estimate.d.sequential: Estimate d using sequential method

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

Description

Estimate d using sequential method

Usage

estimate.d.sequential(geno.matrix, fit.matrix, d.hat.MLE, d.hat.RDB, d.range,
  d.max.adj = 1.1)

Arguments

geno.matrix	Genotype matrix generated in generate.geno.matrix or read in.
fit.matrix	Fitness matrix generated in sim.stick.data or read in.
d.hat.MLE	The MLE estimate of d from estimate.d.MLE
d.hat.RDB	The estimate of d from estimate.d.RDB
d.range	Interval of d where MLE was searched. Defines when valid MLE exists (see details).
d.max.adj	When forced to use the maximum estimator, the estimate is adjusted upwards by this factor (see details). Default = 1.1 (inflate observation 10%).

Details

If a valid MLE exists, function returns it. When MLE is at the boundary as defined by d.range or less than the observed distance from wild type fitness to the maximum fitness, this is not considered a valid estimate. If MLE is not valid, but RDB estimate exists, it returns RDB estimate. If neither exists, returns the Max estimated. The Max estimate is based on the largest observed fitness times a factor d.max.adj. Name of the returned object indicates the method estimate is based on (MLE, RDB or Max).

Value

Estimate of d. Name indicates methods used.

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)])
d.hat.MLE <- estimate.d.MLE(geno.matrix, fit.matrix,c(0.1, 10),0.001,c(2,1))
d.hat.RDB <- estimate.d.RDB(geno.matrix, fit.matrix,-100)$d.hat.RDB
estimate.d.sequential(geno.matrix, fit.matrix, d.hat.MLE, d.hat.RDB, c(0.1, 10), 1.1)

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