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294 Commits (master)

Author SHA1 Message Date
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
JulioV a851a460e4 Change the way we compute battery episodes 2020-09-22 16:53:51 -04:00
Meng Li f806cb44ac Fix the bug of screen duration features for different segments 2020-09-18 20:25:29 -04:00
JulioV 4dc8d38c66 Optimise assign to day segment 2020-09-16 14:54:20 -04:00
JulioV 3c45f6b152 Refactor assign to day segment 2020-09-14 14:21:36 -04:00
JulioV 98ebf9bd13 Migrate conversation to new file structure 2020-09-01 17:07:07 -04:00
JulioV 8d87f6e497 Migrate app foreground to new file structure 2020-09-01 15:25:35 -04:00
JulioV e643881058 Migrate light to new file structure 2020-09-01 12:01:24 -04:00
JulioV eda58d9d2c Migrate wifi to new file structure 2020-08-31 18:51:06 -04:00
JulioV 77d9d8f025 Migrate bluetooth to new file structure 2020-08-31 17:08:26 -04:00
JulioV 132311da77 Migrate messages to new file structure 2020-08-31 13:34:15 -04:00
JulioV e269062439 Migrate calls to new provider file structure 2020-08-28 17:50:49 -04:00
JulioV 011b9736d5 Refactor the function to fetch provider features 2020-08-28 17:40:23 -04:00
JulioV b0f1477d7e Migrate location providers to new file structure and segments 2020-08-28 13:53:00 -04:00
JulioV 14d2d694ce Migrate messages to new segments 2020-08-26 13:01:58 -04:00
JulioV 31ec5b0da4 Finalise new day segment structure with calls as example 2020-08-26 12:09:53 -04:00
JulioV 026d056378 Simplify window workflow 2020-08-20 14:51:22 -04:00
JulioV a0b5b5982b Setup rules and files to support multiple 2020-08-20 14:45:09 -04:00
Meng Li 00385dc54d Discard useless parameters and related code of example 2020-08-17 10:48:15 -04:00
JulioV b83f8ead44 Refactor snakefiles to smk files and create common.smk 2020-08-11 18:45:50 -04:00
JulioV 3f48a47a14 Fix optional input files for phone sensed bins 2020-08-11 18:02:52 -04:00
JulioV 08ce250839 Unify conversation timestamp for ios 2020-08-11 16:18:06 -04:00
nikunjgoel95 df7a52cd6c Added Sampling Frequency to Doryab Location Features. 2020-08-05 13:02:34 -04:00
Meng Li 973e1669fa Move baselines into a folder; rename column of "num_of_participants" with "num_of_rows" in modeling.py 2020-08-05 07:51:35 -04:00
Meng Li 0b65cc0546 Add example_profile 2020-08-03 17:30:15 -04:00
Meng Li c2b25a146d Replace sensor name with table name in heatmap_days_by_sensors section 2020-08-03 15:19:45 -04:00
Meng Li e13b89b125 Add restore_sql_file rule; notsummarised module; diff platforms for heatmap_days_by_sensors 2020-08-03 13:09:16 -04:00
Meng Li 21c3251066 Delete mystudy.snakefile and add all rules to models.snakefile 2020-07-29 15:25:26 -04:00
Meng Li c498b8d2df Add hours and bins thresholds for analysis section 2020-07-27 22:59:32 -04:00
Meng Li 93157db210 Data cleaning section: replace "day_type" with "day_idx" 2020-07-27 18:27:36 -04:00
Meng Li af6678c70c Update visualization section: add MIN_VALID_BINS_PER_HOUR 2020-07-26 20:11:25 -04:00
JulioV 388f09a003 Add missing wifi table 2020-07-24 16:35:41 -04:00
Meng Li b3aa4d82e1 Overall compliance heatmap: shows all dates for all participants (only supports last certain dates previously) 2020-07-24 12:58:48 -04:00
JulioV 5f771618ae Add screen episode filter parameters 2020-07-23 14:38:59 -04:00
nikunjgoel95 faad8f5a8f Added minutes of data in a day/epoch. 2020-07-23 14:23:32 -04:00
Meng Li b0354393ae Add "corr_method" param to heatmap_features_correlations.py 2020-07-22 20:00:14 -04:00
Meng Li c135b6ef78 Add visualization for data exploration 2020-07-22 16:47:32 -04:00
Meng Li 124843f96e Make phone_valid_sensed_days rule works for different min_valid_hours_per_day thresholds 2020-07-21 20:41:24 -04:00
nikunjgoel95 0ada1292ed Added maximum_gap_allowed parameter 2020-07-21 18:56:43 -04:00
nikunjgoel95 024ae1a549 Added Doryab's location features to rapids. 
