From 47bd69524984189f454b8a6aa1213f3a5db3d7c2 Mon Sep 17 00:00:00 2001 From: JulioV Date: Wed, 3 Feb 2021 09:46:29 -0500 Subject: [PATCH] Deprecate Doryab circadian movement feature until it is fixed --- config.yaml | 2 +- docs/change-log.md | 1 + docs/features/phone-locations.md | 6 +++--- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/config.yaml b/config.yaml index 5f77b184..9e55fdf5 100644 --- a/config.yaml +++ b/config.yaml @@ -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 diff --git a/docs/change-log.md b/docs/change-log.md index e4f1992e..4965eaab 100644 --- a/docs/change-log.md +++ b/docs/change-log.md @@ -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 diff --git a/docs/features/phone-locations.md b/docs/features/phone-locations.md index 76542263..e837e235 100644 --- a/docs/features/phone-locations.md +++ b/docs/features/phone-locations.md @@ -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).