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Setting
The software is implemented as a command line application. More than ten parameters are needed for definition of all properties of a simulation and hence it would not be convenient for the user to set them through the command line.
This is resolved using plain text file named “setting.txt”, which is expected to carry all parameters in format
PARAMETER_name = value
and prefix symbol # is used for comments. Performance of more simulations per one run
of the software is facilitated using vector notation of up to three of the parameters. When a value of one of the
parameters is replaced by a vector of values, the simulation will
be performed for all values of vector. Vectors are expected in format [v1, ... , vn] or
[v1; ... ; vn]. Vector notation is not allowed for parameters NUMBERofGENERATIONS and SEED.
A template of the setting files is provided in this repository. More examples you can find in the repository ConjunctionExamples.
Parameters connected to general mechanism of simulations specifying properties of Chromosome, Individual, Deme and World setting
LOCI = <int>
Sets the number of loci per chromosome.
NUMBERofCHROMOSOMES = <integer>
Sets the number of chromosomes per individual
LAMBDA = <real>
Sets the mean value of Poisson distribution generating number of chiasmata per recombination event. The recombination rate between two loci of known distance can be computed using this parameter using Haldane mapping function Individual.
SELECTIONpressure = <real>
Sets the difference of fitness between completely admixed individuals and the native ones. Values out of range from 0 to 1 are meaningless.
BETA = <real>
Sets the strength of epistasis interaction of simulated loci. Beta smaller than 1 causes negative epistasis, and beta greater than 1 will cause positive epistasis, respectively.
DEMEsize = <int>
Sets the number of individuals per deme. The migration rate is so far fixed to m = 0.5. Therefore choose only powers of 4 for 2d case to ensure, that only integer of individuals will migrate.
NUMBERofGENERATIONS = <int>
The number of generations of simulation.
SEED = <int>
Every simulation has a initiate seed for pseudo-random numbers to ensure a reproducibility. It parameter SEED is not specified, the seed will be generated using time. If one value is specified only, the other seeds will be generated using provided seed. User can also specify a vector of seeds, but it has to have a length equal to total number of simulations defined by setting.
REPLICATES = <int>
specifies how many times should be every simulation performed. Every replicate will have a unique seed defined according parameter SEED (see its description for details).
The summary and log will be always printed to standard output stream and the standard error stream respectively. However, various types of simulation output could be captured during the time of simulation using following parameters.
NUMBERofSAVES = <int>
The number of saves and summary reports during simulation. When the number is higher than one, the saves are equally distributed to number of generations of simulation. For example, 3 saves of 300 generations simulation will results in save of one file after 100 generations, 200 generations and in the end of the simulations.
NAMEofOUTPUTfile = <string>
The name of output file, the sulfix will be added automatically. If more saves are set, the order of the save will be added to name as well. The parameter can be left blank to prevent files to be saved. This option might be useful, when the summary output is sufficient for the analysis.
TYPEofOUTPUTfile = <string>
The file can contain summary very same as the one on the standard output stream or it can contain information about every individual - hybrid indices only or both number of indices and number of junctions. Known types complete, blocks, hybridIndices and hybridIndicesJunctions are saving information individual wise. Types summary and raspberrypi are types printing summaries of demes.
DELAY <int>
Sets the number of generations which should be skipped before computing the generations, where the saves will occurs. For example, 3 saves of 400 generations simulation with DELAY 100 will result in the save of one file after 100 generations, 200 generations and in the end of the simulations.
This defines the world, where the simulation will be performed.
WORLDdefinition -quick = '<string>' <int>
World defined using a -quick flag allows user to define world with minimal needed parameters. Templates are HybridZone,LowMigrationBazykin and InfInf,Arena and the <int> is number of demes per column, nothing, number of demes in both rows and columns and nothing respectively. Complete description of all World templates is in separate page. For the interface reading setting is important to put here string in simple quotes: ''.
The flag -standard activates a Standard description of the World.