Primoz
6ba4a66deb
Squashed commit of the following:
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commit 31a47a5ee4569264e39d7c445525a6e64bb7700a
Author: Primoz <sisko.primoz@gmail.com>
Date: Wed Jul 20 13:49:22 2022 +0000
Environment version change.
commit 5b274ed8993f58e783bda6d82fce936764209c28
Author: Primoz <sisko.primoz@gmail.com>
Date: Tue Jul 19 16:10:07 2022 +0000
Enabled cleaning for all participants + standardization files.
commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924
Author: Primoz <sisko.primoz@gmail.com>
Date: Tue Jul 19 14:14:51 2022 +0000
Features cleaning fixes after testing. Visualization script for phone features values.
commit 176178d73b154c30b9eb9eb4a67514f00d6a924e
Author: Primoz <sisko.primoz@gmail.com>
Date: Tue Jul 19 09:05:14 2022 +0000
Revert "Necessary config changes."
This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0.
commit 26ea6512c9d512f95837e7b047fe510c1d196403
Author: Primoz <sisko.primoz@gmail.com>
Date: Mon Jul 18 13:19:47 2022 +0000
Adding cleaning function condition and cleaning functionality.
commit 575c29eef9c21e6f2d7832871e73bc0941643734
Author: Primoz <sisko.primoz@gmail.com>
Date: Mon Jul 18 12:51:56 2022 +0000
Translation of the cleaning individual RAPIDS function from R to py.
commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0
Author: Primoz <sisko.primoz@gmail.com>
Date: Mon Jul 18 12:02:18 2022 +0000
Necessary config changes.
commit b5669f51612fbd8378848615d639677851ab032f
Author: Primoz <sisko.primoz@gmail.com>
Date: Fri Jul 15 15:26:00 2022 +0000
Modified snakemake rule to dynamically choose script extention.
commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d
Author: Primoz <sisko.primoz@gmail.com>
Date: Fri Jul 15 14:43:08 2022 +0000
Trying to modify the snakefile rule to execute scripts in two languages depended on the provider.
commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9
Author: Primoz <sisko.primoz@gmail.com>
Date: Fri Jul 15 09:49:41 2022 +0000
gitignore: adding required files so that RAPIDS can be run successfully.
commit 71018ab178256970535e78961602ab8c7f0ebb14
Author: Primoz <sisko.primoz@gmail.com>
Date: Fri Jul 15 08:34:19 2022 +0000
Standardization bug fixes
commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc
Author: Primoz <sisko.primoz@gmail.com>
Date: Thu Jul 14 15:28:02 2022 +0000
Seperate rules for empatica vs. nonempatica standardization.
Parameter in config that controls the creation of standardized merged files for individual and all participants..
commit 90f902778565e0896d3bae22ae8551be8b487e67
Author: Primoz <sisko.primoz@gmail.com>
Date: Tue Jul 12 14:23:03 2022 +0000
Preparing for final csvs' standardization.
commit d25dde3998786a9a582f5cda544ee104386778f9
Author: Primoz <sisko.primoz@gmail.com>
Date: Mon Jul 11 12:08:47 2022 +0000
Revert "Changes in config to be reverted."
This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313.
commit 6b23e70857e63deda98eb98d190af9090626c84b
Author: Primoz <sisko.primoz@gmail.com>
Date: Mon Jul 11 12:08:26 2022 +0000
Enabled standardization for rest (previously active) phone features.
Testing still needed.
commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f
Author: Primoz <sisko.primoz@gmail.com>
Date: Mon Jul 11 09:07:55 2022 +0000
Enabled standardization for phone calls.
All steps completed and tested.
commit bea7608e7095021fb7c53a9afa07074448fe4313
Author: Primoz <sisko.primoz@gmail.com>
Date: Mon Jul 11 07:47:51 2022 +0000
Changes in config to be reverted.
commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd
Author: Primoz <sisko.primoz@gmail.com>
Date: Fri Jul 8 14:11:24 2022 +0000
Standardization for the rest of the features.
commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7
Author: Primoz <sisko.primoz@gmail.com>
Date: Fri Jul 8 14:11:08 2022 +0000
README update again
2022-07-20 13:51:22 +00:00
Primoz
887fd7dc72
Merge branch 'empatica_calculating_features'
2022-07-06 11:53:21 +00:00
Primoz
9ea39dc557
Standardization as a Snakefile's rule enabled for all E4 sensors.
2022-06-13 18:17:30 +00:00
Primoz
402059871f
Making standardization as a rule. WIP: done only for BVP.
2022-06-13 14:12:03 +00:00
Primoz
5532043b1f
Patching IBI with BVP - completed.
2022-05-25 19:39:47 +00:00
Primoz
2a8f58f5c8
Patching IBI with BVP. WIP
2022-05-20 13:18:45 +00:00
Primoz
31e36e7400
Alternating Second order and full segment features corresponding to config settings.
2022-05-11 08:50:15 +00:00
Primoz
5638367999
Implementation of the second order features.
2022-04-25 13:07:03 +00:00
=
3c058e4463
Add option to calculate features within windows and store it in CSV (all sensors).
2022-04-13 13:18:23 +00:00
junos
baa94c4c4e
Correct additional error in feature file naming.
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Add the final feature file to the list in Snakefile.
2022-04-06 17:29:17 +02:00
junos
cbc8ae4e03
Add necessary checks for empty data frames.
2022-04-05 18:58:09 +02:00
junos
e84c35a36a
Remove unnecessary parameters from preprocess_esm.
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And correct the newly named interim file.
2022-04-05 18:36:09 +02:00
junos
e2ce68f591
Defer creation of feature files to esm_features rule.
2022-04-05 18:30:04 +02:00
junos
751b04f3f4
Pass scale names to Snakemake correctly.
2022-04-05 18:14:37 +02:00
junos
99245afca3
Try a different approach for preprocessing ESMs.
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It is important that this follows generic RAPIDS pattern.
In the subsequent step of calculating features,
there is an expected file and folder structure of data/interim.
See rules/common.smk/find_features_files()
2022-04-05 18:02:31 +02:00
junos
798ec973b4
[WIP] Add a rule for ESM features.
2022-03-30 10:43:30 +02:00
junos
7173ca13e3
Rename a parameter.
2022-03-30 10:40:53 +02:00
junos
23f0aaba3a
Get the name of the questionnaire from Snakefile.
2022-03-16 18:28:57 +01:00
junos
679f00dc19
Enable selecting any questionnaire as target.
2022-03-16 17:55:44 +01:00
junos
cb116100dd
Move preprocessing to features.
2022-03-16 17:06:42 +01:00
Meng Li
5bad3eb8b5
Data cleaning ( #166 )
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* 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
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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
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
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
Meng Li
d529490999
Migrate fitbit features to new data stream
2021-03-12 12:38:36 -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
1063b4ca65
Add steps summary to fitbitjson_mysql
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
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
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
585bf7bc5d
Add code so new feature providers can be added for the new four sensors
2021-01-14 14:31:40 -05:00
JulioV
51c7739bfc
Revert "Start support for phone_keyboard"
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This reverts commit dd95b4f941
.
2020-12-20 16:29:40 -05:00
JulioV
dd95b4f941
Start support for phone_keyboard
2020-12-14 13:42:22 -05:00
JulioV
614e759551
Refactor day segments to time segments
2020-12-02 18:41:03 -05:00