vignette start

Author: KatjaDanielzik

DESCRIPTION

@@ -9,9 +9,14 @@ Authors@R:
            comment=c(ORCID="0000-0003-2973-7869")))
 URL: https://github.com/KatjaDanielzik/BayesVolcano
 BugReports: https://github.com/KatjaDanielzik/BayesVolcano/issues    
-Description: BayesVolcano takes posterior draws from Bayesian models fits and 
-    facilitates the calculation of pi-values for chosen effect sizes and plotting 
-    of Volcano plots (effect size on x-axis, pi-value on y-axis).
+Description: Bayesian models are used to estimate effect sizes (e.g., gene expression changes,
+    protein abundance differences, drug response effects) while accounting for uncertainty, 
+    small sample sizes, and complex experimental designs.
+    However, Bayesian outputs are often difficult to interpret at a glance.
+    One way to quickly identify important biological changes of frequentist analysis 
+    are volcano plots (using fold-changes and p-values).
+    Bayesian volcano plots bring together the uncertainty aware power of Bayesian 
+    models and the familiar visualization of volcano plots.
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
@@ -27,11 +32,10 @@ Imports:
     tidyr
 Suggests:
     brms,
-    rstanarm,
-    cmdstanr,
     rstan,
     knitr,
     rmarkdown,
     testthat (>= 3.0.0)
 LazyData: true
 Config/testthat/edition: 3
+VignetteBuilder: knitr

vignettes/.gitignore

@@ -0,0 +1,2 @@
+*.html
+*.R

vignettes/BayesVolcano.Rmd

@@ -0,0 +1,20 @@
+---
+title: "BayesVolcano"
+author: Katja Danielzik (katja.danielzik@uni-due.de)
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{BayesVolcano}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup}
+library(BayesVolcano)
+```