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
b335561a55
Correct the name of a field.
2021-11-17 18:50:06 +01:00
fcec3e2f93
Implement the necessary functions for PSQL.
2021-11-17 18:49:25 +01:00
7a1e4f7139
Add the format file copied from MySQL.
2021-11-17 18:46:16 +01:00
f340b89c58
Temporary revert PHONE_LOCATIONS BARNETT provider to use R script
2021-09-23 18:16:13 -04:00
a3fb718aea
Refactor PHONE_LOCATIONS DORYAB provider to compute features based on location episodes
2021-09-23 17:40:06 -04:00
a8a178486b
Refactor PHONE_CALLS RAPIDS provider to compute features based on call episodes or events
2021-09-15 10:28:37 -04:00
2e553dc9e7
Add tqdm package to environment.yaml
2021-08-16 11:04:03 -04:00
3ac12e7dad
Fix the bug of step intraday features when INCLUDE_ZERO_STEP_ROWS is False
2021-08-11 12:40:40 -04:00
35eebe8a51
Bug fixed: set ratiovalidyielded mins/hours value to the range 0 to 1
2021-08-09 17:56:29 -04:00
3e69966c91
Update error message
2021-08-04 15:33:02 -04:00
4ddb2845a6
Update initialize_params
2021-08-04 15:33:02 -04:00
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
7f1c502ea0
Fixed bug: Added local_segment column if no data left after filtered
2021-08-04 11:06:31 -04:00
b52059b027
Ensure date/time format is maintained
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Within the 'determine which is home' for loop, 'xx' is the midpoint of two datetime objects. When the midpoint is calculated to be midnight, only the date is returned. This can be replicated with:
mydates <- as.POSIXct("2018-01-01 00:00:00", tz = "UTC")
mydates
[1] "2018-01-01 UTC"
This results in 'hourofday' being NA as an hour cannot be found. By adding the suggested format wrapper, the time is maintained and 'hourofday' can be determined. It can then successfully be applied to the embedded if-statement within the loop.
mydates <- format(as.POSIXct("2018-01-01 00:00:00", tz = "UTC"), "%Y-%m-%d %H:%M:%S")
mydates
[1] "01-01-2018 00:00:00"
2021-07-23 10:12:11 -04:00
5a465873c4
Tested fitbit heartrate intraday feature
2021-07-21 10:24:02 -04:00
6fa1875bf3
Add app foreground episode count
2021-07-01 16:20:16 -04:00
bc5c0c9a4f
Fix app episode length bug
2021-07-01 16:20:16 -04:00
065a926a87
Change own to custom categories name
2021-07-01 16:20:16 -04:00
e74c745f86
Add own categories to app foreground features
2021-07-01 16:20:16 -04:00
5892b6d838
Fix create_participants_files.R to handle numeric PIDs
2021-07-01 16:20:16 -04:00
97ef8a8368
Set color range and avoid SettingWithCopyWarning
2021-06-29 09:50:19 -04:00
1c57320ab3
Update segment labels and fix the bug when we do not have any labels for event segments
2021-06-29 09:49:24 -04:00
cefcb0635b
Update heatmap of recorded phone sensors
2021-06-29 09:49:24 -04:00
bc06477d89
Update heatmap of sensor row count
2021-06-29 09:49:24 -04:00
e98a8ff7ca
Update histogram of phone data yield
2021-06-29 09:49:24 -04:00
f436f1f530
Update heatmap of correlation matrix
2021-06-29 09:49:23 -04:00
4d37696158
Update heatmaps of overall data yield
2021-06-29 09:48:30 -04:00
f374c67bd5
Bug fixed: Added unknown activity case
2021-06-23 19:04:55 -04:00
3e4d167adc
Bug fixed: sort bt_address alphabetically before picking the most frequent bt_address
2021-06-22 17:40:00 -04:00
f248b6c97d
Fix bugs of Fitbit mutation scripts
2021-06-11 18:18:33 -04:00
4b8698a4c6
adding app_episode with the changes as mentioned in the comments
2021-06-10 14:17:56 -04:00
65d5cb7bd4
Bug fixed: countscansmostuniquedevice stays the same for all time segments
2021-06-10 10:49:22 -04:00
e123a14082
Improve aware_csv msg when CSV files don't exist
