Rescaling factor changes with ECM cycles

[Carolin Dahms]

Dear fastsimcoal users,

I observed that when increasing the number of ECM cycles, in my case from -l10 -L40 to -l40 -L60, the rescaling factor decreases.

With less cycles, and I suspect particularly due to the lower number of cycles where monomorphic sites are still included, the rescaling factor is always 1 (from 50 independent runs with 250k simulations) producing less reasonable, too large parameters estimates.

While I will continue using larger mumebr of cycles, I was wondering if someone has a explanation why below a certain cycle threshold the rescaling factor is high (ie 1), does that seem suspicious that something is wrogn with my model in general?

thanks for any hints,

Carolin

tpl:

//Parameters for the coalescence simulation program : fastsimcoal.exe
5 samples to simulate :
//Population effective sizes (number of genes)
NCHA
NNIN
NIND
NGBR
NCHE
//Haploid samples sizes
36
36
36
36
36
//Growth rates: negative growth implies population expansion
0
0
0
0
0
//Number of migration matrices : 0 implies no migration between demes
5
//Migration matrix 0
0 MIGCN 0 0 0
MIGNC 0 MIGNI 0 0
0 MIGIN 0 MIGIG 0
0 0 MIGGI 0 MIGGE
0 0 0 MIGEG 0
//Migration matrix 1
0 MIGCN 0 0 0
MIGNC 0 MIGNI 0 0
0 MIGIN 0 MIGIG 0
0 0 MIGGN 0 0
0 0 0 0 0
//Migration matrix 2
0 MIGCN 0 0 0
MIGNC 0 MIGNI 0 0
0 MIGIN 0 0 0
0 0 0 0 0
0 0 0 0 0
//Migration matrix 3
0 MIGCN 0 0 0
MIGNC 0 0 0 0
0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
//Migration matrix 4
0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
//historical event: time, source, sink, migrants, new deme size, new growth rate, migration matrix index
4 historical event
TCALT 4 3 1 RSGBR 0 1
TEAUT 3 2 1 RSIND 0 2
TWAUT 2 1 1 RSNIN 0 3
TDIV 0 1 1 RSANC 0 4
//Number of independent loci [chromosome]
1 0
//Per chromosome: Number of contiguous linkage Block: a block is a set of contiguous loci
1
//per Block:data type, number of loci, per generation recombination and mutation rates and optional parameters
FREQ 1 0 1.93e-8 OUTEXP       

est:

// Priors and rules file
// *********************
[PARAMETERS]
//#isInt? #name   #dist.#min  #max
//all Ns are in number of haploid individuals
1  NANC         unif    1000    900000   output reference
1  NIND         unif    1000    700000   output
1  NCHA         unif    1000    100000   output
1  NNIN         unif    1000    700000   output
1  NGBR         unif    1000    700000   output
1  NCHE         unif    1000    700000   output
0  RSGBR        logunif 0.1     10       hide
0  RSIND        logunif 0.1     10       hide
0  RSCHA        logunif 0.1     10       hide
0  RSNIN        logunif 0.1     10       hide
0  RSANC        logunif 0.1     10       output
0  MIGCN        logunif 1e-10 1e-1   output
0  MIGNC        logunif 1e-10 1e-1   output
0  MIGGE        logunif 1e-10 1e-1   output
0  MIGEG        logunif 1e-10 1e-1   output
0  MIGIG        logunif 1e-10 1e-1   output
0  MIGGI        logunif 1e-10 1e-1   output
0  MIGIN        logunif 1e-10 1e-1   output
0  MIGNI        logunif 1e-10 1e-1   output
1  TCALT        unif    1000    10000   output
1  TEAUT        unif    TCALT    700000   output paramInRange
1  TWAUT        unif    TEAUT    700000   output paramInRange
1  TDIV         unif    TWAUT    900000   output paramInRange
[COMPLEX PARAMETERS]
1 NACHA = NCHA * RSCHA output
1 NANIN = NNIN * RSNIN output
0 RSANC = NANC/NNIN hide
0 2N = 2 * NANC hide
0 THETA = 2N * 1.93e-8 output                                                                                                                                                                                                                                                                                     

command: 

-m -0 -C5 -n250000 -L40 -s0 -M -x -l10 --foldedSFS