RRphylo: retrieve.angles – R documentation

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retrieve.angles

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"))

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`	if `"yes"` results are saved to a .csv file in your working directory.

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,write2csv="no")
  # for a focal species
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="no",focus="species",
    species="Sap", write2csv="no")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="no",focus="both",
    node=68,species="Sap",write2csv="no")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="no",focus="none",
    write2csv="no")

 # 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,write2csv="no")
  # for a focal species
    retrieve.angles(evo.p,wishlist="angleDir",random="no",focus="species",
    species="Sap", write2csv="no")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="angleDir",random="no",focus="both",
    node=68,species="Sap",write2csv="no")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="angleDir",random="no",focus="none",
    write2csv="no")

 # 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,write2csv="no")
  # for a focal species
    retrieve.angles(evo.p,wishlist="angles.between.species",random="no",
    focus="species", species="Sap", write2csv="no")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="angles.between.species",random="no",
    focus="both",node=68,species="Sap",write2csv="no")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="angles.between.species",random="no",
    focus="none",write2csv="no")


# 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,write2csv="no")
  # for a focal species
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="yes", focus="species",
    species="Sap", write2csv="no")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="yes",focus="both",
    node=68,species="Sap",write2csv="no")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="yes",focus="none",
    write2csv="no")

 # 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,write2csv="no")
  # for a focal species
    retrieve.angles(evo.p,wishlist="angleDir",random="yes",focus="species",
    species="Sap", write2csv="no")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="angleDir",random="yes",focus="both",
    node=68, species="Sap",write2csv="no")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="angleDir",random="yes",focus="none",
    write2csv="no")

 # 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,write2csv="no")
  # for a focal species
    retrieve.angles(evo.p,wishlist="angles.between.species",random="yes",
    focus="species", species="Sap", write2csv="no")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="angles.between.species",random="yes",
    focus="both",node=68,species="Sap",write2csv="no")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="angles.between.species",random="yes",
    focus="none",write2csv="no")
    
## End(Not run)

RRphylo

Phylogenetic Ridge Regression Methods for Comparative Studies

v2.5.0

GPL-2

Authors