Write vignette on how to modify runMacs() and how to use other simulators for founders

[gregorgorjanc]

Essentially turn this script into

https://github.com/gaynorr/AlphaSimR_Examples/blob/master/misc/ManualMaCS.R

https://github.com/gaynorr/AlphaSimR_Examples/blob/master/misc/msprime.R

and show how to bring in stdpopsim results and SlendR results too

[gaynorr]

The msprime example predates importHaplo, so it uses newMapPop with its list arguments. The importHaplo functions uses data.frames / matrices for arguments which are probably easier for most to grasp.

Here is an old example using importHaplo to read in down sampled data. Note that it shows the use of the optional raw format for haplotype data.

library(AlphaSimR)

# Create a large population
founderPop = quickHaplo(nInd=100, nChr=10, segSites=1e5)

# Extract the genetic map and select a subset of sites
genMap = getGenMap(founderPop)
take = sample(nrow(genMap), 10000)
take = sort(take) # Not required, but preserves chromosome order later
genMap = genMap[take,]

# Extract selected marker haplotypes
# Use "raw" format to reduce memory usage
haplo = pullMarkerHaplo(founderPop, genMap$id, asRaw=TRUE)

# Create a new founder population with reduced set of markers
newFounderPop = importHaplo(haplo, genMap)

[gaynorr]

Another example of importHaplo is here: https://github.com/gaynorr/AlphaSimR_Examples/blob/master/misc/ASR_ImportExternalData.R

[gregorgorjanc]

@hannesbecher can you help with this so we clearly document & demonstrate how to use MaCS (less relevant going forward) and msprime/stdpopsim (more relevant going forward) with AlphaSimR?