Refactor fused location resampling
JulioV
parent
c0c32d9f9e
commit
6b1e006b82
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@ -25,6 +25,7 @@ if config["PHONE_VALID_SENSED_BINS"]["COMPUTE"] or config["PHONE_VALID_SENSED_DA
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=pids, sensor=table))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=pids, sensor=table))
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files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_timestamps.csv", pid=config["PIDS"]))
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if config["PHONE_VALID_SENSED_DAYS"]["COMPUTE"]:
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files_to_compute.extend(expand("data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins.csv",
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@ -163,7 +164,8 @@ for provider in config["LOCATIONS"]["PROVIDERS"].keys():
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["LOCATIONS"]["DB_TABLE"]))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["LOCATIONS"]["DB_TABLE"]))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_processed_{locations_to_use}.csv", pid=config["PIDS"], sensor=config["LOCATIONS"]["DB_TABLE"], locations_to_use=config["LOCATIONS"]["LOCATIONS_TO_USE"]))
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files_to_compute.extend(expand("data/interim/{pid}/{sensor}_processed_{locations_to_use}.csv", pid=config["PIDS"], sensor=config["LOCATIONS"]["DB_TABLE"], locations_to_use=config["LOCATIONS"]["LOCATIONS_TO_USE"]))
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files_to_compute.extend(expand("data/interim/{pid}/{sensor}_processed_{locations_to_use}_with_datetime.csv", pid=config["PIDS"], sensor=config["LOCATIONS"]["DB_TABLE"], locations_to_use=config["LOCATIONS"]["LOCATIONS_TO_USE"]))
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files_to_compute.extend(expand("data/interim/{pid}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["LOCATIONS"]["PROVIDERS"][provider]["SRC_LANGUAGE"], provider_key=provider, sensor_key="LOCATIONS".lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/{sensor_key}.csv", pid=config["PIDS"], sensor_key="LOCATIONS".lower()))
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@ -26,6 +26,16 @@ def optional_phone_sensed_bins_input(wildcards):
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return expand("data/raw/{{pid}}/{table}_with_datetime.csv", table = tables_platform)
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def optional_phone_sensed_timestamps_input(wildcards):
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platform = infer_participant_platform("data/external/"+wildcards.pid)
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if platform == "android":
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tables_platform = [table for table in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"] if table not in [config["CONVERSATION"]["DB_TABLE"]["IOS"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]]] # for android, discard any ios tables that may exist
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elif platform == "ios":
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tables_platform = [table for table in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"] if table not in [config["CONVERSATION"]["DB_TABLE"]["ANDROID"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"]]] # for ios, discard any android tables that may exist
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return expand("data/raw/{{pid}}/{table}_raw.csv", table = tables_platform)
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# Features.smk #########################################################################################################
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def find_features_files(wildcards):
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feature_files = []
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@ -111,7 +111,7 @@ rule ios_activity_recognition_deltas:
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rule locations_python_features:
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input:
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sensor_data = expand("data/raw/{{pid}}/{sensor}_processed_{locations_to_use}.csv", sensor=config["LOCATIONS"]["DB_TABLE"], locations_to_use=config["LOCATIONS"]["LOCATIONS_TO_USE"]),
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sensor_data = expand("data/interim/{{pid}}/{sensor}_processed_{locations_to_use}_with_datetime.csv", sensor=config["LOCATIONS"]["DB_TABLE"], locations_to_use=config["LOCATIONS"]["LOCATIONS_TO_USE"]),
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day_segments_labels = "data/interim/day_segments/{pid}_day_segments_labels.csv"
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params:
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provider = lambda wildcards: config["LOCATIONS"]["PROVIDERS"][wildcards.provider_key],
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@ -123,7 +123,7 @@ rule locations_python_features:
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rule locations_r_features:
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input:
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sensor_data = expand("data/raw/{{pid}}/{sensor}_processed_{locations_to_use}.csv", sensor=config["LOCATIONS"]["DB_TABLE"], locations_to_use=config["LOCATIONS"]["LOCATIONS_TO_USE"]),
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sensor_data = expand("data/interim/{{pid}}/{sensor}_processed_{locations_to_use}_with_datetime.csv", sensor=config["LOCATIONS"]["DB_TABLE"], locations_to_use=config["LOCATIONS"]["LOCATIONS_TO_USE"]),
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day_segments_labels = "data/interim/day_segments/{pid}_day_segments_labels.csv"
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params:
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provider = lambda wildcards: config["LOCATIONS"]["PROVIDERS"][wildcards.provider_key],
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@ -70,7 +70,7 @@ rule readable_datetime:
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day_segments_type = config["DAY_SEGMENTS"]["TYPE"],
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include_past_periodic_segments = config["DAY_SEGMENTS"]["INCLUDE_PAST_PERIODIC_SEGMENTS"]
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wildcard_constraints:
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sensor = '.*(' + '|'.join([re.escape(x) for x in PHONE_SENSORS]) + ').*' # only process smartphone sensors, not fitbit
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sensor = '(' + '|'.join([re.escape(x) for x in PHONE_SENSORS]) + ')' # only process smartphone sensors, not fitbit
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output:
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"data/raw/{pid}/{sensor}_with_datetime.csv"
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script:
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@ -86,6 +86,14 @@ rule phone_sensed_bins:
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script:
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"../src/data/phone_sensed_bins.R"
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rule phone_sensed_timestamps:
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input:
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all_sensors = optional_phone_sensed_timestamps_input
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output:
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"data/interim/{pid}/phone_sensed_timestamps.csv"
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script:
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"../src/data/phone_sensed_timestamps.R"
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rule phone_valid_sensed_days:
