## Compositional bar plot
plot(coda, order = "A")
-
Working with (reference) groups
@@ -252,29 +247,59 @@Working with repeated measurementsNote that the presence of repeated measurements may affect some calculations (read the documentation carefully).
-
Log-ratio transformations -
+
+
+Log-ratio transformations +
The amount of every part is limited to the whole. The absolute amount of the whole is noninformative since it is typically due to artifacts on the measurement procedure. Thus only relative changes are relevant. If the relative amount of one part increases, the amounts of other parts must decrease, introducing spurious anticorrelation.
Use cases
-Glass compositions
+
+
+
Glass compositions
+Ceramic compositions
+
+## Data from Day et al. 2011
+data("kommos", package = "folio")
+
+## Remove rows with missing values
+kommos <- remove_NA(kommos, margin = 1)
+
+## Coerce to a compositional matrix
+coda <- as_composition(kommos)
+#> 2 qualitative variables were removed: type, date.
+
+## Set groups
+set_groups(coda) <- kommos$type
+
+## Compositional bar plot
+plot(coda, order = "Ca")
+
+## Data from Day et al. 2011
+data("kommos", package = "folio")
+
+## Remove rows with missing values
+kommos <- remove_NA(kommos, margin = 1)
+
+## Coerce to a compositional matrix
+coda <- as_composition(kommos)
+#> 2 qualitative variables were removed: type, date.
+
+## Set groups
+set_groups(coda) <- kommos$type
+## Compositional bar plot
+plot(coda, order = "Ca")
+## CLR
+clr <- transform_clr(coda)
+plot(clr, border = c("#EE7733", "#0077BB", "#33BBEE", "#EE3377"))
+## PCA
+clr_pca <- pca(clr, scale = FALSE)
+
+viz_individuals(clr_pca, highlight = get_groups(coda), pch = 16,
+ col = c("#EE7733", "#0077BB", "#33BBEE", "#EE3377"))
+viz_variables(clr_pca)
+
References
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diff --git a/nexus/pkgdown.yml b/nexus/pkgdown.yml
index 840e83ddc..4f105c1d0 100644
--- a/nexus/pkgdown.yml
+++ b/nexus/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
articles:
bibliography: bibliography.html
nexus: nexus.html
-last_built: 2023-09-04T15:59Z
+last_built: 2023-09-05T14:36Z
urls:
reference: https://packages.tesselle.org/nexus/reference
article: https://packages.tesselle.org/nexus/articles
diff --git a/nexus/reference/Rplot004.png b/nexus/reference/Rplot004.png
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--- a/nexus/reference/as_amounts.html
+++ b/nexus/reference/as_amounts.html
@@ -108,13 +108,13 @@