Merge branch 'ml_pipeline' of repo.ijs.si:junoslukan/straw2analysis into ml_pipeline

# Conflicts:
#	exploration/ml_pipeline_daily.py - deleted

.gitignore

@@ -6,3 +6,8 @@ __pycache__/
 /config/*.ipynb
 /statistical_analysis/*.ipynb
 /machine_learning/intermediate_results/
+/data/features/
+/data/baseline/
+/data/*input*.csv
+/data/daily*
+/data/intradaily*

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "rapids"]
+	path = rapids
+	url = https://repo.ijs.si/junoslukan/rapids.git
+	branch = master

.idea/misc.xml

@@ -4,4 +4,17 @@
   <component name="PyCharmProfessionalAdvertiser">
     <option name="shown" value="true" />
   </component>
+  <component name="RMarkdownSettings">
+    <option name="renderProfiles">
+      <map>
+        <entry key="file://$PROJECT_DIR$/rapids/src/visualization/merge_heatmap_sensors_per_minute_per_time_segment.Rmd">
+          <value>
+            <RMarkdownRenderProfile>
+              <option name="outputDirectoryUrl" value="file://$PROJECT_DIR$/rapids/src/visualization" />
+            </RMarkdownRenderProfile>
+          </value>
+        </entry>
+      </map>
+    </option>
+  </component>
 </project>

.idea/snakemake-settings.xml

@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="SmkProjectSettings" sdk="Python 3.10 (snakemake)" enabled="true" />
+</project>

.idea/vcs.xml

@@ -2,5 +2,6 @@
 <project version="4">
   <component name="VcsDirectoryMappings">
     <mapping directory="$PROJECT_DIR$" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/rapids" vcs="Git" />
   </component>
 </project>

README.md

@@ -32,4 +32,130 @@ To install:
    
    ```
    DB_PASSWORD=database-password
-   ```
+   ```
+   
+# RAPIDS
+
+To install RAPIDS, follow the [instructions on their webpage](https://www.rapids.science/1.6/setup/installation/). 
+
+Here, I include additional information related to the installation and specific to the STRAW2analysis project.
+The installation was tested on Windows using Ubuntu 20.04 on Windows Subsystem for Linux ([WSL2](https://docs.microsoft.com/en-us/windows/wsl/install)).
+
+## Custom configuration
+### Credentials
+
+As mentioned under [Database in RAPIDS documentation](https://www.rapids.science/1.6/snippets/database/), a `credentials.yaml` file is needed to connect to a database.
+It should contain:
+
+```yaml
+PSQL_STRAW:
+  database: staw
+  host: 212.235.208.113
+  password: password
+  port: 5432
+  user: staw_db
+```
+
+where`password` needs to be specified as well.
+
+## Possible installation issues
+### Missing dependencies for RPostgres
+
+To install `RPostgres` R package (used to connect to the PostgreSQL database), an error might occur:
+
+```text
+------------------------- ANTICONF ERROR ---------------------------
+Configuration failed because libpq was not found. Try installing:
+   * deb: libpq-dev (Debian, Ubuntu, etc)
+   * rpm: postgresql-devel (Fedora, EPEL)
+   * rpm: postgreql8-devel, psstgresql92-devel, postgresql93-devel, or postgresql94-devel (Amazon Linux)
+   * csw: postgresql_dev (Solaris)
+   * brew: libpq (OSX)
+If libpq is already installed, check that either:
+  (i)  'pkg-config' is in your PATH AND PKG_CONFIG_PATH contains a libpq.pc file; or
+  (ii) 'pg_config' is in your PATH.
+If neither can detect , you can set INCLUDE_DIR
+and LIB_DIR manually via:
+  R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
+--------------------------[ ERROR MESSAGE ]----------------------------
+  <stdin>:1:10: fatal error: libpq-fe.h: No such file or directory
+compilation terminated.
+```
+
+The library requires `libpq` for compiling from source, so install accordingly.
+
+### Timezone environment variable for tidyverse (relevant for WSL2)
+
+One of the R packages, `tidyverse` might need access to the `TZ` environment variable during the installation.
+On Ubuntu 20.04 on WSL2 this triggers the following error:
+
+```text
+> install.packages('tidyverse')
+
+ERROR: configuration failed for package ‘xml2’
+System has not been booted with systemd as init system (PID 1). Can't operate.
+Failed to create bus connection: Host is down
+Warning in system("timedatectl", intern = TRUE) :
+  running command 'timedatectl' had status 1
+Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
+  namespace ‘xml2’ 1.3.1 is already loaded, but >= 1.3.2 is required
+Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
+Execution halted
+ERROR: lazy loading failed for package ‘tidyverse’
+```
+
+This happens because WSL2 does not use the `timedatectl` service, which provides this variable.
+
+```bash
+~$ timedatectl
+System has not been booted with systemd as init system (PID 1). Can't operate.
+Failed to create bus connection: Host is down
+```
+
+and later 
+
+```bash 
+Warning message:
+In system("timedatectl", intern = TRUE) :
+  running command 'timedatectl' had status 1
+Execution halted
+```
+
+This can be amended by setting the environment variable manually before attempting to install `tidyverse`:
+
+```bash
+export TZ='Europe/Ljubljana'
+```
+
+## Possible runtime issues
+### Unix end of line characters
+
+Upon running rapids, an error might occur:
+
+```bash
+/usr/bin/env: ‘python3\r’: No such file or directory
+```
+
+This is due to Windows style end of line characters. 
+To amend this, I added a `.gitattributes` files to force `git` to checkout `rapids` using Unix EOL characters.
+If this still fails, `dos2unix` can be used to change them.
+
+### System has not been booted with systemd as init system (PID 1)
+
+See [the installation issue above](#Timezone-environment-variable-for-tidyverse-(relevant-for-WSL2)).
+
+## Update RAPIDS
+
+To update RAPIDS, first pull and merge [origin]( https://github.com/carissalow/rapids), such as with:
+
+```commandline
+git fetch --progress "origin" refs/heads/master
+git merge --no-ff origin/master
+```
+
+Next, update the conda and R virtual environment.
+
+```bash
+R -e 'renv::restore(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/focal/latest"))'
+```
+

