Initialize time series chapter

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: OMA
 Title: Orchestrating Microbiome Analysis with Bioconductor
-Version: 0.98.37
+Version: 0.98.38
 Date: 2025-03-13
 Authors@R:
     c(
@@ -63,6 +63,8 @@ Suggests:
     igraph,
     IntegratedLearner,
     knitr,
+    lme4,
+    lmerTest,
     Maaslin2,
     maaslin3,
     mediation,

inst/assets/_book.yml

@@ -60,9 +60,13 @@ book:
         - pages/cross_correlation.qmd
         - pages/multiassay_ordination.qmd
         - pages/integrated_learner.qmd
-    - part: "Machine learning & statistical modeling"
+    - part: "Machine learning"
       chapters:
         - pages/machine_learning.qmd
+    - part: "Time series"
+      chapters:
+        - pages/time_series.qmd
+        - pages/time_diversity.qmd
     - part: "Workflows"
       chapters:
         - pages/introductory_workflow.qmd

inst/assets/bibliography.bib

@@ -2551,7 +2551,7 @@ @article{Marchesi2015
   publisher = {Springer Science and Business Media LLC},
   author = {Marchesi,  Julian R. and Ravel,  Jacques},
   year = {2015},
-  month = jul 
+  month = jul
 }
 
 @article{Nickols2024,
@@ -2563,3 +2563,18 @@ @article{Nickols2024
   year = {2024},
   month = dec
 }
+
+@article{Schmidt2018,
+  title = {The Human Gut Microbiome: From Association to Modulation},
+  volume = {172},
+  ISSN = {0092-8674},
+  url = {http://dx.doi.org/10.1016/j.cell.2018.02.044},
+  DOI = {10.1016/j.cell.2018.02.044},
+  number = {6},
+  journal = {Cell},
+  publisher = {Elsevier BV},
+  author = {Schmidt,  Thomas S.B. and Raes,  Jeroen and Bork,  Peer},
+  year = {2018},
+  month = mar,
+  pages = {1198–1215}
+}

inst/pages/beta_diversity.qmd

@@ -177,7 +177,7 @@ between two points is always the shortest possible distance.
 
 :::
 
-## Divergence
+## Divergence {#sec-divergence}
 
 Divergence measure refers to a difference in community composition
 between the given sample(s) and a reference sample. This can be
@@ -479,7 +479,6 @@ tse_sub <- runMDS(
 
 Then let's do the same with rarefaction:
 
-
 ```{r}
 #| label = "MDS plot based on the Bray-Curtis distances using rarefaction."