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26 Commits (master)

Author SHA1 Message Date
Primoz 87e5209a9f Squashed commit of the following: 
commit 8a6b52a97c
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Nov 29 11:35:49 2022 +0000

    Switch to 30_before ERS with corresponding targets.

commit 244a053730
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Nov 29 11:19:43 2022 +0000

    Change output files settings to nonstandardized.

commit be0324fd01
Author: Primoz <sisko.primoz@gmail.com>
Date:   Mon Nov 28 12:44:25 2022 +0000

    Fix some bugs and set categorical columns as categories dtypes.

commit 99c2fab8f9
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Nov 16 09:50:18 2022 +0000

    Fix a bug in the making of the individual model (when there is no target in the participants columns).

commit 286de93bfd
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Nov 15 11:21:51 2022 +0000

    Fix some bugs and extend ERS and cleaning scripts with multiple stress event targets logic.

commit ab803ee49c
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Nov 15 10:14:07 2022 +0000

    Add additional appraisal targets.

commit 621f11b2d9
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Nov 15 09:53:31 2022 +0000

    Fix a bug related to wrong user input (duplicated events).

commit bd41f42a5d
Author: Primoz <sisko.primoz@gmail.com>
Date:   Mon Nov 14 15:07:36 2022 +0000

    Rename target_ to segmenting_ method.

commit a543ce372f
Author: Primoz <sisko.primoz@gmail.com>
Date:   Mon Nov 14 15:04:16 2022 +0000

    Add comments for event_related_script understanding.

commit 74b454b07b
Author: Primoz <sisko.primoz@gmail.com>
Date:   Fri Nov 11 09:15:12 2022 +0000

    Apply changes to string answers to make them language-generic.

commit 6ebe83e47e
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Nov 10 12:42:52 2022 +0000

    Improve the ERS extract method with a couple of validations.

commit 00350ef8ca
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Nov 10 10:32:58 2022 +0000

    Change config for stressfulness event target method.

commit e4985c9121
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Nov 10 10:29:11 2022 +0000

    Override stressfulness event target with extracted values from csv.

commit a668b6e8da
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Nov 10 09:37:27 2022 +0000

    Extract ERS and stress event targets to csv files (completed).

commit 9199b53ded
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Nov 9 15:11:51 2022 +0000

    Get, join and start processing required ERS stress event data.

commit f3c6a66da9
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Nov 8 15:53:43 2022 +0000

    Begin with stress events in the ERS script.

commit 0b3e9226b3
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Nov 8 14:44:24 2022 +0000

    Make small corrections in ERS file.

commit 2d83f7ddec
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Nov 8 11:32:05 2022 +0000

    Begin the ERS logic for 90-minutes events.

commit 1da72a7cbe
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Nov 8 09:45:37 2022 +0000

    Rename targets method in config.

commit 9f441afc16
Author: Primoz <sisko.primoz@gmail.com>
Date:   Fri Nov 4 15:09:04 2022 +0000

    Begin ERS logic for 90-minutes events.

commit c1c9f4d05a
Merge: 62f46ea3 7ab0280d
Author: Primoz <sisko.primoz@gmail.com>
Date:   Fri Nov 4 09:11:58 2022 +0000

    Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning

commit 62f46ea376
Author: Primoz <sisko.primoz@gmail.com>
Date:   Fri Nov 4 09:11:53 2022 +0000

    Prepare method-based logic for ERS generating.

commit 7ab0280d7e
Author: Primoz <sisko.primoz@gmail.com>
Date:   Fri Nov 4 08:58:08 2022 +0000

    Correctly rename stressful event target variable.

commit eefa9f3f4d
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Nov 3 14:49:54 2022 +0000

    Add new target: stressfulness_event.

commit 5e8174dd41
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Nov 3 13:52:45 2022 +0000

    Add new target: stressfulness_period.

commit 35c1a762e7
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Nov 3 13:51:18 2022 +0000