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input:
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phone_sensed_bins = "data/interim/{pid}/phone_sensed_bins.csv"
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@ -112,21 +120,35 @@ rule unify_ios_android:
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rule process_location_types:
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input:
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locations = "data/raw/{pid}/{sensor}_with_datetime.csv",
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phone_sensed_bins = rules.phone_sensed_bins.output,
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day_segments = "data/interim/day_segments/{pid}_day_segments.csv"
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locations = "data/raw/{pid}/{sensor}_raw.csv",
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phone_sensed_timestamps = "data/interim/{pid}/phone_sensed_timestamps.csv",
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params:
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bin_size = config["PHONE_VALID_SENSED_BINS"]["BIN_SIZE"],
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timezone = config["LOCATIONS"]["TIMEZONE"],
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consecutive_threshold = config["LOCATIONS"]["FUSED_RESAMPLED_CONSECUTIVE_THRESHOLD"],
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time_since_valid_location = config["LOCATIONS"]["FUSED_RESAMPLED_TIME_SINCE_VALID_LOCATION"],
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day_segments_type = config["DAY_SEGMENTS"]["TYPE"],
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locations_to_use = "{locations_to_used}"
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locations_to_use = "{locations_to_use}"
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wildcard_constraints:
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locations_to_use = '(ALL|GPS|FUSED_RESAMPLED)'
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output:
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"data/raw/{pid}/{sensor}_processed_{locations_to_used}.csv"
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"data/interim/{pid}/{sensor}_processed_{locations_to_use}.csv"
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script:
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"../src/data/process_location_types.R"
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rule readable_datetime_location_processed:
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input:
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sensor_input = expand("data/interim/{{pid}}/{sensor}_processed_{locations_to_use}.csv", sensor=config["LOCATIONS"]["DB_TABLE"], locations_to_use=config["LOCATIONS"]["LOCATIONS_TO_USE"]),
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day_segments = "data/interim/day_segments/{pid}_day_segments.csv"
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params:
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timezones = None,
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fixed_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"],
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day_segments_type = config["DAY_SEGMENTS"]["TYPE"],
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include_past_periodic_segments = config["DAY_SEGMENTS"]["INCLUDE_PAST_PERIODIC_SEGMENTS"]
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wildcard_constraints:
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locations_to_use = '(ALL|GPS|FUSED_RESAMPLED)'
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output:
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expand("data/interim/{{pid}}/{sensor}_processed_{locations_to_use}_with_datetime.csv", sensor=config["LOCATIONS"]["DB_TABLE"], locations_to_use=config["LOCATIONS"]["LOCATIONS_TO_USE"])
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script:
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"../src/data/readable_datetime.R"
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rule application_genres:
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input:
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"data/raw/{pid}/{sensor}_with_datetime.csv"
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@ -0,0 +1,18 @@
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source("renv/activate.R")
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library(dplyr)
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library(readr)
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library(tidyr)
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library(purrr)
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all_sensors = snakemake@input[["all_sensors"]]
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sensor_timestamps <- tibble(files = all_sensors) %>%
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mutate(timestamps = map(files,~ read_csv(.,col_types = cols_only(timestamp = col_double()))),
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sensor = row_number(),
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files = NULL) %>%
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unnest(timestamps) %>%
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mutate(timestamp = (timestamp %/% 1000) * 1000) %>%
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distinct(timestamp, .keep_all = TRUE) %>%
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arrange(timestamp)
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write.csv(sensor_timestamps, snakemake@output[[1]], row.names = FALSE)
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@ -3,21 +3,15 @@ library(dplyr)
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library(readr)
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library(tidyr)
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source("src/data/assign_to_day_segment.R")
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bin_size <- snakemake@params[["bin_size"]]
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timezone <- snakemake@params[["timezone"]]
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consecutive_threshold <- snakemake@params[["consecutive_threshold"]]
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time_since_valid_location <- snakemake@params[["time_since_valid_location"]]
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location_to_used <- snakemake@params[["time_since_valocation_to_usedlid_location"]]
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day_segments <- read.csv(snakemake@input[["day_segments"]])
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day_segments_type <- snakemake@params[["day_segments_type"]]
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locations_to_use <- snakemake@params[["locations_to_use"]]
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phone_sensed_bins <- read_csv(snakemake@input[["phone_sensed_bins"]], col_types = cols(local_date = col_character()))
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locations <- read_csv(snakemake@input[["locations"]], col_types = cols()) %>% filter(provider == "fused") %>%
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filter(double_latitude != 0 & double_longitude != 0)
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phone_sensed_timestamps <- read_csv(snakemake@input[["phone_sensed_timestamps"]], col_types = cols_only(timestamp = col_double()))
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locations <- read.csv(snakemake@input[["locations"]]) %>%
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filter(double_latitude != 0 & double_longitude != 0) %>%
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drop_na(double_longitude, double_latitude)
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locations_to_use <- snakemake@params["locations_to_use"]
