This documentation is for developers of poppr. The accessors here are preferred over accessing the elements via the @ symbol. Please use these in your code when accessing MLG objects.
Usage
visible(x)
visible(x) <- value
MLG2df(x)
distname(x)
distenv(x)
distname(x) <- value
distenv(x) <- value
distargs(x)
distargs(x) <- value
distalgo(x)
distalgo(x) <- value
cutoff(x)
cutoff(x) <- valueDetails
These accessors are intended for internal use only. They only affect
MLG objects, not genind objects. Only visible and MLG2df are general for
all forms of MLG. The distargs and cutoff are specific for use in
mlg.filter or any function that offers filtering as an option. The argument
"value" will always take the type defined in the MLG
class.
Examples
# \dontrun{
# 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
# Visibility ------------------------------
visible(m) # original
#> [1] "original"
visible(m) <- "contracted"
m # shows contracted MLGS
#> 20 contracted mlgs with a cutoff of 0 based on the function diss.dist
#> [1] 8 5 5 2 3 1 4 9 6 4 5 9 7 10 2 4 2 4 10 2
# Conversion to data frame ----------------
MLG2df(m) # Grab the internal data frame
#> expanded original contracted custom
#> 1 8 8 8 8
#> 2 5 5 5 5
#> 3 5 5 5 5
#> 4 2 2 2 2
#> 5 3 3 3 3
#> 6 1 1 1 1
#> 7 4 4 4 4
#> 8 9 9 9 9
#> 9 6 6 6 6
#> 10 4 4 4 4
#> 11 5 5 5 5
#> 12 9 9 9 9
#> 13 7 7 7 7
#> 14 10 10 10 10
#> 15 2 2 2 2
#> 16 4 4 4 4
#> 17 2 2 2 2
#> 18 4 4 4 4
#> 19 10 10 10 10
#> 20 2 2 2 2
# Distance function handling --------------
distname(m) # nei.dist
#> [1] "diss.dist"
distargs(m) # list()
#> list()
distalgo(m) # farthest
#> [1] "farthest_neighbor"
cutoff(m)
#> expanded contracted
#> 0 0
distname(m) <- substitute("diss.dist")
distargs(m) <- list(percent = TRUE)
distalgo(m) <- "average"
cutoff(m)["contracted"] <- 0.2
# }