Add merge metrics module for analysis rules
parent
301bd0bf1d
commit
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@ -92,7 +92,6 @@ packrat/*
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!packrat/packrat.opts
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!packrat/packrat.opts
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.snakemake/
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.snakemake/
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# exclude data from source control by default
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# exclude data from source control by default
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# exclude data from source control by default
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data/external/*
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data/external/*
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!/data/external/.gitkeep
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!/data/external/.gitkeep
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@ -108,3 +107,6 @@ reports/
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*.Rproj
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*.Rproj
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.RData
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.RData
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.Rhistory
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.Rhistory
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# analysis part
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models/*
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@ -2,6 +2,7 @@ configfile: "config.yaml"
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include: "rules/packrat.snakefile"
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include: "rules/packrat.snakefile"
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include: "rules/preprocessing.snakefile"
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include: "rules/preprocessing.snakefile"
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include: "rules/features.snakefile"
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include: "rules/features.snakefile"
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include: "rules/models.snakefile"
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include: "rules/reports.snakefile"
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include: "rules/reports.snakefile"
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rule all:
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rule all:
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@ -55,6 +56,14 @@ rule all:
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expand("data/processed/{pid}/fitbit_step_{day_segment}.csv",
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expand("data/processed/{pid}/fitbit_step_{day_segment}.csv",
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pid = config["PIDS"],
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pid = config["PIDS"],
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day_segment = config["STEP"]["DAY_SEGMENTS"]),
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day_segment = config["STEP"]["DAY_SEGMENTS"]),
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# Models
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expand("models/input/merged_single_participant/{pid}/{source}_{day_segment}.csv",
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pid = config["PIDS"],
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source = config["METRICS_FOR_ANALYSIS"]["SOURCES"],
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day_segment = config["METRICS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
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expand("models/input/merged_all_participants/{source}_{day_segment}.csv",
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source = config["METRICS_FOR_ANALYSIS"]["SOURCES"],
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day_segment = config["METRICS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
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# Reports
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# Reports
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expand("reports/figures/{pid}/{sensor}_heatmap_rows.html", pid=config["PIDS"], sensor=config["SENSORS"]),
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expand("reports/figures/{pid}/{sensor}_heatmap_rows.html", pid=config["PIDS"], sensor=config["SENSORS"]),
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expand("reports/figures/{pid}/compliance_heatmap.html", pid=config["PIDS"]),
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expand("reports/figures/{pid}/compliance_heatmap.html", pid=config["PIDS"]),
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@ -122,3 +122,10 @@ STEP:
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SEDENTARY_BOUT: ["countsedentarybout", "maxdurationsedentarybout", "mindurationsedentarybout", "avgdurationsedentarybout", "stddurationsedentarybout"]
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SEDENTARY_BOUT: ["countsedentarybout", "maxdurationsedentarybout", "mindurationsedentarybout", "avgdurationsedentarybout", "stddurationsedentarybout"]
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ACTIVE_BOUT: ["countactivebout", "maxdurationactivebout", "mindurationactivebout", "avgdurationactivebout", "stddurationactivebout"]
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ACTIVE_BOUT: ["countactivebout", "maxdurationactivebout", "mindurationactivebout", "avgdurationactivebout", "stddurationactivebout"]
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THRESHOLD_ACTIVE_BOUT: 10 # steps
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THRESHOLD_ACTIVE_BOUT: 10 # steps
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METRICS_FOR_ANALYSIS:
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SOURCES: &sources ["phone_metrics", "fitbit_metrics", "phone_fitbit_metrics"]
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DAY_SEGMENTS: *day_segments
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PHONE_METRICS: [accelerometer, applications_foreground, battery, call_incoming, call_missed, call_outgoing, google_activity_recognition, light, location_barnett, screen, sms_received, sms_sent]
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FITBIT_METRICS: [fitbit_heartrate, fitbit_step]
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PHONE_FITBIT_METRICS: "" # This array is merged in the input_merge_features_of_single_participant function in models.snakefile
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@ -0,0 +1,21 @@
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def input_merge_metrics_of_single_participant(wildcards):
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if wildcards.source == "phone_fitbit_metrics":
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return expand("data/processed/{pid}/{metrics}_{day_segment}.csv", pid=wildcards.pid, metrics=config["METRICS_FOR_ANALYSIS"]["PHONE_METRICS"] + config["METRICS_FOR_ANALYSIS"]["FITBIT_METRICS"], day_segment=wildcards.day_segment)
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else:
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return expand("data/processed/{pid}/{metrics}_{day_segment}.csv", pid=wildcards.pid, metrics=config["METRICS_FOR_ANALYSIS"][wildcards.source.upper()], day_segment=wildcards.day_segment)
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rule merge_metrics_of_single_participant:
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input:
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metric_files = input_merge_metrics_of_single_participant
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output:
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"models/input/merged_single_participant/{pid}/{source}_{day_segment}.csv"
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script:
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"../src/models/merge_metrics_of_single_participant.R"
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rule merge_metrics_of_all_participants:
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input:
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metric_files = expand("models/input/merged_single_participant/{pid}/{{source}}_{{day_segment}}.csv", pid=config["PIDS"])
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output:
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"models/input/merged_all_participants/{source}_{day_segment}.csv"
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script:
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"../src/models/merge_metrics_of_all_participants.R"
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@ -0,0 +1,16 @@
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source("packrat/init.R")
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library(tidyr)
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library(purrr)
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library(dplyr)
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library(stringr)
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metric_files <- snakemake@input[["metric_files"]]
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metrics_of_all_participants <- data_frame(filename = metric_files) %>% # create a data frame
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mutate(file_contents = map(filename, ~ read.csv(., stringsAsFactors = F, colClasses = c(local_date = "character"))),
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pid = str_match(filename, ".*/(p[0-9]{2})/.*")[,2]) %>%
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unnest() %>%
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select(-filename)
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write.csv(metrics_of_all_participants, snakemake@output[[1]], row.names = FALSE)
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@ -0,0 +1,13 @@
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source("packrat/init.R")
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library(tidyr)
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library(purrr)
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library(dplyr)
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metric_files <- snakemake@input[["metric_files"]]
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metrics_of_single_participant <- metric_files %>%
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map(read.csv, stringsAsFactors = F, colClasses = c(local_date = "character")) %>%
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reduce(full_join, by="local_date")
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write.csv(metrics_of_single_participant, snakemake@output[[1]], row.names = FALSE)
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