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### test-summary-score.R ---
#----------------------------------------------------------------------
## Author: Thomas Alexander Gerds
## Created: Apr 12 2020 (07:48)
## Version:
## Last-Updated: May 31 2022 (11:43)
## By: Thomas Alexander Gerds
## Update #: 8
#----------------------------------------------------------------------
##
### Commentary:
##
### Change Log:
#----------------------------------------------------------------------
##
### Code:
library(testthat)
library(survival)
library(riskRegression)
library(data.table)
context("riskRegression")
# {{{ "binary"
for (y in c("binary","survival","competing.risks")){
print(y)
set.seed(2)
d1 <- sampleData(n=112,outcome=y)
d2 <- sampleData(n=80,outcome=y)
if (y=="binary"){
f1 <- glm(Y~X2+X8,data=d1,family="binomial")
f2 <- glm(Y~X1+X2+X5+X8+X6,data=d1,family="binomial")
ff <- Y~1
}
if (y=="survival"){
f1 <- coxph(Surv(time,event)~X2+X8,data=d1,x=1L,y=1L)
f2 <- coxph(Surv(time,event)~X1+X2+X5+X8+X6,data=d1,x=1L,y=1L)
ff <- Hist(time,event)~1
}
if (y=="competing.risks"){
f1 <- CSC(Hist(time,event)~X2+X8,data=d1)
f2 <- CSC(Hist(time,event)~X1+X2+X5+X8+X6,data=d1)
ff <- Hist(time,event)~1
}
# with null and se
x <- Score(list(model.1=f1,model.2=f2),formula=ff,data=d2)
xa <- Score(list(model.1=f1,model.2=f2),formula=ff,data=d2,metric="auc")
xb <- Score(list(model.1=f1,model.2=f2),formula=ff,data=d2,metric="brier")
for (X in list(x,xa,xb)){
suppressMessages(expect_output(print(X)))
expect_output(print(summary(X)))
expect_output(print(summary(X,what="contrast")))
expect_output(print(summary(X,what="score")))
}
# without null with se
x <- Score(list(model.1=f1,model.2=f2),formula=ff,data=d2,null.model=0L)
xa <- Score(list(model.1=f1,model.2=f2),formula=ff,data=d2,metric="auc",null.model=0L)
xb <- Score(list(model.1=f1,model.2=f2),formula=ff,data=d2,metric="brier",null.model=0L)
for (X in list(x,xa,xb)){
suppressMessages(expect_output(print(X)))
expect_output(print(summary(X)))
expect_output(print(summary(X,what="contrast")))
expect_output(print(summary(X,what="score")))
}
# without null without se
x <- Score(list(model.1=f1,model.2=f2),formula=ff,data=d2,null.model=0L,se.fit=0L)
xa <- Score(list(model.1=f1,model.2=f2),formula=ff,data=d2,metric="auc",null.model=0L,se.fit=0L)
xb <- Score(list(model.1=f1,model.2=f2),formula=ff,data=d2,metric="brier",null.model=0L,se.fit=0L)
for (X in list(x,xa,xb)){
suppressMessages(expect_output(print(X)))
expect_output(print(summary(X)))
expect_output(print(summary(X,what="contrast")))
expect_output(print(summary(X,what="score")))
}
}
# }}}
######################################################################
### test-summary-score.R ends here
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