rapids/rules/models.snakefile

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)

def optional_input_days_to_include(wildcards):
    if config["METRICS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["ENABLED"]:
        # This input automatically trigers the rule days_to_analyse in mystudy.snakefile
        return ["data/interim/{pid}/days_to_analyse" + \
                    "_" + str(config["METRICS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_BEFORE_SURGERY"]) + \
                    "_" + str(config["METRICS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_IN_HOSPITAL"]) + \
                    "_" + str(config["METRICS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_AFTER_DISCHARGE"]) + ".csv"]
    else:
        return []

def optional_input_valid_sensed_days(wildcards):
    if config["METRICS_FOR_ANALYSIS"]["DROP_VALID_SENSED_DAYS"]["ENABLED"]:
        # This input automatically trigers the rule phone_valid_sensed_days in preprocessing.snakefile
        return ["data/interim/{pid}/phone_valid_sensed_days.csv"]
    else:
        return []

rule merge_metrics_for_individual_model:
    input:
        metric_files = input_merge_metrics_of_single_participant,
        phone_valid_sensed_days = optional_input_valid_sensed_days,
        days_to_include = optional_input_days_to_include
    params:
        source = "{source}"
    output:
        "data/processed/{pid}/metrics_for_individual_model/{source}_{day_segment}_original.csv"
    script:
        "../src/models/merge_metrics_for_individual_model.R"

rule merge_metrics_for_population_model:
    input:
        metric_files = expand("data/processed/{pid}/metrics_for_individual_model/{{source}}_{{day_segment}}_original.csv", pid=config["PIDS"])
    output:
        "data/processed/metrics_for_population_model/{source}_{day_segment}_original.csv" 
    script:
        "../src/models/merge_metrics_for_population_model.R"

rule clean_metrics_for_individual_model:
    input:
        rules.merge_metrics_for_individual_model.output
    params:
        cols_nan_threshold = config["METRICS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
        cols_var_threshold = config["METRICS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
        rows_nan_threshold = config["METRICS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
        participants_day_threshold = config["METRICS_FOR_ANALYSIS"]["PARTICIPANTS_DAY_THRESHOLD"]
    output:
        "data/processed/{pid}/metrics_for_individual_model/{source}_{day_segment}_clean.csv"
    script:
        "../src/models/clean_metrics_for_model.R"

rule clean_metrics_for_population_model:
    input:
        rules.merge_metrics_for_population_model.output
    params:
        cols_nan_threshold = config["METRICS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
        cols_var_threshold = config["METRICS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
        rows_nan_threshold = config["METRICS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
        participants_day_threshold = config["METRICS_FOR_ANALYSIS"]["PARTICIPANTS_DAY_THRESHOLD"]
    output:
        "data/processed/metrics_for_population_model/{source}_{day_segment}_clean.csv"
    script:
        "../src/models/clean_metrics_for_model.R"