Package {hyper.gam}

Type: Package
Title: Generalized Additive Models with Hyper Column
Version: 0.3.3
Date: 2026-08-25
Description: An interactive HTML widget of the perspective plot for generalized additive models; an alternative solution of the function mgcv::vis.gam(). This R package author has retired from academic research. Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications. Backward compatibility with user-code published in <doi:10.1093/bioinformatics/btaf182> and <doi:10.1093/bioinformatics/btaf430> is not maintained in versions >= 0.3.0 (June 2026) of this package. The authors of those publications are the appropriate contacts for reproducibility inquiries.
Encoding: UTF-8
License: GPL-2
Language: en-US
Depends: R (≥ 4.6)
Imports: cli, mgcv, plotly
Suggests: htmlwidgets
Config/roxygen2/version: 8.1.0
Config/roxygen2/markdown: TRUE
NeedsCompilation: no
Packaged: 2026-08-25 18:49:22 UTC; tingtingzhan
Author: Tingting Zhan [aut, cre], Erjia Cui ORCID iD [ctb] (up to v0.2.3)
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Repository: CRAN
Date/Publication: 2026-08-25 22:10:02 UTC

hyper.gam: Generalized Additive Models with Hyper Column

Description

An interactive HTML widget of the perspective plot for generalized additive models; an alternative solution of the function mgcv::vis.gam(). This R package author has retired from academic research. Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications. Backward compatibility with user-code published in doi:10.1093/bioinformatics/btaf182 and doi:10.1093/bioinformatics/btaf430 is not maintained in versions >= 0.3.0 (June 2026) of this package. The authors of those publications are the appropriate contacts for reproducibility inquiries.

Note

This R package author has retired from academic research.

Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications.

Backward compatibility with user-code published in the following publications is not maintained in versions ⁠>= 0.3.0⁠ of this package. The authors of those publications are the appropriate contacts for reproducibility inquiries.

doi:10.1093/bioinformatics/btaf182

doi:10.1093/bioinformatics/btaf430

Author(s)

Maintainer: Tingting Zhan tingtingzhan@gmail.com

Authors:

Other contributors:

Trace on gam Model

Description

Trace on the surface of a gam model.

Usage

trace_gam(
  object,
  formula,
  newdata = data,
  newid = seq_len(min(3L, nrow(newdata))),
  ...
)

Arguments

object

a gam model

formula

one-sided formula

newdata

data.frame, the test set

newid

integer scalar or vector, row indices of newdata to be visualized. Default 1:3, i.e., the first three test subjects.

...

additional parameters, to be passed into the function plot_ly

Value

The function trace_gam() returns a pretty htmlwidgets created by R package plotly.

Note

The maintainer is not aware of any functionality of projection of arbitrary curves in package plotly.

Examples

library(mgcv)
# ?s
# ?ti

Alternative perspective Plot for gam Model

Description

An interactive perspective plot for gam model, rendered as an htmlwidgets using the package plotly.

Usage

widget_gam(x, ..., colorscale)

Arguments

x

a gam model

...

parameters of the function vis.gam

colorscale

to be passed into the function add_surface

Value

The function widget_gam() returns a pretty htmlwidgets created by R package plotly.

Note

The internal utility functions persp_gam_int() and newd_gam_int() are based on the function vis.gam.

Examples

library(mgcv)
colorscale = list(c(0, 1), c('white', 'lightgreen'))

# examples from ?mgcv::te
test1 = \(x,z,sx=0.3,sz=0.4) { 
 x = x*20
 (pi**sx*sz)*(1.2*exp(-(x-0.2)^2/sx^2-(z-0.3)^2/sz^2)+
  0.8*exp(-(x-0.7)^2/sx^2-(z-0.8)^2/sz^2))
}
n = 500
x = runif(n)/20; z = runif(n);
xs = seq(0,1,length=30)/20; zs = seq(0,1,length=30)
pr = data.frame(x=rep(xs,30),z=rep(zs,rep(30,30)))
truth = matrix(test1(pr$x,pr$z),30,30)
persp(xs,zs,truth); title("truth")
f = test1(x,z)
y = f + rnorm(n)*0.2
b1 = gam(y ~ s(x,z))
b2 = gam(y ~ te(x,z))
b3 = gam(y ~ ti(x) + ti(z) + ti(x,z))
b4 = gam(y ~ ti(x) + ti(x,z,mc=c(0,1))) ## note z constrained!

widget_gam(b1, colorscale = colorscale)
widget_gam(b2, colorscale = colorscale)
widget_gam(b3, colorscale = colorscale)
widget_gam(b4, colorscale = colorscale)