simGG.simspline {simPH} | R Documentation |
Plot simulated penalised spline hazards from Cox Proportional Hazards Models
Description
simGG.simspline
uses ggplot2 to plot
quantities of interest from simspline
objects, including relative
hazards, first differences, hazard ratios, and hazard rates.
Usage
## S3 method for class 'simspline'
simGG(
obj,
SmoothSpline = TRUE,
FacetTime = NULL,
from = NULL,
to = NULL,
rug = TRUE,
rug_position = "identity",
xlab = NULL,
ylab = NULL,
zlab = NULL,
title = NULL,
method = "auto",
lcolour = "#2B8CBE",
lsize = 1,
pcolour = "#A6CEE3",
psize = 1,
alpha = 0.2,
type = "ribbons",
...
)
Arguments
obj |
a |
SmoothSpline |
logical whether or not to fit the simulations with
smoothing splines. Creates a smoother plot. See |
FacetTime |
a numeric vector of points in time where you would like to
plot Hazard Rates in a facet grid. Only relevant if
|
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
|
zlab |
a label for the plot's z-axis. Only relevant if
|
title |
the plot's main title. |
method |
what type of smoothing method to use to summarize the center of the simulation distribution. |
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 simspline
objects, including relative hazards, first
differences, hazard ratios, and hazard rates. If currently does not support
hazard rates for multiple strata.
You can to plot hazard rates for a range of values of Xj
in two
dimensional plots at specific points in time. Each plot is arranged in a
facet grid.
Note: A dotted line is created at y = 1 (0 for first difference), i.e. no effect, for time-varying hazard ratio graphs. No line is created for hazard rates.
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
coxsimLinear
, simGG.simtvc
,
ggplot2
Examples
# Load Carpenter (2002) data
data("CarpenterFdaData")
# Load survival package
library(survival)
# Run basic model
# From Keele (2010) replication data
M1 <- coxph(Surv(acttime, censor) ~ prevgenx + lethal + deathrt1 +
acutediz + hosp01 + pspline(hospdisc, df = 4) +
pspline(hhosleng, df = 4) + mandiz01 + femdiz01 +
peddiz01 + orphdum + natreg + vandavg3 + wpnoavg3 +
pspline(condavg3, df = 4) + pspline(orderent, df = 4) +
pspline(stafcder, df = 4), data = CarpenterFdaData)
# Simulate Relative Hazards for orderent
Sim1 <- coxsimSpline(M1, bspline = "pspline(stafcder, df = 4)",
bdata = CarpenterFdaData$stafcder,
qi = "Hazard Ratio",
Xj = seq(1100, 1700, by = 10),
Xl = seq(1099, 1699, by = 10), spin = TRUE, nsim = 100)
# Plot relative hazard
simGG(Sim1, alpha = 0.5)
## Not run:
# Simulate Hazard Rate for orderent
Sim2 <- coxsimSpline(M1, bspline = "pspline(orderent, df = 4)",
bdata = CarpenterFdaData$orderent,
qi = "Hazard Rate",
Xj = seq(1, 30, by = 2), ci = 0.9, nsim = 10)
# Create a time grid plot
# Find all points in time where baseline hazard was found
unique(Sim2$sims$Time)
# Round time values so they can be exactly matched with FacetTime
Sim2$sims$Time <- round(Sim2$sims$Time, digits = 2)
# Create plot
simGG(Sim2, FacetTime = c(6.21, 25.68, 100.64, 202.36),
type = 'ribbons', alpha = 0.5)
# Simulated Fitted Values of stafcder
Sim3 <- coxsimSpline(M1, bspline = "pspline(stafcder, df = 4)",
bdata = CarpenterFdaData$stafcder,
qi = "Hazard Ratio",
Xj = seq(1100, 1700, by = 10),
Xl = seq(1099, 1699, by = 10), ci = 0.90)
# Plot simulated Hazard Ratios
simGG(Sim3, xlab = "\nFDA Drug Review Staff", type = 'lines', alpha = 0.2)
simGG(Sim3, xlab = "\nFDA Drug Review Staff", alpha = 0.2,
SmoothSpline = TRUE, type = 'points')
## End(Not run)