phylotools (version 0.1.2)

phylotools-package: Phylogenetic tools for ecologists

Description

This package currently consists of a few functions for handling DNA-barcoding sequences to build supermatrix for further analysis with RAxML etc. Much more functions for conducting phylogenetic analysis would be added in the future, especially for community phylogentic analysis.

Details

Package:

phylotools

Type:

Package

Version:

0.1.2

Date:

2010-8-18

License:

GLP-2

LazyLoad:

yes

References

Kress W., Erickson D., Jones F., Swenson N., Perez R., Sanjur O., Bermingham E., Plant DNA barcodes and community phylogeny of a tropical forest dynamics plot in Panama. Proceedings of the National Academy of Sciences of the United States of America. 2009 18621-18626

Examples

###############################################
## Example Part I###Building Supermatrix########
###############################################

### Build super matrix
dir <- system.file("extdata", package = "phylotools")
setwd(dir)

## Supermatrix with "rbcla","matk","trnH-psbA"
supermat <- supermat(rbcl = "rbcla.phy", matk = "matK.phy", 
          trn = c("trn1.phy", "trn2.phy","trn3.phy","trn4.phy"))	   
## Save to file
write.mat(supermat, "result.phy")

## Delete file
unlink("result.phy")



###############################################
## Example Part II###Create a image plot#######
###############################################

## Create an Image with legend from named numerical vectors
x <- rnorm(600)
labmat <- expand.grid(paste("X",1:30, sep = ""), 
                  paste("Y", 1:20, sep = ""))
                  
lab <- paste(labmat[,1], labmat[,2], sep = "")
imagevect(x, labels = lab, col = cm.colors(10))



###############################################
## Example Part III###Handling fasta project###
###############################################

## Handling Fasta files
library(seqRFLP)
## loading data
data(fil.fas)
## Get the names of the sequences
col1 <- gnames.fas(fil.fas)
## Generating new names
col2 <- paste("seq", 1:length(col1), sep = "")
reftable.rename <- data.frame(col1, col2)
renamed <- rename.fasta(fil.fas, reftable.rename)

##Generate split factor levels.
index <- rep(NA, length(col2))
level1 <- seq(1, length(col2), by = 2)
index[level1] <- 1
index[-level1] <- 2

## Reference table
reftable.split <- data.frame(col2, index)

## split the fasta object
fasta.split(renamed, reftable.split)



#################################################
## Example Part IV###Phylosor for very large data
#################################################
## Make sure the PhyloCom can be invoked by command line
## res <- phylocom.phylosor(sample.file = "sample",
##                                phylo = "phylo")



#################################################
## Example Part V###Rescale the FDP data #######
## to different scales ##########################
#################################################
## 20m                                
## plotscale(inputdata = BCI, len = 1000, wid = 500,
##           scale = 20)
## 50m                                
## plotscale(inputdata = BCI, len = 1000, wid = 500, 
##           scale = 50)
## 100m                                
## plotscale(inputdata = BCI, len = 1000, wid = 500, 
##          scale = 100)



##################################################
## Example Part VI### 
## Lineages inequality and 
## Mean Gini Coefficient amonge 
## lineages caused by imperfect sampling 
##################################################
data(bird.orders)
rtr1 <- del.tree.tip(bird.orders,3)
inequality(bird.orders, rtr1[[1]], h = 25.25103)


data(bird.orders)
to.drop <- c("Craciformes", "Galliformes", "Gruiformes")
droped <- drop.tip(bird.orders, to.drop)
meangini(tree = bird.orders, subtree = droped, 
         times = 10, plot = TRUE)
meangini(tree = bird.orders, subtree = droped, 
         times = 50, plot = TRUE)
meangini(tree = bird.orders, subtree = droped, 
          times = 100, plot = TRUE)
meangini(tree = bird.orders, subtree = droped, 
          times = 200, plot = TRUE)