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Add hours and bins thresholds for analysis section

pull/95/head
Meng Li 2020-07-27 22:59:32 -04:00
parent 93157db210
commit c498b8d2df
2 changed files with 27 additions and 19 deletions
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16
Snakefile
View File

@ -206,7 +206,9 @@ if config["PARAMS_FOR_ANALYSIS"]["COMPUTE"]:
files_to_compute.extend(expand("data/processed/data_for_population_model/targets_{summarised}.csv",
summarised = config["PARAMS_FOR_ANALYSIS"]["SUMMARISED"]))
files_to_compute.extend(expand(
expand("data/processed/data_for_population_model/{{rows_nan_threshold}}|{{cols_nan_threshold}}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_nancellsratio.csv",
expand("data/processed/data_for_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{{rows_nan_threshold}}|{{cols_nan_threshold}}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_nancellsratio.csv",
min_valid_hours_per_day=config["OVERALL_COMPLIANCE_HEATMAP"]["MIN_VALID_HOURS_PER_DAY"],
min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"],
days_before_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_BEFORE_THRESHOLD"],
days_after_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_AFTER_THRESHOLD"],
cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
@ -216,7 +218,9 @@ if config["PARAMS_FOR_ANALYSIS"]["COMPUTE"]:
rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"]))
files_to_compute.extend(expand(
expand("data/processed/data_for_population_model/{{rows_nan_threshold}}|{{cols_nan_threshold}}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}.csv",
expand("data/processed/data_for_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{{rows_nan_threshold}}|{{cols_nan_threshold}}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}.csv",
min_valid_hours_per_day=config["OVERALL_COMPLIANCE_HEATMAP"]["MIN_VALID_HOURS_PER_DAY"],
min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"],
days_before_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_BEFORE_THRESHOLD"],
days_after_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_AFTER_THRESHOLD"],
cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
@ -227,7 +231,9 @@ if config["PARAMS_FOR_ANALYSIS"]["COMPUTE"]:
rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"]))
files_to_compute.extend(expand(
expand("data/processed/output_population_model/{{rows_nan_threshold}}|{{cols_nan_threshold}}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}_{cv_method}_baseline.csv",
expand("data/processed/output_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{{rows_nan_threshold}}|{{cols_nan_threshold}}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}_{cv_method}_baseline.csv",
min_valid_hours_per_day=config["OVERALL_COMPLIANCE_HEATMAP"]["MIN_VALID_HOURS_PER_DAY"],
min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"],
days_before_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_BEFORE_THRESHOLD"],
days_after_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_AFTER_THRESHOLD"],
cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
@ -239,7 +245,9 @@ if config["PARAMS_FOR_ANALYSIS"]["COMPUTE"]:
rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"]))
files_to_compute.extend(expand(
expand("data/processed/output_population_model/{{rows_nan_threshold}}|{{cols_nan_threshold}}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{{model}}/{cv_method}/{source}_{day_segment}_{summarised}_{{scaler}}/{result}.csv",
expand("data/processed/output_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{{rows_nan_threshold}}|{{cols_nan_threshold}}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{{model}}/{cv_method}/{source}_{day_segment}_{summarised}_{{scaler}}/{result}.csv",
min_valid_hours_per_day=config["OVERALL_COMPLIANCE_HEATMAP"]["MIN_VALID_HOURS_PER_DAY"],
min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"],
days_before_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_BEFORE_THRESHOLD"],
days_after_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_AFTER_THRESHOLD"],
cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],

