In chaolab2019/chaoUtility: chao lab utility

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title: "A Quick introudction for chaolab utility" output: github_document

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overview

library(chaoUtility)

chaoUtility focuses on some useful tools for chao lab, include:

general functions:Boot_p() and checktype()

phylogeny fucntions:

-phylo2phytree() : input phylo object(ultrmetric or non-ultrametric), return chaophytree object

-phyExpandData() : input abundance data, label,chaophytree object, return tibble with abundance or incidence data.

-phyExpandData() : input abundance data, label,chaophytree object, return tibble with abundance or incidence data.

-phylengthbyT() : input vector of ageT, chaophytree object, return matrix with label and new branch.length (default rootExtend =T ,if rootExtend=T and ageT>treeH, root.length=ageT-treeH), non ultrametric tree example

-phyBranchAL() : input abundance data,phylo object,vector of ageTs, return Chaophyabu object (default rootExtend =T ,remove0=T)

-phyBranchALinc() : input incidence_raw data,phylo object,vector of ageTs, return Chaophyabu object (default rootExtend =T ,remove0=T)

-phy_BranchAL_IncBootP() : input incidence bootstrp p,phylo object,vector of ageTs, return ChaophyincBP object (default rootExtend =T ,remove0=T) : the inode formular is 1-(1-p1)(1-p2)

-phylo2chaolabphy()

HOW TO RUN chaoUtility:

The chaoUtility package can be downloaded with a standard R installation procedure using the following commands.

## install the latest version from github
install.packages('devtools')
library(devtools)
install_github('chaolab2019/chaoUtility')

Boot_p

We first describe the main function Boot_p() with default arguments:

Boot_p(x,zero=TRUE,Bootype="One",datatype="abundance")

Argument	Description
x	a matrix, data.frame, lists of species abundances or incidence data.
zero	reserves zero frequency or not. Default is TRUE.
Bootype	character : "One" or "JADE" or "SAR". `Bootype = "One"` or `Bootype = "JADE"` or `Bootype = "SAR"` "One": from #99 2013 Entropy and the species accumulation curve Appendix S2: Estimating species relative abundance. "JADE": from #107 Unveiling the species-rank abundance distribution by generalizing the Good-Turing sample coverage theory. "SAR": :sampleing which was drawn without replacement (based on one parameter estimated method)
datatype	data type of input data: individual-based abundance data (`datatype = "abundance"`), or species by sampling-units incidence frequency (`datatype = "incidence_freq"` or `datatype = "incidence"`),or species by sampling-units incidence matrix (`datatype = "incidence_raw"`).

EXAMPLES

without replacement:

library(chaoUtility)
data(bird)
bird.abun<- bird$abun
Boot_p(bird$abun,zero=FALSE,Bootype="SAR",datatype="abundance",rho=0.8)

data(incdata)
Boot_p(incdata,zero=FALSE,Bootype="SAR",datatype="incidence",rho=0.8)

with replacement:One

library(chaoUtility)
data(bird)
bird.inc <- bird$inci
bird.abun<- bird$abun
Boot_p(bird$abun, datatype="abundance")

References

• Chao, A., Wang, Y. T., and Jost, L. (2013). Entropy and the species accumulation curve: a novel estimator of entropy via discovery rates of new species. Methods in Ecology and Evolution, 4, 1091-1110.
• Chao, A., Hsieh, T. C., Chazdon, R. L., Colwell, R. K., and Gotelli, N. J. (2015). Unveiling the species-rank abundance distribution by generalizing the Good-Turing sample coverage theory. Ecology 96, 1189-1201.

