# Variable Selection in Linear Mixed Models for SNP Data

## Documentation for package ‘ggmix’ version 0.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

admixed | Simulated Dataset with 1D Geography
coef.ggmix_fit | Make predictions from a 'ggmix_fit' object
coef.ggmix_gic | Make predictions from a 'ggmix_gic' object
fn_eta_lasso_fullrank | Functions related to eta parameter used in optim and kkt checks
gen_structured_model | Simulation Scenario from Bhatnagar et al. (2018+) ggmix paper
ggmix | Fit Linear Mixed Model with Lasso or Group Lasso Regularization
ggmix_data_object | Constructor functions for the different ggmix objects
gic | Generalised Information Criterion
gic.default | Generalised Information Criterion
gic.ggmix_fit | Generalised Information Criterion
grr_beta0 | Check of KKT Conditions for Linear Mixed Model
grr_sigma2 | Check of KKT Conditions for Linear Mixed Model
gr_eta_lasso_fullrank | Functions related to eta parameter used in optim and kkt checks
karim | Karim's Simulated Data
kkt_check | Check of KKT Conditions for Linear Mixed Model
lambdalasso | Estimation of Lambda Sequence for Linear Mixed Model with Lasso Penalty
lambdalasso.default | Estimation of Lambda Sequence for Linear Mixed Model with Lasso Penalty
lambdalasso.fullrank | Estimation of Lambda Sequence for Linear Mixed Model with Lasso Penalty
lmmlasso | Estimation of Linear Mixed Model with Lasso Penalty
lmmlasso.default | Estimation of Linear Mixed Model with Lasso Penalty
lmmlasso.fullrank | Estimation of Linear Mixed Model with Lasso Penalty
logliklasso | Estimation of Log-likelihood for Linear Mixed Model with Lasso Penalty
logliklasso.default | Estimation of Log-likelihood for Linear Mixed Model with Lasso Penalty
logliklasso.fullrank | Estimation of Log-likelihood for Linear Mixed Model with Lasso Penalty
new_fullrank_K | Constructor functions for the different ggmix objects
new_fullrank_kinship | Constructor functions for the different ggmix objects
new_fullrank_UD | Constructor functions for the different ggmix objects
new_lowrank_K | Constructor functions for the different ggmix objects
new_lowrank_kinship | Constructor functions for the different ggmix objects
new_lowrank_UD | Constructor functions for the different ggmix objects
plot.ggmix_fit | Plot Method for 'ggmix_fit' object
plot.ggmix_gic | Plot the Generalised Information Criteria curve produced by 'gic'
plotCoef | Plot Method for 'ggmix_fit' object
plotGIC | Plot the Generalised Information Criteria curve produced by 'gic'
predict.ggmix_fit | Make predictions from a 'ggmix_fit' object
predict.ggmix_gic | Make predictions from a 'ggmix_gic' object
print.ggmix_fit | Print Method for Objects of Class 'ggmix_fit'
print.ggmix_gic | Print Method for Objects of Class 'ggmix_fit'
random.effects | Extract Random Effects
random.effects.default | Extract Random Effects
ranef | Extract Random Effects
ranef.default | Extract Random Effects
ranef.ggmix_gic | Extract Random Effects
sigma2lasso | Estimation of Sigma2 for Linear Mixed Model with Lasso Penalty
sigma2lasso.default | Estimation of Sigma2 for Linear Mixed Model with Lasso Penalty
sigma2lasso.fullrank | Estimation of Sigma2 for Linear Mixed Model with Lasso Penalty