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Update fitbit sleep intraday docs & config file

feature/plugin_sentimental
Meng Li 2021-02-25 20:12:33 -05:00
parent 9a49644fc6
commit 2d5e966530
2 changed files with 23 additions and 18 deletions
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12
config.yaml
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@ -382,26 +382,22 @@ FITBIT_SLEEP_SUMMARY:
# See https://www.rapids.science/latest/features/fitbit-sleep-intraday/ # See https://www.rapids.science/latest/features/fitbit-sleep-intraday/
FITBIT_SLEEP_INTRADAY: FITBIT_SLEEP_INTRADAY:
TABLE: fitbit_data TABLE: fitbit_data
INCLUDE_SLEEP_LATER_THAN: &include_sleep_later_than
0 # a number ranged from 0 (midnight) to 1439 (23:59)
REFERENCE_TIME: &reference_time
MIDNIGHT # chosen from "MIDNIGHT" and "START_OF_THE_SEGMENT"
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False
FEATURES: FEATURES:
LEVELS_AND_TYPES_COMBINING_ALL: True LEVELS_AND_TYPES_COMBINING_ALL: True
LEVELS_AND_TYPES: [countepisode, sumduration, maxduration, minduration, avgduration, medianduration, stdduration] LEVELS_AND_TYPES: [countepisode, sumduration, maxduration, minduration, avgduration, medianduration, stdduration]
RATIOS_TYPE: [count, duration] RATIOS_TYPE: [count, duration]
RATIOS_SCOPE: [ACROSS_LEVELS, ACROSS_TYPES, WITHIN_LEVELS, WITHIN_TYPES] RATIOS_SCOPE: [ACROSS_LEVELS, ACROSS_TYPES, WITHIN_LEVELS, WITHIN_TYPES]
ROUTINE: [starttimefirstmainsleep, endtimelastmainsleep, starttimefirstnap, endtimelastnap] ROUTINE: [starttimefirstmainsleep, endtimelastmainsleep, starttimefirstnap, endtimelastnap]
SLEEP_LEVELS: SLEEP_LEVELS:
CLASSIC: [awake, restless, asleep] CLASSIC: [awake, restless, asleep]
STAGES: [wake, deep, light, rem] STAGES: [wake, deep, light, rem]
UNIFIED: [awake, asleep] UNIFIED: [awake, asleep]
SLEEP_TYPES: [main, nap] SLEEP_TYPES: [main, nap]
INCLUDE_SLEEP_LATER_THAN: *include_sleep_later_than INCLUDE_SLEEP_LATER_THAN: 0 # a number ranged from 0 (midnight) to 1439 (23:59)
REFERENCE_TIME: *reference_time REFERENCE_TIME: MIDNIGHT # chosen from "MIDNIGHT" and "START_OF_THE_SEGMENT"
SRC_FOLDER: "rapids" # inside src/features/fitbit_sleep_intraday SRC_FOLDER: "rapids" # inside src/features/fitbit_sleep_intraday
SRC_LANGUAGE: "python" SRC_LANGUAGE: "python"

29
docs/features/fitbit-sleep-intraday.md
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@ -5,8 +5,7 @@ Sensor parameters description for `[FITBIT_SLEEP_INTRADAY]`:
|Key                              | Description | |Key                              | Description |
|----------------|----------------------------------------------------------------------------------------------------------------------------------- |----------------|-----------------------------------------------------------------------------------------------------------------------------------
|`[TABLE]`| Database table name or file path where the sleep intraday data is stored. The configuration keys in [Device Data Source Configuration](../../setup/configuration/#device-data-source-configuration) control whether this parameter is interpreted as table or file. |`[TABLE]`| Database table name or file path where the sleep intraday data is stored. The configuration keys in [Device Data Source Configuration](../../setup/configuration/#device-data-source-configuration) control whether this parameter is interpreted as table or file.
|`[INCLUDE_SLEEP_LATER_THAN]`| All resampled sleep rows (bin interval: one minute) that started after this time will be included in the feature computation. It is a number ranging from 0 (midnight) to 1439 (23:59) which denotes the number of minutes after midnight. If a segment is longer than one day, this value is for every day.
|`[REFERENCE_TIME]`| The reference point from which the `[ROUTINE]` features are to be computed. Chosen from `MIDNIGHT` and `START_OF_THE_SEGMENT`, default is `MIDNIGHT`. If you have multiple time segments per day it might be more informative to set this flag to `START_OF_THE_SEGMENT`.