exploration/debug_heatmap.py

@@ -0,0 +1,323 @@
+# ---
+# jupyter:
+#   jupytext:
+#     formats: ipynb,py:percent
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.13.0
+#   kernelspec:
+#     display_name: straw2analysis
+#     language: python
+#     name: straw2analysis
+# ---
+
+# %%
+import os, sys
+import importlib
+import pandas as pd
+import numpy as np
+
+# import plotly.graph_objects as go
+from importlib import util
+from pathlib import Path
+import yaml
+
+# %%
+phone_data_yield = pd.read_csv(
+    "../rapids/data/interim/p011/phone_yielded_timestamps_with_datetime.csv",
+    parse_dates=["local_date_time"],
+)
+time_segments_labels = pd.read_csv(
+    "../rapids/data/interim/time_segments/p011_time_segments_labels.csv"
+)
+
+# %%
+phone_data_yield["assigned_segments"] = phone_data_yield[
+    "assigned_segments"
+].str.replace(r"_RR\d+SS#", "#")
+time_segments_labels["label"] = time_segments_labels["label"].str.replace(
+    r"_RR\d+SS$", ""
+)
+
+
+# %% tags=[]
+def filter_data_by_segment(data, time_segment):
+    data.dropna(subset=["assigned_segments"], inplace=True)
+    if data.shape[0] == 0:  # data is empty
+        data["local_segment"] = data["timestamps_segment"] = None
+        return data
+
+    datetime_regex = "[0-9]{4}[\-|\/][0-9]{2}[\-|\/][0-9]{2} [0-9]{2}:[0-9]{2}:[0-9]{2}"
+    timestamps_regex = "[0-9]{13}"
+    segment_regex = "\[({}#{},{};{},{})\]".format(
+        time_segment, datetime_regex, datetime_regex, timestamps_regex, timestamps_regex
+    )
+    data["local_segment"] = data["assigned_segments"].str.extract(
+        segment_regex, expand=True
+    )
+    data = data.drop(columns=["assigned_segments"])
+    data = data.dropna(subset=["local_segment"])
+    if (
+        data.shape[0] == 0
+    ):  # there are no rows belonging to time_segment after droping na
+        data["timestamps_segment"] = None
+    else:
+        data[["local_segment", "timestamps_segment"]] = data["local_segment"].str.split(
+            pat=";", n=1, expand=True
+        )
+
+    # chunk episodes
+    if (
+        (not data.empty)
+        and ("start_timestamp" in data.columns)
+        and ("end_timestamp" in data.columns)
+    ):
+        data = chunk_episodes(data)
+
+    return data
+
+
+# %% tags=[]
+time_segment = "daily"
+phone_data_yield_per_segment = filter_data_by_segment(phone_data_yield, time_segment)
+
+# %%
+phone_data_yield.tail()
+
+# %%
+phone_data_yield_per_segment.tail()
+
+
+# %%
+def getDataForPlot(phone_data_yield_per_segment):
+    # calculate the length (in minute) of per segment instance
+    phone_data_yield_per_segment["length"] = (
+        phone_data_yield_per_segment["timestamps_segment"]
+        .str.split(",")
+        .apply(lambda x: int((int(x[1]) - int(x[0])) / (1000 * 60)))
+    )
+    # calculate the number of sensors logged at least one row of data per minute.
+    phone_data_yield_per_segment = (
+        phone_data_yield_per_segment.groupby(
+            ["local_segment", "length", "local_date", "local_hour", "local_minute"]
+        )[["sensor", "local_date_time"]]
+        .max()
+        .reset_index()
+    )
+    # extract local start datetime of the segment from "local_segment" column
+    phone_data_yield_per_segment["local_segment_start_datetimes"] = pd.to_datetime(
+        phone_data_yield_per_segment["local_segment"].apply(
+            lambda x: x.split("#")[1].split(",")[0]
+        )
+    )
+    # calculate the number of minutes after local start datetime of the segment
+    phone_data_yield_per_segment["minutes_after_segment_start"] = (
+        (
+            phone_data_yield_per_segment["local_date_time"]
+            - phone_data_yield_per_segment["local_segment_start_datetimes"]
+        )
+        / pd.Timedelta(minutes=1)
+    ).astype("int")
+
+    # impute missing rows with 0
+    columns_for_full_index = phone_data_yield_per_segment[
+        ["local_segment_start_datetimes", "length"]
+    ].drop_duplicates(keep="first")
+    columns_for_full_index = columns_for_full_index.apply(
+        lambda row: [
+            [row["local_segment_start_datetimes"], x] for x in range(row["length"] + 1)
+        ],
+        axis=1,
+    )
+    full_index = []
+    for columns in columns_for_full_index:
+        full_index = full_index + columns
+    full_index = pd.MultiIndex.from_tuples(
+        full_index,
+        names=("local_segment_start_datetimes", "minutes_after_segment_start"),
+    )
+    phone_data_yield_per_segment = (
+        phone_data_yield_per_segment.set_index(
+            ["local_segment_start_datetimes", "minutes_after_segment_start"]
+        )
+        .reindex(full_index)
+        .reset_index()
+        .fillna(0)
+    )
+
+    # transpose the dataframe per local start datetime of the segment and discard the useless index layer
+    phone_data_yield_per_segment = phone_data_yield_per_segment.groupby(
+        "local_segment_start_datetimes"
+    )[["minutes_after_segment_start", "sensor"]].apply(
+        lambda x: x.set_index("minutes_after_segment_start").transpose()
+    )
+    phone_data_yield_per_segment.index = phone_data_yield_per_segment.index.get_level_values(
+        "local_segment_start_datetimes"
+    )
+    return phone_data_yield_per_segment
+
+
+# %%
+data_for_plot_per_segment = getDataForPlot(phone_data_yield_per_segment)
+
+# %%
+# calculate the length (in minute) of per segment instance
+phone_data_yield_per_segment["length"] = (
