Description Usage Arguments Details Value
This function finds which feature ratios explain the most variance. This is a computationally expensive procedure that we approximate with the heuristic described below.
1 2 |
counts |
A data.frame or matrix. A "count matrix" with subjects as rows and features as columns. Note that this matrix does not necessarily have to contain counts. |
ndim |
An integer. The number of ratios to find. |
nclust |
An integer. The number of clusters to build from the data. |
nsearch |
An integer. The number of clusters to search exhaustively. |
ndenom |
An integer. The number of best denominators to use when searching for the best numerators. |
This function resembles the method described by Michael Greenacre in "Variable Selection in Compositional Data Analysis Using Pairwise Logratios", except that we have modified the method to use a heuristic that scales to high-dimensional data.
For each ratio, the heuristic will search CLR-based clusters
for the best denominator, and then will search ALR-based clusters
for the best numerator. It does this by dividing the
transformed data into nclust
clusters, calculating
vegan::rda
on the geometric mean of each cluster, then
searching the best clusters exhaustively. The ndenom
argument toggles how many best denominators to use during the
next step. This process is repeated ndim
times, finding
that number of ratios that explain the most variance.
A list of: (1) "best", the best ratios and the variance they explain, (2) "all", all ratios tested and the variance they explain, (3) "Z", the standardized data used by the constrained PCA, and (4) "Y", the final ratios used to constrain the PCA.
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