8000 Example and tests for --model_file · Issue #16 · xin-huang/dadi-cli · GitHub
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Example and tests for --model_file #16

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RyanGutenkunst opened this issue May 19, 2022 · 7 comments
Open

Example and tests for --model_file #16

RyanGutenkunst opened this issue May 19, 2022 · 7 comments

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@RyanGutenkunst
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The functionality for using custom model files (--model_file) should be document, and there should be tests of that functionality in the test suite.
@xin-huang
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I have a question that whether we can use demes to generate models for dadi
I saw dadi is in https://github.com/popsim-consortium/demes-paper/blob/main/software-table.tex
Then how to use demes with dadi?

@tjstruck
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tjstruck commented May 24, 2022 •
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dadi has a function:
dadi.Spectrum.from_demes
Which takes the arguments:
g = demes file name
sampled_demes = list of population IDs
sample_sizes = population sample sizes
pts = list of gird points

You can see some unpolished examples in the dadi/examples/demes_test/testing_demes_v_dadi.py

@tjstruck
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tjstruck commented May 24, 2022 •
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I've added a section, "User defined demographic models", after the "Generating caches for DFE inference" section describing using the --model-file option and a bit on making the custom models for demographic inference and cache generation.

@xin-huang
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implemented by #19

@RyanGutenkunst
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@tjstruck I don't see any tests of this functionality in the test suite. Am I missing something?

@tjstruck
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tjstruck commented Sep 26, 2022 •
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It looks like I started implementing tests but never finished (there are tests in test_GenerateCache). I've put together tests for importing (test_Models.py) and inferring (test_InferDM.py) custom models.

Do we want a separate test file for running dadi-cli bash through the subprocess package?

@RyanGutenkunst
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I wouldn't anticipate errors in dadi-cli arising from subprocess, so I would put that as a low priority, unless we've encountered problems along those lines.

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@RyanGutenkunst @xin-huang @tjstruck
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