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294 Commits (master)

Author SHA1 Message Date
junos e5cc02501f Set the timezone.csv path in config. 
Take into account that TZCODES_FILE can be created with a rule.
 2021-12-15 18:09:30 +01:00
junos 1f54195437 Configure timezone file to be created automatically. 2021-12-08 18:21:29 +01:00
junos 0b8a493ff2 Incorporate mulitple timezones into RAPIDS. 2021-12-01 18:20:27 +01:00
junos f0d29d0d1a Incorporate DB query for usernames into snakemake workflow. 2021-12-01 18:14:27 +01:00
junos da5ff0f36e Correct small errors in settings. 2021-11-29 18:04:06 +01:00
junos 181e4f0118 Add parameters to yaml file. 
And use these in the prepare_participants_file function.
 2021-11-29 16:57:50 +01:00
junos 39bd244511 [WIP] Prepare yaml files. 
These will be used to create participants files.
 2021-11-24 19:11:19 +01:00
Meng Li 5bad3eb8b5
Data cleaning (#166) 
* Refactor data cleaning module: move it from example workflow to main directory

* Replace NAs with 0 in selected event-based features

* Add one step to drop highly correlated features

Co-authored-by: Weiyu <weiyuhuang7@gmail.com>
 2021-11-19 10:34:36 -05:00
Meng Li f340b89c58 Temporary revert PHONE_LOCATIONS BARNETT provider to use R script 2021-09-23 18:16:13 -04:00
Meng Li a3fb718aea Refactor PHONE_LOCATIONS DORYAB provider to compute features based on location episodes 2021-09-23 17:40:06 -04:00
Meng Li a8a178486b Refactor PHONE_CALLS RAPIDS provider to compute features based on call episodes or events 2021-09-15 10:28:37 -04:00
JulioV 834bd3b93d Refactor in Python of Barnett provider 
Co-authored-by: Shirley Hayati <sahayati@ucdavis.edu>
Co-authored-by: JulioV <JulioV@users.noreply.github.com>
 2021-08-04 15:33:02 -04:00
Meng Li cefcb0635b Update heatmap of recorded phone sensors 2021-06-29 09:49:24 -04:00
Meng Li bc06477d89 Update heatmap of sensor row count 2021-06-29 09:49:24 -04:00
Meng Li e98a8ff7ca Update histogram of phone data yield 2021-06-29 09:49:24 -04:00
Meng Li f436f1f530 Update heatmap of correlation matrix 2021-06-29 09:49:23 -04:00
Meng Li 4d37696158 Update heatmaps of overall data yield 2021-06-29 09:48:30 -04:00
kirtirajk 4b8698a4c6 adding app_episode with the changes as mentioned in the comments 2021-06-10 14:17:56 -04:00
Meng Li 9687081fbe Refactor the rule phone_locations_add_doryab_extra_columns 2021-05-28 09:48:36 -04:00
Meng Li 0d6f51be8b Refactor location features from Doryab provider & add a new strategy to infer home location & fix bugs 2021-05-26 17:36:52 -04:00
JulioV 32472461ec - Fix bug when no phone data yield is needed to process location data 
- Remove location rows with the same timestamp based on their accuracy
 2021-05-26 14:04:29 -04:00
Meng Li edf71e055d Add the EXCLUDE_SLEEP module for steps intraday features 2021-05-21 15:23:21 -04:00
JulioV 9c56422529 Add calories intraday features 2021-04-20 12:00:38 -04:00
JulioV c48c1c8f24 Optimize Barnett's computation multi-day segments 2021-03-28 15:29:07 -04:00
JulioV d0858f8833 Fix overlapping periodic time segments 2021-03-28 15:29:07 -04:00
Meng Li a5eb535126 Update visualizations docs & add time flag for heatmap of overall data yield 2021-03-23 21:40:55 -04:00
