SIB fastsimcoal2
University of Berne

fast sequential Markov coalescent simulation of genomic data under complex evolutionary models

Visual inspection of the the validity of modeled scenarios

Building a complex model in par files can be difficult. Unfortunately, we have not been able to provide an easy way to construct these input files. However, we have written an R program called called ParFileInterpreter-v6.3.r to help visualize the scenario you have modeled.

executing the script

To do this you need to run the script from the R console or open it in RStudio and run it from there.

Alternatively, you can copy the script in the directory where you have your par file and type the command

    Rscript ParFileInterpreter-v6.3.r test.par

This assumes that the program Rscript is in a folder in your path and that your scenario is described in the file test.par
Note that the script requires to install two non-default  R libraries: plotrix and diagram

By default, the scenario will be drawn in a pdf file called <par file name>.pdf, where <par file name> is simply the name of your par file. In the above example, it would create a pdf file called test.par.pdf

pdf file

For instance, the analysis of the file test.par leads to  test.par.pdf shown below



In this pdf, circles represent populations. Gray circles represent sampled populations, and white circles represent non-sampled "ghost" populations. The population (deme) numbers on the x axis correspond to those in the par file. The area of the circles is proportional to the population sizes.

The numbers in the rightmost column correspond to the times of historical events, which can be population splits (in black), episodes of gene flow  (in blue), or population resizes (in brown).

The orange arrows represent migration rates (in Nm units), with direction indicating flow backward in time. Note that the leftmost column indicates the migration matrix number used in the par file at a given time.

The age of demes sampled in the past are shown below the population circles.

Horizontal arrows represent population splits (solid black arrows) or admixture events (dashed blue arrows), considered backward in time.

Pink arrows on top of population circles (like above deme 6 and 7 above) indicate onsets of exponential growth (or decline).

modifying the R script

The R script should not be modified by non R experts, except to specify the name of the par file directly in the R script

if(length(args)) {
} else { 

R experts can of course customize the R scripts for their own needs.

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Last updated by L. Excoffier on 18.11.15
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