From ab0199e6dd94d7784e7378172a661b73c3fccf36 Mon Sep 17 00:00:00 2001
From: aduvermy <arnaud.duvermy@ens-lyon.fr>
Date: Thu, 18 Jan 2024 17:29:31 +0100
Subject: [PATCH] removing part returning error
---
vignettes/tutorials/htrfit.Rmd | 51 ----------------------------------
1 file changed, 51 deletions(-)
diff --git a/vignettes/tutorials/htrfit.Rmd b/vignettes/tutorials/htrfit.Rmd
index cc567c0..25cd389 100644
--- a/vignettes/tutorials/htrfit.Rmd
+++ b/vignettes/tutorials/htrfit.Rmd
@@ -583,57 +583,6 @@ resSimu <- evaluation_report(list_tmb = l_tmb,
resSimu$performances
```
-## Evaluate model inference involving mixed effects
-
-For certain experimental scenarios, such as those involving a high number of levels or longitudinal data, the utilization of mixed effects within your design formula can be beneficial. The **HTRfit** simulation framework also offers the capability to assess this type of design formula.
-
-
-```{r example-evalMixed, warning = FALSE, message = FALSE}
-## -- init a design with a high number of levels
-input_var_list <- init_variable( name = "varA", mu = 0.2, sd = 0.74, level = 60) %>%
- init_variable( name = "varB", mu = 0.27, sd = 0.6, level = 2) %>%
- add_interaction( between_var = c("varA", "varB"), mu = 0.44, sd = 0.89)
-## -- simulate RNAseq data
-mock_data <- mock_rnaseq(input_var_list,
- n_genes = 30, ## small number to prevent excessively lengthy vignette construction
- min_replicates = 10,
- max_replicates = 10,
- basal_expression = 5 )
-## -- prepare data & fit a model with mixed effect
-data2fit = prepareData2fit(countMatrix = mock_data$counts,
- metadata = mock_data$metadata,
- normalization = F,
- response_name = "kij")
-l_tmb <- fitModelParallel(formula = kij ~ varB + (varB | varA),
- data = data2fit,
- group_by = "geneID",
- family = glmmTMB::nbinom2(link = "log"),
- n.cores = 1)
-## -- evaluation
-resSimu <- evaluation_report(list_tmb = l_tmb,
- dds = NULL,
- mock_obj = mock_data,
- coeff_threshold = 0.27,
- alt_hypothesis = "greater")
-```
-
-```{r example-outputResSimuMixed_id, warning = FALSE, message = FALSE, fig.align = 'center', fig.height = 4, fig.width = 5}
-## -- identity plot
-###### 1) Model params
-resSimu$identity$params
-###### Dispersion params
-resSimu$identity$dispersion
-```
-
-```{r example-outputResSimuMixed_metric, warning = FALSE, message = FALSE, fig.align = 'center', fig.height = 4, fig.width = 7}
-## -- precision-recall curve
-resSimu$precision_recall$params
-## -- ROC curve
-resSimu$roc$params
-## -- Performances metrics
-resSimu$performances
-```
-
## Structure of evaluation report object
```{r example-str_eval_report, warning = FALSE, message = FALSE}
--
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