The format of the column(s) containing the Fitbit sensor data can be `JSON` or `PLAIN_TEXT`. The data in `JSON` format is obtained directly from the Fitbit API. We support `PLAIN_TEXT` in case you already parsed your data and don't have access to your participants' Fitbit accounts anymore. If your data is in `JSON` format then summary and intraday data come packed together. The format of the column(s) containing the Fitbit sensor data can be `JSON` or `PLAIN_TEXT`. The data in `JSON` format is obtained directly from the Fitbit API. We support `PLAIN_TEXT` in case you already parsed your data and don't have access to your participants' Fitbit accounts anymore. If your data is in `JSON` format then summary and intraday data come packed together.
@ -48,9 +47,12 @@ We provide examples of the input format that RAPIDS expects, note that both exam
|type_episode_id |local_date_time |duration |level |is_main_sleep |type | |type_episode_id |local_date_time |duration |level |is_main_sleep |type |
|---------------- |------------------- |--------- |---------- |-------------- |-------------- | |---------------- |------------------- |--------- |---------- |-------------- |-------------- |
|0 |2020-10-10 15:36:30 |60 |restless |1 |stages | |0 |2020-10-10 15:36:30 |60 |restless |0 |classic |
|0 |2020-10-10 15:37:30 |660 |asleep |1 |stages | |0 |2020-10-10 15:37:30 |660 |asleep |0 |classic |
|0 |2020-10-10 15:48:30 |60 |restless |1 |stages | |0 |2020-10-10 15:48:30 |60 |restless |0 |classic |
|... |... |... |... |... |... |
|1 |2020-10-10 01:46:30 |420 |light |1 |stages |
|1 |2020-10-10 01:53:30 |1230 |deep |1 |stages |
## RAPIDS provider ## RAPIDS provider
@ -76,6 +78,8 @@ Parameters description for `[FITBIT_SLEEP_INTRADAY][PROVIDERS][RAPIDS]`:
|`[FEATURES]` | Features to be computed from sleep intraday data, see table below | |`[FEATURES]` | Features to be computed from sleep intraday data, see table below |
|`[SLEEP_LEVELS]` | Fitbit’s sleep API Version 1 only provides `CLASSIC` records. However, Version 1.2 provides 2 types of records: `CLASSIC` and `STAGES`. `STAGES` is only available in devices with a heart rate sensor and even those devices will fail to report it if the battery is low or the device is not tight enough. While `CLASSIC` contains 3 sleep levels (`awake`, `restless`, and `asleep`), `STAGES` contains 4 sleep levels (`wake`, `deep`, `light`, `rem`). To make it consistent, RAPIDS grouped them into 2 `UNIFIED` sleep levels: `awake` (`CLASSIC`: `awake` and `restless`; `STAGES`: `wake`) and `asleep` (`CLASSIC`: `asleep`; `STAGES`: `deep`, `light`, and `rem`). |`[SLEEP_LEVELS]` | Fitbit’s sleep API Version 1 only provides `CLASSIC` records. However, Version 1.2 provides 2 types of records: `CLASSIC` and `STAGES`. `STAGES` is only available in devices with a heart rate sensor and even those devices will fail to report it if the battery is low or the device is not tight enough. While `CLASSIC` contains 3 sleep levels (`awake`, `restless`, and `asleep`), `STAGES` contains 4 sleep levels (`wake`, `deep`, `light`, `rem`). To make it consistent, RAPIDS grouped them into 2 `UNIFIED` sleep levels: `awake` (`CLASSIC`: `awake` and `restless`; `STAGES`: `wake`) and `asleep` (`CLASSIC`: `asleep`; `STAGES`: `deep`, `light`, and `rem`).
|`[SLEEP_TYPES]` | Types of sleep to be included in the feature extraction computation. Fitbit provides 2 types of sleep: `main`, `nap`. |`[SLEEP_TYPES]` | Types of sleep to be included in the feature extraction computation. Fitbit provides 2 types of sleep: `main`, `nap`.
|`[INCLUDE_SLEEP_LATER_THAN]`| All resampled sleep rows (bin interval: one minute) that started after this time will be included in the feature computation. It is a number ranging from 0 (midnight) to 1439 (23:59) which denotes the number of minutes after midnight. If a segment is longer than one day, this value is for every day.
|`[REFERENCE_TIME]`| The reference point from which the `[ROUTINE]` features are to be computed. Chosen from `MIDNIGHT` and `START_OF_THE_SEGMENT`, default is `MIDNIGHT`. If you have multiple time segments per day it might be more informative to set this flag to `START_OF_THE_SEGMENT`.
