Variable Selection in Linear Mixed Models for SNP Data

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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