bb62497ba6
Patching IBI with BVP - selecting appropriate pipeline entry point. WIP
2022-05-24 11:07:18 +00:00
2a8f58f5c8
Patching IBI with BVP. WIP
2022-05-20 13:18:45 +00:00
6864cfe775
Changes after thorough testing with available data.
2022-05-13 13:35:34 +00:00
c1564f0cae
Changed wrapper method calculate_feature to its newest version (for TEMP and ACC).
2022-05-11 14:21:21 +00:00
31e36e7400
Alternating Second order and full segment features corresponding to config settings.
2022-05-11 08:50:15 +00:00
9cf9e1fe14
Testing and modifying the code with different E4 data.
2022-05-10 11:36:49 +00:00
f62a1302dd
Cr-features corrections for ACC and TEMP sensors
2022-05-09 11:01:52 +00:00
5638367999
Implementation of the second order features.
2022-04-25 13:07:03 +00:00
66451160e9
Calculating HRV features with IBI.csv.
2022-04-20 10:44:51 +00:00
8c8fe1fec7
Modifications, mostly imports, after changes in cr-features module.
2022-04-19 13:24:46 +00:00
075c64d1e5
HRV: changed wrapper calcFeat method with specialized one.
2022-04-14 11:51:53 +00:00
c05b047c2d
Correct outstanding baseline feature mistake.
2022-04-13 17:05:16 +02:00
53ec52a954
Disable (SOME) feature cleaning for ESM data.
2022-04-13 16:01:31 +02:00
3c058e4463
Add option to calculate features within windows and store it in CSV (all sensors).
2022-04-13 13:18:23 +00:00
144f0d0dcf
Account for missing baseline data.
2022-04-13 14:56:28 +02:00
ed5314aa98
Merge remote-tracking branch 'origin/master'
2022-04-12 17:27:25 +02:00
a6a37c7bd9
Drop NaN targets.
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This mirrors INNER join in merge_features_and_targets_for_individual_model.py:
data = pd.concat([sensor_features, targets[["target"]]], axis=1, join="inner")
2022-04-12 17:01:49 +02:00
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
2022-04-12 16:59:42 +02:00
4ad261fae5
Rename baseline features AGAIN.
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Correct other mistakes.
2022-04-12 16:55:01 +02:00
74cf4ada1c
Cr-feat window length for all empaticas sensors.
2022-04-12 14:00:44 +00:00
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
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
b1f356c3f7
Extract a function to be used elsewhere.
2022-04-08 15:36:32 +02:00
7ff3dcf5fc
Move and rename target variable.
2022-04-06 18:21:09 +02:00
50c0defca7
Select target columns (no parsing necessary).
2022-04-06 18:16:49 +02:00
ac86221662
[WIP] Add a rule to parse targets.
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Does nothing for now.
2022-04-06 17:47:03 +02:00
d326a1b09d
Include the constant directly in main.py.
2022-04-05 19:08:43 +02:00
2e545e81f0
Include feature calculations for different scales.
2022-04-05 19:05:34 +02:00
cbc8ae4e03
Add necessary checks for empty data frames.
2022-04-05 18:58:09 +02:00
751b04f3f4
Pass scale names to Snakemake correctly.
2022-04-05 18:14:37 +02:00
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
ed298a9479
Implement the basic feature extraction steps.
2022-04-05 15:46:02 +02:00
c050174ca3
Various minimal changes.
2022-03-31 09:16:00 +00:00
a357138f6e
Added CF for HRV and shortened test data
2022-03-30 15:01:24 +00:00
470993eeb0
Modification of getSampleRate method for all CF scripts.
2022-03-30 15:00:11 +00:00
3af8de6235
Create feature provider script.
2022-03-30 10:40:53 +02:00
9478dc94f2
Add an else.
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This is to make sure that in case the reversing fails, we do not get any output items.
Snakemake will inform us of an error in this event.
2022-03-30 10:40:53 +02:00
ab0b9227d7
Added ACC calculated features and shorter version of ACC data.
2022-03-29 09:41:51 +00:00
a9244a60fc
Corrections for TEMP cf src script.
2022-03-28 14:26:37 +00:00
8b76c96e47
Cleaning existing CF mains' and preparing src script for ACC.
2022-03-28 14:18:29 +00:00
ca59a54d8f
Get a sample rate from two sequential timestamps.
2022-03-28 13:50:08 +00:00
393dab72f5
Added components for the temperature features extraction.
2022-03-28 12:37:02 +00:00
f389ac9d89
Delete CF features folder
2022-03-25 16:24:52 +00:00
191e53e543
Added cf provider for EDA feature processing.
2022-03-23 15:13:53 +00:00
2da0911d4c
Skeleton file main.py for EDA CalcFt. integration.
2022-03-22 12:48:43 +00:00
c6144f8403
Reverse JCQ items.
2022-03-16 18:55:46 +01:00
23f0aaba3a
Get the name of the questionnaire from Snakefile.
2022-03-16 18:28:57 +01:00
679f00dc19
Enable selecting any questionnaire as target.
2022-03-16 17:55:44 +01:00
1374eda171
Flatten questionnaire ID dict.
2022-03-16 17:38:09 +01:00
19b9da0ba3
Separate function definitions from main.
2022-03-16 16:49:28 +01:00
ef57103bac
Add questionnaire ID key.
2022-03-15 13:41:33 +01:00
5f293211a7
Reformat.
2022-03-15 13:28:51 +01:00
d470eef27e
Add a rule to preprocess and clean ESM.
2022-03-09 18:38:46 +01:00
d4a4bbbff0
Remove unused columns.
