Package: gremlin 1.1.0

gremlin: Mixed-Effects REML Incorporating Generalized Inverses

Fit linear mixed-effects models using restricted (or residual) maximum likelihood (REML) and with generalized inverse matrices to specify covariance structures for random effects. In particular, the package is suited to fit quantitative genetic mixed models, often referred to as 'animal models'. Implements the average information algorithm as the main tool to maximize the restricted log-likelihood, but with other algorithms available.

Authors:Matthew Wolak [cre, aut]

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gremlin.pdf |gremlin.html✨
gremlin/json (API)
NEWS

# Install 'gremlin' in R:
install.packages('gremlin', repos = c('https://matthewwolak.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/matthewwolak/gremlin/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

average-informationlinear-mixed-modelsmaximum-likelihoodmixed-models

3.85 score 5 stars 14 scripts 182 downloads 2 mentions 35 exports 3 dependencies

Last updated 12 days agofrom:ca41ec5343. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 07 2024
R-4.5-win-x86_64OKNov 07 2024
R-4.5-linux-x86_64OKNov 07 2024
R-4.4-win-x86_64OKNov 07 2024
R-4.4-mac-x86_64OKNov 07 2024
R-4.4-mac-aarch64OKNov 07 2024
R-4.3-win-x86_64OKNov 07 2024
R-4.3-mac-x86_64OKNov 07 2024
R-4.3-mac-aarch64OKNov 07 2024

Exports:aialgChkccFunccFun1ccFun2ccFun3ccFun4chol2inv_iiconTransdeltaSEemfixefgradFungradFun_fdgremlingremlinControlgremlinRgremlinSetupmatlist2vechmkModMatsnpar.gremlinnu2theta_lambdanu2theta_noTransnu2theta_transnuAI2thetaAIinv_lambdanuVar2thetaVar_lambdaremlremlItstart2thetastTranstheta2nu_lambdatheta2nu_transtrtugug_tracevech2matlist

Dependencies:latticeMatrixnlme

Readme and manuals

Help Manual

Help pageTopics
Mixed-Effects REML Incorporating Generalized Inversesgremlin-package
Optimization Algorithm Checks.algChk
anova() for gremlin objectsanova.gremlin
Convergence Criteria Checks for REML.ccFun ccFun, ccFun1 ccFun1, ccFun2 ccFun2, ccFun3 ccFun3, ccFun4
Partial sparse matrix inverse from a Cholesky factorization.chol2inv_ii
(Co)variance parameter transformations.conTrans covFun matlist2vech nu2theta_lambda nu2theta_noTrans nu2theta_trans nuAI2thetaAIinv_lambda nuVar2thetaVar_lambda start2theta stTrans theta2nu_lambda theta2nu_trans vech2matlist
Delta Method to Calculate Standard Errors for Functions of (Co)variances.deltaSE deltaSE.default deltaSE.formula deltaSE.list
Fixed Effect Estimates of 'class' 'gremlin'fixed.effects fixef fixef.gremlin
Mixed-effect modeling functions.getCall.gremlin gremlin gremlinR gremlinSetup mkModMats update update.gremlin
Advanced Options for Mixed-effect modeling functions.gremlinControl
Methods to extract log-likelihood and information criterion of a gremlin model.AIC.gremlin logLik.gremlin npar.gremlin
Weight gain data.Mrode11
Number of observations in data from gremlin model fit objectsnobs.gremlin
REML optimization algorithms for mixed-effect models.ai em gradFun gradFun_fd reml tugug_trace
Mixed-effect model Restricted Maximum Likelihood (REML) iterations.remlIt remlIt.default remlIt.gremlinR
Residuals of 'class' 'gremlin'resid.gremlin residuals.gremlin
Time to execute the gremlin modelruntime
Gremlin model summary.print.summary.gremlin summary.gremlin
Matrix trace methods.tr tr.default tr.dgCMatrix tr.dsCMatrix