R/JADE.R In iNextPD: Interpolation and Extrapolation for Phylogenetic Diversity

Defines functions EstComDisPhat.undePhat.dete

```Phat.dete <- function(x, zero=FALSE){
n <- sum(x)
f1 <- sum(x==1)
f2 <- sum(x==2)
f3 <- sum(x==3)
if(f2==0){
f1 <- max(f1 - 1, 0)
f2 <- 1
}
A1 <- f1 / n * ((n-1)*f1 / ((n-1)*f1 + 2*max(f2,1)))
A2 <- f2 / choose(n, 2) * ((n-2)*f2 / ((n-2)*f2 + 3*max(f3,1)))^2

if(zero==FALSE) x <- x[x>0]
q.solve <- function(q){
e <- A1 / sum(x/n*exp(-q*x))
out <- sum((x/n * (1 - e * exp(-q*x)))^2) - sum(choose(x,2)/choose(n,2)) + A2
abs(out)
}
#q <- tryCatch(uniroot(q.solve, lower=0, upper=1)\$root, error = function(e) {1})
q <- tryCatch(optimize(q.solve, c(0,1))\$min, error = function(e) {1})
e <- A1 / sum(x/n*exp(-q*x))
o <- x/n * (1 - e * exp(-q*x))
o
}

Phat.unde <- function(x){
n <- sum(x)
f1 <- sum(x==1)
f2 <- sum(x==2)
f3 <- sum(x==3)
f4 <- max(sum(x == 4), 1)
f0.hat <- ceiling(ifelse(f2 == 0, (n - 1) / n * f1 * (f1 - 1) / 2, (n - 1) / n * f1 ^ 2/ 2 / f2))  #estimation of unseen species via Chao1
if(f0.hat < 0.5){
return(NULL)
}
if(f2==0){
f1 <- max(f1 - 1, 0)
f2 <- 1
}
A1 <- f1 / n * ((n-1)*f1 / ((n-1)*f1 + 2*max(f2,1)))
A2 <- f2 / choose(n, 2) * ((n-2)*f2 / ((n-2)*f2 + 3*max(f3,1)))^2
R <- A1^2/A2
j <- 1:f0.hat
f.solve <- function(x){
out <- sum(x^j)^2 / sum((x^j)^2) - R
abs(out)
}
b <-  tryCatch(optimize(f.solve, lower=(R-1)/(R+1), upper=1, tol=1e-5)\$min, error = function(e) {(R-1)/(R+1)})
a <- A1 / sum(b^j)
p <- a * b^j
if(f0.hat ==1 ) p <- A1
p
}

EstComDis <- function(x){
phat <- sort(c(Phat.unde(x), Phat.dete(x)), decreasing = TRUE)
phat <- phat[phat>0]
phat
}
```

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iNextPD documentation built on May 2, 2019, 3:31 a.m.