2021-06-01 10:57:17 -04:00
9687081fbe
Refactor the rule phone_locations_add_doryab_extra_columns
2021-05-28 09:48:36 -04:00
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
32472461ec
- Fix bug when no phone data yield is needed to process location data
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- Remove location rows with the same timestamp based on their accuracy
2021-05-26 14:04:29 -04:00
9b21196f35
Fixed `expected_minutes` to account for different time segments. ( #136 )
2021-05-26 11:44:48 -04:00
edf71e055d
Add the EXCLUDE_SLEEP module for steps intraday features
2021-05-21 15:23:21 -04:00
5e451f99b0
Added phone keyboard features including docs/tests ( #134 )
2021-05-21 11:45:27 -04:00
e9cd9c94d7
Fix PID matching when joining data from participants
2021-05-11 16:49:04 -04:00
32818a4802
Fix parse of pids with more than 1 devices
2021-05-11 16:42:20 -04:00
809845143f
Test & fix bugs of sleep intraday features
2021-04-27 14:40:14 -04:00
7c7f34ec45
Test & fix bugs of sleep summary features
2021-04-27 14:40:14 -04:00
50fe09cfac
Update data streams mutation of fitbit data
2021-04-27 14:40:14 -04:00
66d9a9d640
Update params & docs of sleep features
2021-04-27 14:33:19 -04:00
4beafd233d
Fix crash when scraping data for an app that does not exist
2021-04-22 14:28:52 -04:00
ea8094e028
Fix length of periodic segments on days with DLS
2021-04-22 11:32:10 -04:00
9c56422529
Add calories intraday features
2021-04-20 12:00:38 -04:00
00a3335623
Add device_id column for sleep intraday episodes
2021-04-08 11:21:28 -04:00
286d317af4
Fix crash when there are no periodic segments to assign
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This includes a simplification of how periodic segments are computed based on all local dates in the data independently of their time zones
2021-04-07 12:03:25 -04:00
9551669d47
Fix periodic segments bug when there are no segments to assign
2021-04-06 20:29:30 -04:00
78173c54ab
Convert date time object to string in assign_tz_code() function
2021-04-06 23:28:53 +00:00
1025e6d9d8
Fix datetime labels of event segments across multiple tzs
2021-04-06 13:58:58 -04:00
8909876cff
Add local_segment column for phone data yield features
2021-04-05 21:13:36 +00:00
68125dc1bf
Fix the bug of phone data yield features when the input is empty
2021-04-05 20:57:05 +00:00
46f5e24814
Fix Fitbit tz inference from phone data
2021-04-05 11:51:57 -04:00
636b64c61a
Revert "Added more keyboard features."
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This reverts commit 94c72e3172
2021-04-05 11:25:00 -04:00
68e12a2563
Fix bugs of bluetooth feature extraction when number of unique bt_address is 2
2021-04-05 14:09:50 +00:00
8414977331
Fix the bug of utils.py when one participant have multi timezones
2021-04-03 21:20:10 -04:00
94c72e3172
Added more keyboard features.
2021-04-01 20:54:13 -04:00
1ea5b74eff
Fix the bug of utils.py when one participant have multi timezones
2021-03-31 19:34:14 -04:00
136dfef56b
Fix the bug of Analysis Workflows while parsing targets with updated segments
2021-03-30 16:41:50 -04:00
99dae079d5
Add iOS BT and Wifi visible to formats for old devices
2021-03-30 15:32:50 -04:00
30ad3cd586
Validate participant files without device ids
2021-03-28 15:29:08 -04:00
87fbbbe402
Refactor and simplify time segments
2021-03-28 15:29:07 -04:00
c48c1c8f24
Optimize Barnett's computation multi-day segments
2021-03-28 15:29:07 -04:00
d0858f8833
Fix overlapping periodic time segments
2021-03-28 15:29:07 -04:00
junos
=
Primoz
Meng Li
Sam
JulioV
Weiyu
Shirley
Hannah Roberts
kirtirajk
Nikunj Goel