455 lines
12 KiB
Python
455 lines
12 KiB
Python
# -*- coding: utf-8 -*-
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# ---
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# jupyter:
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# jupytext:
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# formats: ipynb,py:percent
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# text_representation:
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# extension: .py
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# format_name: percent
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# format_version: '1.3'
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# jupytext_version: 1.14.5
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# kernelspec:
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# display_name: straw2analysis
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# language: python
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# name: straw2analysis
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# ---
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# %%
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import datetime
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import seaborn as sns
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import participants.query_db
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from features.esm import (
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QUESTIONNAIRE_IDS,
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clean_up_esm,
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get_esm_data,
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increment_answers,
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preprocess_esm,
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reassign_question_ids,
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)
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from features.esm_COPE import DICT_COPE_QUESTION_IDS
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from features.esm_JCQ import reverse_jcq_demand_control_scoring
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from features.esm_SAM import DICT_SAM_QUESTION_IDS, extract_stressful_events
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# import os
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# import sys
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# nb_dir = os.path.split(os.getcwd())[0]
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# if nb_dir not in sys.path:
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# sys.path.append(nb_dir)
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# %%
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save_figs = False
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export_data = True
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# %%
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participants_inactive_usernames = participants.query_db.get_usernames(
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collection_start=datetime.date.fromisoformat("2020-08-01")
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)
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df_esm_inactive = get_esm_data(participants_inactive_usernames)
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# %%
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df_esm_preprocessed = preprocess_esm(df_esm_inactive)
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# %% [markdown]
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# # PANAS
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# %%
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df_esm_PANAS = df_esm_preprocessed[
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(
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df_esm_preprocessed["questionnaire_id"]
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== QUESTIONNAIRE_IDS["PANAS_positive_affect"]
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)
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df_esm_preprocessed["questionnaire_id"]
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== QUESTIONNAIRE_IDS["PANAS_negative_affect"]
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)
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]
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df_esm_PANAS_clean = clean_up_esm(df_esm_PANAS)
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# %% [markdown]
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# Group by participants, date, and subscale and calculate daily means.
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# %%
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df_esm_PANAS_daily_means = (
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df_esm_PANAS_clean.groupby(["participant_id", "date_lj", "questionnaire_id"])
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.esm_user_answer_numeric.agg("mean")
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.reset_index()
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.rename(columns={"esm_user_answer_numeric": "esm_numeric_mean"})
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)
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# %% [markdown]
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# Next, calculate mean, median, and standard deviation across all days for each participant.
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# %%
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df_esm_PANAS_summary_participant = (
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df_esm_PANAS_daily_means.groupby(["participant_id", "questionnaire_id"])
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.esm_numeric_mean.agg(["mean", "median", "std"])
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.reset_index(col_level=1)
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)
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df_esm_PANAS_summary_participant[
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"PANAS subscale"
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] = df_esm_PANAS_daily_means.questionnaire_id.astype("category").cat.rename_categories(
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{8.0: "positive affect", 9.0: "negative affect"}
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)
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# %%
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df_esm_PANAS_summary_participant.groupby("PANAS subscale").describe()["mean"]
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# %%
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df_esm_PANAS_summary_participant.groupby("PANAS subscale").describe()["std"]
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# %%
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df_esm_PANAS_summary_participant.query("std == 0")
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# %%
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fig1 = sns.displot(
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data=df_esm_PANAS_summary_participant, x="mean", hue="PANAS subscale", binwidth=0.2
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)
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fig1.set_axis_labels(x_var="participant mean", y_var="frequency")
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if save_figs:
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fig1.figure.savefig("PANAS_mean_participant.pdf", dpi=300)
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# %%
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sns.displot(
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data=df_esm_PANAS_summary_participant,
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x="median",
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hue="PANAS subscale",
