createParams {poolABC}

Draw parameters from the priors

Description

This function creates a named vector of parameters that can be used as input in the command line of the scrm package. Please note that this function needs to be adjusted if you wish to test the effect of different prior distributions.

Usage

createParams(
  Nref,
  ratio,
  split,
  pool,
  seq,
  CW,
  WC,
  CC = NA,
  WW = NA,
  ANC = NA,
  bT,
  bCW = NA,
  bWC = NA,
  model,
  digits = 5
)

Arguments

Nref

The minimum and maximum value of the uniform distribution for the effective population size of the reference population (Nref).

ratio

The minimum and maximum value of the distribution from which the relative size of the present-day and ancestral populations are drawn. The size of these populations is set as a ratio of the size of the Nref population. All of these ratios are drawn from a log10 uniform distribution.

split

The minimum and maximum values, at the 4Nref scale, of the uniform distribution from which the values of the times of the split events are draw. Both the time of the recent split event and the distance between the two split events are drawn from this distribution.

pool

The minimum and maximum values of the uniform distribution from which the value of the error associated with DNA pooling is drawn. More specifically, this value is related with the unequal individual contribution to the pool.

seq

The minimum and maximum values of the uniform distribution from which the value of the error associated with DNA sequencing is drawn. This parameter should be supplied as a decimal number between zero and one.

CW

The minimum and maximum value of the uniform distribution from which the migration rate between the two divergent ecotypes inhabiting the same location is drawn. We consider that this parameter is drawn on a m scale. This is the migration rate from ecotype C to ecotype W.

WC

The minimum and maximum value of the uniform distribution from which the migration rate between the two divergent ecotypes inhabiting the same location is drawn. We consider that this parameter is drawn on a m scale. This is the migration rate from ecotype W to ecotype C.

CC

The minimum and maximum value of the uniform distribution from which the migration rate between similar ecotypes inhabiting different locations is drawn. We consider that this parameter is drawn on a m scale. This is the migration between the two C ecotypes at two different locations.

WW

The minimum and maximum value of the uniform distribution from which the migration rate between similar ecotypes inhabiting different locations is drawn. We consider that this parameter is drawn on a m scale. This is the migration between the two W ecotypes at two different locations.

ANC

The minimum and maximum value of the uniform distribution from which the migration rate between the two ancestral populations is drawn. We consider that this parameter is drawn on a m scale.

bT

The minimum and maximum values of the distribution from which the proportion of the simulated loci where no migration occurs between divergent ecotypes is drawn. The maximum value should not be higher than one.

bCW

The minimum and maximum values of the distribution from which the proportion of the simulated loci where no migration occurs from the C ecotype towards the W ecotype is drawn. The maximum value should not be higher than one.

bWC

The minimum and maximum values of the distribution from which the proportion of the simulated loci where no migration occurs from the W ecotype towards the C ecotype is drawn. The maximum value should not be higher than one.

model

Either "2pops", "Single" or "Parallel" indicating for which model should parameters be drawn.

digits

An optional integer indicating the number of decimal places to use when rounding certain parameters. The default is five.

Value

a vector with one named entry per relevant parameter. Each entry is the sampled value from the prior for that particular parameter.

Examples

# for a model with two populations
createParams(Nref = c(25000, 25000), ratio = c(0.1, 3), pool = c(5, 250), seq = c(0.0001, 0.001),
split = c(0, 3), CW = c(1e-13, 1e-3), WC = c(1e-13, 1e-3), bT = c(0, 0.2), model = "2pops")

# for a single origin scenario
createParams(Nref = c(25000, 25000), ratio = c(0.1, 3), pool = c(5, 250), seq = c(0.0001, 0.001),
split = c(0, 3), CW = c(1e-13, 1e-3), WC = c(1e-13, 1e-3), CC =  c(1e-13, 1e-3),
WW = c(1e-13, 1e-3), ANC = c(1e-13, 1e-3), bT = c(0, 0.2), bCW = c(0, 0.5),
bWC = c(0, 0.5), model = "Single")