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phylo2phytree

examples ultrametictree

library(chaoUtility)
data(treesample)
newphy<-phylo2phytree(treesample)

class(newphy)

newphy$tips

newphy$nodes

newphy$phytree


newphy$treeH

library(ape)
plot(treesample)
tiplabels()
nodelabels()
library(dplyr)
nodetext<-newphy$phytree %>% filter(tgroup!="Tip") %>% pull(label)
nodelabels(text=nodetext,adj=c(0,2.2))
edgelabels(treesample$edge.length, bg="black", col="white", font=2)

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examples non ultrametictree

text<-"(((((((A:4,B:4):6,C:5):8,D:6):3,E:21):10,((F:4,G:12):14,H:8):13):13,((I:5,J:2):30,(K:11,L:11):2):17):4,M:56);"
library(ape)
tree2<-read.tree(text=text)

library(chaoUtility)
tree2.phytree<-phylo2phytree(tree2)

library(dplyr)
nodetext<-tree2.phytree$phytree %>% filter(tgroup!="Tip") %>% pull(label)
plot(tree2)
nodelabels(text=nodetext)
edgelabels(tree2$edge.length, bg="black", col="white", font=2)

tree2.phytree$treeH

as.data.frame(tree2.phytree$phytree)

tree2.phytree$leaves

tree2.phytree$nodes

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examples non ultrametictree

text<-"(((((((A:4,B:4):6,C:5):8,D:6):3,E:21):10,((F:4,G:12):14,H:8):13):13,((I:5,J:2):30,(K:11,L:11):2):17):4,M:56);"
library(ape)
tree2<-read.tree(text=text)

library(chaoUtility)
tree2.phytree<-phylo2phytree(tree2)

library(dplyr)
nodetext<-tree2.phytree$phytree %>% filter(tgroup!="Tip") %>% pull(label)
plot(tree2)
nodelabels(text=nodetext)
edgelabels(tree2$edge.length, bg="black", col="white", font=2)

tree2.phytree$treeH

as.data.frame(tree2.phytree$phytree)

tree2.phytree$leaves

tree2.phytree$nodes

phyExpandData

EXAMPLES:abundance data

library(chaoUtility)
data(phybird.new)
bird.abu <- phybird.new$abun
bird.lab <- rownames(phybird.new$abun)
bird.phy <- phybird.new$chaophytree

bird.abu

bird.lab


phyExpandData(x=bird.abu, labels=bird.lab, phy=bird.phy, datatype="abundance")

examples incidence simple data

library(chaoUtility)
data(phyincisimple)
data.inc <- phyincisimple$inci.simple.data
data.lab<-rownames(data.inc)
phy.inc<-phyincisimple$tree.simple.phytree

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examples incidence simple data

library(chaoUtility)
data(phyincisimple.new)
data.inc <- phyincisimple.new$inci.simple.data
data.lab<-rownames(data.inc)
phy.inc<-phyincisimple.new$tree.simple.phytree



phylotree<-phyincisimple.new$tree.simple
plot(phylotree)
nodetext<-phy.inc$phytree %>% filter(tgroup!="Tip") %>% pull(label)
nodelabels(text=nodetext)
edgelabels(phylotree$edge.length, bg="black", col="white", font=2)

data.inc

dataNtree<-phyExpandData(data.inc, labels=data.lab, phy=phy.inc, datatype="incidence_raw")
as.data.frame(dataNtree)

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phyLengthbyT

EXAMPLES

library(chaoUtility)
data(phybird)
bird.phy <- phybird$chaophytree


bird.phy$treeH

phyLengthbyT(Ts=c(90,75,55), phy=bird.phy, datatype="abundance")

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examples non ultrametric tree by reference t

text<-"(((((((A:4,B:4):6,C:5):8,D:6):3,E:21):10,((F:4,G:12):14,H:8):13):13,((I:5,J:2):30,(K:11,L:11):2):17):4,M:56);"
library(ape)
tree2<-read.tree(text=text)

examples non ultrametric tree by reference t

text<-"(((((((A:4,B:4):6,C:5):8,D:6):3,E:21):10,((F:4,G:12):14,H:8):13):13,((I:5,J:2):30,(K:11,L:11):2):17):4,M:56);"
library(ape)
tree2<-read.tree(text=text)

library(chaoUtility)
phytree<-phylo2phytree(tree2)

phytree$treeH

phyLengthbyT(Ts=c(75,55,50), phy=phytree, datatype="abundance",rootExtend=T)

library(dplyr)
nodetext<-phytree$phytree %>% filter(tgroup!="Tip") %>% pull(label)
plot(tree2)
nodelabels(text=nodetext)
edgelabels(tree2$edge.length, bg="black", col="white", font=2)

as.data.frame(phytree$phytree)

