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293 Commits (imputation_and_cleaning)

Author SHA1 Message Date
Primoz a668b6e8da Extract ERS and stress event targets to csv files (completed). 2022-11-10 09:37:27 +00:00
Primoz f3c6a66da9 Begin with stress events in the ERS script. 2022-11-08 15:53:43 +00:00
Primoz cf38d9f175 Implement ERS generating logic. 2022-10-17 15:07:33 +00:00
Primoz f3ca56cdbf Start with ERS logic integration within Snakemake. 2022-10-14 14:46:28 +00:00
Primoz 001d400729 Clean features and create input files based on all possible targets. 2022-10-06 14:28:12 +00:00
Primoz eaf4340afd Small imputation and cleaning corrections. 2022-09-20 08:03:48 +00:00
Primoz 18b63127de Removed all standardizaton rules and configurations. 2022-09-19 06:16:26 +00:00
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." 
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. 
Correct other mistakes.
 2022-04-12 16:55:01 +02:00
junos 9ab0c8f289 Add a rule for model baselines. 
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. 
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. 
Does nothing for now.
 2022-04-06 17:47:03 +02:00
junos baa94c4c4e Correct additional error in feature file naming. 
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. 
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. 
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. 
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. 
Take into account that TZCODES_FILE can be created with a rule.
 2021-12-15 18:09:30 +01:00