pqrBayes: fit Bayesian penalized quantile regression for linear, binary...

In pqrBayes: Bayesian Penalized Quantile Regression

fit Bayesian penalized quantile regression for linear, binary LASSO, group LASSO, or varying coefficient models

Description

fit Bayesian penalized quantile regression for linear, binary LASSO, group LASSO, or varying coefficient models

Usage

pqrBayes(
  g,
  y,
  u = NULL,
  e,
  d = NULL,
  quant = 0.5,
  iterations = 10000,
  burn.in = NULL,
  spline = NULL,
  robust = TRUE,
  sparse = TRUE,
  model = "linear",
  hyper = NULL,
  debugging = FALSE
)

Arguments

g	the matrix of predictors (subject to selection). Users do not need to specify an intercept which will be automatically included.
y	the response variable.
u	a vector of effect modifying variable of the quantile varying coefficient model. When fitting a linear model or group LASSO, u = NULL.
e	a matrix of clinical covariates not subject to selection.
d	a positive integer denotes the group size. When fitting a linear model or varying coefficient model, d = NULL.
quant	the quantile level specified by users. The default value is 0.5.
iterations	the number of MCMC iterations. The default value is 10,000.
burn.in	the number of burn-in iterations. If NULL, the first half of MCMC iterations will be used as burn-ins.
spline	a list of the number of interior knots (kn) for B-spline and the degree of B-spline basis (degree). When fitting LASSO, binary LASSO and group LASSO, spline = NULL.
robust	logical flag. If TRUE, robust methods will be used. Otherwise, non-robust methods will be used. The default value is TRUE.
sparse	logical flag. If TRUE, spike-and-slab priors will be adopted to impose exact sparsity on regression coefficients. Otherwise, Laplacian shrinkage will be adopted. The default value is TRUE.
model	the model to be fitted. Users can specify "linear" for a linear model (i.e., LASSO), "binary" for binary LASSO, "group" for group LASSO and "VC" for a varying coefficient model.
hyper	a named list of hyper-parameters. The default value is NULL.
debugging	logical flag. If TRUE, progress will be output to the console and extra information will be returned. The default value is FALSE.

Details

The linear quantile regression model described in "data" is:

Y_{i}=\sum_{k=1}^{q} E_{ik} \beta_k +\sum_{j=0}^{p}X_{ij}\gamma_j +\epsilon_{i},

where \beta_k's are the regression coefficients for clinical covariates and \gamma_j's are the regression coefficients of \boldsymbol X.

The binary quantile regression model described in "data" is:

\tilde{Y}_{i}=\sum_{k=1}^{q} E_{ik} \beta_k +\sum_{j=0}^{p}X_{ij}\gamma_j +\epsilon_{i},

where \beta_k's are the regression coefficients for clinical covariates and \gamma_j's are the regression coefficients of \boldsymbol X.

Y_{i}=1 if \tilde{Y}_{i}>0 and Y_{i}=0 otherwise.

The group LASSO model described in "data" is:

Y_{i}=\sum_{k=1}^{q} E_{ik} \beta_k + X_{i0}\gamma_0+ \sum_{j=1}^{m}\boldsymbol{X_{ij}^\top}\boldsymbol{\gamma_j} +\epsilon_{i},

where \beta_k's are the regression coefficients for clinical covariates and \boldsymbol{\gamma_j} = (\gamma_{j1},\dots,\gamma_{jd})^\top is the vector of regression coefficients of the n \times d matrix \boldsymbol X_{j}.

The quantile varying coefficient model described in "data" is:

Y_{i}=\sum_{k=1}^{q} E_{ik} \beta_k +\sum_{j=0}^{p}\gamma_j(V_i)X_{ij} +\epsilon_{i},

where \beta_k's are the regression coefficients for the clinical covariates, and \gamma_j's are the varying intercept and varying coefficients for predictors (e.g. genetic factors), respectively.

