Include event in state space model / data

jmseq/NAMESPACE

@@ -1,10 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(predict,testdata)
 export(ctstanfit.fold)
 export(fit.poissontsplit)
 export(kalmanwide)
 export(listmodels)
 export(tabulate.predictions)
-export(test.imputed)
 export(trainsplit.long)
 export(trainsplit.surv)

jmseq/R/jmseqfunctions.R

@@ -68,12 +68,25 @@ listmodels <- function(biomarkers, timeinvar.long) {
                                   TDpredNames=NULL, 
                                   TIpredNames = timeinvar.long,
                                   LAMBDA=diag(numbio))
+    model.lmmdriftdiffevent <- ctsem::ctModel(type='stanct',
+        manifestNames=c(biomarkers,'event'),
+        latentNames=c(biomarkers,'event'),
+        MANIFESTMEANS=matrix(rep(0, numbio+1), nrow=numbio+1),
+        #DRIFT=0, #
+        #DIFFUSION=0,
+        CINT=matrix(paste0(rep('slope', numbio), 1:(numbio+1)), nrow=numbio+1),
+        time="Time",
+        TDpredNames=NULL,
+        TIpredNames = timeinvar.long,
+        LAMBDA=diag(numbio+1))
+    model.lmmdriftdiffevent$manifesttype[3] <- 1
 
     models.list <- list(model.lmm=model.lmm,
                         model.nolmm=model.nolmm,
                         model.lmmdiff=model.lmmdiff,
                         model.lmmdrift=model.lmmdrift,
-                        model.lmmdriftdiff=model.lmmdriftdiff)
+                        model.lmmdriftdiff=model.lmmdriftdiff,
+                        model.lmmdriftdiffevent=model.lmmdriftdiffevent)
     return(models.list)
 }
 

jmseq/vignettes/jmseq.Rmd

@@ -50,6 +50,14 @@ data(pbc, package="jmseq")
 pbc
 list2env(pbc, envir=environment())
 
+#include event in long data
+surv2 <- copy(dataSurv)
+setnames(surv2,'Time.cens','Time')
+dataLong <- merge(dataLong,surv2,all=TRUE)
+dataLong[,FinalObs := c(rep(0,.N-1),1),by=id]
+dataLong[FinalObs==0,event:= 0]
+dataLong[,trt:=trt[!is.na(trt)],by=id]
+
 nfolds <- 4
 landmark.time <- 5
 maxtime <- 15