    Improve filtering by esm_session and device_id.

commit 02264b21fd
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Nov 3 09:30:12 2022 +0000

    Add logic for target selection in ERS processing.

commit 0ce8723bdb
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Nov 2 14:01:21 2022 +0000

    Extend imputation logic within the cleaning script.

commit 30b38bfc02
Author: Primoz <sisko.primoz@gmail.com>
Date:   Fri Oct 28 09:00:13 2022 +0000

    Fix the generating procedure of ERS file for participants with multiple devices.

commit cd137af15a
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Oct 27 14:20:15 2022 +0000

    Config for 30 minute EMA segments.

commit 3c0585a566
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Oct 27 14:12:56 2022 +0000

    Remove obsolete comments.

commit 6b487fcf7b
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Oct 27 14:11:42 2022 +0000

    Set E4 data yield to 1 if it is over 1. Optimize E4 data_yield script.

commit 5d17c92e54
Merge: a31fdd14 0d143e6a
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Oct 26 14:18:20 2022 +0000

    Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning

commit a31fdd1479
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Oct 26 14:18:08 2022 +0000

    Start to test empatica_data_yield precieved error.

commit 936324d234
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Oct 26 14:17:27 2022 +0000

    Switch config for 30 minutes event related segments.

commit da0a4596f8
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Oct 26 14:16:25 2022 +0000

    Add additional ESM processing logic for ERS csv extraction.

commit d4d74818e6
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Oct 26 14:14:32 2022 +0000

    Fix a bug - missing time_segment column when df is empty

commit 14ff59914b
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Oct 26 09:59:46 2022 +0000

    Fix to correct dtypes.

commit 6ab0ac5329
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Oct 26 09:57:26 2022 +0000

    Optimize memory consumption with dtype definition while reading csv file.

commit 0d143e6aad
Merge: 8acac501 b92a3aa3
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Oct 25 15:28:27 2022 +0000

    Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning

commit 8acac50125
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Oct 25 15:26:43 2022 +0000

    Add safenet when features dataframe is empty.

commit b92a3aa37a
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Oct 25 15:25:22 2022 +0000

    Remove unwanted output or other error producing code.

commit bfd637eb9c
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Oct 25 08:53:44 2022 +0000

    Improve strings formatting in straw_events file.

commit 0d81ad5756
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Oct 19 13:35:04 2022 +0000

    Debug assignment of segments to rows

commit cea451d344
Merge: e88bbd54 cf38d9f1
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Oct 18 09:15:06 2022 +0000

    Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning

commit e88bbd548f
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Oct 18 09:15:00 2022 +0000

    Add new daily segment and filter by segment in the cleaning script.

commit cf38d9f175
Author: Primoz <sisko.primoz@gmail.com>
Date:   Mon Oct 17 15:07:33 2022 +0000

    Implement ERS generating logic.

commit f3ca56cdbf
Author: Primoz <sisko.primoz@gmail.com>
Date:   Fri Oct 14 14:46:28 2022 +0000

    Start with ERS logic integration within Snakemake.

commit 797aa98f4f
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Oct 12 15:51:50 2022 +0000

    Config for ERS testing.

commit 9baff159cd
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Oct 12 15:51:23 2022 +0000

    Changes needed for testing and starting of the Event-Related Segments.

commit 0f21273508
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Oct 12 12:32:51 2022 +0000

    Bugs fix

commit 55517eb737
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Oct 12 12:23:11 2022 +0000

    Necessary commit before proceeding.

commit de15a52dba
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Oct 11 08:36:23 2022 +0000

    Bug fix

commit 1ad25bb572
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Oct 11 08:26:17 2022 +0000

    Few modifications of some imputation values in cleaning script and feature extraction.

commit 9884b383cf
Author: Primoz <sisko.primoz@gmail.com>
Date:   Mon Oct 10 16:45:38 2022 +0000