JulioV d6c22fdbc7 Fix an import bug and docs 2021-03-15 19:35:58 -04:00
JulioV 4528ab3641 Replace SRC LANGUAGE and FOLDER with SCRIPT 2021-03-14 22:14:13 -04:00
JulioV f4b2bd1fb2 Cleanup data/ 2021-03-14 13:36:22 -04:00
Meng Li ffaa8f8a1c Update create_example_participant_files rule 2021-03-12 20:04:43 -05:00
Meng Li 2b6447105a Migrate analysis example to new data stream 2021-03-12 19:52:34 -05:00
JulioV fae0c2ac05 Swap TABLE for CONTAINER 2021-03-12 18:14:49 -05:00
Meng Li d529490999 Migrate fitbit features to new data stream 2021-03-12 12:38:36 -05:00
JulioV 1b8453bec4 Remove unused params from config.yaml 2021-03-11 14:57:34 -05:00
JulioV 2ee45995f2 Update config docs and create participant files script 2021-03-11 14:40:33 -05:00
JulioV a420f5ef92 Add sleep summary to fitbitjson_mysql 2021-03-11 14:37:22 -05:00
Meng Li 35968e2fd0 Migrate phone log sensor to new data stream 2021-03-11 14:37:22 -05:00
JulioV 47e1b33816 Add hr intraday to fitbitjson_mysql 2021-03-11 14:37:22 -05:00
JulioV 47f449555a Add hr summary to fitbitjson_mysql 2021-03-11 14:37:22 -05:00
JulioV 72f6b2d621 Add steps intraday to fitbitjson_mysql 2021-03-11 14:37:22 -05:00
Meng Li 4825962361 Migrate phone screen sensor to new data stream 2021-03-11 14:35:34 -05:00
Meng Li c1682d8cd3 Migrate phone calls sensor to new data stream 2021-03-11 14:35:34 -05:00
JulioV 6970954358 Change MUTATION structure 2021-03-11 14:35:34 -05:00
JulioV 1063b4ca65 Add steps summary to fitbitjson_mysql 2021-03-11 14:35:34 -05:00
JulioV 8c79cfc56f Fix OS specific dependcies 2021-03-11 14:35:34 -05:00
JulioV 41711fcdb7 Rename download_data add support for py containers 2021-03-11 14:35:34 -05:00
JulioV f65e3c8b1a Migrate empatica sensors to new data stream 2021-03-11 14:35:34 -05:00
JulioV fb054b539f Add support for multiple time zones 2021-03-11 14:35:34 -05:00
JulioV 6c51c6c239 Move phone_conversation to aware_mysql stream 2021-03-11 14:35:34 -05:00
JulioV ab1a3dbf79 Move phone_activity_recognition to aware_mysql stream 2021-03-11 14:35:34 -05:00
JulioV dc11cb593d Add support for smartphone sources and schemas. 
Initial support for accelerometer
Update docs for automatically create participants
Update docs for initial multiple time zones
 2021-03-11 14:35:33 -05:00
Meng Li 8377c12efb Add sleep intraday features with RAPIDS provider 2021-02-26 17:47:01 -05:00
nikunjgoel95 3d6caea6c4 Added the timeathome feature using infer_home_location.py as interim file. 2021-02-24 16:57:25 -05:00
JulioV 2e46f56111 Empatica zips must be placed in pid folder and small fixes 2021-02-21 17:32:41 -05:00
JulioV 4b9857562b Add support for zip input files 2021-02-21 17:32:41 -05:00
JulioV 8c726f5d4f Start empatica support 2021-02-21 17:32:41 -05:00
Meng Li b67f990816 Add new `FITBIT_DATA_YIELD` `RAPIDS` provider 2021-02-02 18:30:21 -05:00
JulioV 4c1e311135 Add error msg for invalid phone data yield sensors 2021-01-14 14:31:40 -05:00
JulioV 585bf7bc5d Add code so new feature providers can be added for the new four sensors 2021-01-14 14:31:40 -05:00
JulioV 8fd1d9dc29 Add four new sensors without providers 2021-01-14 14:31:40 -05:00
JulioV 51c7739bfc Revert "Start support for phone_keyboard" 
This reverts commit dd95b4f941.
