# --- # jupyter: # jupytext: # formats: ipynb,py:percent # text_representation: # extension: .py # format_name: percent # format_version: '1.3' # jupytext_version: 1.11.4 # kernelspec: # display_name: straw2analysis # language: python # name: straw2analysis # --- # %% # %matplotlib inline import datetime import os import sys import seaborn as sns import yaml from sklearn import linear_model from sklearn.model_selection import LeaveOneGroupOut, cross_val_score nb_dir = os.path.split(os.getcwd())[0] if nb_dir not in sys.path: sys.path.append(nb_dir) # %% import participants.query_db from features import esm, helper, proximity # %% [markdown] # # 1. Get the relevant data # %% participants_inactive_usernames = participants.query_db.get_usernames( collection_start=datetime.date.fromisoformat("2020-08-01") ) # Consider only two participants to simplify. ptcp_2 = participants_inactive_usernames[0:2] # %% [markdown] # ## 1.1 Labels # %% df_esm = esm.get_esm_data(ptcp_2) df_esm_preprocessed = esm.preprocess_esm(df_esm) # %% df_esm_PANAS = df_esm_preprocessed[ (df_esm_preprocessed["questionnaire_id"] == 8) | (df_esm_preprocessed["questionnaire_id"] == 9) ] df_esm_PANAS_clean = esm.clean_up_esm(df_esm_PANAS) # %% [markdown] # ## 1.2 Sensor data # %% df_proximity = proximity.get_proximity_data(ptcp_2) df_proximity = helper.get_date_from_timestamp(df_proximity) df_proximity = proximity.recode_proximity(df_proximity) # %% [markdown] # ## 1.3 Standardization/personalization # %% [markdown] # # 2. Grouping/segmentation # %% df_esm_PANAS_daily_means = ( df_esm_PANAS_clean.groupby(["participant_id", "date_lj", "questionnaire_id"]) .esm_user_answer_numeric.agg("mean") .reset_index() .rename(columns={"esm_user_answer_numeric": "esm_numeric_mean"}) ) # %% df_esm_PANAS_daily_means = ( df_esm_PANAS_daily_means.pivot( index=["participant_id", "date_lj"], columns="questionnaire_id", values="esm_numeric_mean", ) .reset_index(col_level=1) .rename(columns={8.0: "PA", 9.0: "NA"}) .set_index(["participant_id", "date_lj"]) ) # %% df_proximity_daily_counts = proximity.count_proximity( df_proximity, ["participant_id", "date_lj"] ) # %% df_proximity_daily_counts # %% [markdown] # # 3. Join features (and export to csv?) # %% df_full_data_daily_means = df_esm_PANAS_daily_means.join( df_proximity_daily_counts ).reset_index() # %% [markdown] # # 4. Machine learning model and parameters # %% lin_reg_proximity = linear_model.LinearRegression() # %% [markdown] # ## 4.1 Validation method # %% logo = LeaveOneGroupOut() logo.get_n_splits( df_full_data_daily_means[["freq_prox_near", "prop_prox_near"]], df_full_data_daily_means["PA"], groups=df_full_data_daily_means["participant_id"], ) # %% [markdown] # ## 4.2 Fit results (export?) # %% cross_val_score( lin_reg_proximity, df_full_data_daily_means[["freq_prox_near", "prop_prox_near"]], df_full_data_daily_means["PA"], groups=df_full_data_daily_means["participant_id"], cv=logo, n_jobs=-1, scoring="r2", ) # %% lin_reg_proximity.fit( df_full_data_daily_means[["freq_prox_near", "prop_prox_near"]], df_full_data_daily_means["PA"], ) # %% lin_reg_proximity.score( df_full_data_daily_means[["freq_prox_near", "prop_prox_near"]], df_full_data_daily_means["PA"], ) # %% [markdown] # # Merging these into a pipeline # %% from machine_learning import pipeline # %% with open("../machine_learning/config/minimal_features.yaml", "r") as file: sensor_features_params = yaml.safe_load(file) # %% sensor_features = pipeline.SensorFeatures(**sensor_features_params) sensor_features.data_types # %% sensor_features.get_sensor_data("proximity") # %% sensor_features.set_sensor_data() # %% sensor_features.get_sensor_data("proximity") # %% sensor_features.calculate_features() # %% sensor_features.get_features("proximity", "all") # %% with open("../machine_learning/config/minimal_labels.yaml", "r") as file: labels_params = yaml.safe_load(file) # %% labels = pipeline.Labels(**labels_params) labels.questionnaires # %% labels.set_labels() # %% labels.get_labels("PANAS") # %%