View source: R/plot.penmodel_c.R
plot.penmodel_c | R Documentation |
penmodel_c
Plots penetrance curves for each event estimated from the fitted competing risks model and overlays non-parametric cumulative incidence curves estimated from the data without proabands.
## S3 method for class 'penmodel_c' plot(x, agemax = 80, print = TRUE, conf.int = FALSE, add.CIF = TRUE, MC = 100, col = c("blue", "red", "blue", "red"), lty = c(1, 1, 2, 2), xlab = "Age at onset", ylab = "Penetrance", ylim = NULL, ...)
x |
An object class of |
agemax |
Maximum age of disease onset or maximum age. Default is 80 years of age. |
print |
Logical; if |
conf.int |
Logical; if |
add.CIF |
Logical; if |
MC |
Number of simulated samples used to calculate confidence intervals with a Monte-Carlo method.
If |
col |
Colors of lines for male carriers, female carriers, male noncarrers, and female noncarriers. Default is |
lty |
Types of lines for male carriers, female carriers, male noncarriers, and female noncarriers. Default is |
xlab |
Title for the x-axis. Default is |
ylab |
Title for the y-axis. Default is |
ylim |
Limits for the y-axis. Default is |
... |
Other parameters to be passed through to plotting functions. |
The 95% confidence intervals for the parametric penetrance curves are
obtained based on simulations of the parameters, assuming a multivariate normal distribution for the estimated
parameters with their variance-covariance matrix. See penetrance_c
for more details.
Returns the following summary values:
coefficients |
Parameter estimates from the competing risks model. |
pen70 |
Penetrance estimates by age 70, specific to gender and mutation-status subgroups. |
age |
Vector of ages of onsest ranging from |
pen1 |
Penetrance estimates for event 1 at each age in |
pen2 |
Penetrance estimates for event 2 at each age in |
lower1 |
Lower limits of 95% confidence interval estimates for penetrance for event 1 at each age in |
upper1 |
Upper limits of 95% confidence interval estimates for penetrance for event 1 at each age in |
lower2 |
Lower limits of 95% confidence interval estimates for penetrance for event 2 at each age in |
upper2 |
Upper limits of 95% confidence interval estimates for penetrance for event 2 at each age in |
Yun-Hee Choi
penmodel_c, print.penmodel_c, summary.penmodel_c,
print.summary.penmodel_c, simfam_c
## Not run: # Simulated family data set.seed(4321) fam2 <- simfam_c(N.fam = 500, design = "pop+", variation = "frailty", competing=TRUE, base.dist = "Weibull", frailty.dist = "cgamma", depend=c(2, 2, 2), allelefreq = 0.02, base.parms = list(c(0.01, 3), c(0.01, 3)), vbeta = list(c(-1.13, 2.35),c(-1, 2))) # Fit family data fit2 <- penmodel_c(formula1 = Surv(time, status==1)~ gender + mgene, formula2 = Surv(time, status==2)~ gender + mgene, cluster = "famID", gvar = "mgene", frailty.dist = "cgamma", parms=list(c(0.01, 3, -1, 2.3), c(0.01, 3, -1, 2), c(2, 2, 2)), data=fam2, design="pop+", base.dist="Weibull", robust=TRUE) # Plot penetrance function curves with 95 plot(fit2, conf.int=TRUE, MC=200, ylim=c(0, 0.7)) ## End(Not run)
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