I just
fixed
a small bug in the S3 plot
method for phyl.RMA
.
phyl.RMA
does reduced major axis (RMA) regression taking
phylogeny into account. The plot
method plots a
phylomorphospace of the two characters, and overlays both the null
hypothesis (to be specified by the user, but defaults to β1 =
1.0) and the fitted RMA regression line.
Here's in example starting with a fitted RMA model:
library(phytools)
obj
##
## Coefficients:
## (Intercept) x
## 3.214059 2.375175
##
## VCV matrix:
## x y
## x 0.005793694 0.006437997
## y 0.006437997 0.032684872
##
## Model for the covariance structure of the error is "BM"
##
## Estimates (or set values):
## lambda log(L)
## 1.0000 -107.8858
##
## Hypothesis test based on Clarke (1980; Biometrika):
## r2 T df P
## 0.218877 8.754613 74.108564 0.000000
##
## Note that the null hypothesis test is h0 = 1
plot(obj)
The fix guarantees that both the null hypothesis & fitted model RMA regression lines pass through the ML reconstructed ancestral state value for the root node of both x & y. (For some reason, this was not the case before - although it should have been.)
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