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Update docs & links in config.yaml

pull/128/head
Meng Li 2021-03-10 18:51:55 -05:00 committed by JulioV
parent 93baff9f83
commit cf0afeb08d
4 changed files with 31 additions and 13 deletions
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18
config.yaml
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@ -474,6 +474,7 @@ EMPATICA_DATA_STREAMS:
# Sensors ------
# See https://www.rapids.science/latest/features/empatica-accelerometer/
EMPATICA_ACCELEROMETER:
TABLE: ACC
PROVIDERS:
@ -483,6 +484,7 @@ EMPATICA_ACCELEROMETER:
SRC_FOLDER: "dbdp" # inside src/features/empatica_accelerometer
SRC_LANGUAGE: "python"
# See https://www.rapids.science/latest/features/empatica-heartrate/
EMPATICA_HEARTRATE:
TABLE: HR
PROVIDERS:
@ -492,6 +494,7 @@ EMPATICA_HEARTRATE:
SRC_FOLDER: "dbdp" # inside src/features/empatica_heartrate
SRC_LANGUAGE: "python"
# See https://www.rapids.science/latest/features/empatica-temperature/
EMPATICA_TEMPERATURE:
TABLE: TEMP
PROVIDERS:
@ -501,6 +504,7 @@ EMPATICA_TEMPERATURE:
SRC_FOLDER: "dbdp" # inside src/features/empatica_heartrate
SRC_LANGUAGE: "python"
# See https://www.rapids.science/latest/features/empatica-electrodermal-activity/
EMPATICA_ELECTRODERMAL_ACTIVITY:
TABLE: EDA
PROVIDERS:
@ -510,6 +514,7 @@ EMPATICA_ELECTRODERMAL_ACTIVITY:
SRC_FOLDER: "dbdp" # inside src/features/empatica_electrodermal_activity
SRC_LANGUAGE: "python"
# See https://www.rapids.science/latest/features/empatica-blood-volume-pulse/
EMPATICA_BLOOD_VOLUME_PULSE:
TABLE: BVP
PROVIDERS:
@ -519,6 +524,7 @@ EMPATICA_BLOOD_VOLUME_PULSE:
SRC_FOLDER: "dbdp" # inside src/features/empatica_blood_volume_pulse
SRC_LANGUAGE: "python"
# See https://www.rapids.science/latest/features/empatica-inter-beat-interval/
EMPATICA_INTER_BEAT_INTERVAL:
TABLE: IBI
PROVIDERS:
@ -528,6 +534,7 @@ EMPATICA_INTER_BEAT_INTERVAL:
SRC_FOLDER: "dbdp" # inside src/features/inter_beat_interval
SRC_LANGUAGE: "python"
# See https://www.rapids.science/latest/features/empatica-tags/
EMPATICA_TAGS:
TABLE: TAGS
PROVIDERS: # None implemented yet
@ -537,21 +544,28 @@ EMPATICA_TAGS:
# PLOTS #
########################################################################################################################
# Data quality
# Data quality ------
# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#1-histograms-of-phone-data-yield
HISTOGRAM_PHONE_DATA_YIELD:
PLOT: False
# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#2-heatmaps-of-overall-data-yield
HEATMAP_PHONE_DATA_YIELD_PER_PARTICIPANT_PER_TIME_SEGMENT:
PLOT: False
# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#3-heatmap-of-recorded-phone-sensors
HEATMAP_SENSORS_PER_MINUTE_PER_TIME_SEGMENT:
PLOT: False
# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#4-heatmap-of-sensor-row-count
HEATMAP_SENSOR_ROW_COUNT_PER_TIME_SEGMENT:
PLOT: False
SENSORS: [PHONE_ACCELEROMETER, PHONE_ACTIVITY_RECOGNITION, PHONE_APPLICATIONS_FOREGROUND, PHONE_BATTERY, PHONE_BLUETOOTH, PHONE_CALLS, PHONE_CONVERSATION, PHONE_LIGHT, PHONE_LOCATIONS, PHONE_MESSAGES, PHONE_SCREEN, PHONE_WIFI_CONNECTED, PHONE_WIFI_VISIBLE]
# Features
# Features ------
# See https://www.rapids.science/latest/visualizations/feature-visualizations/#1-heatmap-correlation-matrix
HEATMAP_FEATURE_CORRELATION_MATRIX:
PLOT: False
MIN_ROWS_RATIO: 0.5

6
docs/features/add-new-features.md
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@ -16,20 +16,24 @@ You can add new features to any existing sensors (see list below) by adding a ne
As a tutorial, we will add a new provider for `PHONE_ACCELEROMETER` called `VEGA` that extracts `feature1`, `feature2`, `feature3` in Python and that it requires a parameter from the user called `MY_PARAMETER`.
??? info "Existing Sensors"
An existing sensor is any of the phone or Fitbit sensors with a configuration entry in `config.yaml`:
An existing sensor of any device with a configuration entry in `config.yaml`:
Smartphone (AWARE)
- Phone Accelerometer
- Phone Activity Recognition
- Phone Applications Crashes
- Phone Applications Foreground
- Phone Applications Notifications
- Phone Battery
- Phone Bluetooth
- Phone Calls
- Phone Conversation
- Phone Data Yield
- Phone Keyboard
- Phone Light
- Phone Locations
- Phone Log
- Phone Messages
- Phone Screen
- Phone WiFI Connected