+    phone_data_yield_per_segment["timestamps_segment"]
+    .str.split(",")
+    .apply(lambda x: int((int(x[1]) - int(x[0])) / (1000 * 60)))
+)
+
+# %%
+phone_data_yield_per_segment.tail()
+
+# %%
+# calculate the number of sensors logged at least one row of data per minute.
+phone_data_yield_per_segment = (
+    phone_data_yield_per_segment.groupby(
+        ["local_segment", "length", "local_date", "local_hour", "local_minute"]
+    )[["sensor", "local_date_time"]]
+    .max()
+    .reset_index()
+)
+
+# %%
+# extract local start datetime of the segment from "local_segment" column
+phone_data_yield_per_segment["local_segment_start_datetimes"] = pd.to_datetime(
+    phone_data_yield_per_segment["local_segment"].apply(
+        lambda x: x.split("#")[1].split(",")[0]
+    )
+)
+
+# %%
+# calculate the number of minutes after local start datetime of the segment
+phone_data_yield_per_segment["minutes_after_segment_start"] = (
+    (
+        phone_data_yield_per_segment["local_date_time"]
+        - phone_data_yield_per_segment["local_segment_start_datetimes"]
+    )
+    / pd.Timedelta(minutes=1)
+).astype("int")
+
+# %%
+columns_for_full_index = phone_data_yield_per_segment[
+    ["local_segment_start_datetimes", "length"]
+].drop_duplicates(keep="first")
+columns_for_full_index = columns_for_full_index.apply(
+    lambda row: [
+        [row["local_segment_start_datetimes"], x] for x in range(row["length"] + 1)
+    ],
+    axis=1,
+)
+
+# %%
+full_index = []
+for columns in columns_for_full_index:
+    full_index = full_index + columns
+full_index = pd.MultiIndex.from_tuples(
+    full_index, names=("local_segment_start_datetimes", "minutes_after_segment_start")
+)
+
+# %%
+phone_data_yield_per_segment.tail()
+
+# %% [markdown]
+# # A workaround
+
+# %%
+phone_data_yield_per_segment["local_segment_start_datetimes", "minutes_after_segment_start"] = phone_data_yield_per_segment[
+    ["local_segment_start_datetimes", "minutes_after_segment_start"]
+].drop_duplicates(keep="first")
+
+# %%
+phone_data_yield_per_segment.set_index(
+    ["local_segment_start_datetimes", "minutes_after_segment_start"],
+    verify_integrity=True,
+).reindex(full_index)
+
+# %%
+phone_data_yield_per_segment.head()
+
+
+# %% [markdown]
+# # Retry
+
+# %%
+def getDataForPlot(phone_data_yield_per_segment):
+    # calculate the length (in minute) of per segment instance
+    phone_data_yield_per_segment["length"] = (
+        phone_data_yield_per_segment["timestamps_segment"]
+        .str.split(",")
+        .apply(lambda x: int((int(x[1]) - int(x[0])) / (1000 * 60)))
+    )
+    # calculate the number of sensors logged at least one row of data per minute.
+    phone_data_yield_per_segment = (
+        phone_data_yield_per_segment.groupby(
+            ["local_segment", "length", "local_date", "local_hour", "local_minute"]
+        )[["sensor", "local_date_time"]]
+        .max()
+        .reset_index()
+    )
+    # extract local start datetime of the segment from "local_segment" column
+    phone_data_yield_per_segment["local_segment_start_datetimes"] = pd.to_datetime(
+        phone_data_yield_per_segment["local_segment"].apply(
+            lambda x: x.split("#")[1].split(",")[0]
+        )
+    )
+    # calculate the number of minutes after local start datetime of the segment
+    phone_data_yield_per_segment["minutes_after_segment_start"] = (
+        (
+            phone_data_yield_per_segment["local_date_time"]
+            - phone_data_yield_per_segment["local_segment_start_datetimes"]
+        )
+        / pd.Timedelta(minutes=1)
+    ).astype("int")
+
+    # impute missing rows with 0
+    columns_for_full_index = phone_data_yield_per_segment[
+        ["local_segment_start_datetimes", "length"]
+    ].drop_duplicates(keep="first")
+    columns_for_full_index = columns_for_full_index.apply(
+        lambda row: [
+            [row["local_segment_start_datetimes"], x] for x in range(row["length"] + 1)
+        ],
+        axis=1,
+    )
+    full_index = []
+    for columns in columns_for_full_index:
+        full_index = full_index + columns
+    full_index = pd.MultiIndex.from_tuples(
+        full_index,
+        names=("local_segment_start_datetimes", "minutes_after_segment_start"),
+    )
+    phone_data_yield_per_segment = phone_data_yield_per_segment.drop_duplicates(subset=["local_segment_start_datetimes", "minutes_after_segment_start"],keep="first")
+    phone_data_yield_per_segment = (
+        phone_data_yield_per_segment.set_index(
+            ["local_segment_start_datetimes", "minutes_after_segment_start"]
+        )
+        .reindex(full_index)
+        .reset_index()
+        .fillna(0)
+    )
+
+    # transpose the dataframe per local start datetime of the segment and discard the useless index layer
+    phone_data_yield_per_segment = phone_data_yield_per_segment.groupby(
+        "local_segment_start_datetimes"
+    )[["minutes_after_segment_start", "sensor"]].apply(
+        lambda x: x.set_index("minutes_after_segment_start").transpose()
+    )
+    phone_data_yield_per_segment.index = phone_data_yield_per_segment.index.get_level_values(
+        "local_segment_start_datetimes"
+    )
+    return phone_data_yield_per_segment
+
+
+# %%
+phone_data_yield_per_segment = filter_data_by_segment(phone_data_yield, time_segment)
+
+# %%
+data_for_plot_per_segment = getDataForPlot(phone_data_yield_per_segment)
+
+# %%