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binwidth=0.2,
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)
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# %%
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fig2 = sns.displot(
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data=df_esm_PANAS_summary_participant, x="std", hue="PANAS subscale", binwidth=0.05
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)
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fig2.set_axis_labels(x_var="participant standard deviation", y_var="frequency")
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if save_figs:
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fig2.figure.savefig("PANAS_std_participant.pdf", dpi=300)
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# %%
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df_esm_PANAS_summary_participant[df_esm_PANAS_summary_participant["std"] < 0.1]
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# %% [markdown]
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# # Stress appraisal measure
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# %%
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df_SAM_all = extract_stressful_events(df_esm_inactive)
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# %%
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df_SAM_all.head()
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# %%
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df_esm_SAM = df_esm_preprocessed[
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(
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df_esm_preprocessed["questionnaire_id"]
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>= QUESTIONNAIRE_IDS["appraisal_stressfulness_event"]
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)
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& (
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df_esm_preprocessed["questionnaire_id"]
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<= QUESTIONNAIRE_IDS["appraisal_stressfulness_period"]
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)
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]
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df_esm_SAM_clean = clean_up_esm(df_esm_SAM)
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# %% [markdown]
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# ## Stressful events
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# %%
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df_esm_SAM_event = df_esm_SAM_clean[
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df_esm_SAM_clean["questionnaire_id"]
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== QUESTIONNAIRE_IDS["appraisal_stressfulness_event"]
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].assign(stressful_event=lambda x: (x.esm_user_answer_numeric > 0))
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# %%
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df_esm_SAM_daily_events = (
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df_esm_SAM_event.groupby(["participant_id", "date_lj"])
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.stressful_event.agg("mean")
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.reset_index()
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.rename(columns={"stressful_event": "SAM_event_ratio"})
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)
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# %% [markdown]
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# Calculate the daily mean of YES (1) or NO (0) answers to the question about stressful events. This is then the daily ratio of EMA sessions that included a stressful event.
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# %%
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df_esm_SAM_event_summary_participant = (
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df_esm_SAM_daily_events.groupby(["participant_id"])
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.SAM_event_ratio.agg(["mean", "median", "std"])
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.reset_index(col_level=1)
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)
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# %%
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fig6 = sns.displot(data=df_esm_SAM_event_summary_participant, x="mean", binwidth=0.1)
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fig6.set_axis_labels(
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x_var="participant proportion of stressful events", y_var="frequency"
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)
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if save_figs:
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fig6.figure.savefig("SAM_events_mean_participant.pdf", dpi=300)
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# %%
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sns.displot(data=df_esm_SAM_event_summary_participant, x="std", binwidth=0.05)
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# %% [markdown]
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# ### Threat and challenge
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# %% [markdown]
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# * Example of threat: "Did this event make you feel anxious?"
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# * Example of challenge: "How eager are you to tackle this event?"
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# * Possible answers:
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# 0 - Not at all,
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# 1 - Slightly,
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# 2 - Moderately,
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# 3 - Considerably,
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# 4 - Extremely
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# %%
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df_esm_SAM_daily = (
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df_esm_SAM_clean.groupby(["participant_id", "date_lj", "questionnaire_id"])
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.esm_user_answer_numeric.agg("mean")
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.reset_index()
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.rename(columns={"esm_user_answer_numeric": "esm_numeric_mean"})
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)
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# %%
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df_esm_SAM_daily_threat_challenge = df_esm_SAM_daily[
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(df_esm_SAM_daily["questionnaire_id"] == QUESTIONNAIRE_IDS["appraisal_threat"])
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| (df_esm_SAM_daily["questionnaire_id"] == QUESTIONNAIRE_IDS["appraisal_challenge"])
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]
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# %%
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df_esm_SAM_summary_participant = (
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df_esm_SAM_daily.groupby(["participant_id", "questionnaire_id"])
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.esm_numeric_mean.agg(["mean", "median", "std"])
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.reset_index(col_level=1)
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)
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# %%
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df_esm_SAM_event_stressfulness_summary_participant = df_esm_SAM_summary_participant[
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df_esm_SAM_summary_participant["questionnaire_id"]
