Reference

Model Fitting

Main functions for fitting the ggmix model

ggmix()

Fit Linear Mixed Model with Lasso or Group Lasso Regularization

gic()

Generalised Information Criterion

Methods for objects of class ggmix_fit and ggmix_gic

Method functions to extract relevant information from fitted objects

predict(<ggmix_fit>) coef(<ggmix_fit>)

Make predictions from a ggmix_fit object

predict(<ggmix_gic>) coef(<ggmix_gic>)

Make predictions from a ggmix_gic object

print(<ggmix_fit>) print(<ggmix_gic>)

Print Method for Objects of Class ggmix_fit

plot(<ggmix_fit>) plotCoef()

Plot Method for ggmix_fit object

plot(<ggmix_gic>) plotGIC()

Plot the Generalised Information Criteria curve produced by gic

ranef() random.effects()

Extract Random Effects

Datasets

Two datasets that ship with the package to illustrate usage

karim

Karim's Simulated Data

admixed

Simulated Dataset with 1D Geography

Diagnostic Plots

Plots for assessing model fit

plot(<ggmix_gic>) plotGIC()

Plot the Generalised Information Criteria curve produced by gic

Simulate Data

Simulate data with different geographies

gen_structured_model()

Simulation Scenario from Bhatnagar et al. (2018+) ggmix paper

Internal Utility Functions

Functions not really meant for the user

logliklasso()

Estimation of Log-likelihood for Linear Mixed Model with Lasso Penalty

lmmlasso()

Estimation of Linear Mixed Model with Lasso Penalty

kkt_check() grr_sigma2() grr_beta0()

Check of KKT Conditions for Linear Mixed Model

lambdalasso()

Estimation of Lambda Sequence for Linear Mixed Model with Lasso Penalty

sigma2lasso()

Estimation of Sigma2 for Linear Mixed Model with Lasso Penalty

gr_eta_lasso_fullrank() fn_eta_lasso_fullrank()

Functions related to eta parameter used in optim and kkt checks

new_fullrank_kinship() new_fullrank_K() new_fullrank_UD() new_lowrank_kinship() new_lowrank_K() new_lowrank_UD()

Constructor functions for the different ggmix objects