| Package | File | Line | Code |
1 | adiv | optimEH.R | 9 | if(is.binary.tree(phyl.phylo))\r" |
2 | adiv | orisaved.R | 16 | if(is.binary.tree(phyl.phylo))\r" |
3 | geiger | diversitree.R | 209 | \t## ape is.binary.tree() can let a few nasties through - for\r" |
4 | geiger | diversitree.R | 212 | \tif ( bifurcating && (!is.binary.tree(tree) ||\r" |
5 | geiger | likelihood.R | 47 | \tif(!is.binary.tree(phy)) stop(\"'phy' is not fully dichotomous.\")" |
6 | geiger | likelihood.R | 288 | if(ct$binary) if(!is.binary.tree(phy)) stop(\"'phy' should be a binary tree\")" |
7 | ggrasp | ggrasp.cluster.R | 277 | if (!is.binary.tree(nj_tree))" |
8 | ggrasp | ggrasp.create.R | 65 | \t\tis.binary <- is.binary.tree;" |
9 | jackalope | create_haplotypes.R | 124 | if (!ape~~is.binary.tree(phy)) {" |
10 | mvMORPH | pruning.r | 8 | if(!is.binary.tree(tree)) tree <- multi2di(tree, random=FALSE)" |
11 | pez | shape.R | 111 | #' @importFrom ape is.binary.tree" |
12 | pez | shape.R | 165 | if(!is.binary.tree(data$phy) & \"colless\" %in% names(functions))" |
13 | phyext2 | phyext2.R | 555 | \tif(!is.binary.tree(tr))\r" |
14 | phylocurve | fast_geomorph_functions.R | 197 | if (!is.binary.tree(phy)) \r" |
15 | phylocurve | fast_geomorph_functions.R | 411 | if (!is.binary.tree(tree)) \r" |
16 | phylocurve | fast_geomorph_functions.R | 435 | if (!is.binary.tree(tree)) {\r" |
17 | phylocurve | phylocurve.R | 4 | if(!is.binary.tree(original_tree)) phy <- reorder(multi2di(phy),\"postorder\") else\r" |
18 | phylocurve | phylocurve.R | 30 | if(!is.binary.tree(original_tree))\r" |
19 | phylocurve | phylocurve.R | 50 | if(!is.binary.tree(original_tree)) phy <- reorder(multi2di(phy),\"postorder\") else\r" |
20 | phylocurve | phylocurve.R | 98 | if(!is.binary.tree(original_tree))\r" |
21 | phylocurve | phylocurve.R | 856 | if(!is.binary.tree(tree))\r" |
22 | phylocurve | phylocurve.R | 1251 | if(!is.binary.tree(model$evo.model.args$tree)) FLAG <- TRUE else FLAG <- FALSE\r" |
23 | phyloTop | phyloCheck.R | 25 | if(!is.binary.tree(tree)||!is.rooted(tree)) {\r" |
24 | phyloTop | phyloCheck.R | 29 | if(!is.binary.tree(tree)||!is.rooted(tree)) {stop(\"Unable to coerce the tree to be binary and rooted.\")}\r |
25 | rase | rase_source.r | 752 | if (!is.binary.tree(tree)) {" |
26 | RPANDA | MC.rescale.R | 7 | \tif(!is.binary.tree(phylo)){stop(\"tree must not contain any polytomies\")}" |
27 | RPANDA | MC.rescale_geog.R | 13 | if(!is.binary.tree(phylo)){stop(\"tree must not contain any polytomies\")}" |
28 | Rphylip | Rphylip.R | 2834 | \tif(!is.binary.tree(tree)){\r" |
29 | RRphylo | RRphylo.R | 13 | #' @importFrom ape multi2di Ntip is.binary.tree Nnode dist.nodes drop.tip subtrees nodelabels\r" |
30 | RRphylo | RRphylo.R | 129 | if (is.binary.tree(tree))\r" |
31 | RRphylo | RRphylo.R | 140 | if (is.binary.tree(tree) == FALSE)\r" |
32 | RRphylo | RRphylo.R | 149 | if (is.binary.tree(tree) == FALSE)\r" |
33 | RRphylo | RRphylo.R | 174 | if (is.binary.tree(tree) == FALSE) {\r" |
34 | RRphylo | RRphylo.R | 245 | if (is.binary.tree(tree) == FALSE) {\r" |
35 | RRphylo | StableTraitsR.R | 48 | if (is.binary.tree(tree)) t <- tree else t <- multi2di(tree,random=FALSE)\r" |
36 | RRphylo | StableTraitsR.R | 64 | if (is.binary.tree(tree)==FALSE){\r" |
37 | TKF | MinSqTree.R | 46 | if(!is.binary.tree(stree)){" |