# plotp.Predict

##### Plot Effects of Variables Estimated by a Regression Model Fit Using plotly

Uses `plotly`

graphics (without using ggplot2) to plot the effect
of one or two predictors
on the linear predictor or X beta scale, or on some transformation of
that scale. The first argument specifies the result of the
`Predict`

function. The predictor is always plotted in its
original coding. Hover text shows point estimates, confidence
intervals, and on the leftmost x-point, adjustment variable settings.

If `Predict`

was run with no variable settings, so that each
predictor is varied one at a time, the result of `plotp.Predict`

is a list with two elements. The first, named `Continuous`

, is a
`plotly`

object containing a single graphic with all the
continuous predictors varying. The second, named `Categorical`

,
is a `plotly`

object containing a single graphic with all the
categorical predictors varying. If there are no categorical
predictors, the value returned by by `plotp.Predict`

is a single
`plotly`

object and not a list of objects.

If `rdata`

is given, a spike histogram is drawn showing
the location/density of data values for the \(x\)-axis variable. If
there is a superposition variable that generated separate
curves, the data density specific to each class of points is shown.
The histograms are drawn by `histSpikeg`

.

To plot effects instead of estimates (e.g., treatment differences as a
function of interacting factors) see `contrast.rms`

and
`summary.rms`

.

Unlike `ggplot.Predict`

, `plotp.Predict`

does not handle
`groups`

, `anova`

, or `perim`

arguments.

##### Usage

```
# S3 method for Predict
plotp(data, subset, xlim, ylim, xlab, ylab,
rdata=NULL, nlevels=3, vnames=c('labels','names'),
histSpike.opts=list(frac=function(f) 0.01 +
0.02 * sqrt(f - 1)/sqrt(max(f, 2) - 1), side=1, nint=100),
ncols=3, width=800, ...)
```

##### Arguments

- data
a data frame created by

`Predict`

- subset
a subsetting expression for restricting the rows of

`data`

that are used in plotting. For example, predictions may have been requested for males and females but one wants to plot only females.- xlim
ignored unless predictors were specified to

`Predict`

. Specifies the x-axis limits of the single plot produced.- ylim
Range for plotting on response variable axis. Computed by default and includes the confidence limits.

- xlab
Label for

`x`

-axis when a single plot is made, i.e., when a predictor is specified to`Predict`

. Default is one given to`asis, rcs`

, etc., which may have been the`"label"`

attribute of the variable.- ylab
Label for

`y`

-axis. If`fun`

is not given, default is`"log Odds"`

for`lrm`

,`"log Relative Hazard"`

for`cph`

, name of the response variable for`ols`

,`TRUE`

or`log(TRUE)`

for`psm`

, or`"X * Beta"`

otherwise. Specify`ylab=NULL`

to omit`y`

-axis labels.- rdata
a data frame containing the original raw data on which the regression model were based, or at least containing the \(x\)-axis and grouping variable. If

`rdata`

is present and contains the needed variables, the original data are added to the graph in the form of a spike histogram using`histSpikeg`

in the Hmisc package.- nlevels
A non-numeric x-axis variable with

`nlevels`

or fewer unique values will cause a horizontal dot plot to be drawn instead of an x-y plot.- vnames
applies to the case where multiple plots are produced separately by predictor. Set to

`'names'`

to use variable names instead of labels for these small plots.- histSpike.opts
a list containing named elements that specifies parameters to

`histSpikeg`

when`rdata`

is given. The`col`

parameter is usually derived from other plotting information and not specified by the user.- ncols
number of columns of plots to use when plotting multiple continuous predictors

- width
width in pixels for

`plotly`

graphics- …
ignored

##### Value

a `plotly`

object or a list containing two elements, each
one a `plotly`

object

##### References

Fox J, Hong J (2009): Effect displays in R for multinomial and proportional-odds logit models: Extensions to the effects package. J Stat Software 32 No. 1.

##### See Also

`Predict`

, `rbind.Predict`

,
`datadist`

, `predictrms`

,
`contrast.rms`

, `summary.rms`

,
`rms`

, `rmsMisc`

, `plot.Predict`

,
`ggplot.Predict`

,
`histSpikeg`

,
`Overview`

##### Examples

```
# NOT RUN {
n <- 350 # define sample size
set.seed(17) # so can reproduce the results
age <- rnorm(n, 50, 10)
blood.pressure <- rnorm(n, 120, 15)
cholesterol <- rnorm(n, 200, 25)
sex <- factor(sample(c('female','male'), n,TRUE))
label(age) <- 'Age' # label is in Hmisc
label(cholesterol) <- 'Total Cholesterol'
label(blood.pressure) <- 'Systolic Blood Pressure'
label(sex) <- 'Sex'
units(cholesterol) <- 'mg/dl' # uses units.default in Hmisc
units(blood.pressure) <- 'mmHg'
# Specify population model for log odds that Y=1
L <- .4*(sex=='male') + .045*(age-50) +
(log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male')) +
.01 * (blood.pressure - 120)
# Simulate binary y to have Prob(y=1) = 1/[1+exp(-L)]
y <- ifelse(runif(n) < plogis(L), 1, 0)
ddist <- datadist(age, blood.pressure, cholesterol, sex)
options(datadist='ddist')
fit <- lrm(y ~ blood.pressure + sex * (age + rcs(cholesterol,4)),
x=TRUE, y=TRUE)
p <- plotp(Predict(fit))
p$Continuous
p$Categorical
# When using Rmarkdown html notebook, best to use
# prList(p) to render the two objects
plotp(Predict(fit), rdata=llist(blood.pressure, age))$Continuous
# spike histogram plot for two of the predictors
p <- Predict(fit, name=c('age','cholesterol')) # Make 2 plots
plotp(p)
p <- Predict(fit, age, sex)
plotp(p, rdata=llist(age,sex))
# rdata= allows rug plots (1-dimensional scatterplots)
# on each sex's curve, with sex-
# specific density of age
# If data were in data frame could have used that
p <- Predict(fit, age=seq(20,80,length=100), sex='male', fun=plogis)
# works if datadist not used
plotp(p, ylab='P')
# plot predicted probability in place of log odds
# Compute predictions for three predictors, with superpositioning or
# conditioning on sex, combined into one graph
p1 <- Predict(fit, age, sex)
p2 <- Predict(fit, cholesterol, sex)
p3 <- Predict(fit, blood.pressure, sex)
p <- rbind(age=p1, cholesterol=p2, blood.pressure=p3)
plotp(p, ncols=2, rdata=llist(age, cholesterol, sex))
# }
```

*Documentation reproduced from package rms, version 5.1-3.1, License: GPL (>= 2)*