exploration/expl_app_categories.py

@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: percent
 #       format_version: '1.3'
-#       jupytext_version: 1.11.4
+#       jupytext_version: 1.13.0
 #   kernelspec:
 #     display_name: straw2analysis
 #     language: python
@@ -74,3 +74,29 @@ rows_os_manufacturer = df_category_not_found["package_name"].str.contains(
 # %%
 with pd.option_context("display.max_rows", None, "display.max_columns", None):
     display(df_category_not_found.loc[~rows_os_manufacturer])
+
+# %% [markdown]
+# # Export categories
+
+# %% [markdown]
+# Rename all of "not_found" to "system" or "other".
+
+# %%
+df_app_categories_to_export = df_app_categories.copy()
+rows_os_manufacturer_full = (df_app_categories_to_export["package_name"].str.contains(
+    "|".join(manufacturers + custom_rom + other), case=False
+)) & (df_app_categories_to_export["play_store_genre"] == "not_found")
+df_app_categories_to_export.loc[rows_os_manufacturer_full, "play_store_genre"] = "System"
+
+# %%
+rows_not_found = (df_app_categories_to_export["play_store_genre"] == "not_found")
+df_app_categories_to_export.loc[rows_not_found, "play_store_genre"] = "Other"
+
+# %%
+df_app_categories_to_export["play_store_genre"].value_counts()
+
+# %%
+df_app_categories_to_export.rename(columns={"play_store_genre": "genre"},inplace=True)
+df_app_categories_to_export.to_csv("../data/app_categories.csv", columns=["package_hash","genre"],index=False)
+
+# %%

exploration/expl_esm_labels.py

@@ -7,7 +7,7 @@
 #       extension: .py
 #       format_name: percent
 #       format_version: '1.3'
-#       jupytext_version: 1.11.2
+#       jupytext_version: 1.13.0
 #   kernelspec:
 #     display_name: straw2analysis
 #     language: python
@@ -17,6 +17,7 @@
 # %%
 import os
 import sys
+import datetime
 
 import seaborn as sns
 
@@ -26,6 +27,7 @@ if nb_dir not in sys.path:
 import participants.query_db
 from features.esm import *
 from features.esm_JCQ import *
+from features.esm_SAM import *
 
 # %%
 participants_inactive_usernames = participants.query_db.get_usernames(
@@ -99,6 +101,12 @@ df_esm_PANAS_summary_participant[df_esm_PANAS_summary_participant["std"] < 0.1]
 # %% [markdown]
 # # Stress appraisal measure
 
+# %%
+df_SAM_all = extract_stressful_events(df_esm_inactive)
+
+# %%
+df_SAM_all.head()
+
 # %%
 df_esm_SAM = df_esm_preprocessed[
     (df_esm_preprocessed["questionnaire_id"] >= 87)

