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Deprecate Doryab circadian movement feature until it is fixed

pull/125/head v0.4.2
JulioV 2021-02-03 09:46:29 -05:00
parent 6e59452c34
commit 47bd695249
3 changed files with 5 additions and 4 deletions
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2
config.yaml
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@ -238,7 +238,7 @@ PHONE_LOCATIONS:
PROVIDERS:
DORYAB:
COMPUTE: False
FEATURES: ["locationvariance","loglocationvariance","totaldistance","averagespeed","varspeed","circadianmovement","numberofsignificantplaces","numberlocationtransitions","radiusgyration","timeattop1location","timeattop2location","timeattop3location","movingtostaticratio","outlierstimepercent","maxlengthstayatclusters","minlengthstayatclusters","meanlengthstayatclusters","stdlengthstayatclusters","locationentropy","normalizedlocationentropy"]
FEATURES: ["locationvariance","loglocationvariance","totaldistance","averagespeed","varspeed", "numberofsignificantplaces","numberlocationtransitions","radiusgyration","timeattop1location","timeattop2location","timeattop3location","movingtostaticratio","outlierstimepercent","maxlengthstayatclusters","minlengthstayatclusters","meanlengthstayatclusters","stdlengthstayatclusters","locationentropy","normalizedlocationentropy"]
ACCURACY_LIMIT: 51 # meters, drops location coordinates with an accuracy higher than this. This number means there's a 68% probability the true location is within this radius
DBSCAN_EPS: 10 # meters
DBSCAN_MINSAMPLES: 5

1
docs/change-log.md
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@ -10,6 +10,7 @@
- Remove sampling frequency dependance in Doryab location provider
- Update documentation of Doryab location provider
- Add new `FITBIT_DATA_YIELD` `RAPIDS` provider
- Deprecate Doryab circadian movement feature until it is fixed
## v0.4.1
- Fix bug when no error message was displayed for an empty `[PHONE_DATA_YIELD][SENSORS]` when resampling location data
## v0.4.0

6
docs/features/phone-locations.md
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@ -121,7 +121,7 @@ Features description for `[PHONE_LOCATIONS][PROVIDERS][DORYAB]`:
|totaldistance |meters |Total distance travelled in a time segment using the haversine formula.
|averagespeed |km/hr |Average speed in a time segment considering only the instances labeled as Moving.
|varspeed |km/hr |Speed variance in a time segment considering only the instances labeled as Moving.
|circadianmovement |- | \"It encodes the extent to which a person's location patterns follow a 24-hour circadian cycle.\" [Doryab et al.](../../citation#doryab-locations).
|{--circadianmovement--} |- | Not suggested for use at the moment, see Observations below. \"It encodes the extent to which a person's location patterns follow a 24-hour circadian cycle.\" [Doryab et al.](../../citation#doryab-locations).
|numberofsignificantplaces |places |Number of significant locations visited. It is calculated using the DBSCAN/OPTICS clustering algorithm which takes in EPS and MIN_SAMPLES as parameters to identify clusters. Each cluster is a significant place.
|numberlocationtransitions |transitions |Number of movements between any two clusters in a time segment.
|radiusgyration |meters |Quantifies the area covered by a participant
@ -142,8 +142,8 @@ Features description for `[PHONE_LOCATIONS][PROVIDERS][DORYAB]`:
**Significant Locations Identified**
Significant locations are determined using DBSCAN clustering on locations that a patient visit over the course of the period of data collection.
**The Circadian Calculation**
For a detailed description of how this is calculated, see [Canzian et al](../../citation#doryab-locations).
**Circadian Movement Calculation**
Note Feb 3 2021. It seems the implementation of this feature is not correct, we suggest not to use this feature until a fix is in place. For a detailed description of how this should be calculated, see [Saeb et al](https://pubmed.ncbi.nlm.nih.gov/28344895/).
**Fine Tuning Clustering Parameters**
Based on an experiment where we collected fused location data for 7 days with a mean accuracy of 86 & SD of 350.874635, we determined that `EPS/MAX_EPS`=100 produced closer clustering results to reality. Higher values (>100) missed out some significant places like a short grocery visit while lower values (<100) picked up traffic lights and stop signs while driving as significant locations. We recommend you set `EPS` based on the accuracy of your location data (the more accurate your data is, the lower you should be able to set EPS).