Features description for `[FITBIT_STEPS_INTRADAY][PROVIDERS][RAPIDS][LEVELS_AND_TYPES]`: Features description for `[FITBIT_STEPS_INTRADAY][PROVIDERS][RAPIDS][LEVELS_AND_TYPES]`:
@ -163,18 +167,23 @@ Parameters description for `[FITBIT_SLEEP_INTRADAY][PROVIDERS][PRICE]`:
|----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|`[COMPUTE]` | Set to `True` to extract `FITBIT_SLEEP_INTRADAY` features from the `PRICE` provider | |`[COMPUTE]` | Set to `True` to extract `FITBIT_SLEEP_INTRADAY` features from the `PRICE` provider |
|`[FEATURES]` | Features to be computed from sleep intraday data, see table below |`[FEATURES]` | Features to be computed from sleep intraday data, see table below
|`[DAY_TYPE]` | The features of this provider can be computed using daily averages/medians that were extracted on `WEEKEND` days only, `WEEK` days only, or `ALL` days| |`[SLEEP_LEVELS]` | Fitbit’s sleep API Version 1 only provides `CLASSIC` records. However, Version 1.2 provides 2 types of records: `CLASSIC` and `STAGES`. `STAGES` is only available in devices with a heart rate sensor and even those devices will fail to report it if the battery is low or the device is not tight enough. While `CLASSIC` contains 3 sleep levels (`awake`, `restless`, and `asleep`), `STAGES` contains 4 sleep levels (`wake`, `deep`, `light`, `rem`). To make it consistent, RAPIDS grouped them into 2 `UNIFIED` sleep levels: `awake` (`CLASSIC`: `awake` and `restless`; `STAGES`: `wake`) and `asleep` (`CLASSIC`: `asleep`; `STAGES`: `deep`, `light`, and `rem`).
|`[INCLUDE_EPISODES_INTERSECTING]` | This parameter contains 2 values: `[START_TIME]` and `[LENGTH]`. Only `main` sleep episodes that ended later than `[START_TIME]` or start before `[START_TIME]` + `[LENGTH]` are taken into account to compute the features described below. Both `[START_TIME]` and `[LENGTH]` are in minutes. `[START_TIME]` is a number ranging from 0 (midnight) to 1439 (23:59) which denotes the number of minutes after midnight. `[LENGTH]` is a number smaller than 1440 (24 hours). | |`[DAY_TYPE]` | The features of this provider can be computed using daily averages/standard deviations that were extracted on `WEEKEND` days only, `WEEK` days only, or `ALL` days|
|`[GROUP_EPISODES_WITHIN]` | This parameter contains 2 values: `[START_TIME]` and `[LENGTH]`. Only `main` sleep episodes that intersect or contain the period between [`START_TIME`, `START_TIME` + `LENGTH`] are taken into account to compute the features described below. Both `[START_TIME]` and `[LENGTH]` are in minutes. `[START_TIME]` is a number ranging from 0 (midnight) to 1439 (23:59) which denotes the number of minutes after midnight. `[LENGTH]` is a number smaller than 1440 (24 hours). |
Features description for `[FITBIT_STEPS_INTRADAY][PROVIDERS][PRICE]`: Features description for `[FITBIT_STEPS_INTRADAY][PROVIDERS][PRICE]`:
|Feature                                                             |Units |Description | |Feature                                                             |Units |Description |
|------------------------------------- |----------------- |-------------------------------------------------------------| |------------------------------------- |----------------- |-------------------------------------------------------------|
|avgratioawaketoinbedmain`[DAY_TYPE]` |- | Average daily ratio between daily awake time and in-bed time inferred from `main` sleep episodes. An sleep episode can have `CLASSIC` or `STAGES` levels, awake time is formed by the `[awake, restless]` `CLASSIC` levels and the `[wake]` `STAGES` level. In turn, in-bed time is the total duration of all `main` sleep episodes for each day. You can include daily ratios that were computed on weekend days, week days or both depending on the value of the `DAY_TYPE` flag. |avgduration`[LEVEL]`main`[DAY_TYPE]` |minutes | Average duration of daily `LEVEL` sleep episodes. You can include daily average that were computed on weekend days, week days or both depending on the value of the `DAY_TYPE` flag.
