Rename merge metrics for models and add filter valid sensed days

Co-authored-by: Meng Li <AnnieLM1996@gmail.com>
pull/95/head
JulioV 2020-03-12 17:31:46 -04:00
parent 63310b7b90
commit 3d4c26754e
7 changed files with 35 additions and 26 deletions

3
.gitignore vendored
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@ -107,6 +107,3 @@ reports/
*.Rproj *.Rproj
.RData .RData
.Rhistory .Rhistory
# analysis part
models/*

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@ -57,11 +57,11 @@ rule all:
pid = config["PIDS"], pid = config["PIDS"],
day_segment = config["STEP"]["DAY_SEGMENTS"]), day_segment = config["STEP"]["DAY_SEGMENTS"]),
# Models # Models
expand("models/input/merged_single_participant/{pid}/{source}_{day_segment}.csv", expand("data/processed/{pid}/metrics_for_individual_model/{source}_{day_segment}.csv",
pid = config["PIDS"], pid = config["PIDS"],
source = config["METRICS_FOR_ANALYSIS"]["SOURCES"], source = config["METRICS_FOR_ANALYSIS"]["SOURCES"],
day_segment = config["METRICS_FOR_ANALYSIS"]["DAY_SEGMENTS"]), day_segment = config["METRICS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
expand("models/input/merged_all_participants/{source}_{day_segment}.csv", expand("data/processed/metrics_for_population_model/{source}_{day_segment}.csv",
source = config["METRICS_FOR_ANALYSIS"]["SOURCES"], source = config["METRICS_FOR_ANALYSIS"]["SOURCES"],
day_segment = config["METRICS_FOR_ANALYSIS"]["DAY_SEGMENTS"]), day_segment = config["METRICS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
# Reports # Reports

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@ -130,3 +130,4 @@ METRICS_FOR_ANALYSIS:
PHONE_METRICS: [accelerometer, applications_foreground, battery, call_incoming, call_missed, call_outgoing, google_activity_recognition, light, location_barnett, screen, sms_received, sms_sent] 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] 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 PHONE_FITBIT_METRICS: "" # This array is merged in the input_merge_features_of_single_participant function in models.snakefile
DROP_VALID_SENSED_DAYS: True

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@ -4,18 +4,22 @@ def input_merge_metrics_of_single_participant(wildcards):
else: 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) 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: rule merge_metrics_for_individual_model:
input: input:
metric_files = input_merge_metrics_of_single_participant metric_files = input_merge_metrics_of_single_participant,
phone_valid_sensed_days = "data/interim/{pid}/phone_valid_sensed_days.csv"
params:
drop_valid_sensed_days = config["METRICS_FOR_ANALYSIS"]["DROP_VALID_SENSED_DAYS"],
source = "{source}"
output: output:
"models/input/merged_single_participant/{pid}/{source}_{day_segment}.csv" "data/processed/{pid}/metrics_for_individual_model/{source}_{day_segment}.csv"
script: script:
"../src/models/merge_metrics_of_single_participant.R" "../src/models/merge_metrics_for_individual_model.R"
rule merge_metrics_of_all_participants: rule merge_metrics_for_population_model:
input: input:
metric_files = expand("models/input/merged_single_participant/{pid}/{{source}}_{{day_segment}}.csv", pid=config["PIDS"]) metric_files = expand("data/processed/{pid}/metrics_for_individual_model/{{source}}_{{day_segment}}.csv", pid=config["PIDS"])
output: output:
"models/input/merged_all_participants/{source}_{day_segment}.csv" "data/processed/metrics_for_population_model/{source}_{day_segment}.csv"
script: script:
"../src/models/merge_metrics_of_all_participants.R" "../src/models/merge_metrics_for_population_model.R"

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@ -0,0 +1,20 @@
source("packrat/init.R")
library(tidyr)
library(purrr)
library(dplyr)
metric_files <- snakemake@input[["metric_files"]]
phone_valid_sensed_days <- read.csv(snakemake@input[["phone_valid_sensed_days"]])
drop_valid_sensed_days <- snakemake@params[["drop_valid_sensed_days"]]
source <- snakemake@params[["source"]]
metrics_for_individual_model <- metric_files %>%
map(read.csv, stringsAsFactors = F, colClasses = c(local_date = "character")) %>%
reduce(full_join, by="local_date")
if(drop_valid_sensed_days && source == "phone_metrics"){
metrics_for_individual_model <- merge(metrics_for_individual_model, phone_valid_sensed_days, by="local_date") %>% select(-valid_hours)
}
write.csv(metrics_for_individual_model, snakemake@output[[1]], row.names = FALSE)

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@ -1,13 +0,0 @@
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)