magellan: Functions generating the fitness of the mutants' genotypes in...

In YoannAnciaux/inferenceFitnessLandscape: What the Package Does (One Line, Title Case)

Description

Functions generating the fitness of the mutants' genotypes in genotype_table The mutants are generated by a call to the fl_generate binary from MAGELLAN. See Rstudio. Warning : These functions return malthusian fitnesses (also called log fitnesses). i.e. they use the argument "-L" in MAGELLAN.

Usage

model_Fix(nb_mut, genotype_table, fitness_wt, f, path2_fl_generate)

model_Mult(nb_mut, genotype_table, fitness_wt, s, S, d, path2_fl_generate)

model_HoC(nb_mut, genotype_table, fitness_wt, H, path2_fl_generate)

model_NK(nb_mut, genotype_table, fitness_wt, K, r, path2_fl_generate)

model_Ising(nb_mut, genotype_table, fitness_wt, i, I, c, path2_fl_generate)

model_EggBox(nb_mut, genotype_table, fitness_wt, e, E, path2_fl_generate)

model_Optimum(nb_mut, genotype_table, fitness_wt, o, O, p, P,
  path2_fl_generate)

Arguments

nb_mut	A natural number. Number of mutations (or loci in MAGELLAN) used to form the different genotypes from genotype_table.
genotype_table	A matrix of 0 and 1. The rows correspond to different genotypes and the columns to the mutations that are considered for these genotypes. A genotype (at a certain row) has a given mutation when there is a 1 in the corresponding column. A row with only zeros correspond to the wild type.
fitness_wt	A real number. Fitness of the wild type used as reference.
f	A real number. Add a fixed contribution
path2_fl_generate	File path to the binary fl_generate of MAGELLAN.
s	A real number. Mean fitness selection coefficient per locus (fitness is then fitness_wt + s)
S	A real number. Stdev for fitness for each locus (if 0 use fix fitness)
d	A real number. Can set a diminishing (negative) or increasing (positive) return as you approach the peak
H	A positive real number. Stdev for fitness for House-of-Cards (normal centered on 0)
K	A positive integer. Kaufman NK with N=nb_mut and K<=N
r	A logical value. If TRUE interacting loci are chosen at random. If FALSE they are the neighbors.
i	A real number. Mean cost for incompatibility.
I	A positive real number. Stdev cost for incompatibility (if 0 use fix cost)
c	A logical value. If TRUE last interacs with first (loci are arranged on a circle).
e	A real number. Every other genotype is +/- e
E	A positive real number. Add noise on the mean effect for eggbox
o	A real number. Optimum to target.
O	A positive real number. The spread around the optimal point, the larger the less selection for optimum
p	A real number. The mean production value for each non 0 allele.
P	A positive real number. The associated stdev.

Value

A vector of real numbers. Each element is the fitness of the corresponding random mutants in genotype_table. They are in the same order as the rows of genotype_table.

YoannAnciaux/inferenceFitnessLandscape documentation built on Oct. 31, 2019, 1:19 a.m.