simGG.simpoly {simPH} | R Documentation |
Plot simulated polynomial quantities of interest from Cox Proportional Hazards Models
Description
simGG.simpoly
uses ggplot2 to plot simulated relative
quantities of interest from a simpoly
class object.
Usage
## S3 method for class 'simpoly'
simGG(
obj,
from = NULL,
to = NULL,
rug = TRUE,
rug_position = "identity",
xlab = NULL,
ylab = NULL,
title = NULL,
method = "auto",
spalette = "Set1",
legend = "legend",
leg.name = "",
lcolour = "#2B8CBE",
lsize = 1,
pcolour = "#A6CEE3",
psize = 1,
alpha = 0.2,
type = "ribbons",
...
)
Arguments
obj |
a |
from |
numeric time to start the plot from. Only relevant if
|
to |
numeric time to plot to. Only relevant if
|
rug |
logical indicating whether or not to include a rug plot showing
the distribution of values in the sample used to estimate the |
rug_position |
character string. The position adjustment to use for
overlapping points in the rug plot. Use |
xlab |
a label for the plot's x-axis. |
ylab |
a label of the plot's y-axis. The default uses the value of
|
title |
the plot's main title. |
method |
what type of smoothing method to use to summarize the center of the simulation distribution. |
spalette |
colour palette for when there are multiple sets of
comparisons to plot. Default palette is |
legend |
specifies what type of legend to include (if applicable). The
default is |
leg.name |
name of the legend (if applicable). |
lcolour |
character string colour of the smoothing line. The default is
hexadecimal colour |
lsize |
size of the smoothing line. Default is 1. See
|
pcolour |
character string colour of the simulated points or ribbons
(when there are not multiple sets of simulations). Default is hexadecimal
colour |
psize |
size of the plotted simulation points. Default is
|
alpha |
numeric. Alpha (e.g. transparency) for the points, lines, or
ribbons. Default is |
type |
character string. Specifies how to plot the simulations. Can be
|
... |
Additional arguments. (Currently ignored.) |
Details
Uses ggplot2 to plot the quantities of interest from
simpoly
objects.
Value
a gg
ggplot
class object
References
Gandrud, Christopher. 2015. simPH: An R Package for Illustrating Estimates from Cox Proportional Hazard Models Including for Interactive and Nonlinear Effects. Journal of Statistical Software. 65(3)1-20.
See Also
coxsimPoly
and ggplot2
Examples
# Load Carpenter (2002) data
data("CarpenterFdaData")
# Load survival package
library(survival)
# Run basic model
M1 <- coxph(Surv(acttime, censor) ~ prevgenx + lethal +
deathrt1 + acutediz + hosp01 + hhosleng + mandiz01 +
femdiz01 + peddiz01 + orphdum + natreg +
I(natreg^2) + I(natreg^3) + vandavg3 + wpnoavg3 +
condavg3 + orderent + stafcder, data = CarpenterFdaData)
# Simulate simpoly First Difference
Sim1 <- coxsimPoly(M1, b = "natreg", qi = "First Difference",
pow = 3, Xj = seq(1, 150, by = 5), nsim = 100)
# Plot simulations
simGG(Sim1, rug_position = 'jitter')
## Not run:
# Simulate simpoly Hazard Ratio with spin probibility interval
Sim2 <- coxsimPoly(M1, b = "natreg", qi = "Hazard Ratio",
pow = 3, Xj = seq(1, 150, by = 5), spin = TRUE,
nsim = 100)
# Plot simulations
simGG(Sim2, type = 'ribbons', rug_position = 'jitter')
Sim3 <- coxsimPoly(M1, b = "natreg", qi = "Hazard Rate",
pow = 3, Xj = c(1, 150), nsim = 100)
# Plot simulations
simGG(Sim3, type = 'lines')
## End(Not run)