30
rules/models.snakefile
View File

@ -99,7 +99,7 @@ rule nan_cells_ratio_of_cleaned_features:
rule merge_features_and_targets:
input:
cleaned_features = "data/processed/data_for_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_clean.csv",
cleaned_features = "data/processed/data_for_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_clean.csv",
demographic_features = "data/processed/data_for_population_model/demographic_features.csv",
targets = "data/processed/data_for_population_model/targets_{summarised}.csv",
params:
@ -108,28 +108,28 @@ rule merge_features_and_targets:
numerical_operators = config["PARAMS_FOR_ANALYSIS"]["NUMERICAL_OPERATORS"],
categorical_operators = config["PARAMS_FOR_ANALYSIS"]["CATEGORICAL_OPERATORS"]
output:
"data/processed/data_for_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}.csv"
"data/processed/data_for_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}.csv"
script:
"../src/models/merge_features_and_targets.py"
rule baseline:
input:
"data/processed/data_for_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}.csv"
"data/processed/data_for_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}.csv"
params:
cv_method = "{cv_method}",
rowsnan_colsnan_days_colsvar_threshold = "{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}",
demographic_features = config["PARAMS_FOR_ANALYSIS"]["DEMOGRAPHIC_FEATURES"]
output:
"data/processed/output_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}_{cv_method}_baseline.csv"
"data/processed/output_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}_{cv_method}_baseline.csv"
log:
"data/processed/output_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}_{cv_method}_notes.log"
"data/processed/output_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}_{cv_method}_notes.log"
script:
"../src/models/baseline.py"
rule modeling:
input:
data = "data/processed/data_for_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}.csv"
data = "data/processed/data_for_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}.csv"
params:
model = "{model}",
cv_method = "{cv_method}",
@ -142,21 +142,21 @@ rule modeling:
model_hyperparams = config["PARAMS_FOR_ANALYSIS"]["MODEL_HYPERPARAMS"],
rowsnan_colsnan_days_colsvar_threshold = "{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}"
output:
fold_predictions = "data/processed/output_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{model}/{cv_method}/{source}_{day_segment}_{summarised}_{scaler}/fold_predictions.csv",
fold_metrics = "data/processed/output_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{model}/{cv_method}/{source}_{day_segment}_{summarised}_{scaler}/fold_metrics.csv",
overall_results = "data/processed/output_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{model}/{cv_method}/{source}_{day_segment}_{summarised}_{scaler}/overall_results.csv",
fold_feature_importances = "data/processed/output_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{model}/{cv_method}/{source}_{day_segment}_{summarised}_{scaler}/fold_feature_importances.csv"
fold_predictions = "data/processed/output_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{model}/{cv_method}/{source}_{day_segment}_{summarised}_{scaler}/fold_predictions.csv",
fold_metrics = "data/processed/output_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{model}/{cv_method}/{source}_{day_segment}_{summarised}_{scaler}/fold_metrics.csv",
overall_results = "data/processed/output_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{model}/{cv_method}/{source}_{day_segment}_{summarised}_{scaler}/overall_results.csv",
fold_feature_importances = "data/processed/output_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{model}/{cv_method}/{source}_{day_segment}_{summarised}_{scaler}/fold_feature_importances.csv"
log:
"data/processed/output_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{model}/{cv_method}/{source}_{day_segment}_{summarised}_{scaler}/notes.log"
"data/processed/output_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{model}/{cv_method}/{source}_{day_segment}_{summarised}_{scaler}/notes.log"
script:
"../src/models/modeling.py"
rule merge_population_model_results:
input:
overall_results = "data/processed/output_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{model}/{cv_method}/{source}_{day_segment}_{summarised}_{scaler}/overall_results.csv",
nan_cells_ratio = "data/processed/data_for_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_nancellsratio.csv",
baseline = "data/processed/output_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}_{cv_method}_baseline.csv"
overall_results = "data/processed/output_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{model}/{cv_method}/{source}_{day_segment}_{summarised}_{scaler}/overall_results.csv",
nan_cells_ratio = "data/processed/data_for_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_nancellsratio.csv",
baseline = "data/processed/output_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}_{cv_method}_baseline.csv"
output:
"data/processed/output_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{model}/{cv_method}/{source}_{day_segment}_{summarised}_{scaler}/merged_population_model_results.csv"
"data/processed/output_population_model/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{model}/{cv_method}/{source}_{day_segment}_{summarised}_{scaler}/merged_population_model_results.csv"
script:
"../src/models/merge_population_model_results.py"