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Make phone_valid_sensed_days rule works for different min_valid_hours_per_day thresholds

pull/95/head
Meng Li 2020-07-21 20:41:24 -04:00
parent 0ada1292ed
commit 124843f96e
4 changed files with 7 additions and 7 deletions
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2
Snakefile
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@ -22,7 +22,7 @@ if config["PHONE_VALID_SENSED_DAYS"]["COMPUTE"]:
if len(config["PHONE_VALID_SENSED_BINS"]["TABLES"]) == 0: if len(config["PHONE_VALID_SENSED_BINS"]["TABLES"]) == 0:
raise ValueError("If you want to compute PHONE_VALID_SENSED_DAYS, you need to add at least one table to [PHONE_VALID_SENSED_BINS][TABLES] in config.yaml") raise ValueError("If you want to compute PHONE_VALID_SENSED_DAYS, you need to add at least one table to [PHONE_VALID_SENSED_BINS][TABLES] in config.yaml")
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"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_valid_sensed_days.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}h.csv", pid=config["PIDS"], min_valid_hours_per_day=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_HOURS_PER_DAY"]))
if config["MESSAGES"]["COMPUTE"]: if config["MESSAGES"]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["MESSAGES"]["DB_TABLE"])) files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["MESSAGES"]["DB_TABLE"]))

4
config.yaml
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@ -32,11 +32,11 @@ PHONE_VALID_SENSED_BINS:
BIN_SIZE: 5 # (in minutes) BIN_SIZE: 5 # (in minutes)
# Add as many sensor tables as you have, they all improve the computation of PHONE_VALID_SENSED_BINS and PHONE_VALID_SENSED_DAYS. # Add as many sensor tables as you have, they all improve the computation of PHONE_VALID_SENSED_BINS and PHONE_VALID_SENSED_DAYS.
# If you are extracting screen or Barnett's location features, screen and locations tables are mandatory. # If you are extracting screen or Barnett's location features, screen and locations tables are mandatory.
TABLES: [locations] TABLES: []
PHONE_VALID_SENSED_DAYS: PHONE_VALID_SENSED_DAYS:
COMPUTE: False COMPUTE: False
MIN_VALID_HOURS_PER_DAY: 16 # (out of 24) MIN_HOURS_PER_DAY MIN_VALID_HOURS_PER_DAY: [16, 18, 20] # (out of 24) MIN_HOURS_PER_DAY
MIN_VALID_BINS_PER_HOUR: 6 # (out of 60min/BIN_SIZE bins) MIN_VALID_BINS_PER_HOUR: 6 # (out of 60min/BIN_SIZE bins)
# Communication SMS features config, TYPES and FEATURES keys need to match # Communication SMS features config, TYPES and FEATURES keys need to match

6
rules/preprocessing.snakefile
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@ -22,7 +22,7 @@ rule download_dataset:
"../src/data/download_dataset.R" "../src/data/download_dataset.R"
PHONE_SENSORS = [] PHONE_SENSORS = []
PHONE_SENSORS.extend([config["MESSAGES"]["DB_TABLE"], config["CALLS"]["DB_TABLE"], config["BARNETT_LOCATION"]["DB_TABLE"], config["BLUETOOTH"]["DB_TABLE"], config["BATTERY"]["DB_TABLE"], config["SCREEN"]["DB_TABLE"], config["LIGHT"]["DB_TABLE"], config["ACCELEROMETER"]["DB_TABLE"], config["APPLICATIONS_FOREGROUND"]["DB_TABLE"],config["WIFI"]["DB_TABLE"], config["CONVERSATION"]["DB_TABLE"]["ANDROID"], config["CONVERSATION"]["DB_TABLE"]["IOS"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]]) PHONE_SENSORS.extend([config["MESSAGES"]["DB_TABLE"], config["CALLS"]["DB_TABLE"], config["BARNETT_LOCATION"]["DB_TABLE"], config["DORYAB_LOCATION"]["DB_TABLE"], config["BLUETOOTH"]["DB_TABLE"], config["BATTERY"]["DB_TABLE"], config["SCREEN"]["DB_TABLE"], config["LIGHT"]["DB_TABLE"], config["ACCELEROMETER"]["DB_TABLE"], config["APPLICATIONS_FOREGROUND"]["DB_TABLE"],config["WIFI"]["DB_TABLE"], config["CONVERSATION"]["DB_TABLE"]["ANDROID"], config["CONVERSATION"]["DB_TABLE"]["IOS"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]])
rule readable_datetime: rule readable_datetime:
input: input:
@ -51,10 +51,10 @@ rule phone_valid_sensed_days:
input: input:
phone_sensed_bins = "data/interim/{pid}/phone_sensed_bins.csv" phone_sensed_bins = "data/interim/{pid}/phone_sensed_bins.csv"
params: params:
min_valid_hours_per_day = config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_HOURS_PER_DAY"], min_valid_hours_per_day = "{min_valid_hours_per_day}",
min_valid_bins_per_hour = config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"] min_valid_bins_per_hour = config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]
output: output:
"data/interim/{pid}/phone_valid_sensed_days.csv" "data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}h.csv"
script: script:
"../src/data/phone_valid_sensed_days.R" "../src/data/phone_valid_sensed_days.R"

2
src/data/phone_valid_sensed_days.R
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@ -3,7 +3,7 @@ library("dplyr")
library("tidyr") library("tidyr")
phone_sensed_bins <- read.csv(snakemake@input[["phone_sensed_bins"]]) phone_sensed_bins <- read.csv(snakemake@input[["phone_sensed_bins"]])
min_valid_hours_per_day <- snakemake@params[["min_valid_hours_per_day"]] min_valid_hours_per_day <- as.integer(snakemake@params[["min_valid_hours_per_day"]])
min_valid_bins_per_hour <- snakemake@params[["min_valid_bins_per_hour"]] min_valid_bins_per_hour <- snakemake@params[["min_valid_bins_per_hour"]]
output_file <- snakemake@output[[1]] output_file <- snakemake@output[[1]]