Add merge metrics module for analysis rules

.gitignore

@@ -92,7 +92,6 @@ packrat/*
 !packrat/packrat.opts
 .snakemake/
 
-# exclude data from source control by default
 # exclude data from source control by default
 data/external/*
 !/data/external/.gitkeep
@@ -108,3 +107,6 @@ reports/
 *.Rproj
 .RData
 .Rhistory
+
+# analysis part
+models/*

Snakefile

@@ -2,6 +2,7 @@ configfile: "config.yaml"
 include: "rules/packrat.snakefile"
 include: "rules/preprocessing.snakefile"
 include: "rules/features.snakefile"
+include: "rules/models.snakefile"
 include: "rules/reports.snakefile"
 
 rule all:
@@ -55,6 +56,14 @@ rule all:
         expand("data/processed/{pid}/fitbit_step_{day_segment}.csv",
                             pid = config["PIDS"],
                             day_segment = config["STEP"]["DAY_SEGMENTS"]),
+        # Models
+        expand("models/input/merged_single_participant/{pid}/{source}_{day_segment}.csv",
+                                pid = config["PIDS"],
+                                source = config["METRICS_FOR_ANALYSIS"]["SOURCES"],
+                                day_segment = config["METRICS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
+        expand("models/input/merged_all_participants/{source}_{day_segment}.csv",
+                                source = config["METRICS_FOR_ANALYSIS"]["SOURCES"],
+                                day_segment = config["METRICS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
         # Reports
         expand("reports/figures/{pid}/{sensor}_heatmap_rows.html", pid=config["PIDS"], sensor=config["SENSORS"]),
         expand("reports/figures/{pid}/compliance_heatmap.html", pid=config["PIDS"]),

config.yaml

@@ -122,3 +122,10 @@ STEP:
     SEDENTARY_BOUT: ["countsedentarybout", "maxdurationsedentarybout", "mindurationsedentarybout", "avgdurationsedentarybout", "stddurationsedentarybout"]
     ACTIVE_BOUT: ["countactivebout", "maxdurationactivebout", "mindurationactivebout", "avgdurationactivebout", "stddurationactivebout"]
   THRESHOLD_ACTIVE_BOUT: 10 # steps
+
+METRICS_FOR_ANALYSIS:
+  SOURCES: &sources ["phone_metrics", "fitbit_metrics", "phone_fitbit_metrics"]
+  DAY_SEGMENTS: *day_segments
+  PHONE_METRICS: [accelerometer, applications_foreground, battery, call_incoming, call_missed, call_outgoing, google_activity_recognition, light, location_barnett, screen, sms_received, sms_sent]
+  FITBIT_METRICS: [fitbit_heartrate, fitbit_step]
+  PHONE_FITBIT_METRICS: "" # This array is merged in the input_merge_features_of_single_participant function in models.snakefile

rules/models.snakefile

@@ -0,0 +1,21 @@
+def input_merge_metrics_of_single_participant(wildcards):
+    if wildcards.source == "phone_fitbit_metrics":
+        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)
+    else:
+        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)
+
+rule merge_metrics_of_single_participant:
+    input:
+        metric_files = input_merge_metrics_of_single_participant
+    output:
+        "models/input/merged_single_participant/{pid}/{source}_{day_segment}.csv"
+    script:
+        "../src/models/merge_metrics_of_single_participant.R"
+
+rule merge_metrics_of_all_participants:
+    input:
+        metric_files = expand("models/input/merged_single_participant/{pid}/{{source}}_{{day_segment}}.csv", pid=config["PIDS"])
+    output:
+        "models/input/merged_all_participants/{source}_{day_segment}.csv" 
+    script:
+        "../src/models/merge_metrics_of_all_participants.R"

src/models/merge_metrics_of_all_participants.R

@@ -0,0 +1,16 @@
+source("packrat/init.R")
+
+library(tidyr)
+library(purrr)
+library(dplyr)
+library(stringr)
+
+metric_files  <- snakemake@input[["metric_files"]]
+
+metrics_of_all_participants <- data_frame(filename = metric_files) %>% # create a data frame
+  mutate(file_contents = map(filename, ~ read.csv(., stringsAsFactors = F, colClasses = c(local_date = "character"))),
+         pid = str_match(filename, ".*/(p[0-9]{2})/.*")[,2]) %>%
+  unnest() %>%
+  select(-filename)
+
+write.csv(metrics_of_all_participants, snakemake@output[[1]], row.names = FALSE)

src/models/merge_metrics_of_single_participant.R

@@ -0,0 +1,13 @@
+source("packrat/init.R")
+
+library(tidyr)
+library(purrr)
+library(dplyr)
+
+metric_files  <- snakemake@input[["metric_files"]]
+
+metrics_of_single_participant <- metric_files %>%
+  map(read.csv, stringsAsFactors = F, colClasses = c(local_date = "character")) %>%
+  reduce(full_join, by="local_date")
+
+write.csv(metrics_of_single_participant, snakemake@output[[1]], row.names = FALSE)