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#phybranchal

EXAMPLES-improve performance

 data(AbuALdata)
 adata<-AbuALdata$abudata
 atree<-AbuALdata$tree
 vdata<-adata$EM
 names(vdata)<-rownames(adata)
 vdata

 refTs<-c(400,250,100)
 result<-phyBranchAL_Abu(atree,vdata,datatype="abundance",refTs)

 ##final branch.abu:removed abu=0
 treeNabu<-result$treeNabu
 treeNabu %>% print(n = Inf)

 ##final treeH:removed abu=0
 result$treeH

 ##final branch.length:removed abu=0
 result$BLbyT

 ####result$treeNabu is an object of tbl_tree could change to phylo
 tlb2phylo<-as.phylo(treeNabu)
 plot(tlb2phylo)


 ###this is the original tree
 plot(atree)

#phybranchalinc

EXAMPLES-improve performance

  data(phybird.new)
  bird.abu <- phybird.new$abun   
  bird.inc <- phybird.new$inci   
  bird.lab <- rownames(phybird.new$abun)   
  bird.phy <- phybird.new$chaophytree   
  tree<-as.phylo(bird.phy$phytree)   
  Idata<-bird.inc$North.site   

  Idata

  refTs<-c(80,90,100)   
  result<-phyBranchAL_Inc(tree,Idata,datatype="incidence_raw",refTs)   

 ##final branch.abu:removed abu=0
 treeNabu<-result$treeNabu
 treeNabu %>% print(n = Inf)

 ##final treeH:removed abu=0
 result$treeH

 ##final branch.length:removed abu=0
 result$BLbyT

 ####result$treeNabu is an object of tbl_tree could change to phylo
 tlb2phylo<-as.phylo(treeNabu)
 plot(tlb2phylo)


 ###this is the original tree
 plot(tree)

EXAMPLES

  data(phybird.new)
  bird.abu <- phybird.new$abun   
  bird.inc <- phybird.new$inci   
  bird.lab <- rownames(phybird.new$abun)   
  bird.phy <- phybird.new$chaophytree   
  tree<-as.phylo(bird.phy$phytree)   
  Idata<-bird.inc$North.site   

  refTs<-c(80,90,100)   
  result<-phy_BranchAL_Inc(tree,Idata,datatype="incidence_raw",refTs)   


 ##final branch.abu:removed abu=0
 treeNabu<-result$treeNabu
 treeNabu %>% print(n = Inf)

 ##final treeH:removed abu=0
 result$treeH

 ##final branch.length:removed abu=0
 result$BLbyT

 ####result$treeNabu is an object of tbl_tree could change to phylo
 tlb2phylo<-as.phylo(treeNabu)
 plot(tlb2phylo)


 ###this is the original tree
 plot(atree)

#phybranchalincp

EXAMPLES

  data(phyincPdata)
  pdata <- phyincPdata$pdata
  phylotree <- phyincPdata$tree

  pdata

  refTs<-c(80,90,100)
  result<-phy_BranchAL_IncBootP(phylotree,pdata,refTs,remove0=FALSE)


 ##final treeNincBP:
 treeNincBP<-result$treeNincBP
 treeNincBP %>% print(n = Inf)

 ##final treeH:
 result$treeH

 ##final branch.length:
 result$BLbyT

 ####result$treeNabu is an object of tbl_tree could change to phylo
 tlb2phylo<-as.phylo(treeNincBP)
 plot(tlb2phylo)


 ###this is the original tree
 plot(phylotree)

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chaolab2019/chaoUtility documentation built on Feb. 26, 2020, 2:48 p.m.