phy:

In bomeara/piecewisesim: Does simulations in diversitree (later, others), stopping every certain amount of time

Usage

data("phy")

Format

The format is: List of 10 $ edge : int [1:58, 1:2] 31 32 33 33 37 38 40 40 38 41 ... $ Nnode : int 29 $ tip.label : chr [1:30] "sp7" "sp8" "sp10" "sp11" ... $ tip.state : Named num [1:30] 0 0 0 0 1 1 0 1 1 1 ... ..- attr(*, "names")= chr [1:30] "sp7" "sp8" "sp10" "sp11" ... $ node.label : chr [1:29] "nd1" "nd9" "nd10" "nd11" ... $ node.state : Named num [1:29] 0 0 0 0 0 0 1 1 1 1 ... ..- attr(*, "names")= chr [1:29] "nd1" "nd9" "nd10" "nd11" ... $ edge.length: num [1:58] 33.23 2.4 12.5 1.39 2.68 ... $ orig :'data.frame': 67 obs. of 11 variables: ..$ idx : int [1:67] 2 3 4 6 9 11 12 14 16 17 ... ..$ len : num [1:67] 0.729 7.333 0.37 13.562 29.082 ... ..$ parent : num [1:67] 1 1 2 4 3 6 11 12 14 14 ... ..$ start : num [1:67] 12.4 12.4 13.1 13.5 19.7 ... ..$ state : num [1:67] 0 0 0 0 0 0 0 0 0 0 ... ..$ extinct: logi [1:67] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ split : logi [1:67] TRUE TRUE TRUE TRUE TRUE TRUE ... ..$ idx2 : num [1:67] 41 42 43 44 45 46 47 48 49 50 ... ..$ parent2: num [1:67] 40 40 41 43 42 44 46 47 48 48 ... ..$ name : chr [1:67] NA NA NA NA ... ..$ name2 : chr [1:67] "nd2" "nd3" "nd4" "nd5" ... ..- attr(*, "t")= num 60.5 ..- attr(*, "hist")='data.frame': 1 obs. of 6 variables: .. ..$ idx : num 21 .. ..$ t : num 48.7 .. ..$ from: num 0 .. ..$ to : num 1 .. ..$ x0 : num 48 .. ..$ tc : num 0.742 $ hist :'data.frame': 1 obs. of 8 variables: ..$ idx : num 21 ..$ t : num 48.7 ..$ from : num 0 ..$ to : num 1 ..$ x0 : num 48 ..$ tc : num 0.742 ..$ idx2 : int 37 ..$ name2: chr "nd14" $ edge.state : num [1:76] 0 0 0 0 0 0 0 0 0 1 ... - attr(*, "class")= chr "phylo" - attr(*, "order")= chr "cladewise"

Examples

data(phy)
## maybe str(phy) ; plot(phy) ...

bomeara/piecewisesim documentation built on May 12, 2019, 11:36 p.m.