Description Usage Arguments Details Value See Also Examples
View source: R/diversity.range.R
Generates multiple populations stochastically from an identical source, and measures the resulting diversity over time in each.
1 2 3 4 |
m.rate |
Mutation rate (per genome per generation). |
runtime |
Number of bacterial generations over which to simulate. |
equi.pop |
Equilibrium effective population size. |
iterations |
Number of populations to simulate. |
n.points |
Number of equidistant points to sample diversity during |
genomelength |
Genome length. |
bottle.times |
Vector of population bottleneck times. |
bottle.size |
Size of population bottleneck. |
feedback |
Number of generations between each simulation report. |
makeplot |
Should resulting diversity be plotted? |
area |
Should 95% central quantile of genetic diversity be shaded? If |
colline |
Colour of lines (if |
colarea |
Colour of shaded area (if |
ref.strain |
Reference strain, if required. |
init.freq |
Initial frequency of strains in starting population (if |
libr |
Library of initial sequences. |
nuc |
Nucleotides at polymorphic sites, corresponding to |
... |
Additional arguments to be passed to |
Provides an empirical estimate of the expected genetic diversity (pairwise SNP distance) over time, with associated uncertainty. Initial population can be specified using the libr
, nuc
and init.freq
arguments, otherwise population is grown from a single genotype. Resolution can be improved by increasing n.points
, and accuracy by increasing iterations
(at the expense of accuracy).
A iterations
by n.points
matrix with diversity over time for each simulation.
1 2 3 4 | iterations <- 10
K <- diversity.range(m.rate=0.0005, runtime=1000, equi.pop=1000,
iterations=iterations, n.points=100, genomelength=100000, feedback=100,
makeplot=TRUE, area=TRUE, colline="blue", colarea=rgb(0,0,1,0.4))
|
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