exploration/ml_pipeline_classification.py

@@ -0,0 +1,385 @@
+# ---
+# jupyter:
+#   jupytext:
+#     formats: ipynb,py:percent
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.13.0
+#   kernelspec:
+#     display_name: straw2analysis
+#     language: python
+#     name: straw2analysis
+# ---
+
+# %% jupyter={"source_hidden": true}
+# %matplotlib inline
+import datetime
+import importlib
+import os
+import sys
+
+import numpy as np
+import matplotlib.pyplot as plt
+import pandas as pd
+import seaborn as sns
+
+from sklearn import linear_model, svm, naive_bayes, neighbors, tree, ensemble 
+from sklearn.model_selection import LeaveOneGroupOut, cross_validate
+from sklearn.dummy import DummyClassifier
+from sklearn.impute import SimpleImputer
+
+from lightgbm import LGBMClassifier
+import xgboost as xg
+from IPython.core.interactiveshell import InteractiveShell
+InteractiveShell.ast_node_interactivity = "all"
+
+nb_dir = os.path.split(os.getcwd())[0]
+if nb_dir not in sys.path:
+    sys.path.append(nb_dir)
+
+import machine_learning.labels
+import machine_learning.model
+
+# %% [markdown]
+# # RAPIDS models
+
+# %% [markdown]
+# ## Set script's parameters
+cv_method_str = 'logo' # logo, halflogo, 5kfold # Cross-validation method (could be regarded as a hyperparameter)
+n_sl = 1 # Number of largest/smallest accuracies (of particular CV) outputs
+
+# %% jupyter={"source_hidden": true}
+model_input = pd.read_csv("../data/stressfulness_event_nonstandardized/input_appraisal_stressfulness_event_mean.csv")
+
+# %% jupyter={"source_hidden": true}
+index_columns = ["local_segment", "local_segment_label", "local_segment_start_datetime", "local_segment_end_datetime"]
+model_input.set_index(index_columns, inplace=True)
+model_input['target'].value_counts()
+
+# %% jupyter={"source_hidden": true}
+# bins = [-10, -1, 1, 10] # bins for z-scored targets
+bins = [0, 1, 4] # bins for stressfulness (1-4) target
+model_input['target'], edges = pd.cut(model_input.target, bins=bins, labels=['low', 'high'], retbins=True, right=True) #['low', 'medium', 'high']
+model_input['target'].value_counts(), edges
+# model_input = model_input[model_input['target'] != "medium"]
+model_input['target'] = model_input['target'].astype(str).apply(lambda x: 0 if x == "low" else 1)
+
+model_input['target'].value_counts()
+
+if cv_method_str == 'halflogo':
+    model_input['pid_index'] = model_input.groupby('pid').cumcount()
+    model_input['pid_count'] = model_input.groupby('pid')['pid'].transform('count')
+
+    model_input["pid_index"] = (model_input['pid_index'] / model_input['pid_count'] + 1).round()
+    model_input["pid_half"] = model_input["pid"] + "_" +  model_input["pid_index"].astype(int).astype(str)
+
+    data_x, data_y, data_groups = model_input.drop(["target", "pid", "pid_index", "pid_half"], axis=1), model_input["target"], model_input["pid_half"]
+else:
+    data_x, data_y, data_groups = model_input.drop(["target", "pid"], axis=1), model_input["target"], model_input["pid"]
+
+
+# %% jupyter={"source_hidden": true}
+categorical_feature_colnames = ["gender", "startlanguage"]
+additional_categorical_features = [col for col in data_x.columns if "mostcommonactivity" in col or "homelabel" in col]
+categorical_feature_colnames += additional_categorical_features
+
+categorical_features = data_x[categorical_feature_colnames].copy()
+mode_categorical_features = categorical_features.mode().iloc[0]
+
+# fillna with mode
+categorical_features = categorical_features.fillna(mode_categorical_features)
+
+# one-hot encoding
+categorical_features = categorical_features.apply(lambda col: col.astype("category"))
+if not categorical_features.empty:
+    categorical_features = pd.get_dummies(categorical_features)
+
+numerical_features = data_x.drop(categorical_feature_colnames, axis=1)
+train_x = pd.concat([numerical_features, categorical_features], axis=1)
+train_x.dtypes
+
+# %% jupyter={"source_hidden": true}
+cv_method = None # Defaults to 5 k-folds in cross_validate method
+if cv_method_str == 'logo' or cv_method_str == 'half_logo':
+    cv_method = LeaveOneGroupOut()
+    cv_method.get_n_splits(
+        train_x,
+        data_y,
+        groups=data_groups,
+    )
+
+# %% jupyter={"source_hidden": true}
+imputer = SimpleImputer(missing_values=np.nan, strategy='median')
+
+# %% [markdown]
+# ### Baseline: Dummy Classifier (most frequent)
+dummy_class = DummyClassifier(strategy="most_frequent")
+
+# %% jupyter={"source_hidden": true}
+dummy_classifier = cross_validate(
+    dummy_class,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=cv_method,
+    n_jobs=-1,
+    error_score='raise',
+    scoring=('accuracy', 'average_precision', 'recall', 'f1')
+)
+# %% jupyter={"source_hidden": true}
+print("Acc", np.mean(dummy_classifier['test_accuracy']))
+print("Precision", np.mean(dummy_classifier['test_average_precision']))
+print("Recall", np.mean(dummy_classifier['test_recall']))
+print("F1", np.mean(dummy_classifier['test_f1']))
+print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-dummy_classifier['test_accuracy'], n_sl)[:n_sl])[::-1])
+print(f"Smallest {n_sl} ACC:", np.sort(np.partition(dummy_classifier['test_accuracy'], n_sl)[:n_sl]))
+
+# %% [markdown]
+# ### Logistic Regression
+
+# %% jupyter={"source_hidden": true}
+logistic_regression = linear_model.LogisticRegression()
+
+# %% jupyter={"source_hidden": true}
+log_reg_scores = cross_validate(
+    logistic_regression,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=cv_method,
+    n_jobs=-1,
+    scoring=('accuracy', 'precision', 'recall', 'f1')
+)
+# %% jupyter={"source_hidden": true}
+print("Acc", np.mean(log_reg_scores['test_accuracy']))
+print("Precision", np.mean(log_reg_scores['test_precision']))
+print("Recall", np.mean(log_reg_scores['test_recall']))
+print("F1", np.mean(log_reg_scores['test_f1']))
+print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-log_reg_scores['test_accuracy'], n_sl)[:n_sl])[::-1])
+print(f"Smallest {n_sl} ACC:", np.sort(np.partition(log_reg_scores['test_accuracy'], n_sl)[:n_sl]))
+
+# %% [markdown]
+# ### Support Vector Machine
+
+# %% jupyter={"source_hidden": true}
+svc = svm.SVC()
+
+# %% jupyter={"source_hidden": true}
+svc_scores = cross_validate(
+    svc,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=cv_method,
+    n_jobs=-1,
+    scoring=('accuracy', 'precision', 'recall', 'f1')
+)
+# %% jupyter={"source_hidden": true}
+print("Acc", np.mean(svc_scores['test_accuracy']))
+print("Precision", np.mean(svc_scores['test_precision']))
+print("Recall", np.mean(svc_scores['test_recall']))
+print("F1", np.mean(svc_scores['test_f1']))
+print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-svc_scores['test_accuracy'], n_sl)[:n_sl])[::-1])
+print(f"Smallest {n_sl} ACC:", np.sort(np.partition(svc_scores['test_accuracy'], n_sl)[:n_sl]))