 2020-12-20 16:29:40 -05:00
JulioV 41f19ed781 Merge branch 'hotfix/v0.2.3' into develop 2020-12-18 11:27:39 -05:00
JulioV 1b65f11b89 Fix participant IDS in the example analysis workflow 2020-12-18 11:27:04 -05:00
JulioV dd95b4f941 Start support for phone_keyboard 2020-12-14 13:42:22 -05:00
Meng Li 58ed986a61 Update PIDS in example_config.yaml 2020-12-04 18:45:16 -05:00
Meng Li 9a0e57301b Update 4 plots for time_segments 2020-12-03 21:00:32 -05:00
JulioV 88743b9a14 Update rule to create analysis workflow participant files 2020-12-03 12:48:32 -05:00
JulioV 614e759551 Refactor day segments to time segments 2020-12-02 18:41:03 -05:00
Meng Li 0bd43c139c Update plot#1: histogram_phone_data_yield 2020-12-01 14:21:33 -05:00
Meng Li 70991d6667 Add dates filter while parsing fitbit data 2020-11-30 12:34:14 -05:00
Meng Li 5178be585d Rename modeling.py to modelling.py & Update example_config.yaml 2020-11-25 22:35:38 -05:00
JulioV 5f51c94ac6 Separate device data configuration and update docs 2020-11-25 19:42:11 -05:00
Meng Li b4a512faf3 Add analysis example workflow 2020-11-25 16:34:05 -05:00
JulioV ced3305ddb Update R feature scripts to add sensor and provider names automatically 2020-11-25 14:49:42 -05:00
JulioV f02ca2624d Add phone yield sensor 2020-11-24 19:12:16 -05:00
Meng Li deba6b9e4f Update sleep summary features for segments 2020-11-23 12:01:00 -05:00
Meng Li a71efd6b85 Split FITBIT_STEPS into FITBIT_STEPS_SUMMARY and FITBIT_STEPS_INTRADAY 2020-11-11 21:16:48 -05:00
Meng Li b7e22b7440 Fix fitbit_parse_heartrate rule's table parameter 2020-11-11 20:23:41 -05:00
Meng Li 9fc36f67e2 Split FITBIT_HEARTRATE into FITBIT_HEARTRATE_SUMMARY and FITBIT_HEARTRATE_INTRADAY 2020-11-11 17:27:46 -05:00
JulioV 6ac4c05772 Merge branch 'day_segments' of https://github.com/carissalow/rapids into day_segments 2020-11-06 17:18:02 -05:00
JulioV 2aa44fc504 Change SENSOR_DATA to DEVICE_DATA 2020-11-04 17:16:46 -05:00
Meng Li 82873c285d Make sure feature rules of all sensors support both Python and R scripts 2020-11-04 14:05:25 -05:00
Meng Li 39632c66f5 Update steps features for segments 2020-10-30 18:57:04 -04:00
Meng Li ed7585c2bf Update heartrate features for segments 2020-10-27 17:55:57 -04:00
JulioV d5931c75d8 Refactor script to create participants files 2020-10-27 17:13:16 -04:00
Meng Li c8176b2d90 Fix MissingInputException issue of download_fitbit_data rule 2020-10-27 14:59:47 -04:00
Meng Li 2601ccde87 Fix minor bug of download_fitbit_data rule 2020-10-27 13:40:10 -04:00
JulioV b986599226 Add support to read fitbit data from csv files 2020-10-26 17:17:53 -04:00
JulioV 234588c94d Expose episode threshold between rows parameter 2020-10-26 15:28:19 -04:00
JulioV 1d04aa6807 Add check for non-overlapping event day segments 2020-10-23 12:15:26 -04:00
JulioV 47adb8bc4b Add tz support to fitbit 2020-10-22 14:38:40 -04:00
JulioV cff83a7ceb Implement parse fitbit data 2020-10-22 13:08:52 -04:00
JulioV c266f6dd10 Update participant files structure and fitbit download rule 2020-10-20 19:12:01 -04:00
JulioV 24bf62a7ab Update file names 2020-10-19 15:07:12 -04:00
Meng Li 29dcd1f284 Add accelerometer features of RAPIDS provider 2020-10-13 11:42:36 -04:00
Meng Li 236b1cd809 Update AR module for segments; Refactor input format 2020-10-07 18:11:06 -04:00
JulioV 6b1e006b82 Refactor fused location resampling 2020-10-07 11:51:31 -04:00
Meng Li f1717e59e7 Update screen&battery episodes features with different segment format 2020-09-29 17:13:34 -04:00
JulioV 0dafdd1340 Redo resample episodes in R, new battery episodes 2020-09-29 15:18:48 -04:00
JulioV 303d1472ed Change how we compute AR episodes 2020-09-22 17:32:51 -04:00