A class to store multilocus genotypes in genclone objects. This is intended for internal use only.
mlg
a list containing four vectors, one for each type of MLG manipulation.
visible
a character specifying which MLG type is to be displayed and accessed.
distname
the name of the distance function or matrix used to collapse mlgs.
distenv
the environment that contains the distance function or matrix
distargs
the arguments provided to compute the distance function.
distalgo
the algorithm used to contract multilocus genotypes.
cutoff
Two numbers specifying the cutoff value for expanding and collapsing MLGs.
# These examples will simply show you what you can do with these set.seed(5000) (x <- sample(10, 20, replace = TRUE))#> [1] 8 5 5 2 3 1 4 9 6 4 5 9 7 10 2 4 2 4 10 2(m <- new("MLG", x))#> 20 original mlgs. #> [1] 8 5 5 2 3 1 4 9 6 4 5 9 7 10 2 4 2 4 10 2#> [1] "original"m[] # adding braces after the object will always return a vector of#> [1] 8 5 5 2 3 1 4 9 6 4 5 9 7 10 2 4 2 4 10 2# the same type as defined in "visible" m + 1 # You can do math on the numeric ones#> [1] 9 6 6 3 4 2 5 10 7 5 6 10 8 11 3 5 3 5 11 3#> Warning: ‘+’ not meaningful for factors#> [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA#> 20 original mlgs. #> [1] 8 5 5 2 3 1 4 9 6 4 5 9 7 10 2 4 2 4 10 2m[, "custom"]#> [1] 8 5 5 2 3 1 4 9 6 4 5 9 7 10 2 4 2 4 10 2 #> Levels: 1 2 3 4 5 6 7 8 9 10# Important for subsetting, if you subset the object, normally, it will # return a vector unless you specify all = TRUE m[1:10] # original vector#> [1] 8 5 5 2 3 1 4 9 6 4m[1:10, all = TRUE] # still class MLG#> 10 original mlgs. #> [1] 8 5 5 2 3 1 4 9 6 4