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Transform Fit fido Parameters to other representations

Source: R/fido_transforms.R
fido_transforms.Rd

These are a collection of convenience functions for transforming fido fit objects to a number of different representations including ILR bases, CLR coordinates, ALR coordinates, and proportions.

Usage

to_proportions(m)

to_alr(m, d)

to_ilr(m, V = NULL)

to_clr(m)

# S3 method for class 'pibblefit'
to_proportions(m)

# S3 method for class 'orthusfit'
to_proportions(m)

# S3 method for class 'pibblefit'
to_alr(m, d)

# S3 method for class 'orthusfit'
to_alr(m, d)

# S3 method for class 'pibblefit'
to_ilr(m, V = NULL)

# S3 method for class 'orthusfit'
to_ilr(m, V = NULL)

# S3 method for class 'pibblefit'
to_clr(m)

# S3 method for class 'orthusfit'
to_clr(m)

Arguments

m

object of class pibblefit or orthusfit (e.g., output of pibble or orthus)

d

(integer) multinomial category to take as new alr reference

V

(matrix) contrast matrix for ILR basis to transform into to (defaults to create_default_ilr_base(D))

Value

object

Details

For orthus, transforms only appleid to log-ratio parameters

Note: that there is a degeneracy of representations for a covariance matrix represented in terms of proportions. As such the function to_proportions does not attempt to transform parameters Sigma or prior Xi and instead just removes them from the pibblefit object returned.