Co-authored-by: JulioV <juliovhz@gmail.com>
 2020-07-16 14:26:43 -04:00
JulioV d2704296f3 Refactor valid sensed bins and days 2020-07-09 13:01:50 -04:00
JulioV 06edf53016 Add support for multi-platform participants 2020-06-30 17:34:18 -04:00
JulioV 6608e47918
Fix conversation plugin bug that mixed android tables with ios 2020-06-25 16:38:24 -04:00
JulioV 1bdb52dd65 Add functionality to exlcude step data based on sleep 2020-06-24 13:33:58 -04:00
JulioV 36017d5dca Refactor Snakefile and docs. Rename SMS scripts 2020-06-23 11:33:34 -04:00
Meng Li a121c0fe7b Split accelerometer features in config file; drop count; add more stats features 2020-06-22 12:01:17 -04:00
nikunjgoel95 1409de2832 Added Converstion Features. 
Updated config.yaml, Snakefile, Features.Snakefile and documentation.
 2020-06-19 01:27:28 -04:00
Meng Li e133b8b530 Refactor fitbit sleep features 2020-06-12 18:44:05 -04:00
Meng Li dcc7ca14e3 Refactor fitbit heartrate features 2020-06-12 16:04:03 -04:00
JulioV 8fbafcbe0c Fix location bug and improve fused resampling 2020-06-11 12:25:49 -04:00
Meng Li 0115fd14f6 Refactor fitbit step features 2020-06-05 21:29:39 -04:00
Meng Li adb170c3fa Fix step feature extraction input bug 2020-06-04 14:40:32 -04:00
JulioV 53db3fbaac
Fix bug so download_dataset receives the right fitbit table name 2020-06-01 18:54:19 -04:00
kaguillera 7f6448c431 Add Travis CI 2020-05-18 19:24:34 -04:00
Meng Li 34ffe4abaf Add the rule to merge population model results 2020-05-15 18:49:14 -04:00
Meng Li 8df8a5c2b3 Add baseline 2020-05-15 18:45:45 -04:00
Meng Li 8c8378f74a Split modeling module into two rules; Add RandomOverSampler for resampling; Add log; Fix bug of AUC 2020-05-15 18:42:03 -04:00
Meng Li 5fab99d8df Add one rule to calculate the ratio of cells with missing values for cleaned features 2020-05-15 18:25:07 -04:00
Meng Li 6e99e69f8c Save cleaned features with different data cleaning threasholds under different folders 2020-05-15 17:59:14 -04:00
Meng Li 915bdd04b1 Parse Fitbit summary and intraday data; Extract Fitbit daily features from summary data 2020-05-15 17:51:00 -04:00
JulioV c30bf4d24f
Update renv.snakefile 2020-05-06 18:00:44 -04:00
JulioV f0674122ff Replace packrat with renv 2020-05-01 19:46:04 -04:00
Meng Li 7cbb227214 Add modeling module 2020-04-29 18:53:54 -04:00
Meng Li 9ddb50ed59 Split days threshold of data cleaning into days_before_surgery and days_after_discharge 
Co-authored-by: JulioV <juliovhz@gmail.com>
 2020-04-29 14:37:40 -04:00
Meng Li 490599c742 Implement AR features for iOS 
Co-authored-by: JulioV <juliovhz@gmail.com>
 2020-04-20 18:05:54 -04:00
Meng Li 5696b4f6d4 Add merge module for demographic features and target 2020-04-16 14:20:16 -04:00
Meng Li eac721de84 Add demographic_features and targets module; refactor analysis code 
Co-authored-by: JulioV <juliovhz@gmail.com>
 2020-04-16 12:38:28 -04:00
JulioV 010114c1aa Add wifi features 2020-04-13 13:24:52 -04:00
Mingze Cao 8cc93c8791 Refactor battery feature: replace "metrics" with "features" 
Co-authored-by: Meng Li <AnnieLM1996@gmail.com>
 2020-04-09 15:06:25 -05:00
Mingze Cao 2d7d3bfccf Refactor location_barnett features: replace "metrics" with "features" 
Co-authored-by: Meng Li <AnnieLM1996@gmail.com>
 2020-04-09 12:20:39 -05:00
Mingze Cao c2fbc3ad7a Refactor sms feature: replace "metrics" with "features" 
Co-authored-by: Meng Li <AnnieLM1996@gmail.com>
 2020-04-08 15:02:58 -05:00
Mingze Cao 97c83caebc Refactor fitbit_heartrate feature: replace "metrics" with "features" 
Co-authored-by: Meng Li <AnnieLM1996@gmail.com>
