 3.6.0'
- type: software
  title: boot
  abstract: 'boot: Bootstrap Functions (Originally by Angelo Canty for S)'
  notes: Imports
  repository: https://CRAN.R-project.org/package=boot
  authors:
  - family-names: Canty
    given-names: Angelo
    email: cantya@mcmaster.ca
  - family-names: Ripley
    given-names: Brian
    email: ripley@stats.ox.ac.uk
  year: '2024'
  doi: 10.32614/CRAN.package.boot
- type: software
  title: gsl
  abstract: 'gsl: Wrapper for the Gnu Scientific Library'
  notes: Imports
  url: https://github.com/RobinHankin/gsl
  repository: https://CRAN.R-project.org/package=gsl
  authors:
  - family-names: Hankin
    given-names: Robin K. S.
    email: hankin.robin@gmail.com
    orcid: https://orcid.org/0000-0001-5982-0415
  year: '2024'
  doi: 10.32614/CRAN.package.gsl
- type: software
  title: lme4
  abstract: 'lme4: Linear Mixed-Effects Models using ''Eigen'' and S4'
  notes: Imports
  url: https://github.com/lme4/lme4/
  repository: https://CRAN.R-project.org/package=lme4
  authors:
  - family-names: Bates
    given-names: Douglas
    orcid: https://orcid.org/0000-0001-8316-9503
  - family-names: Maechler
    given-names: Martin
    orcid: https://orcid.org/0000-0002-8685-9910
  - family-names: Bolker
    given-names: Ben
    email: bbolker+lme4@gmail.com
    orcid: https://orcid.org/0000-0002-2127-0443
  - family-names: Walker
    given-names: Steven
    orcid: https://orcid.org/0000-0002-4394-9078
  year: '2024'
  doi: 10.32614/CRAN.package.lme4
- type: software
  title: parallel
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
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  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
- type: software
  title: stats
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
- type: software
  title: utils
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
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  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
- type: software
  title: ggplot2
  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Suggests
  url: https://ggplot2.tidyverse.org
  repository: https://CRAN.R-project.org/package=ggplot2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
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  - family-names: Pedersen
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  - family-names: Takahashi
    given-names: Kohske
  - family-names: Wilke
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  - family-names: Woo
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  - family-names: Brand
    given-names: Teun
    name-particle: van den
    orcid: https://orcid.org/0000-0002-9335-7468
  year: '2024'
  doi: 10.32614/CRAN.package.ggplot2
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
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- type: software
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  abstract: 'markdown: Render Markdown with ''commonmark'''
  notes: Suggests
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  repository: https://CRAN.R-project.org/package=markdown
  authors:
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    given-names: Yihui
    email: xie@yihui.name
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  year: '2024'
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- type: software
  title: piecewiseSEM
  abstract: 'piecewiseSEM: Piecewise Structural Equation Modeling'
  notes: Suggests
  url: https://github.com/jslefche/
  repository: https://CRAN.R-project.org/package=piecewiseSEM
  authors:
  - family-names: Lefcheck
    given-names: Jon
    email: lefcheckj@si.edu
  - family-names: Byrnes
    given-names: Jarrett
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  version: <= 2.3.0
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  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
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    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2024'
  doi: 10.32614/CRAN.package.rmarkdown

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  • Avg Commits per committer: 171.5
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  • Commits: 3
  • Committers: 2
  • Avg Commits per committer: 1.5
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Last synced: over 2 years ago

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  • Average comments per issue: 2.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 31
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
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  • Average time to close issues: about 2 months
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  • Issue authors: 6
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  • murphymv (1)
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Pull Request Authors
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Top Labels
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Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 6,615 last-month
  • Total docker downloads: 166
  • Total dependent packages: 1
  • Total dependent repositories: 4
  • Total versions: 9
  • Total maintainers: 1
cran.r-project.org: semEff

Automatic Calculation of Effects for Piecewise Structural Equation Models

  • Versions: 9
  • Dependent Packages: 1
  • Dependent Repositories: 4
  • Downloads: 6,615 Last month
  • Docker Downloads: 166
Rankings
Downloads: 7.8%
Dependent repos count: 14.6%
Average: 17.2%
Docker downloads count: 17.3%
Stargazers count: 17.4%
Dependent packages count: 18.1%
Forks count: 27.8%
Maintainers (1)
murphymv@gmail.com
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.6.0 depends
  • boot * imports
  • gsl * imports
  • lme4 * imports
  • parallel * imports
  • stats * imports
  • utils * imports
  • ggplot2 * suggests
  • knitr * suggests
  • markdown * suggests
  • piecewiseSEM * suggests
  • rmarkdown * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action 4.1.4 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/update-citation-cff.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite