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adeverse / ade4

Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences
http://adeverse.github.io/ade4/
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Values of the low dimensional space on the mcoa output #25

Open llrs opened 3 years ago

llrs commented 3 years ago

Many thanks for providing this package. It has been very useful for some of the analysis together with other packages on Bioconductor. However I have a question, I would like to calculate the inner average variance explained (AVE) of mcoa.

The inner AVE is defined as:

ave_inner <- function(C, Y) {
  suppressWarnings({sum(C * cor(Y)^2/2, na.rm = TRUE)/(sum(C)/2)})
}

where C is a matrix modelling the relationships between each ktab and Y are the components of the common low dimension space for the samples. If I understood correctly the published manuscript, C would be a matrix such as: C <- matrix(c(0, 1, 1, 0), nrow = 2). However, I am not sure I understood the details on the manual page for the output of mcoa. I'm not sure what are the values for the samples on the ktab on the common space. Is this the SynVar data.frame of the output of mcoa?