tune_lucid: A wrapper function to perform model selection for LUCID

In USCbiostats/LUCIDus: Latent Unknown Clustering Integrating Multi-View Data

A wrapper function to perform model selection for LUCID

Description

Given a grid of K and L1 penalties (incluing Rho_G, Rho_Z_mu and Rho_Z_Cov), fit LUCID model over all combinations of K and L1 penalties to determine the optimal penalty.

Usage

tune_lucid(
  G,
  Z,
  Y,
  CoG = NULL,
  CoY = NULL,
  family = "normal",
  K = 2:5,
  Rho_G = 0,
  Rho_Z_Mu = 0,
  Rho_Z_Cov = 0,
  ...
)

Arguments

G	Exposures, a numeric vector, matrix, or data frame. Categorical variable should be transformed into dummy variables. If a matrix or data frame, rows represent observations and columns correspond to variables.
Z	Omics data, a numeric matrix or data frame. Rows correspond to observations and columns correspond to variables.
Y	Outcome, a numeric vector. Categorical variable is not allowed. Binary outcome should be coded as 0 and 1.
CoG	Optional, covariates to be adjusted for estimating the latent cluster. A numeric vector, matrix or data frame. Categorical variable should be transformed into dummy variables.
CoY	Optional, covariates to be adjusted for estimating the association between latent cluster and the outcome. A numeric vector, matrix or data frame. Categorical variable should be transformed into dummy variables.
family	Distribution of outcome. For continuous outcome, use "normal"; for binary outcome, use "binary". Default is "normal".
K	Number of latent clusters. An integer greater or equal to 2. If K is a vector, model selection on K is performed
Rho_G	A scalar or a vector. This parameter is the LASSO penalty to regularize exposures. If it is a vector, tune_lucid will conduct model selection and variable selection. User can try penalties from 0 to 1.
Rho_Z_Mu	A scalar or a vector. This parameter is the LASSO penalty to regularize cluster-specific means for omics data (Z). If it is a vector, tune_lucid will conduct model selection and variable selection. User can try penalties from 1 to 100.
Rho_Z_Cov	A scalar or a vector. This parameter is the graphical LASSO penalty to estimate sparse cluster-specific variance-covariance matrices for omics data (Z). If it is a vector, tune_lucid will conduct model selection and variable selection. User can try penalties from 0 to 1.
...	Other parameters passed to est_lucid

Value

A list:

best_model	the best model over different combination of tuning parameters
tune_list	a data frame contains combination of tuning parameters and c orresponding BIC
res_model	a list of LUCID models corresponding to each combination of tuning parameters

Examples

## Not run: 
# use simulated data
G <- sim_data$G
Z <- sim_data$Z
Y_normal <- sim_data$Y_normal

# find the optimal model over the grid of K
tune_K <- tune_lucid(G = G, Z = Z, Y = Y_normal, useY = FALSE, tol = 1e-3, 
seed = 1, K = 2:5)

# tune penalties
tune_Rho_G <- tune_lucid(G = G, Z = Z, Y = Y_normal, useY = FALSE, tol = 1e-3,
seed = 1, K = 2, Rho_G = c(0.1, 0.2, 0.3, 0.4))
tune_Rho_Z_Mu <- tune_lucid(G = G, Z = Z, Y = Y_normal, useY = FALSE, tol = 1e-3,
seed = 1, K = 2, Rho_Z_Mu = c(10, 20, 30, 40))
tune_Rho_Z_Cov <- tune_lucid(G = G, Z = Z, Y = Y_normal, useY = FALSE, tol = 1e-3,
seed = 1, K = 2, Rho_Z_Cov = c(0.1, 0.2, 0.3))


## End(Not run)

USCbiostats/LUCIDus documentation built on Dec. 4, 2022, 3:24 p.m.