spawned additional sections for microbiome exploration dedicated to s…

…pecial aspects

13-microbiome-exploration.Rmd

@@ -62,40 +62,6 @@ See also related functions for the analysis of rare and variable taxa
 TODO
 
 
-## Alpha diversity
-
-
-
-## Beta diversity
-
-
-### Community comparisons
-
-PERMANOVA and other methods.
-
-
-### Visualizing beta diversity
-
-Ordination with PCoA, UMAP, and other methods.
-
-
-
-## Differential abundance analysis
-
-A number of methods for differential abundance analysis are available,
-and reviewed elsewhere.
-
-
-## Community composition
-
-Heatmaps
-
-
-## Community typing
-
- - Community State Types (CST)
- - Dirichlet Multinomial Mixtures (DMM)
-
 
 ## Session Info {-}
 

14-microbiome-diversity.Rmd

@@ -0,0 +1,30 @@
+# Microbiome Exploration {#microbiome-exploration}
+
+```{r setup, echo=FALSE, results="asis"}
+library(rebook)
+chapterPreamble()
+```
+
+
+## Alpha diversity
+
+
+
+## Beta diversity
+
+
+### Community comparisons
+
+PERMANOVA and other methods.
+
+
+### Visualizing beta diversity
+
+Ordination with PCoA, UMAP, and other methods.
+
+
+## Session Info {-}
+
+```{r sessionInfo, echo=FALSE, results='asis'}
+prettySessionInfo()
+```

15-microbiome-community.Rmd

@@ -0,0 +1,24 @@
+# Microbiome Community {#microbiome-community}
+
+```{r setup, echo=FALSE, results="asis"}
+library(rebook)
+chapterPreamble()
+```
+
+
+
+## Community composition
+
+Heatmaps
+
+
+## Community typing
+
+- Community State Types (CST)
+- Dirichlet Multinomial Mixtures (DMM)
+
+## Session Info {-}
+
+```{r sessionInfo, echo=FALSE, results='asis'}
+prettySessionInfo()
+```

16-differential-abundance.Rmd

@@ -0,0 +1,18 @@
+# Differential abundance {#differential-abundance}
+
+```{r setup, echo=FALSE, results="asis"}
+library(rebook)
+chapterPreamble()
+```
+
+
+
+A number of methods for differential abundance analysis are available,
+and reviewed elsewhere.
+
+
+## Session Info {-}
+
+```{r sessionInfo, echo=FALSE, results='asis'}
+prettySessionInfo()
+```

15-timeseries.Rmd → 17-timeseries.Rmd

@@ -1,4 +1,4 @@
-# Microbiome time series {#timeseries}
+# Microbiome time series {#microbiome-timeseries}
 
 ```{r setup, echo=FALSE, results="asis"}
 library(rebook)