overfitSS function

Testing search.shift overfit

Testing the robustness of search.shift

(Castiglione et al. 2018 ) results to sampling effects and phylogenetic uncertainty.

overfitSS(RR,oveRR,node=NULL,state=NULL)

Arguments

• RR: an object produced by RRphylo.
• oveRR: an object produced by applying overfitRR on the object provided to the function as RR.
• node, state: arguments passed to search.shift. Arguments node and state can be specified at the same time.

Returns

The function returns a 'RRphyloList' object containing:

$SSclade.list a 'RRphyloList' including the results of each search.shift - clade condition performed within overfitSS.

$SSsparse.list a 'RRphyloList' including the results of each search.shift - sparse condition performed within overfitSS.

$shift.results a list including results for search.shift performed under clade and sparse

conditions. If one or more nodes are specified, the $clade$single.clades object contains the proportion of simulations producing significant and positive or significant and negative rate shifts for each single node, either compared to the rest of the tree ($singles) or to the rest of the tree after removing other shifting clades ($no.others). The object $clade$all.clades.together

includes the same proportions obtained by testing all the specified clades as a whole (i.e. considering them as evolving under a single rate regime). For each node the proportion of tested trees (i.e. where the clade identity was preserved) is also indicated. If a state vector is supplied, the object $sparse contains the percentage of simulations producing significant p-value separated by shift sign ($p.states).

The output always has an attribute "Call" which returns an unevaluated call to the function.

Examples

## Not run:

cc<- 2/parallel::detectCores()
# load the RRphylo example dataset including Ornithodirans tree and data
data("DataOrnithodirans")
DataOrnithodirans$treedino->treedino
log(DataOrnithodirans$massdino)->massdino
DataOrnithodirans$statedino->statedino

# peform RRphylo on Ornithodirans tree and data
RRphylo(tree=treedino,y=massdino,clus=cc)->dinoRates

# perform search.shift under both "clade" and "sparse" condition
search.shift(RR=dinoRates, status.type= "clade")->SSauto
search.shift(RR=dinoRates, status.type= "sparse", state=statedino)->SSstate

## overfitSS routine
# generate a list of subsampled and swapped phylogenies, setting as categories/node
# the state/node under testing
treedino.list<-resampleTree(dinoRates$tree,s = 0.25,categories=statedino,
                        node=rownames(SSauto$single.clades),swap.si = 0.1,swap.si2 = 0.1,nsim=10)

# test the robustness of search.shift
ofRRdino<-overfitRR(RR = dinoRates,y=massdino,phylo.list=treedino.list,clus=cc)
ofSS<-overfitSS(RR = dinoRates,oveRR = ofRRdino,state=statedino,node=rownames(SSauto$single.clades))
## End(Not run)

References

Castiglione, S., Tesone, G., Piccolo, M., Melchionna, M., Mondanaro, A., Serio, C., Di Febbraro, M., & Raia, P. (2018). A new method for testing evolutionary rate variation and shifts in phenotypic evolution. Methods in Ecology and Evolution, 9: 974-983.doi:10.1111/2041-210X.12954

See Also

c("list("overfitSS")", " vignette") ; c("list("search.shift")", " vignette") ; c("list("Alternative-trees")", " vignette")

Author(s)

Silvia Castiglione, Carmela Serio, Giorgia Girardi, Pasquale Raia