sim.measure.attributes-class: Attributes of similarity measures

In AlmaasLab/micInt: Find microbial interactions

Attributes of similarity measures

Description

Accessor and construction functions for dealing with the sim.measure attributes of similarity measures. The sim.measure.attributes extracts or constructs an object showing the attributes, whereas sim_measure_function extracts the similarity function itself.

Usage

sim.measure.attributes(x, ...)

sim_measure_function(x, ...)

## S4 method for signature 'sim.measure'
sim.measure.attributes(x, ...)

## S4 method for signature 'sim.measure'
sim_measure_function(x, ...)

## S4 method for signature 'character'
sim.measure.attributes(x, type_measure, signed)

Arguments

x	An sim.measure
...	Ignored
type_measure	Character, the type of similarity measure which should be repesented
signed	Logical, is the similarity measure signed?

Slots

string

Character, the similarity score's human readable name

type_measure

Character, what type to similarity measure is this (equvialent to type field in sim.measure)

signed

Logical, does this similarity measure return signed results?

Examples

# This measures how well the arguments agree with the signs
# This primary function accept two vectors only
my_measure_simple <- function(x,y){
 (sum((x > 0) & (y > 0)) + sum((x < 0) & (y < 0))) /
  (sum(x > 0) + sum(x < 0))
}
# We extend this function into acception a matrix argument when y is now supplied
my_measure <- function(x,y=NULL){
if(is.null(y)){
n_vectors <- ncol(x)
res <- matrix(NA_real_,n_vectors,n_vectors)
for (i in seq_len(n_vectors)){
    for(j in seq_len(n_vectors)){
    res[i,j] <- my_measure_simple(x[,i],x[,j])
    }
}
    res

}
else{
my_measure_simple(x,y)
}
}

my_sim_score <-sim.measure(my_measure,string= "My measure", categorical = FALSE,
 mean_scaleable = FALSE, signed = FALSE, type = "non-paramtric")
sim_fun <- sim_measure_function(my_sim_score)
sim_fun(c(1,0,-1),c(2,-1,-1))
sim.measure.attributes(my_sim_score)

AlmaasLab/micInt documentation built on April 1, 2022, 10:37 a.m.