Latent Environmental & Genetic InTeraction (LEGIT) Model

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Documentation for package ‘LEGIT’ version 1.4.1

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

Help Pages

best_model	Best model
best_model.elastic_net_var_select	Best model from elastic net variable selection
bootstrap_var_select	Bootstrap variable selection (for IMLEGIT)
elastic_net_var_select	Elastic net for variable selection in IMLEGIT model
example_2way	Simulated example of a 2 way interaction GxE model.
example_2way_lme4	Simulated example of a 3 way interaction GxExZ model
example_3way	Simulated example of a 3 way interaction GxExz model
example_3way_3latent	Simulated example of a 3 way interaction GxExZ model
example_with_crossover	Simulated example of a 2 way interaction GxE model with crossover point.
genetic_var_select	Parallel genetic algorithm variable selection (for IMLEGIT)
GxE_interaction_RoS	Regions of significance using Johnson-Neyman technique
GxE_interaction_test	Testing of the GxE interaction
IMLEGIT	Independent Multiple Latent Environmental & Genetic InTeraction (IMLEGIT) model
IMLEGIT_cv	Cross-validation for the IMLEGIT model
IMLEGIT_net	Independent Multiple Latent Environmental & Genetic InTeraction (IMLEGIT) model with Elastic Net on the latent variables. Do not use on it's own, use elastic_net_var_select instead.
IMLEGIT_to_LEGIT	IMLEGIT to LEGIT
LEGIT	Latent Environmental & Genetic InTeraction (LEGIT) model
LEGIT_cv	Cross-validation for the LEGIT model
LEGIT_to_IMLEGIT	LEGIT to IMLEGIT
longitudinal_folds	Longitudinal folds
nes_var_select	Parallel natural evolutionary variable selection assuming bernouilli distribution (for IMLEGIT)
plot.elastic_net_var_select	Plot function for the output of elastic_net_var_select
plot.LEGIT	Plot
predict.IMLEGIT	Predictions of IMLEGIT fits
predict.LEGIT	Predictions of LEGIT fits
r1nes_var_select	Parallel natural evolutionary variable selection assuming multivariate normal search distribution with a simple covariance matrix parametrization (for IMLEGIT)
rGE	Gene-Environment correlation estimation and testing
rGE.IMLEGIT	Gene-Environment correlation estimation and testing of IMLEGIT models
rGE.LEGIT	Gene-Environment correlation estimation and testing of LEGIT models
stepwise_search	Stepwise search for the best subset of genetic variants or environments with the LEGIT model
stepwise_search_IM	Stepwise search for the best subset of elements in the latent variables with the IMLEGIT model
summary.elastic_net_var_select	Summary function for the output of elastic_net_var_select
summary.IMLEGIT	Summarizing IMLEGIT fits
summary.LEGIT	Summarizing LEGIT fits