仅作个人笔记 - 早期基因流的fastsimcoal2模型的配置

仅作个人笔记使用意思就是只考虑我能不能看懂

1. 只谈两个群体

2. 配置文件来自于fsc论坛
   https://groups.google.com/g/fastsimcoal/c/AKrFl7v0Ft0
   适用于最新版本的fsc

3. 模型是这样的:

   
   early gene flow

4. tpl文件
   I think you can simplify your tpl file. Maybe try something like:

//Parameters for the coalescence simulation program : fastsimcoal.exe
2 samples to simulate
//Population effective sizes (number of genes)
CAPOPSIZE
JUPOPSIZE
//Haploid samples sizes
10
10
//Growth rates: negative growth implies population expansion
0
0
//Number of migration matrices : 0 implies no migration between demes
3
//Migration matrix 0
0 0
0 0
//Migration matrix 1
0 M23
M32 0
//Migration matrix 2
0 0
0 0
//historical event: time, source, sink, migrants, new deme size, new growth rate, migration matrix index
3 historical event
Tmig 0 0 0  MID1  0 1 absoluteResize
Tmig 1 1 0  MID0  0 1  absoluteResize
TDIV 0 1 1  ANCPOPOSIZE  0 2  absoluteResize
//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 3.03e-9 OUTEXP

5. est文件
   For the est file I'd advice to use loguniform distribution for large search ranges

// Priors and rules file
// *********************
[PARAMETERS]
//#isInt? #name   #dist.#min  #max
//all Ns are in number of haploid individuals
1 CAPOPSIZE logunif 1e2    1e8 output
1 JUPOPSIZE logunif  1e2   1e8 output
1 ANCPOPOSIZE unif  1e2   1e8 output
1 MID0 logunif  1e2   1e8 output
1 MID1 logunif  1e2   1e8 output
1 Tmig unif 1  1340000  output bounded
1 TDIV unif  Tmig   1340000 output  paramInRange
0 M23 logunif 1e-7   1 output
0 M32 logunif 1e-7   1 output

[COMPLEX PARAMETERS]