gam_ctr_plot {BioPred}

GAM Contrast Plot

Description

Computes and plots the contrasts between treatment and control group based on a GAM for exploring the relationship be-tween treatment benefit and biomarker.

Usage

gam_ctr_plot(
  yvar,
  censorvar = NULL,
  xvar,
  xvars.adj = NULL,
  sxvars.adj = NULL,
  trtvar = NULL,
  type,
  data,
  k,
  title = "Group Contrast",
  ybreaks = NULL,
  xbreaks = NULL,
  rugcol.var = NULL,
  link.scale = TRUE,
  prt.sum = TRUE,
  prt.chk = FALSE,
  outlier.rm = FALSE
)

Arguments

yvar

Response variable name.

censorvar

Censoring variable name (0-censored, 1-event). Required if type is "s" (survival).

xvar

Biomarker name.

xvars.adj

Potential confounding variables to adjust for using linear terms.

sxvars.adj

Potential confounding variables to adjust for using curves.

trtvar

Treatment variable that the contrast will build upon (treatment-control).

type

Type of response variable. Options are "c" for continuous, "s" for survival, and "b" for binary response.

data

The dataset containing the variables.

k

Upper limit on the degrees of freedom associated with an s smooth.When this k is too large, program will report error saying

title

Title of the plot.

ybreaks

Breaks on the y-axis.

xbreaks

Breaks on the x-axis.

rugcol.var

Variable name that defines the color of the rug.

link.scale

Whether to show the plot (y-axis) in the scale of the link function (linear predictor).

prt.sum

Whether to print summary or not.

prt.chk

Whether to print model diagnosis.

outlier.rm

Whether to remove outliers based on 1.5IQR.

Value

A list containing the p-value table, summarized p-value table, s-value table, summarized s-value table, and the plot.