Refactor fitbit_step features: replace "metrics" with "features"
Co-authored-by: Meng Li <AnnieLM1996@gmail.com> Co-authored-by: JulioV <juliovhz@gmail.com>pull/95/head
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@ -76,7 +76,7 @@ BARNETT_LOCATION:
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BLUETOOTH:
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BLUETOOTH:
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DAY_SEGMENTS: *day_segments
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DAY_SEGMENTS: *day_segments
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METRICS: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
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FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
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GOOGLE_ACTIVITY_RECOGNITION:
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GOOGLE_ACTIVITY_RECOGNITION:
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DAY_SEGMENTS: *day_segments
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DAY_SEGMENTS: *day_segments
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@ -117,7 +117,7 @@ HEARTRATE:
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STEP:
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STEP:
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DAY_SEGMENTS: *day_segments
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DAY_SEGMENTS: *day_segments
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METRICS:
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FEATURES:
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ALL_STEPS: ["sumallsteps", "maxallsteps", "minallsteps", "avgallsteps", "stdallsteps"]
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ALL_STEPS: ["sumallsteps", "maxallsteps", "minallsteps", "avgallsteps", "stdallsteps"]
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SEDENTARY_BOUT: ["countsedentarybout", "maxdurationsedentarybout", "mindurationsedentarybout", "avgdurationsedentarybout", "stddurationsedentarybout", "sumdurationsedentarybout"]
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SEDENTARY_BOUT: ["countsedentarybout", "maxdurationsedentarybout", "mindurationsedentarybout", "avgdurationsedentarybout", "stddurationsedentarybout", "sumdurationsedentarybout"]
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ACTIVE_BOUT: ["countactivebout", "maxdurationactivebout", "mindurationactivebout", "avgdurationactivebout", "stddurationactivebout"]
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ACTIVE_BOUT: ["countactivebout", "maxdurationactivebout", "mindurationactivebout", "avgdurationactivebout", "stddurationactivebout"]
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@ -1073,7 +1073,7 @@ See `Fitbit: Steps Config Code`_
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| ``pid=config["PIDS"],``
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| ``pid=config["PIDS"],``
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| ``fitbit_sensor=config["FITBIT_SENSORS"]),``
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| ``fitbit_sensor=config["FITBIT_SENSORS"]),``
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- Extract Fitbit: Steps Metrics:
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- Extract Fitbit: Steps Features:
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| ``expand("data/processed/{pid}/fitbit_step_{day_segment}.csv",``
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| ``expand("data/processed/{pid}/fitbit_step_{day_segment}.csv",``
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| ``pid=config["PIDS"],``
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| ``pid=config["PIDS"],``
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@ -1089,9 +1089,9 @@ See `Fitbit: Steps Config Code`_
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- **Script:** ``src/data/fitbit_readable_datetime.py`` - See the fitbit_readable_datetime.py_ script.
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- **Script:** ``src/data/fitbit_readable_datetime.py`` - See the fitbit_readable_datetime.py_ script.
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- **Rule:** ``rules/features.snakefile/fitbit_step_metrics`` - See the fitbit_step_metrics.py_ rule.
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- **Rule:** ``rules/features.snakefile/fitbit_step_features`` - See the fitbit_step_features.py_ rule.
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- **Script:** ``src/features/fitbit_step_metrics.py`` - See the fitbit_step_metrics.py_ script.
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- **Script:** ``src/features/fitbit_step_features.py`` - See the fitbit_step_features.py_ script.
