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Minor updates to config and Snakefile

pull/103/head
JulioV 2020-10-28 14:03:02 -04:00
parent 84068ab33c
commit 8f74d3f3b7
2 changed files with 15 additions and 15 deletions
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2
Snakefile
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@ -132,7 +132,7 @@ for provider in config["PHONE_CONVERSATION"]["PROVIDERS"].keys():
for provider in config["PHONE_LOCATIONS"]["PROVIDERS"].keys(): for provider in config["PHONE_LOCATIONS"]["PROVIDERS"].keys():
if config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["COMPUTE"]:
if config["PHONE_LOCATIONS"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED": if config["PHONE_LOCATIONS"]["LOCATIONS_TO_USE"] == "FUSED_RESAMPLED":
if "PHONE_LOCATIONS" in config["PHONE_VALID_SENSED_BINS"]["PHONE_SENSORS"]: if "PHONE_LOCATIONS" in config["PHONE_VALID_SENSED_BINS"]["PHONE_SENSORS"]:
files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
else: else:

28
config.yaml
View File

@ -1,5 +1,5 @@
# Participants to include in the analysis # Participants to include in the analysis
# You must create a file for each participant named pXXX containing their device_id. This can be done manually or automatically # You must create a participant file per person manually or automatically (see PARTICIPANT_FILES below)
PIDS: [test01] PIDS: [test01]
# Use tz codes from https://en.wikipedia.org/wiki/List_of_tz_database_time_zones. Double check your code, for example EST is not US Eastern Time. # Use tz codes from https://en.wikipedia.org/wiki/List_of_tz_database_time_zones. Double check your code, for example EST is not US Eastern Time.
@ -9,7 +9,7 @@ TIMEZONE: &timezone
DATABASE_GROUP: &database_group DATABASE_GROUP: &database_group
MY_GROUP MY_GROUP
# run 'snakemake -j1 create_participants_files' # To create your participant files from the aware_device table or a csv file change config below and run 'snakemake -j1 create_participants_files'
CREATE_PARTICIPANT_FILES: CREATE_PARTICIPANT_FILES:
SOURCE: SOURCE:
TYPE: AWARE_DEVICE_TABLE #AWARE_DEVICE_TABLE or CSV_FILE TYPE: AWARE_DEVICE_TABLE #AWARE_DEVICE_TABLE or CSV_FILE
@ -256,12 +256,12 @@ PHONE_CONVERSATION:
################################################################################ ################################################################################
FITBIT_HEARTRATE: FITBIT_HEARTRATE:
TABLE_FORMAT: JSON # JSON or CSV TABLE_FORMAT: JSON # JSON or CSV. If your JSON or CSV data are files change [SENSOR_DATA][FITBIT][SOURCE][TYPE] to FILES
TABLE: TABLE:
JSON: fitbit_heartrate JSON: fitbit_heartrate
CSV: CSV:
SUMMARY: heartrate_summary.csv SUMMARY: heartrate_summary
INTRADAY: heartrate_intraday.csv INTRADAY: heartrate_intraday
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False
@ -273,12 +273,12 @@ FITBIT_HEARTRATE:
FITBIT_STEPS: FITBIT_STEPS:
TABLE_FORMAT: JSON # JSON or CSV TABLE_FORMAT: JSON # JSON or CSV. If your JSON or CSV data are files change [SENSOR_DATA][FITBIT][SOURCE][TYPE] to FILES
TABLE: TABLE:
JSON: fitbit_steps JSON: fitbit_steps
CSV: CSV:
SUMMARY: steps_summary.csv SUMMARY: steps_summary
INTRADAY: steps_intraday.csv INTRADAY: steps_intraday
EXCLUDE_SLEEP: # you can exclude sleep periods from the step features computation EXCLUDE_SLEEP: # you can exclude sleep periods from the step features computation
EXCLUDE: False EXCLUDE: False
TYPE: FIXED # FIXED OR FITBIT_BASED (configure FITBIT_SLEEP section) TYPE: FIXED # FIXED OR FITBIT_BASED (configure FITBIT_SLEEP section)
@ -297,12 +297,12 @@ FITBIT_STEPS:
INCLUDE_ZERO_STEP_ROWS: False INCLUDE_ZERO_STEP_ROWS: False
FITBIT_SLEEP: FITBIT_SLEEP:
TABLE_FORMAT: JSON # JSON or CSV TABLE_FORMAT: JSON # JSON or CSV. If your JSON or CSV data are files change [SENSOR_DATA][FITBIT][SOURCE][TYPE] to FILES
TABLE: TABLE:
JSON: fitbit_sleep JSON: fitbit_sleep
CSV: CSV:
SUMMARY: sleep_summary.csv SUMMARY: sleep_summary
INTRADAY: sleep_intraday.csv INTRADAY: sleep_intraday
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False
@ -310,12 +310,12 @@ FITBIT_SLEEP:
SUMMARY_FEATURES: ["sumdurationafterwakeup", "sumdurationasleep", "sumdurationawake", "sumdurationtofallasleep", "sumdurationinbed", "avgefficiency", "countepisode"] SUMMARY_FEATURES: ["sumdurationafterwakeup", "sumdurationasleep", "sumdurationawake", "sumdurationtofallasleep", "sumdurationinbed", "avgefficiency", "countepisode"]
FITBIT_CALORIES: FITBIT_CALORIES:
TABLE_FORMAT: JSON # JSON or CSV TABLE_FORMAT: JSON # JSON or CSV. If your JSON or CSV data are files change [SENSOR_DATA][FITBIT][SOURCE][TYPE] to FILES
TABLE: TABLE:
JSON: fitbit_calories JSON: fitbit_calories
CSV: CSV:
SUMMARY: calories_summary.csv SUMMARY: calories_summary
INTRADAY: calories_intraday.csv INTRADAY: calories_intraday
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False