|avgratioduration`[LEVEL]`withinmain`[DAY_TYPE]` |- | Average ratio between daily `LEVEL` time and in-bed time inferred from `main` sleep episodes. `LEVEL` is one of `SLEEP_LEVELS` (e.g. awake-classic or rem-stages). In-bed time is the total duration of all `main` sleep episodes for each day. You can include daily ratios that were computed on weekend days, week days or both depending on the value of the `DAY_TYPE` flag.
|avgstarttimeofepisodemain`[DAY_TYPE]` |minutes | Average start time of the first `main` sleep episode of each day in a time segment. You can include daily start times from episodes detected on weekend days, week days or both depending on the value of the `DAY_TYPE` flag. |avgstarttimeofepisodemain`[DAY_TYPE]` |minutes | Average start time of the first `main` sleep episode of each day in a time segment. You can include daily start times from episodes detected on weekend days, week days or both depending on the value of the `DAY_TYPE` flag.
|avgendtimeofepisodemain`[DAY_TYPE]` |minutes | Average end time of the last `main` sleep episode of each day in a time segment. You can include daily end times from episodes detected on weekend days, week days or both depending on the value of the `DAY_TYPE` flag. |avgendtimeofepisodemain`[DAY_TYPE]` |minutes | Average end time of the last `main` sleep episode of each day in a time segment. You can include daily end times from episodes detected on weekend days, week days or both depending on the value of the `DAY_TYPE` flag.
|avgmidpointofepisodemain`[DAY_TYPE]` |minutes | Average mid time between the start of the first `main` sleep episode and the end of the last `main` sleep episode of each day in a time segment. You can include episodes detected on weekend days, week days or both depending on the value of the `DAY_TYPE` flag. |avgmidpointofepisodemain`[DAY_TYPE]` |minutes | Average mid time between the start of the first `main` sleep episode and the end of the last `main` sleep episode of each day in a time segment. You can include episodes detected on weekend days, week days or both depending on the value of the `DAY_TYPE` flag.
|stdstarttimeofepisodemain`[DAY_TYPE]` |minutes | Standard deviation of start time of the first `main` sleep episode of each day in a time segment. You can include daily start times from episodes detected on weekend days, week days or both depending on the value of the `DAY_TYPE` flag.
|stdendtimeofepisodemain`[DAY_TYPE]` |minutes | Standard deviation of end time of the last `main` sleep episode of each day in a time segment. You can include daily end times from episodes detected on weekend days, week days or both depending on the value of the `DAY_TYPE` flag.
|stdmidpointofepisodemain`[DAY_TYPE]` |minutes | Standard deviation of mid time between the start of the first `main` sleep episode and the end of the last `main` sleep episode of each day in a time segment. You can include episodes detected on weekend days, week days or both depending on the value of the `DAY_TYPE` flag.
|socialjetlag |minutes | Difference in minutes between the avgstarttimeofepisodemain (bed time) of weekends and weekdays. |socialjetlag |minutes | Difference in minutes between the avgstarttimeofepisodemain (bed time) of weekends and weekdays.
|meanssdstarttimeofepisodemain |minutes squared | Same as `avgstarttimeofepisodemain[DAY_TYPE]` but the average is computed over the squared differences of each pair of consecutive start times. |meanssdstarttimeofepisodemain |minutes squared | Same as `avgstarttimeofepisodemain[DAY_TYPE]` but the average is computed over the squared differences of each pair of consecutive start times.
|meanssdendtimeofepisodemain |minutes squared | Same as `avgendtimeofepisodemain[DAY_TYPE]` but the average is computed over the squared differences of each pair of consecutive end times. |meanssdendtimeofepisodemain |minutes squared | Same as `avgendtimeofepisodemain[DAY_TYPE]` but the average is computed over the squared differences of each pair of consecutive end times.