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.. _fitbit-steps-parameters:
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.. _fitbit-steps-parameters:
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@ -1195,8 +1195,8 @@ stddurationactivebout minutes Std duration active bout: The standard
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.. _fitbit_heartrate_metrics: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/features.snakefile#L151
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.. _fitbit_heartrate_metrics: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/features.snakefile#L151
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.. _fitbit_heartrate_metrics.py: https://github.com/carissalow/rapids/blob/master/src/features/fitbit_heartrate_metrics.py
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.. _fitbit_heartrate_metrics.py: https://github.com/carissalow/rapids/blob/master/src/features/fitbit_heartrate_metrics.py
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.. _`Fitbit: Steps Config Code`: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L117
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.. _`Fitbit: Steps Config Code`: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L117
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.. _fitbit_step_metrics: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/features.snakefile#L162
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.. _fitbit_step_features: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/features.snakefile#L162
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.. _fitbit_step_metrics.py: https://github.com/carissalow/rapids/blob/master/src/features/fitbit_step_metrics.py
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.. _fitbit_step_features.py: https://github.com/carissalow/rapids/blob/master/src/features/fitbit_step_features.py
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.. _`Fitbit documentation`: https://help.fitbit.com/articles/en_US/Help_article/1565
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.. _`Fitbit documentation`: https://help.fitbit.com/articles/en_US/Help_article/1565
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.. _`Custom Catalogue File`: https://github.com/carissalow/rapids/blob/master/data/external/stachl_application_genre_catalogue.csv
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.. _`Custom Catalogue File`: https://github.com/carissalow/rapids/blob/master/data/external/stachl_application_genre_catalogue.csv
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.. _top1global: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L108
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.. _top1global: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L108
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@ -160,17 +160,17 @@ rule fitbit_heartrate_metrics:
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script:
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script:
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"../src/features/fitbit_heartrate_metrics.py"
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"../src/features/fitbit_heartrate_metrics.py"
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rule fitbit_step_metrics:
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rule fitbit_step_features:
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input:
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input:
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steps_data = "data/raw/{pid}/fitbit_steps_with_datetime.csv",
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steps_data = "data/raw/{pid}/fitbit_steps_with_datetime.csv",
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params:
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params:
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day_segment = "{day_segment}",
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day_segment = "{day_segment}",
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metrics_all_steps = config["STEP"]["METRICS"]["ALL_STEPS"],
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features_all_steps = config["STEP"]["FEATURES"]["ALL_STEPS"],
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metrics_sedentary_bout = config["STEP"]["METRICS"]["SEDENTARY_BOUT"],
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features_sedentary_bout = config["STEP"]["FEATURES"]["SEDENTARY_BOUT"],
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metrics_active_bout = config["STEP"]["METRICS"]["ACTIVE_BOUT"],
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features_active_bout = config["STEP"]["FEATURES"]["ACTIVE_BOUT"],
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threshold_active_bout = config["STEP"]["THRESHOLD_ACTIVE_BOUT"],
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threshold_active_bout = config["STEP"]["THRESHOLD_ACTIVE_BOUT"],
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include_zero_step_rows = config["STEP"]["INCLUDE_ZERO_STEP_ROWS"]
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include_zero_step_rows = config["STEP"]["INCLUDE_ZERO_STEP_ROWS"]
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output:
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output:
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"data/processed/{pid}/fitbit_step_{day_segment}.csv"
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"data/processed/{pid}/fitbit_step_{day_segment}.csv"
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script:
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script:
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"../src/features/fitbit_step_metrics.py"
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"../src/features/fitbit_step_features.py"
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@ -4,9 +4,9 @@ import datetime as dt
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from features_utils import splitOvernightEpisodes, splitMultiSegmentEpisodes
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from features_utils import splitOvernightEpisodes, splitMultiSegmentEpisodes
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day_segment = snakemake.params["day_segment"]
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day_segment = snakemake.params["day_segment"]
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all_steps = snakemake.params["metrics_all_steps"]
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all_steps = snakemake.params["features_all_steps"]
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sedentary_bout = snakemake.params["metrics_sedentary_bout"]
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sedentary_bout = snakemake.params["features_sedentary_bout"]
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active_bout = snakemake.params["metrics_active_bout"]
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active_bout = snakemake.params["features_active_bout"]
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threshold_active_bout = snakemake.params['threshold_active_bout']
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threshold_active_bout = snakemake.params['threshold_active_bout']
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include_zero_step_rows = snakemake.params["include_zero_step_rows"]
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include_zero_step_rows = snakemake.params["include_zero_step_rows"]
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