 2020-04-08 14:31:43 -05:00
Mingze Cao a53ba242f8 Refactor google_activity_recognition feature: replace "metrics" with "features" 
Co-authored-by: Meng Li <AnnieLM1996@gmail.com>
 2020-04-08 13:36:36 -05:00
Mingze Cao 0809001dfa Refactor light features: replace "metrics" with "features" 
Co-authored-by: Meng Li <AnnieLM1996@gmail.com>
 2020-04-08 13:02:53 -05:00
Mingze Cao f46e8c0666 Refactor applications_foreground features: replace "metrics" with "features" 
Co-authored-by: Meng Li <AnnieLM1996@gmail.com>
 2020-04-08 12:31:43 -05:00
Mingze Cao d1c38016de Refactor call features: replace "metrics" with "features" 
Co-authored-by: Meng Li <AnnieLM1996@gmail.com>
 2020-04-08 10:51:18 -05:00
Mingze Cao e0d19cbc1b Refactor screen features: replace "metrics" with "features" 
Co-authored-by: Meng Li <AnnieLM1996@gmail.com>
 2020-04-08 10:05:16 -05:00
Mingze Cao 3986f4e185 Refactor fitbit_step features: replace "metrics" with "features" 
Co-authored-by: Meng Li <AnnieLM1996@gmail.com>
Co-authored-by: JulioV <juliovhz@gmail.com>
 2020-04-03 16:03:45 -05:00
Mingze Cao 595bdd6f5b Refactor bluetooth features: replace "metrics" with "features" 
Co-authored-by: Meng Li <AnnieLM1996@gmail.com>
Co-authored-by: JulioV <juliovhz@gmail.com>
 2020-04-03 12:07:09 -05:00
Mingze Cao 6045df494d Modify the Accelerometer ‘Metrics’ to Accelerometer ‘Features’ 
Co-authored-by: Meng Li <AnnieLM1996@gmail.com>
Co-authored-by: JulioV <juliovhz@gmail.com>
 2020-04-02 16:36:28 -05:00
Meng Li ea46df63d5 Get targets 
Co-authored-by: JulioV <juliovhz@gmail.com>
 2020-03-26 17:27:23 -04:00
JulioV 0e173872df Refactor select_days_to_analyse, fix merge bugs, add clean metrics for model 2020-03-17 21:15:53 -04:00
Meng Li 7c240a9613 Select days to analyse 
Co-authored-by: JulioV <juliovhz@gmail.com>
 2020-03-17 17:26:30 -04:00
JulioV 3d4c26754e Rename merge metrics for models and add filter valid sensed days 
Co-authored-by: Meng Li <AnnieLM1996@gmail.com>
 2020-03-12 17:31:46 -04:00
Meng Li b23bb0e402 Add INCLUDE_ZERO_STEP_ROWS flag for step sensor 2020-03-09 15:59:51 -04:00
Meng Li aba9f13332 Add merge metrics module for analysis rules 2020-03-09 13:32:14 -04:00
JulioV 12ceb87090 Merge branch 'master' of https://github.com/carissalow/rapids 2020-03-05 10:32:46 -05:00
JulioV ccc283db16 Add day segment parameter to location barnett rule 2020-03-05 10:32:38 -05:00
Meng Li c8b7275084 Add firstuseafterTIME feature for screen sensor 2020-03-04 12:21:36 -05:00
Meng Li 85f4ec2ab6 Delete screen event features and add countepisode and episodepersensedminutes 2020-03-03 17:31:15 -05:00
JulioV c7bc430425 Add priority to download participants rule 2020-03-03 11:08:18 -05:00
JulioV 619a6e6e2b Fix screen delta extraction for iOS and Android 2020-03-02 19:26:20 -05:00
Meng Li fa9029b090 Add overall compliance heatmap for last 7 days 2020-02-25 13:27:17 -05:00
JulioV f22d1834ee Add metric filter to barnett location features 2020-02-21 10:58:35 -05:00
Meng Li 579df6325f Add date filter for download_dataset 2020-02-20 15:51:22 -05:00
Meng Li 3369a97d0e Add device_id and label to heatmaps 2020-02-20 10:16:03 -05:00
Meng Li 76888b412d Add label and dates for external files 2020-02-18 16:41:10 -05:00
JulioV 6bbc916702 Add download_participants functionality 2020-02-10 16:45:34 -05:00
Meng Li 0840235280 Add applications_foreground features 2020-02-07 11:52:55 -05:00
Meng Li 770764ec8a Add heartrate features 2020-02-07 11:35:15 -05:00
Meng Li 3d13940bd3 Fixed heatmap issue#27 2020-02-07 11:14:19 -05:00