+
+# %% [markdown]
+# ### Gaussian Naive Bayes
+
+# %% jupyter={"source_hidden": true}
+gaussian_nb = naive_bayes.GaussianNB()
+
+# %% jupyter={"source_hidden": true}
+gaussian_nb_scores = cross_validate(
+    gaussian_nb,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=cv_method,
+    n_jobs=-1,
+    error_score='raise',
+    scoring=('accuracy', 'precision', 'recall', 'f1')
+)
+# %% jupyter={"source_hidden": true}
+print("Acc", np.mean(gaussian_nb_scores['test_accuracy']))
+print("Precision", np.mean(gaussian_nb_scores['test_precision']))
+print("Recall", np.mean(gaussian_nb_scores['test_recall']))
+print("F1", np.mean(gaussian_nb_scores['test_f1']))
+print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-gaussian_nb_scores['test_accuracy'], n_sl)[:n_sl])[::-1])
+print(f"Smallest {n_sl} ACC:", np.sort(np.partition(gaussian_nb_scores['test_accuracy'], n_sl)[:n_sl]))
+
+# %% [markdown]
+# ### Stochastic Gradient Descent Classifier
+
+# %% jupyter={"source_hidden": true}
+sgdc = linear_model.SGDClassifier()
+
+# %% jupyter={"source_hidden": true}
+sgdc_scores = cross_validate(
+    sgdc,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=cv_method,
+    n_jobs=-1,
+    error_score='raise',
+    scoring=('accuracy', 'precision', 'recall', 'f1')
+)
+# %% jupyter={"source_hidden": true}
+print("Acc", np.mean(sgdc_scores['test_accuracy']))
+print("Precision", np.mean(sgdc_scores['test_precision']))
+print("Recall", np.mean(sgdc_scores['test_recall']))
+print("F1", np.mean(sgdc_scores['test_f1']))
+print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-sgdc_scores['test_accuracy'], n_sl)[:n_sl])[::-1])
+print(f"Smallest {n_sl} ACC:", np.sort(np.partition(sgdc_scores['test_accuracy'], n_sl)[:n_sl]))
+
+# %% [markdown]
+# ### K-nearest neighbors
+
+# %% jupyter={"source_hidden": true}
+knn = neighbors.KNeighborsClassifier()
+
+# %% jupyter={"source_hidden": true}
+knn_scores = cross_validate(
+    knn,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=cv_method,
+    n_jobs=-1,
+    error_score='raise',
+    scoring=('accuracy', 'precision', 'recall', 'f1')
+)
+# %% jupyter={"source_hidden": true}
+print("Acc", np.mean(knn_scores['test_accuracy']))
+print("Precision", np.mean(knn_scores['test_precision']))
+print("Recall", np.mean(knn_scores['test_recall']))
+print("F1", np.mean(knn_scores['test_f1']))
+print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-knn_scores['test_accuracy'], n_sl)[:n_sl])[::-1])
+print(f"Smallest {n_sl} ACC:", np.sort(np.partition(knn_scores['test_accuracy'], n_sl)[:n_sl]))
+
+# %% [markdown]
+# ### Decision Tree
+
+# %% jupyter={"source_hidden": true}
+dtree = tree.DecisionTreeClassifier()
+
+# %% jupyter={"source_hidden": true}
+dtree_scores = cross_validate(
+    dtree,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=cv_method,
+    n_jobs=-1,
+    error_score='raise',
+    scoring=('accuracy', 'precision', 'recall', 'f1')
+)
+# %% jupyter={"source_hidden": true}
+print("Acc", np.mean(dtree_scores['test_accuracy']))
+print("Precision", np.mean(dtree_scores['test_precision']))
+print("Recall", np.mean(dtree_scores['test_recall']))
+print("F1", np.mean(dtree_scores['test_f1']))
+print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-dtree_scores['test_accuracy'], n_sl)[:n_sl])[::-1])
+print(f"Smallest {n_sl} ACC:", np.sort(np.partition(dtree_scores['test_accuracy'], n_sl)[:n_sl]))
+
+# %% [markdown]
+# ### Random Forest Classifier
+
+# %% jupyter={"source_hidden": true}
+rfc = ensemble.RandomForestClassifier()
+
+# %% jupyter={"source_hidden": true}
+rfc_scores = cross_validate(
+    rfc,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=cv_method,
+    n_jobs=-1,
+    error_score='raise',
+    scoring=('accuracy', 'precision', 'recall', 'f1')
+)
+# %% jupyter={"source_hidden": true}
+print("Acc", np.mean(rfc_scores['test_accuracy']))
+print("Precision", np.mean(rfc_scores['test_precision']))
+print("Recall", np.mean(rfc_scores['test_recall']))
+print("F1", np.mean(rfc_scores['test_f1']))
+print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-rfc_scores['test_accuracy'], n_sl)[:n_sl])[::-1])
+print(f"Smallest {n_sl} ACC:", np.sort(np.partition(rfc_scores['test_accuracy'], n_sl)[:n_sl]))
+
+# %% [markdown]
+# ### Gradient Boosting Classifier
+
+# %% jupyter={"source_hidden": true}
+gbc = ensemble.GradientBoostingClassifier()
+
+# %% jupyter={"source_hidden": true}
+gbc_scores = cross_validate(
+    gbc,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=cv_method,
+    n_jobs=-1,
+    error_score='raise',
+    scoring=('accuracy', 'precision', 'recall', 'f1')
+)
+# %% jupyter={"source_hidden": true}
+print("Acc", np.mean(gbc_scores['test_accuracy']))
+print("Precision", np.mean(gbc_scores['test_precision']))
+print("Recall", np.mean(gbc_scores['test_recall']))
+print("F1", np.mean(gbc_scores['test_f1']))
+print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-gbc_scores['test_accuracy'], n_sl)[:n_sl])[::-1])
+print(f"Smallest {n_sl} ACC:", np.sort(np.partition(gbc_scores['test_accuracy'], n_sl)[:n_sl]))
+
+# %% [markdown]
+# ### LGBM Classifier
+
+# %% jupyter={"source_hidden": true}
+lgbm = LGBMClassifier()
+
+# %% jupyter={"source_hidden": true}
+lgbm_scores = cross_validate(
+    lgbm,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=cv_method,
+    n_jobs=-1,
+    error_score='raise',
+    scoring=('accuracy', 'precision', 'recall', 'f1')
+)
+# %% jupyter={"source_hidden": true}
+print("Acc", np.mean(lgbm_scores['test_accuracy']))
+print("Precision", np.mean(lgbm_scores['test_precision']))
+print("Recall", np.mean(lgbm_scores['test_recall']))
+print("F1", np.mean(lgbm_scores['test_f1']))
+print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-lgbm_scores['test_accuracy'], n_sl)[:n_sl])[::-1])
+print(f"Smallest {n_sl} ACC:", np.sort(np.partition(lgbm_scores['test_accuracy'], n_sl)[:n_sl]))
+
+# %% [markdown]
+# ### XGBoost Classifier
+
+# %% jupyter={"source_hidden": true}
+xgb_classifier = xg.sklearn.XGBClassifier()
+
+# %% jupyter={"source_hidden": true}
+xgb_classifier_scores = cross_validate(
+    xgb_classifier,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=cv_method,
+    n_jobs=-1,
+    error_score='raise',
+    scoring=('accuracy', 'precision', 'recall', 'f1')
+)
+# %% jupyter={"source_hidden": true}
+print("Acc", np.mean(xgb_classifier_scores['test_accuracy']))
+print("Precision", np.mean(xgb_classifier_scores['test_precision']))
+print("Recall", np.mean(xgb_classifier_scores['test_recall']))
+print("F1", np.mean(xgb_classifier_scores['test_f1']))
+print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-xgb_classifier_scores['test_accuracy'], n_sl)[:n_sl])[::-1])
+print(f"Smallest {n_sl} ACC:", np.sort(np.partition(xgb_classifier_scores['test_accuracy'], n_sl)[:n_sl]))