2022-03-09 17:58:36 +01:00
085a6d144b
Add files to compute and create an empty script.
2022-03-09 17:32:02 +01:00
42d62f16d0
Add RAPIDS mandatory columns for ESM.
2022-03-09 17:31:37 +01:00
2bef86b1da
Add a format for ESM and add to config.
2022-03-08 15:43:25 +01:00
d8e9a309f7
Rename features and write baseline_interim.
2022-03-08 15:10:36 +01:00
a3a4f04ffe
Setting with : produces NaNs.
2022-03-01 12:02:57 +01:00
aedb8b6785
Write questionnaire data to data/interim.
2022-03-01 12:02:36 +01:00
b5a6317f4b
Calculate JCQ control and demand control ratio.
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Include norms and corresponding quartile.
2022-02-28 18:51:47 +01:00
2fed962644
Calculate JCQ demand score.
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Hardcode question IDs to be reversed.
2022-02-28 18:30:41 +01:00
30ac8b1cd5
Start calculating demand control features.
2022-02-23 19:08:10 +01:00
9a74e74d08
Add the baseline features rule to snakefile.
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Correct age calculation for a single value instead of dataframe.
2022-02-23 18:15:26 +01:00
07da6be398
Add age, gender, and language as features.
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Move calculation of age from merge_baseline_data.py to baseline_features.py.
2022-02-23 18:05:23 +01:00
176367631b
Prepare baseline feature rule.
2022-02-23 11:09:33 +01:00
bf9c764c97
Split baseline data to participants.
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And some csv I/O settings.
2022-02-04 18:37:57 +01:00
16e608db74
First merge baseline datasets.
2022-02-04 18:21:42 +01:00
204f6f50b0
Read the relevant files.
2022-02-04 18:06:02 +01:00
685ed6a546
Set up demographic data download.
2022-02-04 17:37:00 +01:00
463ac0a2aa
Fix bug#169 ( #174 )
2022-01-27 11:27:32 -05:00
10e896ca1d
Add data stream for AWARE Micro server ( #173 )
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* Add data stream for AWARE Micro server
* Fix one documentation typo and one ommission
2022-01-27 10:47:50 -05:00
afa3b8546f
Mutate data in an R script.
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The Python script did not read the timestamp correctly for some reason. All timestamps were 0.
2022-01-26 16:34:19 +01:00
e5dbbfce44
Avoid NA problem in barnett location evaluation ( #172 )
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* Avoid occasional issue where does_not_span evaluates to NA, which breaks the if()
* Restored original warning
2022-01-18 10:16:37 -05:00
8ae26fb845
Fixes issue where 'duration' in the 'ios_calls' dataframe is seen as a character type. ( #171 )
2022-01-18 10:15:53 -05:00
b17a7eff1a
Deal with inexplicable snakemake failure.
2022-01-07 18:11:38 +01:00
e1499a5ae2
Account for missing device_ids.
2021-12-15 20:41:28 +01:00
5a9252e46e
Merge remote-tracking branch 'origin/master'
2021-12-15 18:32:36 +01:00
352598f3da
Use absolute path to avoid RuleException.
2021-12-15 17:27:13 +01:00
70cada8bb8
Consider a subset of columns when dropping.
2021-12-15 16:14:33 +01:00
d2ed73dccf
Debug ValueError for index.
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See exploration/debug_heatmap.py for illustration.
2021-12-15 16:03:04 +01:00
6f451e05ac
Bring back application_name.
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This column still needs to be in the data, so add it in app_add_name.py.
Later, join categories by package hash.
2021-12-15 12:58:27 +01:00
4485c4c95e
Delete columns we don't have.
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Rename light table.
Correct timesegments.
2021-12-08 20:02:47 +01:00
37b3460b76
Use Empatica wristband numbers as provided in CSV.
2021-12-01 17:20:57 +01:00
22f9e0722d
Start preparing the true usernames CSV file.
2021-12-01 11:29:22 +01:00
0be4cd5a8f
Remove unnecessary library.
2021-11-30 17:08:07 +01:00
04ad2d0b81
Source specific container script.
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It is probably not worth the effort of making this general.
2021-11-29 18:19:47 +01:00
da5ff0f36e
Correct small errors in settings.
2021-11-29 18:04:06 +01:00
35d9779026
Prepare the tibble in requested format.
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Write it to a CSV file.
2021-11-29 17:54:16 +01:00
32025cbd8c
Start with a tibble from CSV.
2021-11-29 17:51:07 +01:00
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
ab84109d55
Prepare a function to compile participants data.
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It combines functions from container.R
2021-11-24 19:07:56 +01:00
f9863ec622
Fix small mistakes.
2021-11-24 19:01:30 +01:00
c1f56c61e8
Add a function to pull start and end datetimes.
2021-11-24 18:33:06 +01:00
3acf6ece14
Add a function to pull device IDs.
2021-11-24 18:23:53 +01:00
8b2717122d
Add a function to get participants' IDs.
2021-11-24 18:05:17 +01:00
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
296960f425
Fix the bug of location doryab features when a participant is moving during the whole time segment
2021-11-18 18:42:19 -05:00
3d34036eae
Add firststeptime and laststeptime features to FITBIT_STEPS_INTRADAY RAPIDS provider ( #168 )
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* Add firststeptime and laststeptime features to FITBIT_STEPS_INTRADAY RAPIDS provider
* Update test config files
2021-11-18 18:35:27 -05:00
ed193d2290
Revert "Correct the name of a field."
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This reverts commit b335561a55
2021-11-17 19:16:35 +01:00
Primoz
=
junos
Meng Li
Sam