Fisher's geometric model for diploids Code
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A simulation of Fisher's Geometric Model in two dimensions for
diploids. You can download the most recent version from
https://sourceforge.net/projects/fgm/ or clone the Git repository
Prerequisites:
--------------
(a computer and OS, preferably Linux)
a C++ compiler (http://gcc.gnu.org/)
GNU Scientific Library (http://www.gnu.org/s/gsl/)
Compiling and Installing:
-------------------------
uncompress the file and compile
#> tar -xzvf fgm.YYMMDD.tar.gz
#> make
Running the simulations:
------------------------
After compiling you will get a new executable called a.out. In order
to run a sensible simulation you need to define a number of
parameters. Three example parameter files are included in the .tar
file you can modify them or create your own:
parameters.dat: includes all the simulation parameters such as population size
mutation rates etc. There are no defaults for these!
initPopulation.dat: parameters specifying the initial population. By default a
monomorphic population at distance 2 from the optimum
initEnvironment.dat: initial conditions of the environment. This is useful for
continuing interrupted runs with moving optimum. The
default is optimum on (0,0)
Once all the parameters are ready you can run a simulation:
#> ./a.out initPopulation.dat initEnvironment.dat parameters.dat output
This will create a number of output files, the most important are:
output.ts: This file contains data in columns one generation per line.
the columns are:
1. time (generations)
2. mean fitness
3. maximum allele's fitness
4. number of different alleles
5. optimum location (r)
6. optimum location (theta)
7. fitness variance
8. mean phenotype r
9. mean phenotype phi
10. phenotype variance on x axis
11. phenotype variance on y axis
12. maximum genotype fitness
13. time since last change in the environment's optimum
14. number of polymorphic alleles (with pi > d && pi < d)
15. stable equilibrium for all alleles (with pi > d &&
taking 1/N into account)
16. Heterosis A (wab - (waa+wbb)/2)/wab
17. Heterosis B (wab - max(waa,wbb))/wab
18. maximum difference
output.b: Summary statistics for the whole run in columns:
1. mean fitness
2. fitness variance
3. number of balanced generations
4. total generations
5. did the population adapt
6. if true (1) the fitness is almost 0
more details about the simulation run are stored in the rest of the
output files, details of the colums can be found in the comments of
printStatus function in population.cpp
output.table :each line corresponds to a different allele
output.edges :pairs of parent-offspring alleles (mutated-mutant)
output.r :only used with print states function
in the Git repository there are a number of R and Perl scripts for
formating and plotting the output in some convenient ways but their
usefulness highly depends on the focus of interest
Cite:
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Sellis, D., Callahan, B.J., Petrov, D.A and P.W. Messer. Fitness overdominance as a generic feature of adaptation in diploids. unpub (at least for now)
Bugs:
-----
through sourceforge or at dsellis@stanford.edu
