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Reference to Module API #59
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@@ -6,7 +6,7 @@ format (recommended) or the [ESGPT](https://eventstreamml.readthedocs.io/en/late | |||||||||||||||||||
system works by defining a configuration object that details the underlying concepts, inclusion/exclusion, and | ||||||||||||||||||||
labeling criteria for the cohort/task to be extracted, then using a recursive algorithm to identify all | ||||||||||||||||||||
realizations of valid patient time-ranges of data that satisfy those constraints from the raw data. For more | ||||||||||||||||||||
details on the recursive algorithm, see the `terminology.md` file. | ||||||||||||||||||||
details on the recursive algorithm, see [Algorithm Design](https://eventstreamaces.readthedocs.io/en/latest/technical.html#algorithm-design). | ||||||||||||||||||||
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As indicated above, these cohorts are specified through a combination of concepts (realized as event | ||||||||||||||||||||
_predicate_ functions, _aka_ "predicates") which are _dataset specific_ and inclusion/exclusion/labeling | ||||||||||||||||||||
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@@ -28,10 +28,10 @@ ______________________________________________________________________ | |||||||||||||||||||
In the machine form used by ACES, the configuration file consists of three parts: | ||||||||||||||||||||
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- `predicates`, stored as a dictionary from string predicate names (which must be unique) to either | ||||||||||||||||||||
`PlainPredicateConfig` objects, which store raw predicates with no dependencies on other predicates, or | ||||||||||||||||||||
`DerivedPredicateConfig` objects, which store predicates that build on other predicates. | ||||||||||||||||||||
{py:class}`aces.config.PlainPredicateConfig` objects, which store raw predicates with no dependencies on other predicates, or | ||||||||||||||||||||
{py:class}`aces.config.DerivedPredicateConfig` objects, which store predicates that build on other predicates. | ||||||||||||||||||||
- `trigger`, stored as a string to `EventConfig` | ||||||||||||||||||||
- `windows`, stored as a dictionary from string window names (which must be unique) to `WindowConfig` | ||||||||||||||||||||
- `windows`, stored as a dictionary from string window names (which must be unique) to {py:class}`aces.config.WindowConfig` | ||||||||||||||||||||
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There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Update class references to use consistent and correct Sphinx notation. - {py:class}`aces.config.PlainPredicateConfig`
+ :py:class:`aces.config.PlainPredicateConfig`
- {py:class}`aces.config.DerivedPredicateConfig`
+ :py:class:`aces.config.DerivedPredicateConfig`
- {py:class}`aces.config.WindowConfig`
+ :py:class:`aces.config.WindowConfig` This change corrects the syntax for referencing Python classes in Sphinx documentation, ensuring that the documentation is properly rendered. Committable suggestion
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objects. | ||||||||||||||||||||
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Below, we will detail each of these configuration objects. | ||||||||||||||||||||
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@@ -40,7 +40,7 @@ ______________________________________________________________________ | |||||||||||||||||||
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### Predicates: `PlainPredicateConfig` and `DerivedPredicateConfig` | ||||||||||||||||||||
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#### `PlainPredicateConfig`: Configuration of Predicates that can be Computed Directly from Raw Data | ||||||||||||||||||||
#### {py:class}`aces.config.PlainPredicateConfig`: Configuration of Predicates that can be Computed Directly from Raw Data | ||||||||||||||||||||
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These configs consist of the following four fields: | ||||||||||||||||||||
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@@ -87,7 +87,7 @@ on its source format. | |||||||||||||||||||
be of the univariate regression type and its value, if needed, will be pulled from the corresponding | ||||||||||||||||||||
column. | ||||||||||||||||||||
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#### `DerivedPredicateConfig`: Configuration of Predicates that Depend on Other Predicates | ||||||||||||||||||||
#### {py:class}`aces.config.DerivedPredicateConfig`: Configuration of Predicates that Depend on Other Predicates | ||||||||||||||||||||
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These configuration objects consist of only a single string field--`expr`--which contains a limited grammar of | ||||||||||||||||||||
accepted operations that can be applied to other predicates, containing precisely the following: | ||||||||||||||||||||
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@@ -100,7 +100,7 @@ analytic operations over predicates. | |||||||||||||||||||
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______________________________________________________________________ | ||||||||||||||||||||
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### Events: `EventConfig` | ||||||||||||||||||||
### Events: {py:class}`aces.config.EventConfig` | ||||||||||||||||||||
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The event config consists of only a single field, `predicate`, which specifies the predicate that must be | ||||||||||||||||||||
observed with value greater than one to satisfy the event. There can only be one defined "event" with an | ||||||||||||||||||||
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@@ -110,7 +110,7 @@ The value of its field can be any defined predicate. | |||||||||||||||||||
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______________________________________________________________________ | ||||||||||||||||||||
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### Windows: `WindowConfig` | ||||||||||||||||||||
### Windows: {py:class}`aces.config.WindowConfig` | ||||||||||||||||||||
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Windows contain a tracking `name` field, and otherwise are specified with two parts: (1) A set of four | ||||||||||||||||||||
parameters (`start`, `end`, `start_inclusive`, and `end_inclusive`) that specify the time range of the window, | ||||||||||||||||||||
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```{include} configuration.md | ||
``` | ||
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```{include} terminology.md | ||
```{include} algorithm.md | ||
``` |
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Ensure the class reference uses the correct Sphinx notation.
This correction ensures that the class reference is properly formatted for Sphinx documentation, allowing for correct rendering and linking.
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