Edits to VPH Output package for Alzheimer's simulation#10
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NathanielBlairStahn wants to merge 20 commits intomainfrom
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Edits to VPH Output package for Alzheimer's simulation#10NathanielBlairStahn wants to merge 20 commits intomainfrom
NathanielBlairStahn wants to merge 20 commits intomainfrom
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…xtract_transition_states
zmbc
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Nov 19, 2025
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| # FIXME: Define the cause column somewhere else that makes | ||
| # sense, and deal with different column names in older | ||
| # Vivarium models | ||
| cause_col = 'entity' # Used to be 'cause' |
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It seems like at the least we could make this an argument to the function?
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| This is a wrapper function for DataFrameGroupBy.describe(), | ||
| with `df` grouped by everything except draw and value. |
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Seems like this is no longer true. I don't understand the reason behind the changes here.
| __uri__ = "https://github.com/ihmeuw/vivarium_helpers" | ||
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| __version__ = "0.4.2" | ||
| __version__ = "0.5.0-dev" |
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We should get this set up with https://pypi.org/project/setuptools-scm/
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Adds some functionality to handle outputs from the Alzheimer's simulation. Much of the additions are for better handling pandas Categoricals, which was necessary for loading some large DataFrames into memory. Other changes are updating column names and adding parameters to functions to make them more flexible.
utils.pyfor dealing with Categoricals and printing memory usagedifferencefunction to preserve Categoricals and save memoryextract_transition_statesandget_burdenfunctionsprefilter_queryandmeasureparameters to theratiofunctionlocation_colparameter to theVPHOperatorconstructor, and addlocation_colandopsparameters to theVPHResultsconstructordescribefunction to asummarize_drawsfunction which defaults to computing "mean, lower, upper"