Compositional Data Analysis on Statistics @ Home
http://statsathome.com/tags/compositional-data-analysis/
Recent content in Compositional Data Analysis on Statistics @ HomeHugo -- gohugo.ioen-ENstats.at.home@gmail.com (Justin and Rachel Silverman)stats.at.home@gmail.com (Justin and Rachel Silverman)(c) 2017 Justin and Rachel SilvermanWed, 20 Sep 2017 00:00:00 +0000Plotting a Sequential Binary Partition on a Tree in R
http://statsathome.com/2017/09/20/plotting-a-sequential-binary-partition-on-a-tree-in-r/
Wed, 20 Sep 2017 00:00:00 +0000stats.at.home@gmail.com (Justin and Rachel Silverman)http://statsathome.com/2017/09/20/plotting-a-sequential-binary-partition-on-a-tree-in-r/For users of PhILR (Paper, R Package), and also for users of the ILR transform that wan to make use of the awesome plotting functions in R. I wanted to share a function for plotting a sequential binary partition on a tree using the ggtree package. I recently wrote this for a manuscript but figured it might be of more general use to others as well.
In its simplest form a sequential binary partition can be represented as a binary tree.Building the ILR from the ALR Transform
http://statsathome.com/2017/08/10/building-the-ilr-from-the-alr-transform/
Thu, 10 Aug 2017 00:00:00 +0000stats.at.home@gmail.com (Justin and Rachel Silverman)http://statsathome.com/2017/08/10/building-the-ilr-from-the-alr-transform/Following up on a recent post on limitations of the ALR and Softmax transforms, I wanted to briefly show how we can derive an Isometric Log-Ratio transform from the Additive Log-Ratio (ALR) transform.
The ILR transform is just an orthonormal basis in the simplex with respect to the Aitchison metric (which follows naturally from using log-ratios - I will probably have a post explaining this more in the future). We are going to use the Gram-Schmidt orthonomalization process to build an orthonormal basis given a set of vectors which are not orthonormal (the coordinates defined by our ALR transform).We can do better than the ALR or Softmax Transform
http://statsathome.com/2017/08/09/we-can-do-better-than-the-alr-or-softmax-transform/
Wed, 09 Aug 2017 00:00:00 +0000stats.at.home@gmail.com (Justin and Rachel Silverman)http://statsathome.com/2017/08/09/we-can-do-better-than-the-alr-or-softmax-transform/In multiple places in the Compositional Data Analysis literature (for example here and here) people refer to the Additive Log-Ratio transform (ALR) as “not preserving metric concepts”. But what exactly does this mean and how can we visualize this problem?
Here I am going to briefly describe how this problem can be seen with the ALR transform and then show how the Isometric Log-Ratio (ILR) transform does not have this problem.