Nothing
## ----lib, message=FALSE, warning=FALSE----------------------------------------
library(coxed)
## ----simsurv1-----------------------------------------------------------------
simdata <- sim.survdata(N=1000, T=100, num.data.frames=1)
## ----simatt-------------------------------------------------------------------
attributes(simdata)
## ----data---------------------------------------------------------------------
head(simdata$data, 10)
## ----xdata--------------------------------------------------------------------
head(simdata$xdata, 10)
## ----baseline-----------------------------------------------------------------
head(simdata$baseline, 10)
## ----beta---------------------------------------------------------------------
simdata$betas
## ----cox1---------------------------------------------------------------------
model <- coxph(Surv(y, failed) ~ X1 + X2 + X3, data=simdata$data)
model$coefficients
## ----expxb--------------------------------------------------------------------
head(cbind(simdata$xb, simdata$exp.xb))
## ----ind1---------------------------------------------------------------------
simdata$ind.survive[1,]
## ----data3--------------------------------------------------------------------
head(simdata[[2]]$data, 10)
## ----plot1, fig.align="center", fig.width=6, fig.height=4---------------------
survsim.plot(simdata, df=1, type="baseline")
## ----plot2, fig.align="center", fig.width=7, fig.height=3---------------------
survsim.plot(simdata, df=1, type="hist")
## ----plot3, fig.align="center", fig.width=7, fig.height=7---------------------
survsim.plot(simdata, df=1, type="both")
## ----simdata3-----------------------------------------------------------------
simdata <- sim.survdata(N=700, T=250, xvars=5, censor=.2, num.data.frames = 1)
summary(simdata$data)
## ----simsurv1part2------------------------------------------------------------
simdata <- sim.survdata(N=1000, T=100, num.data.frames=1, beta=c(1, -1.5, 2))
simdata$betas
## ----mv-----------------------------------------------------------------------
summary(martinvanberg)
## ----userdata-----------------------------------------------------------------
mv.data <- dplyr::select(martinvanberg, postel, rgovm, pgovno)
simdata <- sim.survdata(T=100, X=mv.data, num.data.frames = 1)
## ----userdata2----------------------------------------------------------------
head(simdata$data)
## ----simsurv2-----------------------------------------------------------------
simdata <- sim.survdata(N=1000, T=100, num.data.frames=1, covariate=1, low=0, high=1,
beta = c(2, .1, .1))
## ----me-----------------------------------------------------------------------
simdata$marg.effect
## ----medata-------------------------------------------------------------------
head(simdata$marg.effect.data$low$x)
head(simdata$marg.effect.data$low$y)
head(simdata$marg.effect.data$high$x)
head(simdata$marg.effect.data$high$y)
## ----fixhaz1, fig.align="center", fig.width=6, fig.height=4-------------------
simdata <- sim.survdata(N=1000, T=100, num.data.frames=2, fixed.hazard=TRUE)
survsim.plot(simdata, df=1, type="baseline")
survsim.plot(simdata, df=2, type="baseline")
## ----fixhaz2, fig.align="center", fig.width=6, fig.height=4-------------------
simdata <- sim.survdata(N=1000, T=100, num.data.frames=2, fixed.hazard=FALSE)
survsim.plot(simdata, df=1, type="baseline")
survsim.plot(simdata, df=2, type="baseline")
## ----censorx1-----------------------------------------------------------------
simdata <- sim.survdata(N=1000, T=100, num.data.frames=1, censor.cond=FALSE)
logit <- glm(failed ~ X1 + X2 + X3, data=simdata$data, family=binomial(link="logit"))
summary(logit)
## ----censorx2-----------------------------------------------------------------
simdata <- sim.survdata(N=1000, T=100, num.data.frames=1, censor.cond=TRUE)
logit <- glm(failed ~ X1 + X2 + X3, data=simdata$data, family=binomial(link="logit"))
summary(logit)
## ----myhaz--------------------------------------------------------------------
my.hazard <- function(t){
dnorm((log(t) - log(50))/log(10)) /
(log(10)*t*(1 - pnorm((log(t) - log(50))/log(10))))
}
## ----myhazsim-----------------------------------------------------------------
simdata <- sim.survdata(N=1000, T=1000, num.data.frames=1, hazard.fun = my.hazard)
## ----myhazplot, fig.align="center", fig.width=6, fig.height=4-----------------
survsim.plot(simdata, df=1, type="baseline")
## ----tvc1---------------------------------------------------------------------
simdata <- sim.survdata(N=1000, T=100, type="tvc", num.data.frames=1)
head(simdata$data, 20)
## ----tvbeta-------------------------------------------------------------------
simdata <- sim.survdata(N=1000, T=100, type="tvbeta", num.data.frames = 1)
## ----tvbetamat----------------------------------------------------------------
head(simdata$betas, 10)
## ----makecoef-----------------------------------------------------------------
beta.mat <- data.frame(beta1 = (1:100 - 25)^2/2500,
beta2 = .5,
beta3 = -.25)
head(beta.mat)
## ----tvbeta2------------------------------------------------------------------
simdata <- sim.survdata(N=1000, T=100, type="tvbeta", beta=beta.mat, num.data.frames = 1)
## ----tvbeta3------------------------------------------------------------------
head(simdata$data, 10)
## ----tvbeta4------------------------------------------------------------------
head(simdata$betas, 10)
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