diff --git a/vignettes/mindfulness.Rmd b/vignettes/mindfulness.Rmd index 9579055..5943260 100644 --- a/vignettes/mindfulness.Rmd +++ b/vignettes/mindfulness.Rmd @@ -75,6 +75,7 @@ ways. The point of mediation analysis is to provide evidence for one or the other of these possibilities. ```{r libraries} +library(cmdstanr) library(ggdist) library(ggrepel) library(phyloseq) @@ -105,6 +106,12 @@ exper <- mediation_data( exper ``` +```{r check_install} +if (is.null(cmdstan_version(error_on_NA = FALSE))) { + install_cmdstan() +} +``` + This block applies a logistic-normal multinomial model to the microbiome outcome. This is an example where the response variables are all modeled jointly. We'll use a ridge regression model for each of the mediators. This is a