LaRC: Landscape Roughness Calculator

In PsamClark/LaRC: Landscape Roughness Calculator

Description

Function for calculating roughness by sampling across a fitness landscape based on sequence data. Function initially calculates string distances between sequences and and condenses the resultant distance matrix to the number of dimensions requested a linear fit between the fitness value and the dimensions is then calculated and the average slope for this fit is c alculated.The final step is to calculate the sum of the residuals to the fit squared divided by the mean slope to give the roughness/slope. This calculation is repeated several times with bootstrap sampling on the full set and the mean and standard error of the roughness/slope values is calculated.

Usage

LaRC(data_set, dims = 2, nsize = 16, runs = 100, meth = "lcs")

Arguments

data_set	tibble containing paired sequences and fitness values
dims	number of dimensions requested for landscape
nsize	number of data points extracted in each sampling
runs	number of times sampling is performed
meth	string distance calculation method

Value

Returns a list object containing the mean and standard error of the roughness/slope values obtained from sampling.

PsamClark/LaRC documentation built on July 8, 2020, 2:34 p.m.