README for the program popvizard.py
[* see also at very bottom for popvizard2.py]

popvizard.py does visualize population models and samples taken from such population models:
- Wright-Fisher model
- Canning exchangeable model (needs an additional parameter for offspring variance)
- Moran model

Origin of the name: popvizard.py
POPulation VIsualization wiZARD

For each of the models one can specify an exponential growth rate.

Input/Calling syntax
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Example calls are:

python popvizard.py -m WrightFisher
python popvizard.py --model Moran
python popvizard.py --model WrightFisher -r 0.014
python popvizard.py -m Moran  -r -0.011
python popvizard.py -m Canning --offspring 1.5
python popvizard.py --model Canning -o 1.5 --growth 0.01

The number of individuals and other parameters can be given as options:
Check out all options using: 
python popvizard.py --help


Output
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A PDF file is created with two plots: 
- the population history through time 
- and a genealogy of the sample

The default filename is set in the DEFAULT section of the program and is
wf.pdf
which happens to be an ambigous name: wright-fisher, water frog, .... :-)


popvizard2.py
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includes bottlenecks, but is not as well tested as popvizard.py,
the popvizard2 adds the option 
-b or --bottleneck
with option "{g1:ne1,g2,ne2,...}" this forces a particular population size at generationtion gi. Example:

python popvizard2.py -b "{20:10,30:40,40:10}"

you need the quotations!

For generating populations for presentations use something like this:
python popvizard.py --ratio -1 -size "[16,9]" -s 0 -n 20 -ms 10 -t 50 --seed 31 -f coal-2024-0samp-0.pdf
python popvizard.py --ratio -1 -size "[16,9]" -s 2 -n 20 -ms 10 -t 50 --seed 31 -f coal-2024-2samp-1.pdf



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(c) 2025 Peter Beerli