angle.matrix | R Documentation |
This function computes and compares ontogenetic vectors among species in a tree.
angle.matrix(RR,node,Y=NULL,select.axes=c("no","yes"), type=c("phenotypes","rates"),cova=NULL,clus=0.5)
RR |
an object produced by |
node |
the number identifying the most recent common ancestor to all the species the user wants ontogenetic vectors be computed. |
Y |
multivariate trait values at tips. |
select.axes |
if |
type |
specifies weather to perform the analysis on phenotypic
( |
cova |
the covariate to be indicated if its effect on rate values must
be accounted for. Contrary to |
clus |
the proportion of clusters to be used in parallel computing. To
run the single-threaded version of |
The angle.matrix
function takes as objects a phylogenetic
tree (retrieved directly from an RRphylo
object), including
the different ontogenetic stages of each species as polytomies. Names at
tips must be written as species ID and stage number separated by the
underscore. The RRphylo
object angle.matrix
is fed with is
just used to extract the dichotomized version of the phylogeny. This is
necessary because node numbers change randomly at dichotomizing non-binary
trees. However, when performing angle.matrix
with the covariate the
RRphylo
object must be produced without accounting for the
covariate. Furthermore, as the covariate only affects the rates
computation, it makes no sense to use it when computing vectors for
phenotypic variables. Once angles and vectors are computed,
angle.matrix
performs two tests by means of standard major axis
(SMA) regression. For each species pair, the "biogenetic test" verifies
whether the angle between species grows during development, meaning that
the two species becomes less similar to each other during growth. The
"paedomorphosis test" tells whether there is heterochronic shape change in
the data. Under paedomorphosis, the adult stages of one (paedomorphic)
species will resemble the juvenile stages of the other (peramorphic)
species. The test regresses the angles formed by the shapes at different
ontogenetic stages of a species to the shape at the youngest stage of the
other in the pair, against age. Then, it tests whether the two regression
lines (one per species) have different slopes, and whether they have
different signs. If the regression lines point to different directions, it
means that one of the two species in the pair resembles, with age, the
juveniles of the other, indicating paedomorphosis. Ontogenetic vectors of
individual species are further computed, in reference to the MRCA of the
pair, and to the first stage of each species (i.e. intraspecifically).
Importantly, the size of the ontogenetic vectors of rates tell whether the
two species differ in terms of developmental rate, which is crucial to
understand which process is behind paedomorphosis, where it applies.While
performing the analysis, the function prints messages on-screen informing
about tests results. If select.axes = "yes"
, informs the user about
which phenotypic variables are used. Secondly, it specifies whether
ontogenetic vectors to MRCA, and intraspecific ontogenetic vectors
significantly differ in angle or size between species pairs. Then, for each
species pair, it indicates if the biogenetic law and paedomorphosis apply.
A list containing 4 objects:
$regression.matrix a 'list' including 'angles between species' and 'angles between species to MRCA' matrices for all possible combinations of species pairs from the two sides descending from the MRCA. For each matrix, corresponding biogenetic and paedomorphosis tests are reported.
$angles.2.MRCA.and.vector.size a 'data.frame' including angles between the resultant vector of species and the MRCA and the size of the resultant vector computed from species to MRCA, per stage per species.
$ontogenetic.vectors2MRCA a 'data.frame' including angle, size, and corresponding x and y components, of ontogenetic vectors computed between each species and the MRCA. For both angle and size, the p-value for the difference between species pairs is reported.
$ontogenetic.vectors.to.1st.stage a 'list' containing:
$matrices: for all possible combinations of species pairs from the two sides descending form the MRCA, the upper triangle of the matrix contains the angles between different ontogenetic stages for the first species. The same applies to the lower triangle, but for the second species.
$vectors: for all possible combinations of species pairs from the two sides descending form the MRCA, angles and sizes of ontogenetic vectors computed to the first stage of each species. For both, the p-value for the difference between the species pair is reported.
Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto
## Not run: data("DataApes") DataApes$PCstage->PCstage DataApes$Tstage->Tstage DataApes$CentroidSize->CS cc<- 2/parallel::detectCores() RRphylo(tree=Tstage,y=PCstage,clus=cc)->RR # Case 1. without accounting for the effect of a covariate # Case 1.1 selecting shape variables that show significant relationship with age # on phenotypic vectors angle.matrix(RR,node=72,Y=PCstage,select.axes="yes",type="phenotypes",clus=cc) # on rates vectors angle.matrix(RR,node=72,Y=PCstage,select.axes="yes",type="rates",clus=cc) # Case 1.2 using all shape variables # on phenotypic vectors angle.matrix(RR,node=72,Y=PCstage,select.axes="no",type="phenotypes",clus=cc) # on rates vectors angle.matrix(RR,node=72,Y=PCstage,select.axes="no",type="rates",clus=cc) # Case 2. accounting for the effect of a covariate (on rates vectors only) # Case 2.1 selecting shape variables that show significant relationship with age angle.matrix(RR,node=72,Y=PCstage,select.axes="yes",type="rates", cova=CS,clus=cc) # Case 2.2 using all shape variables angle.matrix(RR,node=72,Y=PCstage,select.axes="no",type="rates",cova=CS,clus=cc) ## End(Not run)
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