Primoz
f78aa3e7b3
Preparation for cleaning & imputation
2022-08-26 10:56:14 +00:00
Primoz
a620def209
Generate standardized model input files (NOTE: commented unstandardized sections!)
2022-08-24 13:42:39 +00:00
Primoz
c498ecb742
Include baseline models (+corrections), disable columns drop in cleaning function.
2022-08-23 14:12:14 +00:00
Primoz
6ba4a66deb
Squashed commit of the following:
...
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
5a777ac79f
Working version that integrates both phone and empatica feature calculations.
2022-07-07 15:00:47 +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
9f5edf1c2b
Revert "Add a rule for model baselines."
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The example was for a classification rather than regression problem.
This reverts commit 9ab0c8f289
.
# Conflicts:
# rules/models.smk
2022-04-12 16:59:42 +02:00
junos
4ad261fae5
Rename baseline features AGAIN.
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Correct other mistakes.
2022-04-12 16:55:01 +02:00
junos
9ab0c8f289
Add a rule for model baselines.
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Add baselines and helper functions to main models dir.
2022-04-12 14:23:58 +02:00
junos
f5688f6154
Add a rule to merge sensor and baseline features.
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And select target as before.
2022-04-08 15:42:04 +02:00
junos
50c0defca7
Select target columns (no parsing necessary).
2022-04-06 18:16:49 +02:00
junos
ac86221662
[WIP] Add a rule to parse targets.
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Does nothing for now.
2022-04-06 17:47:03 +02:00
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
Primoz
dc2b462145
Reseting files to defaults - for Minimal Working Example
2022-03-16 13:30:19 +00:00
junos
d470eef27e
Add a rule to preprocess and clean ESM.
2022-03-09 18:38:46 +01:00
junos
aedb8b6785
Write questionnaire data to data/interim.
2022-03-01 12:02:36 +01:00
junos
30ac8b1cd5
Start calculating demand control features.
2022-02-23 19:08:10 +01:00
junos
176367631b
Prepare baseline feature rule.
2022-02-23 11:09:33 +01:00
junos
bf9c764c97
Split baseline data to participants.
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And some csv I/O settings.
2022-02-04 18:37:57 +01:00
junos
16e608db74
First merge baseline datasets.
2022-02-04 18:21:42 +01:00
junos
204f6f50b0
Read the relevant files.
2022-02-04 18:06:02 +01:00
junos
685ed6a546
Set up demographic data download.
2022-02-04 17:37:00 +01:00
junos
ffa7a30575
Make place for STRAW models.
2022-02-04 17:25:24 +01:00
junos
b29f902915
Look into ESM table for device_id.
2021-12-15 20:18:12 +01:00
junos
5a9252e46e
Merge remote-tracking branch 'origin/master'
2021-12-15 18:32:36 +01:00
junos
e5cc02501f
Set the timezone.csv path in config.
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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.
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And use these in the prepare_participants_file function.
2021-11-29 16:57:50 +01:00
junos
39bd244511
[WIP] Prepare yaml files.
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These will be used to create participants files.
2021-11-24 19:11:19 +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