Skip to content

Instantly share code, notes, and snippets.

Embed
What would you like to do?
Terminal I
1 1
2 2
3 4
4 6
5 6
6 6
7 7
8 8
9 9
10 9
11 4
12 5
13 6
14 8
15 9
16 9
17 8
18 9
19 10
20 10
(1,(2,((3,((4,5),(6,(7,(8,(9,10)))))),(11,(12,(13,((14,(15,16)),(17,(18,(19,20))))))))));
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
##Index I
data <- read.table("index.csv",header = T, sep=",")
data
##I values
data[,2]
##Summatory of all I values
total.I <- as.numeric(sum(data[,2]))
##Now the Q index is calculate
##Total I value / each I value
Q <- total.I/data$I
data$Q <- Q
data
##Foun the minimum Q value
min.Q <- min(data$Q)
##Whith the minimum Q value, the W index is calculate
## each Q value / minimum Q value
W <- data$Q/min.Q
data$W <- W
data
#Here, I create the basic function.
vane91 <- function(x){
data <- x
total.I <- as.numeric(sum(data[,2]))
Q <- total.I/data[,2]
data$Q <- Q
min.Q <- min(data$Q)
W <- data$Q/min.Q
data$W <- W
a <- 0
l <- length(data[,1])
#Find the highest W value and his terminal
for (i in seq(1:l)){
if (data[i,4]>a){
a <- data[i,4]
n <- i
}
}
print(data)
print("The terminal which highest W values is:")
print(data[n,1])
print("With W value =")
print(a)
}
vane91(data)
##Remember vane91 use a data frame with just 2 columns (Terminals first and I index second)
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment