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gremlin

R package for mixed-effects REML incorporating Generalized Inverses

https://github.com/matthewwolak/gremlin

Science Score: 10.0%

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

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    CITATION.cff file
  • ○
    codemeta.json file
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    .zenodo.json file
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    DOI references
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    Academic publication links
    Links to: zenodo.org
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    Committers with academic emails
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    Scientific vocabulary similarity
    Low similarity (12.0%) to scientific vocabulary

Keywords

average-information linear-mixed-models maximum-likelihood mixed-models
Last synced: 6 months ago · JSON representation

Repository

R package for mixed-effects REML incorporating Generalized Inverses

Basic Info
  • Host: GitHub
  • Owner: matthewwolak
  • License: gpl-3.0
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 1020 KB
Statistics
  • Stars: 5
  • Watchers: 2
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Topics
average-information linear-mixed-models maximum-likelihood mixed-models
Created almost 9 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

gremlin

DOI

R package for mixed-effects model REML incorporating Generalized Inverses (so, with some mental gymnastics: GREMLIN).

See the latest developments:

Overview of main branches:

  • master branch is the most recent production version (often the same as what is available from the R CRAN mirrors)

    • devel branch is a preview of the next release which should be functional and error/bug free, but proceed with caution

To install gremlin:

  • From R:

    • see the package page for the latest release of gremlin on CRAN where you can download the source.
    • install the latest release of the package directly in R: R install.packages("gremlin") then select your favorite CRAN mirror

  • From GitHub:

```

# Install master branch remotes::install_github("matthewwolak/gremlin")

# Install devel branch remotes::install_github("matthewwolak/gremlin", ref = "devel")

```

Examples

Estimating autosomal additive and dominance genetic variances

``` library(gremlin) library(nadiv) #<-- needed for creating inverse relatedness matrices

Add unique term for including individual effects of additive and dominance

warcolak$IDD <- warcolak$ID

Create generalized inverse matrices

Ainv <- makeAinv(warcolak[, 1:3])$Ainv Dinv <- makeD(warcolak[, 1:3])$Dinv

Basic model structure is as follows:

Fixed effects of sex

ID = autosomal additive genetic variance term

IDD = autosomal dominance genetic variance term

grAD <- gremlin(trait1 ~ sex-1, random = ~ ID + IDD, ginverse = list(ID = Ainv, IDD = Dinv), data = warcolak)

```

Summarize model

```

Summary

nrow(warcolak) summary(grAD) ```

Calculating combinations of (co)variances and quantifying uncertainty

Delta method

```

Calculate proportions of phenotypic variances (and Std. Error)

deltaSE(h2 ~ V1 / (V1 + V2 + V3), grAD) deltaSE(d2 ~ V2 / (V1 + V2 + V3), grAD) ```

Likelihood Ratio Test

  • Hypothesis test: domimance variance=0 `` ## Do this 2 alternative ways - both useupdate()`:

Either fix dominance variance to almost zero

grA_Dfxd <- update(grAD, Gstart = list(0.1, 1e-8), Gcon = list("P", "F"))

Or drop dominance variance from the model

grA <- update(grAD, random = ~ ID)

Compare log-likelihoods

logLik(grA_Dfxd) logLik(grA)

Do the Hypothesis test:

anova(grA, grAD)

```

Owner

  • Name: Matthew
  • Login: matthewwolak
  • Kind: user
  • Location: Auburn, AL, USA
  • Company: Auburn University

GitHub Events

Total
  • Create event: 1
  • Issues event: 2
  • Release event: 1
  • Issue comment event: 3
  • Push event: 14
  • Pull request event: 3
Last Year
  • Create event: 1
  • Issues event: 2
  • Release event: 1
  • Issue comment event: 3
  • Push event: 14
  • Pull request event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 560
  • Total Committers: 1
  • Avg Commits per committer: 560.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
matthewwolak m****k@g****m 560

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 24
  • Average time to close issues: 17 days
  • Average time to close pull requests: 2 minutes
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 1.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 24
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 2
  • Average time to close issues: 17 days
  • Average time to close pull requests: less than a minute
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 3.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • JulienGAMartin (1)
  • JavierMarcuzzi (1)
Pull Request Authors
  • matthewwolak (25)
  • qgevoeco (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 526 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
cran.r-project.org: gremlin

Mixed-Effects REML Incorporating Generalized Inverses

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 526 Last month
Rankings
Forks count: 21.9%
Stargazers count: 22.5%
Dependent packages count: 29.8%
Average: 34.5%
Dependent repos count: 35.5%
Downloads: 62.6%
Maintainers (1)
matthewwolak@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • Matrix * depends
  • methods * imports
  • nlme * imports