retrieve.angles: Extracting a user-specified subset of the evo.dir results

In RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies

Extracting a user-specified subset of the evo.dir results

Description

This function takes the result list produced by evo.dir as the input, and extracts a specific subset of it. The user may specify whether to extract the set of angles between species resultant vectors and the MRCA, the size of resultant vectors, or the set of angles between species.

Usage

retrieve.angles(angles.res,wishlist=c("anglesMRCA","angleDir","angles.between.species"),
  random=c("yes","no"),focus=c("node","species","both","none"),
 node=NULL,species=NULL,write2csv=c("no","yes"),csvfile=NULL)

Arguments

angles.res	the object resulting from evo.dir function.
wishlist	specifies whether to extract angles and sizes ("anglesMRCA") of resultant vectors between individual species and the MRCA, angles and sizes ("angleDir") of vectors between individual species and a fixed reference vector (the same for all species), or angles between species resultant vectors ("angles.between.species").
random	it needs to be "yes" if 'angles.res' object contains randomization results.
focus	it can be "node", "species", "both", or "none", whether the user wants the results for a focal node, or for a given species, for both, or just wants to visualize everything.
node	must be indicated if focus = "node" or "both". As for evo.dir, the node number must refer to the dichotomic version of the original tree, as produced by RRphylo.
species	must be indicated if focus = "species" or "both".
write2csv	has been deprecated; please see the argument csvfile instead.
csvfile	if results should be saved to a .csv file, a character indicating the name of the csv file and the path where it is to be saved. If no path is indicated the file is stored in the working directory. If left unspecified, no file will be saved.

Details

retrieve.angles allows to focalize the extraction to a particular node, species, or both. Otherwise it returns the whole dataset.

Value

retrieve.angles outputs an object of class 'data.frame'.

If wishlist = "anglesMRCA", the data frame includes:

• MRCA the most recent common ancestor the angle is computed to

• species species ID

• angle the angle between the resultant vector of species and the MRCA

• vector.size the size of the resultant vector computed from species to MRCA

If wishlist = "angleDir", the data frame includes:

• MRCA the most recent common ancestor the vector is computed to

• species species ID

• angle.direction the angle between the vector of species and a fixed reference

• vector.size the size of the vector of species

If wishlist = "angles.between.species", the data frame includes:

• MRCA the most recent common ancestor the vector is computed from

• species pair IDs of the species pair the "angle between species" is computed for

• angleBTWspecies2MRCA angle between species resultant vectors to MRCA

• anglesBTWspecies angle between species resultant vectors

Author(s)

Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto

Examples

## Not run: 
    data("DataApes")
    DataApes$PCstage->PCstage
    DataApes$Tstage->Tstage

    cc<- 2/parallel::detectCores()
    RRphylo(tree=Tstage,y=PCstage,clus=cc)->RR

# Case 1. "evo.dir" without performing randomization
    evo.dir(RR,angle.dimension="rates",pair.type="node",
    node=  57,random="no")->evo.p

 # Case 1.1 angles and sizes of resultant vectors between individual species and the MRCA:
  # for a focal node
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="no",focus="node",
    node=68)
  # for a focal species
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="no",focus="species",
    species="Sap")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="no",focus="both",
    node=68,species="Sap")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="no",focus="none")

 # Case 1.2 angles and sizes of vectors between individual species
 #and a fixed reference vector:
  # for a focal node
    retrieve.angles(evo.p,wishlist="angleDir",random="no",focus="node",
    node=68)
  # for a focal species
    retrieve.angles(evo.p,wishlist="angleDir",random="no",focus="species",
    species="Sap")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="angleDir",random="no",focus="both",
    node=68,species="Sap")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="angleDir",random="no",focus="none")

 # Case 1.3 angles between species resultant vectors:
  # for a focal node
    retrieve.angles(evo.p,wishlist="angles.between.species",random="no",
    focus="node", node=68)
  # for a focal species
    retrieve.angles(evo.p,wishlist="angles.between.species",random="no",
    focus="species", species="Sap")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="angles.between.species",random="no",
    focus="both",node=68,species="Sap")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="angles.between.species",random="no",
    focus="none")


# Case 2. "evo.dir" with performing randomization
    evo.dir(RR,angle.dimension="rates",pair.type="node",node=57,
    random="yes",nrep=10)->evo.p

 # Case 2.1 angles and sizes of resultant vectors between individual species and the MRCA:
  # for a focal node
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="yes",focus="node",
    node=68)
  # for a focal species
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="yes", focus="species",
    species="Sap")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="yes",focus="both",
    node=68,species="Sap")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="yes",focus="none")

 # Case 2.2 angles and sizes of vectors between individual species and a fixed reference vector:
  # for a focal node
    retrieve.angles(evo.p,wishlist="angleDir",random="yes",focus="node",
    node=68)
  # for a focal species
    retrieve.angles(evo.p,wishlist="angleDir",random="yes",focus="species",
    species="Sap")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="angleDir",random="yes",focus="both",
    node=68, species="Sap")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="angleDir",random="yes",focus="none")

 # Case 2.3 retrieve angles between species resultant vectors:
  # for a focal node
    retrieve.angles(evo.p,wishlist="angles.between.species",random="yes",
    focus="node", node=68)
  # for a focal species
    retrieve.angles(evo.p,wishlist="angles.between.species",random="yes",
    focus="species", species="Sap")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="angles.between.species",random="yes",
    focus="both",node=68,species="Sap")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="angles.between.species",random="yes",
    focus="none")
    
## End(Not run)

RRphylo documentation built on June 7, 2023, 5:49 p.m.