    Testing new data with AutoML.

commit 2dc89c083c
Author: Primoz <sisko.primoz@gmail.com>
Date:   Fri Oct 7 08:52:12 2022 +0000

    Small changes in cleaning overall

commit 001d400729
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Oct 6 14:28:12 2022 +0000

    Clean features and create input files based on all possible targets.

commit 1e38d9bf1e
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Oct 6 13:27:38 2022 +0000

    Standardization and correlation visualization in overall cleaning script.

commit a34412a18d
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Oct 5 14:16:55 2022 +0000

    E4 data yield corrections. Changes in overal cs - standardization.

commit 437459648f
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Oct 5 13:35:05 2022 +0000

    Errors fix: individual script - treat participants missing data.

commit 53f6cc60d5
Author: Primoz <sisko.primoz@gmail.com>
Date:   Mon Oct 3 13:06:39 2022 +0000

    Config and cleaning script necessary changes ...

commit bbeabeee6f
Author: Primoz <sisko.primoz@gmail.com>
Date:   Mon Oct 3 12:53:31 2022 +0000

    Last changes before processing on the server.

commit 44531c6d94
Author: Primoz <sisko.primoz@gmail.com>
Date:   Fri Sep 30 10:04:07 2022 +0000

    Code cleaning, reworking cleaning individual based on changes in overall script. Changes in thresholds.

commit 7ac7cd5a37
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Sep 29 14:33:21 2022 +0000

    Preparation of the overall cleaning script.

commit 68fd69dada
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Sep 29 11:55:25 2022 +0000

    Cleaning script for individuals: corrections and comments.

commit a4f0d056a0
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Sep 29 11:44:27 2022 +0000

    Fillna for app foreground and activity recognition

commit 6286e7a44c
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Sep 28 12:47:08 2022 +0000

    firstuseafter column removed from contextual imputation

commit 9b3447febd
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Sep 28 12:40:05 2022 +0000

    Contextual imputation correction

commit d6adda30cf
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Sep 28 12:37:51 2022 +0000

    Contextual imputation on time(first/last) features.

commit 8af4ef11dc
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Sep 28 10:02:47 2022 +0000

    Contextual imputation by feature type.

commit 536b9494cd
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Sep 27 14:12:08 2022 +0000

    Cleaning script corrections

commit f0b87c9dd0
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Sep 27 09:54:15 2022 +0000

    Debugging of the empatica data yield integration.

commit 7fcdb873fe
Merge: 5c7bb0f4 bd53dc16
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Sep 27 07:50:29 2022 +0000

    Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning

commit 5c7bb0f4c1
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Sep 27 07:48:32 2022 +0000

    Config changes

commit bd53dc1684
Author: Primoz <sisko.primoz@gmail.com>
Date:   Mon Sep 26 15:54:00 2022 +0000

    Empatica data yield usage in the cleaning script.

commit d9a574c550
Author: Primoz <sisko.primoz@gmail.com>
Date:   Fri Sep 23 13:24:50 2022 +0000

    Changes in the cleaning script and preparation of empatica data yield method.

commit 19aa8707c0
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Sep 22 13:45:51 2022 +0000

    Redefined cleaning steps after revision

commit 247d758cb7
Merge: 90ee99e4 7493aaa6
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Sep 21 07:18:01 2022 +0000

    Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning

commit 90ee99e4b9
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Sep 21 07:16:00 2022 +0000

    Remove TODO comments

commit 7493aaa643
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Sep 20 12:57:55 2022 +0000

    Small changes in cleaning scrtipt and missing vals testing.

commit eaf4340afd
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Sep 20 08:03:48 2022 +0000

    Small imputation and cleaning corrections.

commit a96ea508c6
Author: Primoz <sisko.primoz@gmail.com>
Date:   Mon Sep 19 07:34:02 2022 +0000

    Fill NaN of Empatica's SD second order feature (must be tested).