exploration/ml_pipeline_classification_with_clustering.py

@@ -0,0 +1,184 @@
+# ---
+# jupyter:
+#   jupytext:
+#     formats: ipynb,py:percent
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.13.0
+#   kernelspec:
+#     display_name: straw2analysis
+#     language: python
+#     name: straw2analysis
+# ---
+
+# %% jupyter={"source_hidden": true}
+# %matplotlib inline
+import datetime
+import importlib
+import os
+import sys
+
+import numpy as np
+import matplotlib.pyplot as plt
+import pandas as pd
+import seaborn as sns
+from scipy import stats
+
+from sklearn.model_selection import LeaveOneGroupOut, cross_validate
+from sklearn.impute import SimpleImputer
+
+from sklearn.dummy import DummyClassifier
+from sklearn import linear_model, svm, naive_bayes, neighbors, tree, ensemble
+from lightgbm import LGBMClassifier
+import xgboost as xg 
+
+from sklearn.cluster import KMeans
+
+from IPython.core.interactiveshell import InteractiveShell
+InteractiveShell.ast_node_interactivity = "all"
+
+nb_dir = os.path.split(os.getcwd())[0]
+if nb_dir not in sys.path:
+    sys.path.append(nb_dir)
+
+import machine_learning.labels
+import machine_learning.model
+from machine_learning.classification_models import ClassificationModels
+
+# %% [markdown]
+# # RAPIDS models
+
+# %% [markdown]
+# ## Set script's parameters
+n_clusters = 5 # Number of clusters (could be regarded as a hyperparameter)
+cv_method_str = 'logo' # logo, halflogo, 5kfold # Cross-validation method (could be regarded as a hyperparameter)
+n_sl = 1 # Number of largest/smallest accuracies (of particular CV) outputs
+
+# %% jupyter={"source_hidden": true}
+model_input = pd.read_csv("../data/intradaily_30_min_all_targets/input_JCQ_job_demand_mean.csv")
+index_columns = ["local_segment", "local_segment_label", "local_segment_start_datetime", "local_segment_end_datetime"]
+
+clust_col = model_input.set_index(index_columns).var().idxmax() # age is a col with the highest variance
+
+model_input.columns[list(model_input.columns).index('age'):-1]
+
+lime_cols = [col for col in model_input if col.startswith('limesurvey')]
+lime_cols
+lime_col = 'limesurvey_demand_control_ratio'
+clust_col = lime_col
+
+model_input[clust_col].describe()
+
+
+# %% jupyter={"source_hidden": true}
+
+# Filter-out outlier rows by clust_col 
+model_input = model_input[(np.abs(stats.zscore(model_input[clust_col])) < 3)]
+
+uniq = model_input[[clust_col, 'pid']].drop_duplicates().reset_index(drop=True)
+plt.bar(uniq['pid'], uniq[clust_col])
+
+# %% jupyter={"source_hidden": true}
+# Get clusters by cluster col & and merge the clusters to main df
+km = KMeans(n_clusters=n_clusters).fit_predict(uniq.set_index('pid'))
+np.unique(km, return_counts=True)
+uniq['cluster'] = km
+uniq
+
+model_input = model_input.merge(uniq[['pid', 'cluster']])   
+
+# %% jupyter={"source_hidden": true}
+model_input.set_index(index_columns, inplace=True)
+
+# %% jupyter={"source_hidden": true}
+# Create dict with classification ml models
+cm = ClassificationModels()
+cmodels = cm.get_cmodels()
+
+# %% jupyter={"source_hidden": true}
+for k in range(n_clusters):
+    model_input_subset = model_input[model_input["cluster"] == k].copy()
+    bins = [-10, -1, 1, 10] # bins for z-scored targets
+    model_input_subset.loc[:, 'target'] = \
+        pd.cut(model_input_subset.loc[:, 'target'], bins=bins, labels=['low', 'medium', 'high'], right=False) #['low', 'medium', 'high']
+    model_input_subset['target'].value_counts()
+    model_input_subset = model_input_subset[model_input_subset['target'] != "medium"]
+    model_input_subset['target'] = model_input_subset['target'].astype(str).apply(lambda x: 0 if x == "low" else 1)
+
+    model_input_subset['target'].value_counts()
+    
+    if cv_method_str == 'halflogo':
+        model_input_subset['pid_index'] = model_input_subset.groupby('pid').cumcount()
+        model_input_subset['pid_count'] = model_input_subset.groupby('pid')['pid'].transform('count')
+
+        model_input_subset["pid_index"] = (model_input_subset['pid_index'] / model_input_subset['pid_count'] + 1).round()
+        model_input_subset["pid_half"] = model_input_subset["pid"] + "_" +  model_input_subset["pid_index"].astype(int).astype(str)
+
+        data_x, data_y, data_groups = model_input_subset.drop(["target", "pid", "pid_index", "pid_half"], axis=1), model_input_subset["target"], model_input_subset["pid_half"]
+    else:
+        data_x, data_y, data_groups = model_input_subset.drop(["target", "pid"], axis=1), model_input_subset["target"], model_input_subset["pid"]
+
+    # Treat categorical features
+    categorical_feature_colnames = ["gender", "startlanguage"]
+    additional_categorical_features = [col for col in data_x.columns if "mostcommonactivity" in col or "homelabel" in col]
+    categorical_feature_colnames += additional_categorical_features
+
+    categorical_features = data_x[categorical_feature_colnames].copy()
+    mode_categorical_features = categorical_features.mode().iloc[0]
+
+    # fillna with mode
+    categorical_features = categorical_features.fillna(mode_categorical_features)
+
+    # one-hot encoding
+    categorical_features = categorical_features.apply(lambda col: col.astype("category"))
+    if not categorical_features.empty:
+        categorical_features = pd.get_dummies(categorical_features)
+
+    numerical_features = data_x.drop(categorical_feature_colnames, axis=1)
+    train_x = pd.concat([numerical_features, categorical_features], axis=1)
+
+    # Establish cv method
+    cv_method = None # Defaults to 5 k-folds in cross_validate method
+    if cv_method_str == 'logo' or cv_method_str == 'half_logo':
+        cv_method = LeaveOneGroupOut()
+        cv_method.get_n_splits(
+            train_x,
+            data_y,
+            groups=data_groups,
+        )
+
+    imputer = SimpleImputer(missing_values=np.nan, strategy='median')
+
+    for model_title, model in cmodels.items():
+
+        classifier = cross_validate(
+            model['model'],
+            X=imputer.fit_transform(train_x),
+            y=data_y,
+            groups=data_groups,
+            cv=cv_method,
+            n_jobs=-1,
+            error_score='raise',
+            scoring=('accuracy', 'precision', 'recall', 'f1')
+        )
+        
+        print("\n-------------------------------------\n")
+        print("Current cluster:", k, end="\n")
+        print("Current model:", model_title, end="\n")
+        print("Acc", np.mean(classifier['test_accuracy']))
+        print("Precision", np.mean(classifier['test_precision']))
+        print("Recall", np.mean(classifier['test_recall']))
+        print("F1", np.mean(classifier['test_f1']))
+        print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-classifier['test_accuracy'], n_sl)[:n_sl])[::-1])
+        print(f"Smallest {n_sl} ACC:", np.sort(np.partition(classifier['test_accuracy'], n_sl)[:n_sl]))
+        
+        cmodels[model_title]['metrics'][0] += np.mean(classifier['test_accuracy'])
+        cmodels[model_title]['metrics'][1] += np.mean(classifier['test_precision'])
+        cmodels[model_title]['metrics'][2] += np.mean(classifier['test_recall'])
+        cmodels[model_title]['metrics'][3] += np.mean(classifier['test_f1'])
+
+# %% jupyter={"source_hidden": true}
+# Get overall results
+cm.get_total_models_scores(n_clusters=n_clusters)

