estimate.d.MLE: Find MLE of d

In jtvanleuven/Stickbreaker: Fits Stickbreaking, Multiplicative and Additive Models to Data

Description

Find MLE of d

Usage

estimate.d.MLE(geno.matrix, fit.matrix, d.range, accuracy = 0.001,
  wts = c(2, 1))

Arguments

geno.matrix	Genotype matrix generated in generate.geno.matrix
fit.matrix	Fitness matrix generated in sim.stick.data
d.range	Interval of d to search for maximum over
accuracy	tol to send optimize function
wts	Vector of weights to weight genotypes by. Used when generate.geno.weight.matrix is called (see that function). Default is c(2,1), meaning weight single-mutation genotypes twice as heavily as others. Alternatively, vector of weights corresponding to geno.matrix can be provided.

Details

Maximizes the function calc.stick.logLn using optimize

Value

MLE of d

Examples

n.muts <- length(Khan.data[1,])-1
geno.matrix <- Khan.data[,seq(1, n.muts)]
fit.matrix <- as.matrix(Khan.data[,(n.muts+1)])
estimate.d.MLE(geno.matrix, fit.matrix,c(0.1, 10),0.001,c(2,1))

jtvanleuven/Stickbreaker documentation built on May 20, 2019, 3:18 a.m.