commit 52e11cdcab
Author: Primoz <sisko.primoz@gmail.com>
Date:   Mon Sep 19 07:25:54 2022 +0000

    Configurations for new standardization path.

commit 92aff93e65
Author: Primoz <sisko.primoz@gmail.com>
Date:   Mon Sep 19 07:25:16 2022 +0000

    Remove standardization script.

commit 18b63127de
Author: Primoz <sisko.primoz@gmail.com>
Date:   Mon Sep 19 06:16:26 2022 +0000

    Removed all standardizaton rules and configurations.

commit 62982866cd
Author: Primoz <sisko.primoz@gmail.com>
Date:   Fri Sep 16 13:24:21 2022 +0000

    Phone wifi visible inspection (WIP)

commit 0ce6da5444
Author: Primoz <sisko.primoz@gmail.com>
Date:   Fri Sep 16 11:30:08 2022 +0000

    kNN imputation relocation and execution only on specific columns.

commit e3b78c8a85
Author: Primoz <sisko.primoz@gmail.com>
Date:   Fri Sep 16 10:58:57 2022 +0000

    Impute selected phone features with 0.
    Wifi visible, screen, and light.

commit 7d85f75d21
Author: Primoz <sisko.primoz@gmail.com>
Date:   Fri Sep 16 09:03:30 2022 +0000

    Changes in phone features NaN values script.

commit 385e21409d
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Sep 15 14:16:58 2022 +0000

    Changes in NaN values testing script.

commit 18002f59e1
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Sep 15 10:48:59 2022 +0000

    Doryab bluetooth and locations features fill in NaN values.

commit 3cf7ca41aa
Merge: d27a4a71 d5ab5a03
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Sep 14 15:38:32 2022 +0000

    Merge branch 'imputation_and_cleaning' of https://repo.ijs.si/junoslukan/rapids into imputation_and_cleaning

commit d5ab5a0394
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Sep 14 14:13:03 2022 +0000

    Writing testing scripts to determine the point of manual imputation.

commit dfbb758902
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Sep 13 13:54:06 2022 +0000

    Changes in AutoML params and environment.yml

commit 4ec371ed96
Author: Primoz <sisko.primoz@gmail.com>
Date:   Tue Sep 13 09:51:03 2022 +0000

    Testing auto-sklearn

commit d27a4a71c8
Author: Primoz <sisko.primoz@gmail.com>
Date:   Mon Sep 12 13:44:17 2022 +0000

    Reorganisation and reordering of the cleaning script.

commit 15d792089d
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Sep 1 10:33:36 2022 +0000

    Changes in cleaning script:
    - target extracted from config to remove rows where target is nan
    - prepared sns.heatmap for further missing values analysis
    - necessary changes in config and participant p01
    - picture of heatmap which shows the values state after cleaning

commit cb351e0ff6
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Sep 1 10:06:57 2022 +0000

    Unnecessary line (rows with no target value will be removed in cleaning script).

commit 86299d346b
Author: Primoz <sisko.primoz@gmail.com>
Date:   Thu Sep 1 09:57:21 2022 +0000

    Impute phone and sms NAs with 0

commit 3f7ec80c18
Author: Primoz <sisko.primoz@gmail.com>
Date:   Wed Aug 31 10:18:50 2022 +0000

    Preparation a) phone_calls 0 imputation b) remove rows with NaN target
 2022-12-08 16:04:39 +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
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 f13a91044d Write questionnaire data to data/interim. 2022-03-01 11:39:58 +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
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 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
JulioV 614e759551 Refactor day segments to time segments 2020-12-02 18:41:03 -05:00
Meng Li 5178be585d Rename modeling.py to modelling.py & Update example_config.yaml 2020-11-25 22:35:38 -05:00
Meng Li b4a512faf3 Add analysis example workflow 2020-11-25 16:34:05 -05:00
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