From d3db658f3ec4c529052fe572e4bd2f9c32424ad5 Mon Sep 17 00:00:00 2001
From: TuomasBorman <tvborm@utu.fi>
Date: Mon, 10 Feb 2025 09:53:58 +0200
Subject: [PATCH] up

---
 DESCRIPTION              |  6 ++++--
 inst/pages/mediation.qmd | 11 ++++++-----
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6365492d..56b9ddb1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: OMA
 Title: Orchestrating Microbiome Analysis with Bioconductor
-Version: 0.98.35
-Date: 2025-02-05
+Version: 0.98.36
+Date: 2025-02-10
 Authors@R:
     c(
   person(given = "Tuomas", family = "Borman", role = c("aut", "cre"), email = "tuomas.v.borman@utu.fi", comment = c(ORCID = "0000-0002-8563-8884")),
@@ -49,6 +49,7 @@ Suggests:
     factoextra,
     fido,
     forcats,
+    ggdag,
     ggplot2,
     ggpubr,
     ggtree,
@@ -62,6 +63,7 @@ Suggests:
     IntegratedLearner,
     knitr,
     maaslin3,
+    mediation,
     mia,
     miaTime,
     miaViz,
diff --git a/inst/pages/mediation.qmd b/inst/pages/mediation.qmd
index 87cc5e7f..b49cd5c0 100644
--- a/inst/pages/mediation.qmd
+++ b/inst/pages/mediation.qmd
@@ -115,9 +115,9 @@ by the microbiome is investigated in 3 different steps:
 
 First, we ask whether alpha diversity mediates the effect of living environment
 on BMI. Using the `getMediation` function, the variables X, Y and M are
-specified with the arguments `treatment`, `outcome` and `mediator`, respectively.
-We control for sex and age and limit comparisons to two nationality groups,
-Central Europeans (control) vs. Scandinavians (treatment).
+specified with the arguments `treatment`, `outcome` and `mediator`,
+respectively. We control for sex and age and limit comparisons to two
+nationality groups, Central Europeans (control) vs. Scandinavians (treatment).
 
 ```{r}
 #| label: mediation3
@@ -279,5 +279,6 @@ data also exist [@Xia2021mediation]. However, no one solution has emerged yet to
 become the golden standard in microbiome data analysis, mainly because the
 available approaches can only partially accommodate for the specific properties
 of microbiome data, such as compositionality, sparsity and its hierarchical
-structure. While this chapter proposed a standard approach to mediation analysis,
-in the future fine-tuned solutions for the microbiome may also become common.
+structure. While this chapter proposed a standard approach to mediation
+analysis, in the future fine-tuned solutions for the microbiome may also become
+common.