#' @title Generate a four-parent pedigree
#'
#' @description
#' Generate a four-parent pedigree starting from inbred founders, using a random funnel
#'
#' @seealso \code{\link{fourParentPedigreeSingleFunnel}}, \code{\link{twoParentPedigree}}
#'
#' @param initialPopulationSize The number of F1 lines generated
#' @param selfingGenerations The number of selfing generations at the end of the pedigree
#' @param nSeeds The number of progeny taken from each intercrossing line, or from each F1 if no intercrossing is specified. These lines are then selfed according to selfingGenerations
#' @param intercrossingGenerations The number of generations of random mating performed from the F1 generation. Population size is maintained at that specified by initialPopulationSize
#' @return An object of class \code{detailedPedigree} representing the experimental design, suitable for simulation using simulateMPCross.
#' @export
# This is written in C because otherwise it's just too damn slow (especially for generating the huge populations that we want to use to get numerically accurate results for unit testing)
fourParentPedigreeRandomFunnels <- function(initialPopulationSize, selfingGenerations, nSeeds = 1L, intercrossingGenerations)
{
nonNegativeIntegerArgument(initialPopulationSize)
nonNegativeIntegerArgument(selfingGenerations)
positiveIntegerArgument(nSeeds)
nonNegativeIntegerArgument(intercrossingGenerations)
if(initialPopulationSize <= 2 && intercrossingGenerations > 0)
{
stop("Random mating is impossible with only two lines per generation")
#....and more importantly it means that the sample command below gets screwed up, because we're calling sample(x) where length(x) == 1, which samples from 1:x
}
return(.Call("fourParentPedigreeRandomFunnels", as.integer(initialPopulationSize), as.integer(selfingGenerations), as.integer(nSeeds), as.integer(intercrossingGenerations), PACKAGE="mpMap2"))
}
fourParentPedigreeRandomFunnelsPrototype <- function(initialPopulationSize, selfingGenerations, nSeeds = 1L, intercrossingGenerations)
{
nonNegativeIntegerArgument(initialPopulationSize)
nonNegativeIntegerArgument(selfingGenerations)
positiveIntegerArgument(nSeeds)
nonNegativeIntegerArgument(intercrossingGenerations)
intercrossingGenerations <- as.integer(intercrossingGenerations)
initialPopulationSize <- as.integer(initialPopulationSize)
if(initialPopulationSize <= 2 && intercrossingGenerations > 0)
{
stop("Random mating is impossible with only two lines per generation")
#....and more importantly it means that the sample command below gets screwed up, because we're calling sample(x) where length(x) == 1, which samples from 1:x
}
#Four founders, + 6 pairs + intialPopulationSize funnels
entries <- 4L + 6L + initialPopulationSize + intercrossingGenerations*initialPopulationSize + nSeeds*selfingGenerations*initialPopulationSize
mother <- father <- rep(NA, entries)
observed <- rep(FALSE, entries)
lineNames <- paste0("L", 1:entries)
mother[1:4] <- father[1:4] <- 0L
#Crosses of the founders
mother[5:10] <- c(1L, 3L, 1L, 2L, 1L, 2L)
father[5:10] <- c(2L, 4L, 3L, 4L, 4L, 3L)
#line 5 = 1,2
#line 6 = 3,4
#line 7 = 1,3
#line 8 = 2,4
#line 9 = 1,4
#line10 = 2,3
#The three different funnels:
#lines 5, 6
#lines 7, 8
#lines 9, 10
funnelChoices <- sample(1:3, replace = TRUE, initialPopulationSize)
mother[10+1:initialPopulationSize] <- 4L + 2L*funnelChoices - 1L
father[10+1:initialPopulationSize] <- 4L + 2L*funnelChoices
#Now intercrossing generations
currentIndex <- 11L
if(intercrossingGenerations > 0)
{
lastGenerationStart <- currentIndex
lastGenerationEnd <- currentIndex-1L+initialPopulationSize
for(i in 1:intercrossingGenerations)
{
for(lineCounter in lastGenerationStart:lastGenerationEnd)
{
mother[lineCounter + initialPopulationSize] <- lineCounter
father[lineCounter + initialPopulationSize] <- sample(setdiff(lastGenerationStart:lastGenerationEnd, lineCounter), 1)
}
lastGenerationStart <- lastGenerationStart + initialPopulationSize
lastGenerationEnd <- lastGenerationEnd + initialPopulationSize
}
currentIndex <- lastGenerationStart
}
#The next free spot in the pedigree
nextFree <- currentIndex+initialPopulationSize
#Now the selfing.
#First the case of one generation of selfing
if(selfingGenerations == 1)
{
#The line that we're going to self
for(lineCounter in currentIndex:(currentIndex+initialPopulationSize-1))
{
mother[nextFree:(nextFree+nSeeds-1)] <- father[nextFree:(nextFree+nSeeds-1)] <- lineCounter
observed[nextFree+nSeeds-1] <- TRUE
nextFree <- nextFree + nSeeds
}
}
else if(selfingGenerations > 1)
{
for(lineCounter in currentIndex:(currentIndex+initialPopulationSize-1))
{
#And the number of selfed lines coming off this one
for(seedCounter in 1:nSeeds)
{
father[nextFree:(nextFree+selfingGenerations-1)] <- mother[nextFree:(nextFree+selfingGenerations-1)] <- c(lineCounter, nextFree:(nextFree+selfingGenerations-2))
observed[nextFree+selfingGenerations-1] <- TRUE
nextFree <- nextFree + selfingGenerations
}
}
}
#No selfing
else
{
#...and no intercrossing
if(intercrossingGenerations == 0)
{
observed[11:length(observed)] <- TRUE
}
#If there's no selfing but there is intercrossing then mark the last set of intercrossing lines as observed
else
{
observed[lastGenerationStart:lastGenerationEnd] <- TRUE
}
}
return(new("detailedPedigree", lineNames = lineNames, mother = mother, father = father, initial = 1L:4L, observed = observed, selfing = "infinite", warnImproperFunnels = TRUE))
}
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