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== QUESTIONNAIRE_IDS["appraisal_stressfulness_event"]
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]
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df_esm_SAM_event_stressfulness_summary_participant.describe()["mean"]
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# %%
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df_esm_SAM_event_stressfulness_summary_participant.describe()["std"]
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# %%
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sns.displot(
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data=df_esm_SAM_event_stressfulness_summary_participant, x="mean", binwidth=0.2
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)
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# %%
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df_esm_SAM_threat_challenge_summary_participant = df_esm_SAM_summary_participant[
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(
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df_esm_SAM_summary_participant["questionnaire_id"]
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== QUESTIONNAIRE_IDS["appraisal_threat"]
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)
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| (
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df_esm_SAM_summary_participant["questionnaire_id"]
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== QUESTIONNAIRE_IDS["appraisal_challenge"]
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)
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]
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df_esm_SAM_threat_challenge_summary_participant[
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"event subscale"
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] = df_esm_SAM_threat_challenge_summary_participant.questionnaire_id.astype(
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"category"
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).cat.rename_categories(
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{88: "threat", 89: "challenge"}
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)
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# %%
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sns.displot(
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data=df_esm_SAM_threat_challenge_summary_participant,
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x="mean",
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hue="event subscale",
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binwidth=0.2,
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)
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# %%
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fig3 = sns.displot(
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data=df_esm_SAM_threat_challenge_summary_participant,
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x="std",
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hue="event subscale",
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binwidth=0.1,
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)
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fig3.set_axis_labels(x_var="participant standard deviation", y_var="frequency")
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if save_figs:
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fig3.figure.savefig("SAM_std_participant.pdf", dpi=300)
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# %%
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df_esm_SAM_threat_challenge_summary_participant.groupby("event subscale").describe()[
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"mean"
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]
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# %%
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df_esm_SAM_threat_challenge_summary_participant.groupby("event subscale").describe()[
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"std"
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]
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# %%
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df_esm_SAM_clean.columns
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# %%
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df_esm_SAM_clean.esm_status.value_counts()
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# %%
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if export_data:
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df_esm_SAM_fixed = reassign_question_ids(df_esm_SAM_clean, DICT_SAM_QUESTION_IDS)
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df_esm_SAM_fixed = increment_answers(df_esm_SAM_fixed)
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df_esm_SAM_for_export = df_esm_SAM_fixed[
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[
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"participant_id",
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"username",
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"device_id",
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"_id",
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"esm_trigger",
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"esm_session",
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"esm_notification_id",
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"question_id",
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"questionnaire_id",
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"esm_instructions",
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"double_esm_user_answer_timestamp",
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"datetime_lj",
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"date_lj",
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"time",
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"esm_user_answer",
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"esm_user_answer_numeric",
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]
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]
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df_esm_SAM_for_export.sort_values(
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by=["participant_id", "device_id", "_id"], ignore_index=True, inplace=True
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)
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print(df_esm_SAM_for_export.head())
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df_esm_SAM_for_export.to_csv(
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"../data/raw/df_esm_SAM_threat_challenge.csv", index=False
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)
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# %% [markdown]
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# ## Stressfulness of period
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# %%
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df_esm_SAM_period_summary_participant = df_esm_SAM_summary_participant[
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df_esm_SAM_summary_participant["questionnaire_id"]
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== QUESTIONNAIRE_IDS["appraisal_stressfulness_period"]
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]
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# %%
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df_esm_SAM_period_summary_participant.describe()["mean"]
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# %%
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df_esm_SAM_period_summary_participant.describe()["std"]
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# %%
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sns.displot(data=df_esm_SAM_period_summary_participant, x="mean", binwidth=0.2)
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# %%
