This function computes Local Indicator of Phylogenetic Association (local Moran's I) for each tip of a tree. Tests are based on permutations.
1 2 |
p4d |
a |
trait |
the traits in the |
reps |
a numeric value. Number of repetitions for the estimation of p.values with randomization. |
alternative |
a character string specifying the alternative hypothesis for the tests.
Must be one of |
prox.phylo |
a matrix of phylogenetic proximities or a character string specifying a method to compute it. See Details. |
as.p4d |
logical. Should the results returned as a |
If "prox.phylo
" is a character string,
the phylogenetic proximity matrix is computed internally
using the function proxTips
from the package adephylo.
Different methods are available:
"patristic
","nNodes
","Abouheif
" and "sumDD
".
See proxTips
for details about the methods.
If as.p4d
is FALSE
(default), the function returns a list:
A matrix of LIPA indices computed for each tip of the tree and each trait.
A matrix of p-values (tests of LIPA indices)
Number of permutations for the tests
Alternative hypothesis for the tests
If as.p4d
is TRUE
, the function returns a phylo4d
object
with LIPA values as tips associated data.
Anselin L. (1995) Local Indicators of Spatial Association-LISA. Geographical Analysis 27, 93-115.
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.
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