70 lines
3.5 KiB
Plaintext
70 lines
3.5 KiB
Plaintext
def input_merge_features_of_single_participant(wildcards):
|
|
if wildcards.source == "phone_fitbit_features":
|
|
return expand("data/processed/{pid}/{features}_{day_segment}.csv", pid=wildcards.pid, features=config["PARAMS_FOR_ANALYSIS"]["PHONE_FEATURES"] + config["PARAMS_FOR_ANALYSIS"]["FITBIT_FEATURES"], day_segment=wildcards.day_segment)
|
|
else:
|
|
return expand("data/processed/{pid}/{features}_{day_segment}.csv", pid=wildcards.pid, features=config["PARAMS_FOR_ANALYSIS"][wildcards.source.upper()], day_segment=wildcards.day_segment)
|
|
|
|
def optional_input_days_to_include(wildcards):
|
|
if config["PARAMS_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["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_BEFORE_SURGERY"]) + \
|
|
"_" + str(config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_IN_HOSPITAL"]) + \
|
|
"_" + str(config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_AFTER_DISCHARGE"]) + ".csv"]
|
|
else:
|
|
return []
|
|
|
|
def optional_input_valid_sensed_days(wildcards):
|
|
if config["PARAMS_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_features_for_individual_model:
|
|
input:
|
|
feature_files = input_merge_features_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}/features_for_individual_model/{source}_{day_segment}_original.csv"
|
|
script:
|
|
"../src/models/merge_features_for_individual_model.R"
|
|
|
|
rule merge_targets_for_population_model:
|
|
input:
|
|
data_files = expand("data/processed/{pid}/targets_{{summarised}}.csv", pid=config["PIDS"])
|
|
output:
|
|
"data/processed/features_for_population_model/targets_{summarised}.csv"
|
|
script:
|
|
"../src/models/merge_data_for_population_model.py"
|
|
|
|
rule clean_features_for_individual_model:
|
|
input:
|
|
rules.merge_features_for_individual_model.output
|
|
params:
|
|
cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
|
|
cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
|
|
rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
|
|
participants_day_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANTS_DAY_THRESHOLD"]
|
|
output:
|
|
"data/processed/{pid}/features_for_individual_model/{source}_{day_segment}_clean.csv"
|
|
script:
|
|
"../src/models/clean_features_for_model.R"
|
|
|
|
rule clean_features_for_population_model:
|
|
input:
|
|
rules.merge_features_for_population_model.output
|
|
params:
|
|
cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
|
|
cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
|
|
rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
|
|
participants_day_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANTS_DAY_THRESHOLD"]
|
|
output:
|
|
"data/processed/features_for_population_model/{source}_{day_segment}_clean.csv"
|
|
script:
|
|
"../src/models/clean_features_for_model.R"
|
|
|