Usage
plot_pca_surface(x, pca.term = NULL, weights = NULL, view = NULL,
cond = list(), partial = FALSE, select = NULL, se = -1, n.grid = 30,
too.far = 0, rm.ranef = NULL, col = NA, color = "topo",
contour.col = NULL, nCol = 50, plotCI = FALSE,
add.color.legend = TRUE, plot.type = "contour", xlim = NULL,
ylim = NULL, zlim = NULL, print.summary = getOption("itsadug_print"),
transform = NULL, transform.view = NULL, hide.label = FALSE,
dec = NULL, ...)Arguments
x
A gam object, produced by gam or
bam. pca.term
Text string, name of model predictor that represents a
principle component.
weights
Named list with the predictors that are combined in the PC
and their weights. See examples.
view
A two-value vector containing the names of the two terms to
plot. The two terms should be part of the PC. Note that
variables coerced to factors in the model formula won't work as view
variables.
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.
partial
Logical value: whether or not to plot the partial effect
(TRUE) or the summed effect (FALSE, default).
select
Numeric value, model term. In case partial=TRUE a
model term needs to be selected.
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
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
rm.ranef
Logical: whether or not to remove random effects.
Default is TRUE.
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.
nCol
The number of colors to use in color schemes.
plotCI
Logical: whether or not to plot the confidence intervals.
The value of se determines the size of the CI.
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. plot.type
one of "contour" or "persp" (default is "contour").
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.
zlim
A two item array giving the lower and upper limits for the z-
axis scale. NULL to choose automatically.
print.summary
Logical: whether or not to print a summary.
Default set to the print info messages option
(see infoMessages). transform
Function for transforming the fitted values.
Default is NULL.
transform.view
List with two functions for transforming
the values on the x- and y-axis respectively. If one of the axes
need to be transformed, set the other to NULL (no transformation).
See examples below.
hide.label
Logical: whether or not to hide the label
(i.e., "fitted values"). Default is FALSE.
dec
Numeric: number of decimals for rounding the color legend.
When NULL, no rounding (default). If -1, automatically determined.
Note: if value = -1, 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.