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if(!locations_to_use %in% c("ALL", "FUSED_RESAMPLED", "GPS")){
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print("Unkown location filter, provide one of the following three: ALL, GPS, or FUSED_RESAMPLED")
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quit(save = "no", status = 1, runLast = FALSE)
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@ -31,44 +25,35 @@ if(locations_to_use == "ALL"){
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} else if(locations_to_use == "FUSED_RESAMPLED"){
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locations <- locations %>% filter(provider == "fused")
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if(nrow(locations) > 0){
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sensed_minute_bins <- phone_sensed_bins %>%
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pivot_longer(-local_date, names_to = c("hour", "bin"), names_sep = "_", values_to = "sensor_count") %>%
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mutate(hour = as.integer(hour), bin = as.integer(bin)) %>%
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complete(nesting(local_date, hour), bin = seq(0, 59,1)) %>%
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fill(sensor_count) %>%
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mutate(timestamp = as.numeric(as.POSIXct(paste0(local_date, " ", hour,":", bin,":00"), format = "%Y-%m-%d %H:%M:%S", tz = timezone)) * 1000 ) %>%
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filter(sensor_count > 0) %>%
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select(timestamp)
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resampled_locations <- locations %>%
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select(-assigned_segments) %>%
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bind_rows(sensed_minute_bins) %>%
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mutate(provider = replace_na(provider, "resampled")) %>%
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processed_locations <- locations %>%
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# TODO filter repeated location rows based on the accurcy
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distinct(timestamp, .keep_all = TRUE) %>%
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bind_rows(phone_sensed_timestamps) %>%
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arrange(timestamp) %>%
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# We group and therefore, fill in, missing rows that appear after a valid fused location record and exist
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# within consecutive_threshold minutes from each other
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mutate(consecutive_time_diff = c(1, diff(timestamp)),
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resample_group = cumsum(!is.na(double_longitude) | consecutive_time_diff > (1000 * 60 * consecutive_threshold))) %>%
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resample_group = cumsum(!is.na(double_longitude) | consecutive_time_diff > (1000 * 60 * consecutive_threshold))) %>%
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group_by(resample_group) %>%
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# drop rows that are logged after time_since_valid_location minutes from the last valid fused location
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filter((timestamp - first(timestamp) < (1000 * 60 * time_since_valid_location))) %>%
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fill(-timestamp, -resample_group) %>%
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select(-consecutive_time_diff) %>%
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drop_na(double_longitude, double_latitude, accuracy) %>%
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# Add local date_time
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mutate(utc_date_time = as.POSIXct(timestamp/1000, origin="1970-01-01", tz="UTC"),
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local_date_time = format(utc_date_time, tz = timezone, usetz = F)) %>%
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separate(local_date_time, c("local_date","local_time"), "\\s", remove = FALSE) %>%
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separate(local_time, c("local_hour", "local_minute"), ":", remove = FALSE, extra = "drop") %>%
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mutate(local_hour = as.numeric(local_hour),
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local_minute = as.numeric(local_minute)) %>%
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# Delete resampled rows that exist in the same minute as other original (fused) rows
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group_by(local_date, local_hour, local_minute) %>%
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mutate(n = n()) %>%
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filter(n == 1 | (n > 1 & provider == "fused")) %>%
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select(-n) %>%
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ungroup()
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processed_locations <- assign_to_day_segment(resampled_locations, day_segments, day_segments_type)
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# Filter those rows that are further away than time_since_valid_location since the last fused location
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mutate(time_from_fused = timestamp - first(timestamp)) %>%
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filter(provider == "fused" | (time_from_fused < (1000 * 60 * time_since_valid_location))) %>%
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# Summarise the period to resample for
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summarise(limit = max(timestamp), timestamp = first(timestamp), double_latitude = first(double_latitude), double_longitude = first(double_longitude),
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double_bearing=first(double_bearing), double_speed = first(double_speed), double_altitude=first(double_altitude), provider=first(provider),
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accuracy=first(accuracy), label=first(label)) %>%
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# the limit will be equal to the next timestamp-1 or the last binded timestamp (limit) plus the consecutive_threshold buffer
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# you can think of consecutive_threshold as the period a location row is valid for
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mutate(limit = pmin(lead(timestamp, default = 9999999999999) - 1, limit + (1000 * 60 * consecutive_threshold)),
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n_resample = (limit - timestamp)%/%60001,
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n_resample = if_else(n_resample == 0, 1, n_resample)) %>%
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drop_na(double_longitude, double_latitude) %>%
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uncount(weights = n_resample, .id = "id") %>%
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mutate(provider = if_else(id > 1, "resampled", provider),
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id = id -1,
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timestamp = timestamp + (id * 60000)) %>%
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ungroup() %>%
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select(-resample_group, -limit, -id)
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} else {
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processed_locations <- locations
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}
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