fixing IPA

Author: tagteam

slowtests/test-GLMnet.R

@@ -0,0 +1,36 @@
+### test-GLMnet.R --- 
+#----------------------------------------------------------------------
+## Author: Thomas Alexander Gerds
+## Created: okt 17 2025 (08:17) 
+## Version: 
+## Last-Updated: okt 17 2025 (11:33) 
+##           By: Thomas Alexander Gerds
+##     Update #: 2
+#----------------------------------------------------------------------
+## 
+### Commentary: 
+## 
+### Change Log:
+#----------------------------------------------------------------------
+## 
+### Code:
+library(testthat)
+library(lava)
+library(data.table)
+test_that("penalized logistic regression", {
+    m = lvm(X2~X1+X8)
+    distribution(m,~X2) = binomial.lvm()
+    regression(m,X2~X1+X8) = c(-.05,.07)
+    set.seed(9)
+    d = setDT(sim(m,1100))
+    d[,table(X2)]
+    fit = glm(X2~X1+X8,data = d,family = "binomial")
+    lasso = GLMnet(X2~X1+X8,data = d,family = "binomial",alpha = 1)
+    ridge = GLMnet(X2~X1+X8,data = d,family = "binomial",alpha = 0)
+    
+
+})
+
+
+######################################################################
+### test-GLMnet.R ends here

slowtests/test-ipa.R

@@ -0,0 +1,23 @@
+library(riskRegression)
+library(survival)
+library(data.table)
+library(testthat)
+library(randomForestSRC)
+test_that("ipa cv5 survival",{
+    set.seed(8)
+    learndat=sampleData(200,outcome="survival")
+    testdat=sampleData(123,outcome="survival")
+    cox1a = coxph(Surv(time,event)~X6,data=learndat,x=TRUE,y=TRUE)
+    cox2a = coxph(Surv(time,event)~X7+X8+X9,data=learndat,x=TRUE,y=TRUE)
+    set.seed(5)
+    five <- Score(list("COX1"=cox1a,"COX2"=cox2a),formula=Surv(time,event)~1,data=learndat,times=5,B = 1,split.method="cv5",summary = "ipa",se.fit=TRUE,progress.bar=NULL)
+    set.seed(5)
+    loob <- Score(list("COX1"=cox1a,"COX2"=cox2a),formula=Surv(time,event)~1,data=learndat,times=5,summary = "ipa",split.method="loob",B=100,se.fit=TRUE,progress.bar=NULL,verbose = 0L)
+    set.seed(5)
+    loob_sans <- Score(list("COX1"=cox1a,"COX2"=cox2a),formula=Surv(time,event)~1,data=learndat,times=5,summary = "ipa",split.method="loob",B=100,se.fit=FALSE,progress.bar=NULL,verbose = 0L)
+    set.seed(5)
+    test <- Score(list("COX1"=cox1a,"COX2"=cox2a),formula=Surv(time,event)~1,data=testdat,times=5,summary = "ipa",se.fit=FALSE,progress.bar=NULL,verbose = 0L)
+    set.seed(5)
+    bootcv <- Score(list("COX1"=cox1a,"COX2"=cox2a),formula=Surv(time,event)~1,data=testdat,times=5,summary = "ipa",split.method = "bootcv",B = 5,se.fit=TRUE,progress.bar=NULL,verbose = 0L)
+})
+