updates

drizopoulos · Apr 20, 2024 · ac96a04 · ac96a04
1 parent 2a90f37
commit ac96a04
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Showing 3 changed files with 10 additions and 7 deletions.
diff --git a/Development/interval_CR.R b/Development/interval_CR.R
@@ -57,25 +57,27 @@ eventDF$stop[eventDF$start == eventDF$stop] <- 1e-05
 attr(eventDF$weight, "integrate") <- eventDF$intgr_
 
 
-CoxFit <- coxph(Surv(start, stop, event) ~ DxAge + strata(strt), data = eventDF,
+CoxFit <- coxph(Surv(start, stop, event) ~ density:strata(strt), data = eventDF,
                 weights = eventDF$weight, model = TRUE)
 
 lmeFit <- lme(PSAValue ~ ns(time, k = c(1.49, 3.535), B = c(0, 10.223)) + DxAge,
               data = train.dat,
               random = list(CISNET_ID = pdDiag(form = ~ ns(time, k = c(1.49, 3.535), B = c(0, 10.223)))))
 
-lmeFit <- lme(PSAValue ~ ns(time, k = c(1.49, 3.535), B = c(0, 10.223)) + DxAge,
-              data = train.dat,
-              random = ~ ns(time, k = c(1.49, 3.535), B = c(0, 10.223)) | CISNET_ID)
+lmeFit <- lme(PSAValue ~ ns(time, df = 3) + DxAge,
+              data = train.dat, control = lmeControl(opt = 'optim'),
+              random = ~ ns(time, df = 3) | CISNET_ID)
 
 jmFit <- jm(CoxFit, lmeFit, time_var = "time",
             functional_forms = ~ value(PSAValue):strt +
                 slope(PSAValue,eps = 1, direction = "back"):strt,
-            n_iter = 6500L, n_burnin = 2500L)
+            n_iter = 6500L, n_burnin = 500L)
 summary(jmFit)
 
 iccsjm.model$summary$coef
 
+
+
 Surv_object = CoxFit
 Mixed_objects = lmeFit
 time_var = 'time'

diff --git a/NAMESPACE b/NAMESPACE
@@ -8,7 +8,8 @@ export(area, calibration_metrics, calibration_plot, cumuplot, coef, compare_jm,
 import(Rcpp)
 importFrom("utils", "glob2rx", "tail", "head", "combn")
 importFrom("stats", "coef", "terms", "model.frame", "model.frame.default",
-           "model.matrix", "model.matrix.default", "family", "lm.fit", "sd",
+           "model.matrix", "model.matrix.default", "model.weights", "family",
+           "lm.fit", "sd",
            "ar", "var", "vcov", "optim", "delete.response", "model.response",
            "rnorm", "quantile", "runif", "rlnorm", "cov2cor", "as.formula",
            "gaussian", ".getXlevels", "makepredictcall", "plogis",

diff --git a/R/jm_fit.R b/R/jm_fit.R
@@ -34,7 +34,7 @@ jm_fit <- function (model_data, model_info, initial_values, priors, control) {
         id_h_ <- unlist(mapply2(function (x, ind) if (sum(ind) > 0) x[!duplicated(ind)] else x,
                                 split(id_h, id_h), split(model_data$intgr_ind, id_h)))
     } else {
-        id_h2 <- 0
+        id_h2 <- id_h_ <- 0
     }
     model_data <-
         c(model_data, create_Wlong_mats(model_data, model_info,