edit README; rebuild

friendly · Sep 4, 2023 · 2a55e13 · 2a55e13
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diff --git a/README.Rmd b/README.Rmd
@@ -222,6 +222,8 @@ iris.mod <- lm(cbind(Sepal.Length, Sepal.Width, Petal.Length, Petal.Width) ~
 heplot(iris.mod)
 ```
 
+### Contrasts
+
 Contrasts or other linear hypotheses can be shown as well, and the
 ellipses look better if they are filled. We create contrasts to test the
 differences between `versacolor` and `virginca` and also between
@@ -246,14 +248,30 @@ heplot(iris.mod, hypotheses=hyp,
        fill=TRUE, fill.alpha=0.1)
 ```
 
-All pairwise HE plots are produced using the `pairs` method for MLM
+### All pairwise HE plots
+
+All pairwise HE plots are produced using the `pairs()` method for MLM
 objects.
 
 ```{r, iris3, out.width="100%"}
 pairs(iris.mod, hypotheses=hyp, hyp.labels=FALSE,
       fill=TRUE, fill.alpha=0.1)
 ```
 
+### Covariance ellipses
+
+MANOVA relies on the assumption that within-group covariance matrices are all equal.
+It is useful to visualize these in the space of some of the predictors.
+`covEllipses()` provides this both for classical and robust estimates.
+The figure below shows these for the three Iris species and the 
+pooled covariance matrix, which is the same as the **E** matrix used
+in MANOVA tests.
+```{r iris4, out.width="80%"}
+covEllipses(iris[,1:4], iris$Species)
+covEllipses(iris[,1:4], iris$Species, 
+            fill=TRUE, method="mve", add=TRUE, labels="")
+```
+
 ## References
 
 Anderson, E. (1928). The Problem of Species in the Northern Blue Flags,
@@ -288,5 +306,5 @@ Linear Models in Psychological Research: An R
 Tutorial.](https://doi.org/10.20982/tqmp.13.1.p020) *The Quantitative
 Methods for Psychology*, **13**, 20-45.
 
-Friendly, M. & Sigal, M. (2018): Visualizing Tests for Equality of
-Covariance Matrices, _The American Statistician_, [DOI](https://doi.org/10.1080/00031305.2018.1497537)
+Friendly, M. & Sigal, M. (2018): [Visualizing Tests for Equality of
+Covariance Matrices](https://www.datavis.ca/papers/EqCov-TAS.pdf), _The American Statistician_, [DOI](https://doi.org/10.1080/00031305.2018.1497537)
diff --git a/README.md b/README.md
@@ -202,6 +202,8 @@ heplot(iris.mod)
 
 <img src="man/figures/README-iris1-1.png" width="70%" />
 
+### Contrasts
+
 Contrasts or other linear hypotheses can be shown as well, and the
 ellipses look better if they are filled. We create contrasts to test the
 differences between `versacolor` and `virginca` and also between
@@ -232,7 +234,9 @@ heplot(iris.mod, hypotheses=hyp,
 
 <img src="man/figures/README-iris2-1.png" width="70%" />
 
-All pairwise HE plots are produced using the `pairs` method for MLM
+### All pairwise HE plots
+
+All pairwise HE plots are produced using the `pairs()` method for MLM
 objects.
 
 ``` r
@@ -242,6 +246,23 @@ pairs(iris.mod, hypotheses=hyp, hyp.labels=FALSE,
 
 <img src="man/figures/README-iris3-1.png" width="100%" />
 
+### Covariance ellipses
+
+MANOVA relies on the assumption that within-group covariance matrices
+are all equal. It is useful to visualize these in the space of some of
+the predictors. `covEllipses()` provides this both for classical and
+robust estimates. The figure below shows these for the three Iris
+species and the pooled covariance matrix, which is the same as the **E**
+matrix used in MANOVA tests.
+
+``` r
+covEllipses(iris[,1:4], iris$Species)
+covEllipses(iris[,1:4], iris$Species, 
+            fill=TRUE, method="mve", add=TRUE, labels="")
+```
+
+<img src="man/figures/README-iris4-1.png" width="80%" />
+
 ## References
 
 Anderson, E. (1928). The Problem of Species in the Northern Blue Flags,
@@ -275,6 +296,7 @@ Linear Models in Psychological Research: An R
 Tutorial.](https://doi.org/10.20982/tqmp.13.1.p020) *The Quantitative
 Methods for Psychology*, **13**, 20-45.
 
-Friendly, M. & Sigal, M. (2018): Visualizing Tests for Equality of
-Covariance Matrices, *The American Statistician*,
+Friendly, M. & Sigal, M. (2018): [Visualizing Tests for Equality of
+Covariance Matrices](https://www.datavis.ca/papers/EqCov-TAS.pdf), *The
+American Statistician*,
 [DOI](https://doi.org/10.1080/00031305.2018.1497537)
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   HE_manova: HE_manova.html
   HE_mmra: HE_mmra.html
-last_built: 2023-09-04T16:16Z
+last_built: 2023-09-04T16:50Z
 urls:
   reference: https://friendly.github.io/heplots/reference
   article: https://friendly.github.io/heplots/articles

diff --git a/docs/reference/covEllipses-1.png b/docs/reference/covEllipses-1.png
diff --git a/docs/reference/cqplot-5.png b/docs/reference/cqplot-5.png
diff --git a/docs/reference/ellipse3d.axes.html b/docs/reference/ellipse3d.axes.html
diff --git a/docs/reference/figures/README-iris4-1.png b/docs/reference/figures/README-iris4-1.png
diff --git a/docs/search.json b/docs/search.json
diff --git a/man/figures/README-iris4-1.png b/man/figures/README-iris4-1.png