overfitPGLS function

Testing PGLS_fossil overfit

Testing the robustness of PGLS_fossil results to sampling effects and phylogenetic uncertainty.

overfitPGLS(modform,oveRR=NULL,phylo.list=NULL,data=NULL,...)

Arguments

• modform,: data as passed to PGLS_fossil.
• oveRR: an object produced by applying overfitRR to be provided if PGLS_fossil rescaled according to RRphylo rates should be performed.
• phylo.list: a list of phylogenetic trees to be provided if PGLS_fossil on unscaled trees should be performed.
• data: a data.frame or list including response and predictor variables as named in modform. If not found in data, the variables are taken from current environment.
• ...: further argument passed to PGLS_fossil.

Returns

The function returns a list containing two 'RRphyloList' objects including results of PGLS_fossil performed by using the phylogeny as it is ($tree) and/or rescaled according to RRphylo rates ($RR). The output always has an attribute "Call" which returns an unevaluated call to the function.

Examples

## Not run:

cc<- 2/parallel::detectCores()
library(phytools)
library(ape)

# generate fictional data to test the function
rtree(100)->tree
fastBM(tree)->resp
fastBM(tree,nsim=3)->resp.multi
fastBM(tree)->pred1
fastBM(tree)->pred2
data.frame(y1=resp,x2=pred1,x1=pred2)->dat

# perform RRphylo and PGLS_fossil with univariate/multivariate phenotypic data
PGLS_fossil(modform=y1~x1+x2,data=dat,tree=tree)->pgls_noRR
RRphylo(tree,resp,clus=cc)->RR
PGLS_fossil(modform=resp~pred1+pred2,RR=RR)->pgls_RR

PGLS_fossil(modform=y1~x1+x2,data=list(y1=resp.multi,x2=pred1,x1=pred2),tree=tree)->pgls2_noRR
RRphylo(tree,resp.multi,clus=cc)->RR2
PGLS_fossil(modform=resp.multi~pred1+pred2,tree=tree,RR=RR2)->pgls2_RR

# overfitPGLS routine
# generate a list of subsampled and swapped phylogenies to test
tree.list<-resampleTree(RR$tree,s = 0.25,swap.si=0.1,swap.si2=0.1,nsim=10)

# test the robustnes of PGLS_fossil with univariate/multivariate phenotypic data
ofRR<-overfitRR(RR = RR,y=resp,phylo.list=tree.list,clus=cc)
ofPGLS<-overfitPGLS(oveRR = ofRR,phylo.list=tree.list,modform = y1~x1+x2,data=dat)

ofRR2<-overfitRR(RR = RR2,y=resp.multi,phylo.list=tree.list,clus=cc)
ofPGLS2<-overfitPGLS(oveRR = ofRR2,phylo.list=tree.list,modform = y1~x1+x2,
                     data=list(y1=resp.multi,x2=pred1,x1=pred2))
## 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("overfitPGLS")", " vignette") ; c("list("Alternative-trees")", " vignette")

Author(s)

Silvia Castiglione, Carmela Serio, Giorgia Girardi, Pasquale Raia