itsadug (version 2.0)

pvisgam: Visualization of partial nonlinear interactions.

Description

Produces perspective or contour plot views of gam model predictions of the partial effects interactions. Combines the function plot.gam for interaction surfaces with the function vis.gam. Similar to plot.gam, pvisgam plots the partial interaction surface, without including values for other predictors that are not being shown. Similar to vis.gam the user can set the two predictors to be viewed, and colors are added behind the contours to facilitate interpretation. In contrast to plot.gam, this function allows to plotting of interactions with three of more continuous predictors by breaking it down in two-dimensional surfaces. The code is derivated from the script for vis.gam.

Usage

pvisgam(x, view = NULL, select = NULL, cond = list(), n.grid = 30,
  too.far = 0, col = NA, color = "topo", contour.col = NULL,
  add.color.legend = TRUE, se = -1, type = "link",
  plot.type = "contour", zlim = NULL, xlim = NULL, ylim = NULL,
  nCol = 50, labcex = 0.6, hide.label = FALSE,
  print.summary = getOption("itsadug_print"), dec = NULL, ...)

Arguments

x

A gam object, produced by gam or bam.

view

A two-value vector containing the names of the two main effect terms to be displayed on the x and y dimensions of the plot. Note that variables coerced to factors in the model formula won't work as view variables.

select

A number, selecting a single model term for printing. e.g. if you want the plot for the second smooth term set select=2.

cond

A named list of the values to use for the other predictor terms (not in view). Used for choosing between smooths that share the same view predictors.

n.grid

The number of grid nodes in each direction used for calculating the plotted surface.

too.far

Plot grid nodes that are too far from the points defined by the variables given in view can be excluded from the plot. too.far determines what is too far. The grid is scaled into the unit square along with the view variables and then grid nodes more th

col

The colors for the facets of the plot.

color

The color scheme to use for plots. One of "topo", "heat", "cm", "terrain", "gray" or "bw".

contour.col

sets the color of contours when using plot.

add.color.legend

Logical: whether or not to add a color legend. Default is TRUE. If FALSE (omitted), one could use the function gradientLegend to add a legend manually at any position.

se

If less than or equal to zero then only the predicted surface is plotted, but if greater than zero, then 3 surfaces are plotted, one at the predicted values minus se standard errors, one at the predicted values and one at the predicted values plus se s

type

"link" to plot on linear predictor scale and "response" to plot on the response scale.

plot.type

one of "contour" or "persp" (default is "contour").

zlim

A two item array giving the lower and upper limits for the z- axis scale. NULL to choose automatically.

xlim

A two item array giving the lower and upper limits for the x- axis scale. NULL to choose automatically.

ylim

A two item array giving the lower and upper limits for the y- axis scale. NULL to choose automatically.

nCol

The number of colors to use in color schemes.

labcex

Size of the contour labels.

hide.label

Logical: whether or not to hide the label (i.e., "partial effect"). Default is FALSE.

print.summary

Logical: whether or not to print summary. Default set to the print info messages option (see infoMessages).

dec

Numeric: number of decimals for rounding the color legend. When NULL (default), no rounding. If -1 the values are automatically determined. Note: if value = -1 (default), rounding will be applied also when zlim is provided.

...

other options to pass on to persp, image or contour. In particular ticktype="detailed" will add proper axes labeling to the plots.

Warnings

In contrast to vis.gam, do not specify other predictors in cond that are not to be plotted.

See Also

vis.gam, plot.gam

Other Functions for model inspection: fvisgam, gamtabs, inspect_random, plot_data, plot_parametric, plot_smooth, plot_topo

Examples

data(simdat)

# Model with random effect and interactions:
m1 <- bam(Y ~ te(Time, Trial)+s(Time, Subject, bs='fs', m=1),
    data=simdat)

# Plot summed effects:
vis.gam(m1, view=c("Time", "Trial"), plot.type='contour', color='topo')
# Partial effect of interaction:
pvisgam(m1, view=c("Time", "Trial"), select=1)
# Same:
plot(m1, select=1, scheme=2)
plot(m1, select=1)
# Alternatives:
pvisgam(m1, view=c("Trial", "Time"), select=1)
pvisgam(m1, view=c("Trial", "Time"), select=1, zlim=c(-20,20))

# Notes on the color legend:
# Labels can easily fall off the plot, therefore the numbers are 
# automatically rounded.
# To undo the rounding, set dec=NULL:
pvisgam(m1, view=c("Time", "Trial"), dec=NULL)
# For custom rounding, set dec to a value:
pvisgam(m1, view=c("Time", "Trial"), dec=3)
# To increase the left marging of the plot (so that the numbers fit):
oldmar <- par()$mar
par(mar=oldmar + c(0,0,0,1) ) # add one line to the right
pvisgam(m1, view=c("Time", "Trial"), dec=3)
par(mar=oldmar) # restore to default settings
# see the vignette for examples:
vignette("overview", package="itsadug")