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sns.displot(data=df_esm_SAM_period_summary_participant, x="std", binwidth=0.1)
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# %% [markdown]
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# # Job demand and control
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# %%
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df_esm_JCQ_demand_control = df_esm_preprocessed[
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(df_esm_preprocessed["questionnaire_id"] >= QUESTIONNAIRE_IDS["JCQ_job_demand"])
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& (df_esm_preprocessed["questionnaire_id"] <= QUESTIONNAIRE_IDS["JCQ_job_control"])
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]
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df_esm_JCQ_demand_control_clean = clean_up_esm(df_esm_JCQ_demand_control)
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# %%
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df_esm_JCQ_demand_control_reversed = reverse_jcq_demand_control_scoring(
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df_esm_JCQ_demand_control_clean
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)
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# %%
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df_esm_JCQ_daily = (
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df_esm_JCQ_demand_control_reversed.groupby(
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["participant_id", "date_lj", "questionnaire_id"]
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)
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.esm_user_score.agg("mean")
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.reset_index()
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.rename(columns={"esm_user_score": "esm_score_mean"})
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)
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df_esm_JCQ_summary_participant = (
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df_esm_JCQ_daily.groupby(["participant_id", "questionnaire_id"])
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.esm_score_mean.agg(["mean", "median", "std"])
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.reset_index(col_level=1)
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)
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df_esm_JCQ_summary_participant[
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"JCQ subscale"
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] = df_esm_JCQ_summary_participant.questionnaire_id.astype(
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"category"
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).cat.rename_categories(
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{10: "job demand", 11: "job control"}
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)
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# %%
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df_esm_JCQ_summary_participant.groupby("JCQ subscale").describe()["mean"]
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# %%
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df_esm_JCQ_summary_participant.groupby("JCQ subscale").describe()["std"]
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# %%
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fig4 = sns.displot(
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data=df_esm_JCQ_summary_participant,
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x="mean",
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hue="JCQ subscale",
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binwidth=0.1,
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)
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fig4.set_axis_labels(x_var="participant mean", y_var="frequency")
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if save_figs:
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fig4.figure.savefig("JCQ_mean_participant.pdf", dpi=300)
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# %%
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fig5 = sns.displot(
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data=df_esm_JCQ_summary_participant,
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x="std",
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hue="JCQ subscale",
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binwidth=0.05,
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)
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fig6.set_axis_labels(x_var="participant standard deviation", y_var="frequency")
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if save_figs:
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fig5.figure.savefig("JCQ_std_participant.pdf", dpi=300)
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# %% [markdown]
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# # COPE Inventory
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# %%
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df_esm_COPE = df_esm_preprocessed[
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(df_esm_preprocessed["questionnaire_id"] >= QUESTIONNAIRE_IDS["COPE_active"])
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& (df_esm_preprocessed["questionnaire_id"] <= QUESTIONNAIRE_IDS["COPE_emotions"])
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]
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# %%
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df_esm_COPE_clean = clean_up_esm(df_esm_COPE)
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df_esm_COPE_clean = increment_answers(df_esm_COPE_clean)
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df_esm_COPE_fixed = reassign_question_ids(df_esm_COPE_clean, DICT_COPE_QUESTION_IDS)
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# %%
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if export_data:
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df_esm_COPE_for_export = df_esm_COPE_fixed[
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[
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"participant_id",
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"username",
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"device_id",
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"_id",
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"esm_trigger",
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"esm_session",
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"esm_notification_id",
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"question_id",
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"questionnaire_id",
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"esm_instructions",
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"double_esm_user_answer_timestamp",
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"datetime_lj",
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"date_lj",
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"time",
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"esm_user_answer",
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"esm_user_answer_numeric",
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]
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]
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df_esm_COPE_for_export.sort_values(
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by=["participant_id", "device_id", "_id"], ignore_index=True, inplace=True
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)
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print(df_esm_COPE_for_export.head())
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df_esm_COPE_for_export.to_csv("../data/raw/df_esm_COPE.csv", index=False)
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