fn.ab: Vector of abundances with different methods
In QSutils: Quasispecies Diversity

Description Usage Arguments Details Value Author(s) See Also Examples

Function to simulate haplotype abundances in the quasispecies.

1	fn.ab(n, h = 10000, r = 0.5,fn="pcf")

`n`	Number of counts to compute.
`h`	Highest abundance value.
`r`	A number to compute the abundance. See details.
`fn`	Character indicating which function to use to compute the abundances "pf","pcf" or "dfp", see details. By default "pcf".

The abundances computed as a power of fractions, when fn is "pf", are computed according to the following equation, taking the integer part:

max(h r^{(i-1)},1); ~~ 0<r<1; ~~ i=1..n

The lower r, the faster the decrease in abundance, r is in the range 0 < r < 1.

With "pcf" the abundances are computed by a power of decreasing fractions, as counts, according to the following equation, taking the integer part:

max(h ~ ≤ft( \frac{1}{i} \right) ^r,1); ~~ r>0; ~~i=1..n

The higher r, the faster the decrease in abundances. In this case r corresponds to the power of the function, a value larger than 0, usually in the range 0.5 < r < 4.

If fn is equal to "dfp", the abundances are computed by increasing root powers according to the following equation,taking the integer part:

max(h^{(1/i)},1); ~~ i=1..n

Numeric vector with n decreasing counts, where the first element equals h, and no element is lower than 1.

Mercedes Guerrero-Murillo and Josep Gregori

geom.series,GetRandomSeq, GenerateVars,Diverge

# Simulate a quasispecies alignment.
m1 <- GetRandomSeq(50)
v1 <- GenerateVars(m1,50,2,c(10,1)) 
qs <- c(m1,v1)
w_pf <- fn.ab(length(qs),h=1000,r=1.5,fn="pf")
w_pf
w_pcf <- fn.ab(length(qs),h=1000,r=1.5,fn="pcf")
w_pcf
w_dfp <- fn.ab(length(qs),h=1000,fn="dfp") 
w_dfp