update vignettes

vignettes/htrfit.Rmd

@@ -503,6 +503,8 @@ l_tmb <- fitModelParallel(formula = kij ~ varB + (varB | varA),
                           family = glmmTMB::nbinom2(link = "log"), 
                           log_file = "log.txt",
                           n.cores = 1)
+## -- output
+l_tmb$gene1
 ## -- evaluation
 resSimu <- simulationReport(mock_data, 
                             list_tmb = l_tmb,
@@ -519,3 +521,9 @@ resSimu$dispersionEvaluation$disp_plot
 resSimu$roc_plot
 ```
 
+# About mixed model evaluation
+
+**HTRfit** offers a versatile simulation framework capable of fitting various types of models involving mixed effects, thanks to its implementation of **glmmTMB**. By combining the functionalities of `init_variable()` and `add_interaction()`, **HTRfit** enables the simulation of even the most complex experimental designs. However, it's important to note that as of now, HTRfit supports the evaluation of only *Type I* mixed models. In this context, *Type I* models are defined as those that follow the structure: `~ varA + (1 | varB)` or `~ varA + (varA | varB)`. Models not conforming to this specific form cannot be evaluated using **HTRfit's** current implementation. Nonetheless, you are welcome to extend its capabilities by implementing support for additional model types. 
+
+
+