Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ---- eval=FALSE--------------------------------------------------------------
# install.packages("ahMLE")
## ---- message=FALSE, warning=FALSE--------------------------------------------
library(ahMLE)
## ---- message=FALSE, warning=FALSE--------------------------------------------
require(survival)
require(invGauss)
library(ahMLE)
data(d.oropha.rec)
SData = data.frame(time = d.oropha.rec$time,
constant = 1,
sex = d.oropha.rec$sex,
treatm = d.oropha.rec$treatm,
grade = d.oropha.rec$grade,
age = d.oropha.rec$age,
cond = d.oropha.rec$cond,
tstage = d.oropha.rec$tstage,
nstage = d.oropha.rec$nstage,
event = d.oropha.rec$status)
# Data rescaled
SData$sex = SData$sex - 1
SData$treatm = SData$treatm -1
SData$grade = SData$grade -1
SData$age = (SData$age -60)/10
SData$cond = SData$cond -1
SData$tstage = SData$tstage - 1
## ---- message=FALSE, warning=FALSE, results="hide"----------------------------
formula_input = Surv(time= time, event = event) ~ sex + treatm +grade + age +cond + tstage + nstage
# Use Aalen's OLS method to compute the cumulative beta
beta_aalen = ah(formula_input, data = SData, method = "aalen")
Cbeta_aalen = beta_aalen$cumbeta
# Use (default) maximum likelihood method to compute the cumulative beta
beta_mle= ah(formula_input, data = SData, progbar = TRUE)
Cbeta_mle = beta_mle$cumbeta
## ---- message=FALSE, warning=FALSE, fig.height = 3, fig.width = 6, fig.align = "center"----
old.par <- par(no.readonly = TRUE)
par(mfrow=c(1,1))
par(mar=c(5, 6, 4, 2))
time_grid = beta_aalen$cumbeta[,1]
plot(time_grid,Cbeta_mle[,2],type="l", lwd = 2, col=colors()[258], ylim=c(-0.1,1.1), ylab = "Cumulative beta",xlab = "Days from diagnosis", cex.lab=1)
lines(time_grid,Cbeta_aalen[,2], type="l", lty = 5, lwd =2, col="red")
legend("topright", legend=c("MLE","OLS"), col=c(colors()[258],"red"),lty=c(1,5), cex=1,lwd = 1)
par(old.par)
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