VGAM: plotvgam – R documentation

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plotvgam

Default VGAM Plotting

Description

Component functions of a vgam-class object can be plotted with plotvgam(). These are on the scale of the linear/additive predictor.

Usage

plotvgam(x, newdata = NULL, y = NULL, residuals = NULL,
         rugplot = TRUE, se = FALSE, scale = 0, raw = TRUE,
         offset.arg = 0, deriv.arg = 0, overlay = FALSE,
         type.residuals = c("deviance", "working", "pearson", "response"),
         plot.arg = TRUE, which.term = NULL, which.cf = NULL,
         control = plotvgam.control(...), varxij = 1, ...)

Arguments

`x`	A fitted VGAM object, e.g., produced by `vgam`, `vglm`, or `rrvglm`.
`newdata`	Data frame. May be used to reconstruct the original data set.
`y`	Unused.
`residuals`	Logical. If `TRUE` then residuals are plotted. See `type.residuals`
`rugplot`	Logical. If `TRUE` then a rug plot is plotted at the foot of each plot. These values are jittered to expose ties.
`se`	Logical. If `TRUE` then approximate +-2 pointwise standard error bands are included in the plot.
`scale`	Numerical. By default, each plot will have its own y-axis scale. However, by specifying a value, each plot's y-axis scale will be at least `scale` wide.
`raw`	Logical. If `TRUE` then the smooth functions are those obtained directly by the algorithm, and are plotted without having to premultiply with the constraint matrices. If `FALSE` then the smooth functions have been premultiply by the constraint matrices. The `raw` argument is directly fed into `predict.vgam()`.
`offset.arg`	Numerical vector of length r. These are added to the component functions. Useful for separating out the functions when `overlay` is `TRUE`. If `overlay` is `TRUE` and there is one covariate then using the intercept values as the offsets can be a good idea.
`deriv.arg`	Numerical. The order of the derivative. Should be assigned an small integer such as 0, 1, 2. Only applying to `s()` terms, it plots the derivative.
`overlay`	Logical. If `TRUE` then component functions of the same covariate are overlaid on each other. The functions are centered, so `offset.arg` can be useful when `overlay` is `TRUE`.
`type.residuals`	if `residuals` is `TRUE` then the first possible value of this vector, is used to specify the type of residual.
`plot.arg`	Logical. If `FALSE` then no plot is produced.
`which.term`	Character or integer vector containing all terms to be plotted, e.g., `which.term = c("s(age)", "s(height"))` or `which.term = c(2, 5, 9)`. By default, all are plotted.
`which.cf`	An integer-valued vector specifying which linear/additive predictors are to be plotted. The values must be from the set {1,2,...,r}. By default, all are plotted.
`control`	Other control parameters. See `plotvgam.control`.
`...`	Other arguments that can be fed into `plotvgam.control`. This includes line colors, line widths, line types, etc.
`varxij`	Positive integer. Used if `xij` of `vglm.control` was used, this chooses which inner argument the component is plotted against. This argument is related to `raw = TRUE` and terms such as `NS(dum1, dum2)` and constraint matrices that have more than one column. The default would plot the smooth against `dum1` but setting `varxij = 2` could mean plotting the smooth against `dum2`. See the VGAM website for further information.

Details

In this help file M is the number of linear/additive predictors, and r is the number of columns of the constraint matrix of interest.

Many of plotvgam()'s options can be found in plotvgam.control, e.g., line types, line widths, colors.

Value

The original object, but with the preplot slot of the object assigned information regarding the plot.

Note

While plot(fit) will work if class(fit) is "vgam", it is necessary to use plotvgam(fit) explicitly otherwise.

plotvgam() is quite buggy at the moment.

Author(s)

Thomas W. Yee

Examples

coalminers <- transform(coalminers, Age = (age - 42) / 5)
fit <- vgam(cbind(nBnW, nBW, BnW, BW) ~ s(Age),
            binom2.or(zero = NULL), data = coalminers)
## Not run:  par(mfrow = c(1,3))
plot(fit, se = TRUE, ylim = c(-3, 2), las = 1)
plot(fit, se = TRUE, which.cf = 1:2, lcol = "blue", scol = "orange",
     ylim = c(-3, 2))
plot(fit, se = TRUE, which.cf = 1:2, lcol = "blue", scol = "orange",
     overlay = TRUE) 
## End(Not run)

VGAM

Vector Generalized Linear and Additive Models

v1.1-5

GPL-3

Authors

Thomas Yee [aut, cre], Cleve Moler [ctb] (author of several LINPACK routines)

Initial release

2021-01-13