Users can modify the hyper-parameters by providing a named list of hyper-parameters via the argument ‘hyper’. The list can have the following named components

a0, b0:

shape parameters of the Beta priors (\pi^{a_{0}-1}(1-\pi)^{b_{0}-1}) on \pi_{0}.

c1, c2:

the shape parameter and the rate parameter of the Gamma prior on \nu.

Please check the references for more details about the prior distributions.

Value

an object of class "pqrBayes" is returned, which is a list with components:

obj	a list of posterior samples from the MCMC and other parameters
coefficients	a list of posterior estimates of coefficients

References

Fan, K., Subedi, S., Yang, G., Lu, X., Ren, J. and Wu, C. (2024). Is Seeing Believing? A Practitioner's Perspective on High-dimensional Statistical Inference in Cancer Genomics Studies. Entropy, 26(9).794 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.3390/e26090794")}

Zhou, F., Ren, J., Ma, S. and Wu, C. (2023). The Bayesian regularized quantile varying coefficient model. Computational Statistics & Data Analysis, 107808 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.csda.2023.107808")}

Ren, J., Zhou, F., Li, X., Ma, S., Jiang, Y. and Wu, C. (2023). Robust Bayesian variable selection for gene-environment interactions. Biometrics, 79(2), 684-694 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/biom.13670")}

Ren, J., Zhou, F., Li, X., Chen, Q., Zhang, H., Ma, S., Jiang, Y. and Wu, C. (2020) Semi-parametric Bayesian variable selection for gene-environment interactions. Statistics in Medicine, 39: 617– 638 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/sim.8434")}

Examples

## The quantile (linear and binary) regression model
data(data)
data = data$data_linear
g=data$g
y=data$y
e=data$e
data(data)
data_1=data$data_binary
g_1=data_1$g
y_1=data_1$y
e_1=data_1$e

fit1=pqrBayes(g,y,u=NULL,e,d=NULL,quant=0.5,model="linear")
fit1_1=pqrBayes(g_1,y_1,u=NULL,e_1,d=NULL,quant=0.5,model="binary")


## Non-sparse example (linear model)
sparse <- FALSE
fit2 <- pqrBayes(
  g = g, y = y, u = NULL, e = e, d = NULL,
  quant = 0.5,
  spline = NULL,
  sparse = sparse,
  model = "linear"
)

## Non-robust example (linear model)
robust <- FALSE
fit3 <- pqrBayes(
  g = g, y = y, u = NULL, e = e, d = NULL,
  quant = 0.5,
  spline = NULL,
  robust = robust,
  model = "linear"
)


## The group LASSO model
data(data)
data = data$data_group
g=data$g
y=data$y
e=data$e

fit1=pqrBayes(g,y,u=NULL,e,d=3,quant=0.5,model="group")


## Non-sparse version
sparse <- FALSE
fit2 <- pqrBayes(
  g = g, y = y, u = NULL, e = e, d = 3,
  quant = 0.5, spline = NULL,
  sparse = sparse,
  model = "group"
)

## Non-robust version
robust <- FALSE
fit3 <- pqrBayes(
  g = g, y = y, u = NULL, e = e, d = 3,
  quant = 0.5, spline = NULL,
  robust = robust,
  model = "group"
)

## The quantile varying coefficient model
data(data)
data = data$data_varying
g=data$g
y=data$y
u=data$u
e=data$e

spline = list(kn=2,degree=2)
fit1=pqrBayes(g,y,u,e,quant=0.5,spline = spline,model="VC")



## Non-sparse example
sparse <- FALSE
fit2 <- pqrBayes(
  g = g, y = y, u = u, e = e,
  quant = 0.5,
  spline = spline,
  sparse = sparse,
  model = "VC"
)

## Non-robust example
robust <- FALSE
fit3 <- pqrBayes(
  g = g, y = y, u = u, e = e,
  quant = 0.5,
  spline = spline,
  robust = robust,
  model = "VC"
)

pqrBayes documentation built on June 8, 2025, 12:35 p.m.