new case studies and logo

_quarto-public.yml

@@ -1,6 +1,5 @@
 project:
   output-dir: docs/public
-  post-render: src/move_videos.R # workaround for Quarto issue https://github.com/quarto-dev/quarto-cli/issues/3892
 
 book:
   repo-url: https://github.com/Novartis/bamdd/
@@ -11,12 +10,15 @@ book:
       chapters:
       - src/01a_introduction.qmd
       - src/01b_basic_workflow.qmd
+      - src/01c_priors.qmd
     - part: src/02_case_studies.qmd
       chapters:
       - src/02a_meta_analysis.qmd
       - src/02ab_meta_analysis_trtdiff.qmd
+      - src/02ac_meta_analysis_strata.qmd
       - src/02b_dose_finding.qmd
       - src/02c_dose_escalation.qmd
+      - src/02cb_tte_dose_escalation.qmd
       - src/02e_multiple_imputation.qmd
       - src/02g_longitudinal.qmd
       - src/02h_mmrm.qmd

_quarto.yml

@@ -13,7 +13,7 @@ execute:
    freeze: false
 
 book:
-  title: "(Bayesian) Applied Modelling in Drug Development (BAMDD)"
+  title: "Applied Modelling in Drug Development"
   subtitle: "Flexible regression modelling in Stan via `brms`"
   repo-actions: [issue]
   repo-branch: master
@@ -25,6 +25,8 @@ book:
   - Lukas Widmer - <[email protected]>
   - Andrew Bean - <[email protected]>
   date: today
+  sidebar:
+    logo: bamdd_logo.png
 
 # we use per chapter references
 bibliography:

index.qmd

@@ -34,6 +34,10 @@ appropiate. Key changes to the web-site are tracked here:
 
 
 ::: {.content-visible when-profile="public"}
+- 29th April 2024: Third edition course from Paul Bürkner with the new
+  case studies on probability of success, meta-analytic priors with
+  covariates & time-to-event modelling in Oncology phase I
+  dose-escalation. Pre-read version.
 - 19th April 2024: First public version at [opensource.nibr.com/bamdd](http://opensource.nibr.com/bamdd)
 - 5th January 2024: Release web-site in more modern quarto book
   based format

src/02_case_studies.qmd

@@ -12,15 +12,15 @@ format:
 ```{r, echo = FALSE}
 overview <- dplyr::tribble(
                        ~Problem, ~Technique,
-                       "[Use of historical control data](02a_meta_analysis.qmd)", "nested random effects",
-                       "[Meta-analysis to estimate treatment effects](02ab_meta_analysis_trtdiff.qmd)", "aggregate data modeling & varying exposure times of count data",
-                       "[Dose finding](02b_dose_finding.qmd)", "non-linear models",
-                       "[Oncology dose escalation](02c_dose_escalation.qmd)",  "constrained parameters",
-                       "[Multiple imputation](02e_multiple_imputation.qmd)", "multi-variate outcome modeling",
-                       "[Longitudinal data](02g_longitudinal.qmd)", "longitudinal modeling with different covariance structures (MMRM)",
-                       "[Bayesian Mixed effects Model for Repeated Measures (MMRM)](02h_mmrm.qmd)", "unstructured MMRM for a continuous endpoint",
-                       "[Time-to-event data](02i_time_to_event.qmd)", "parametric time-to-event modeling with customized parametrization by using user-defined contrasts",
-                       "[Network meta-analysis](02j_network_meta_analysis.qmd)", "arm based network meta-analysis"
+                       "@sec-use-hist-control-data", "nested random effects",
+                       "@sec-map-treat-effects", "aggregate data modeling & varying exposure times of count data",
+                       "@sec-dose-finding", "non-linear models",
+                       "@sec-onc-escalation",  "constrained parameters",
+                       "@sec-multiple-imputation", "multi-variate outcome modeling",
+                       "@sec-longitudinal-data", "longitudinal modeling with different covariance structures (MMRM)",
+                       "@sec-mmrm", "unstructured MMRM for a continuous endpoint",
+                       "@sec-tte-data", "parametric time-to-event modeling with customized parametrization by using user-defined contrasts",
+                       "@sec-network-meta", "arm based network meta-analysis"
                    )
 knitr::kable(overview)
 ```

src/02ab_meta_analysis_trtdiff.qmd

@@ -4,7 +4,7 @@ author:
   - Sebastian Weber - <[email protected]>
 ---
 
-# Meta-analysis to estimate treatment effects
+# Meta-analysis to estimate treatment effects {#sec-map-treat-effects}
 
 ```{r, include=FALSE}
 source(here::here("src", "setup.R"))