2
docs/features/phone-data-yield.md
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@ -28,8 +28,8 @@ Sensor parameters description for `[PHONE_DATA_YIELD]`:
PHONE_LOCATIONS
PHONE_LOG
PHONE_SCREEN
PHONE_WIFI_VISIBLE
PHONE_WIFI_CONNECTED
PHONE_WIFI_VISIBLE
```
## RAPIDS provider

18
docs/setup/configuration.md
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@ -74,26 +74,26 @@ Participant files link together multiple devices (smartphones and wearables) to
|-------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `[DEVICE_IDS]` | An array of the strings that uniquely identify each smartphone, you can have more than one for when participants changed phones in the middle of the study, in this case, data from all their devices will be joined and relabeled with the last 1 on this list. |
| `[PLATFORMS]` | An array that specifies the OS of each smartphone in `[DEVICE_IDS]` , use a combination of `android` or `ios` (we support participants that changed platforms in the middle of your study!). You can set `[PLATFORMS]: [infer]` and RAPIDS will infer them automatically (each phone data stream infer this differently, e.g. `aware_mysql` uses the `aware_device` table). |
| `[LABEL]` | A string that is used in reports and visualizations. |
| `[START_DATE]` | A string with format `YYY-MM-DD` . Only data collected *after* this date will be included in the analysis |
| `[END_DATE]` | A string with format `YYY-MM-DD` . Only data collected *before* this date will be included in the analysis |
| `[LABEL]` | A string that is used in reports and visualizations. |
| `[START_DATE]` | A string with format `YYYY-MM-DD` or `YYYY-MM-DD HH:MM:SS`. Only data collected *after* this date time will be included in the analysis. By default, `YYYY-MM-DD` is interpreted as `YYYY-MM-DD 00:00:00`. |
| `[END_DATE]` | A string with format `YYYY-MM-DD` or `YYYY-MM-DD HH:MM:SS`. Only data collected *before* this date time will be included in the analysis. By default, `YYYY-MM-DD` is interpreted as `YYYY-MM-DD 00:00:00`. |
=== "[FITBIT]"
| Key                      | Description |
|------------------|-----------------------------------------------------------------------------------------------------------|
| `[DEVICE_IDS]` | An array of the strings that uniquely identify each Fitbit, you can have more than one in case the participant changed devices in the middle of the study, in this case, data from all devices will be joined and relabeled with the last `device_id` on this list. |
| `[LABEL]` | A string that is used in reports and visualizations. |
| `[START_DATE]` | A string with format `YYY-MM-DD` . Only data collected *after* this date will be included in the analysis |
| `[END_DATE]` | A string with format `YYY-MM-DD` . Only data collected *before* this date will be included in the analysis |
| `[LABEL]` | A string that is used in reports and visualizations. |
| `[START_DATE]` | A string with format `YYYY-MM-DD` or `YYYY-MM-DD HH:MM:SS`. Only data collected *after* this date time will be included in the analysis. By default, `YYYY-MM-DD` is interpreted as `YYYY-MM-DD 00:00:00`. |
| `[END_DATE]` | A string with format `YYYY-MM-DD` or `YYYY-MM-DD HH:MM:SS`. Only data collected *before* this date time will be included in the analysis. By default, `YYYY-MM-DD` is interpreted as `YYYY-MM-DD 00:00:00`. |
=== "[EMPATICA]"
| Key                      | Description |
|------------------|-----------------------------------------------------------------------------------------------------------|
| `[LABEL]` | A string that is used in reports and visualizations. |
| `[START_DATE]` | A string with format `YYY-MM-DD` . Only data collected *after* this date will be included in the analysis |
| `[END_DATE]` | A string with format `YYY-MM-DD` . Only data collected *before* this date will be included in the analysis
| `[LABEL]` | A string that is used in reports and visualizations. |
| `[START_DATE]` | A string with format `YYYY-MM-DD` or `YYYY-MM-DD HH:MM:SS`. Only data collected *after* this date time will be included in the analysis. By default, `YYYY-MM-DD` is interpreted as `YYYY-MM-DD 00:00:00`. |
| `[END_DATE]` | A string with format `YYYY-MM-DD` or `YYYY-MM-DD HH:MM:SS`. Only data collected *before* this date time will be included in the analysis. By default, `YYYY-MM-DD` is interpreted as `YYYY-MM-DD 00:00:00`. |
### Automatic creation of participant files
You can use a CSV file with a row per participant to automatically create participant files.