diff --git a/inst/pages/differential_abundance.qmd b/inst/pages/differential_abundance.qmd
index ce29e849..45083c2b 100644
--- a/inst/pages/differential_abundance.qmd
+++ b/inst/pages/differential_abundance.qmd
@@ -199,11 +199,6 @@ folder for some output files. Lastly, we prevent `Maaslin2()` to create certain
 plots. (Note that `Maaslin2()` prints a lot of some output
 which is suppressed here for convenience.)
 
-```{r}
-#| label: disable_chunks
-knitr::opts_chunk$set(eval = FALSE)
-```
-
 ```{r}
 #| label: run_daa_basic
 #| results: hide
@@ -558,11 +553,6 @@ cohort).
 Note that a similar plot could also be used to illustrate a possible confounding
 effect.
 
-```{r}
-#| label: enable_chunks
-knitr::opts_chunk$set(eval = TRUE)
-```
-
 ### Differential prevalence analysis (DPA) {#sec-DPA}
 
 We show here how to perform DPA with logistic regression. We show the case
diff --git a/inst/pages/integrated_learner.qmd b/inst/pages/integrated_learner.qmd
index 6031ebc5..286f30e8 100644
--- a/inst/pages/integrated_learner.qmd
+++ b/inst/pages/integrated_learner.qmd
@@ -146,11 +146,6 @@ integrates the outputs from these individual models to make the final
 predictions. For "base learners" and "meta learner", we use _random forest_
 and _rank loss minimization_ models, respectively.
 
-```{r}
-#| label: disable_chunks
-knitr::opts_chunk$set(eval = FALSE)
-```
-
 ```{r}
 #| label: fit_model
 
diff --git a/inst/pages/mmuphin_meta_analysis.qmd b/inst/pages/mmuphin_meta_analysis.qmd
index 900e66f2..dfd9466a 100644
--- a/inst/pages/mmuphin_meta_analysis.qmd
+++ b/inst/pages/mmuphin_meta_analysis.qmd
@@ -130,11 +130,6 @@ abundance file, which includes the study names and overall response rate
 (ORR) the response variable along with other metadata. By the end of
 this step, we obtain a batch-adjusted relative abundance matrix.
 
-```{r}
-#| label: disable_chunks
-knitr::opts_chunk$set(eval = FALSE)
-```
-
 ```{r}
 #| label: prepare_input_data
 
diff --git a/inst/pages/msea.qmd b/inst/pages/msea.qmd
index d42b72f6..2fdd35d8 100644
--- a/inst/pages/msea.qmd
+++ b/inst/pages/msea.qmd
@@ -98,11 +98,6 @@ microbial species abundance versus IBD diagnosis. The analysis method we use
 here is "LM", which is the default setting. We also adjust for age and
 antibiotic usage, following the original study.
 
-```{r}
-#| label: disable_chunks
-knitr::opts_chunk$set(eval = FALSE)
-```
-
 ```{r}
 #| label: fit_model_Maaslin2