diff --git a/vignettes/htrfit.Rmd b/vignettes/tutorials/htrfit.Rmd similarity index 93% rename from vignettes/htrfit.Rmd rename to vignettes/tutorials/htrfit.Rmd index 1b63f22eb7ed6c06904e531ec6561e4f226a100d..cc567c0a50df3b2e6d0ac7875517aa5ab6472568 100644 --- a/vignettes/htrfit.Rmd +++ b/vignettes/tutorials/htrfit.Rmd @@ -588,7 +588,51 @@ resSimu$performances For certain experimental scenarios, such as those involving a high number of levels or longitudinal data, the utilization of mixed effects within your design formula can be beneficial. The **HTRfit** simulation framework also offers the capability to assess this type of design formula. -Removed for test +```{r example-evalMixed, warning = FALSE, message = FALSE} +## -- init a design with a high number of levels +input_var_list <- init_variable( name = "varA", mu = 0.2, sd = 0.74, level = 60) %>% + init_variable( name = "varB", mu = 0.27, sd = 0.6, level = 2) %>% + add_interaction( between_var = c("varA", "varB"), mu = 0.44, sd = 0.89) +## -- simulate RNAseq data +mock_data <- mock_rnaseq(input_var_list, + n_genes = 30, ## small number to prevent excessively lengthy vignette construction + min_replicates = 10, + max_replicates = 10, + basal_expression = 5 ) +## -- prepare data & fit a model with mixed effect +data2fit = prepareData2fit(countMatrix = mock_data$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 diff --git a/vignettes/test_vignette.Rmd b/vignettes/tutorials/test_vignette.Rmd similarity index 100% rename from vignettes/test_vignette.Rmd rename to vignettes/tutorials/test_vignette.Rmd