fn.ab: Vector of abundances with different methods

In VHIRHepatiques/QSutils: Quasispecies Diversity

Vector of abundances with different methods

Description

Function to simulate haplotype abundances in the quasispecies.

Usage

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

Arguments

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".

Details

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 ~ \left( \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

Value

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

Author(s)

Mercedes Guerrero-Murillo and Josep Gregori

See Also

geom.series,GetRandomSeq, GenerateVars,Diverge

Examples

# 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

VHIRHepatiques/QSutils documentation built on April 27, 2024, 10:29 p.m.