Omar Daniel Leon Alvarado oleon12

oleon12 / Vane_Wright_Index.R

Created April 26, 2015 04:37

	library(ape)
	library(phangorn)

	##This is the tree who I'll want to calculate Vane-Wright index
	##
	tree <- read.tree("puranius.tre")
	plot(tree)

	##Now a read the table
	##This table have terminal and the number of nodes who belong each terminal

oleon12 / GenBank.R

Last active August 29, 2015 14:21

Here I describe how to download DNA sequences from GenBank in R, using two types of data frames: 1. Without NA and 2. With NA.

	#How to download sequences from GenBank
	#
	#[email protected]

	#######################################################################################
	# Use a data without NA #
	# #
	#This function need a data frame with the two first columns calling Genera and Specie #
	# #
	#######################################################################################

oleon12 / toCharacter_toNumber.R

Last active August 29, 2015 14:21

If you need change numbers treat as characters in a data frame to numeric class, this function will be useful.

	toNum <- function(x){
	for (i in 1:length(x)){
	matrix <- as.matrix(x)
	x[,i] <- as.numeric(matrix[,i])
	}
	}

	#At the end, all characters in the data frame will be numeric type variables.