exploration/ml_pipeline_classification_with_clustering_2_class.py

@@ -0,0 +1,181 @@
+# ---
+# jupyter:
+#   jupytext:
+#     formats: ipynb,py:percent
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.13.0
+#   kernelspec:
+#     display_name: straw2analysis
+#     language: python
+#     name: straw2analysis
+# ---
+
+# %% jupyter={"source_hidden": true}
+# %matplotlib inline
+import datetime
+import importlib
+import os
+import sys
+
+import numpy as np
+import matplotlib.pyplot as plt
+import pandas as pd
+import seaborn as sns
+from scipy import stats
+
+from sklearn.model_selection import LeaveOneGroupOut, cross_validate, train_test_split
+from sklearn.impute import SimpleImputer
+from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score
+
+from sklearn.dummy import DummyClassifier
+from sklearn import linear_model, svm, naive_bayes, neighbors, tree, ensemble
+from lightgbm import LGBMClassifier
+import xgboost as xg 
+
+from sklearn.cluster import KMeans
+
+from IPython.core.interactiveshell import InteractiveShell
+InteractiveShell.ast_node_interactivity = "all"
+
+nb_dir = os.path.split(os.getcwd())[0]
+if nb_dir not in sys.path:
+    sys.path.append(nb_dir)
+
+import machine_learning.labels
+import machine_learning.model
+from machine_learning.classification_models import ClassificationModels
+
+# %% [markdown]
+# # RAPIDS models
+
+# %% [markdown]
+# # Useful method
+def treat_categorical_features(input_set):
+    categorical_feature_colnames = ["gender", "startlanguage"]
+    additional_categorical_features = [col for col in input_set.columns if "mostcommonactivity" in col or "homelabel" in col]
+    categorical_feature_colnames += additional_categorical_features
+        
+    categorical_features = input_set[categorical_feature_colnames].copy()
+    mode_categorical_features = categorical_features.mode().iloc[0]
+
+    # fillna with mode
+    categorical_features = categorical_features.fillna(mode_categorical_features)
+
+    # one-hot encoding
+    categorical_features = categorical_features.apply(lambda col: col.astype("category"))
+    if not categorical_features.empty:
+        categorical_features = pd.get_dummies(categorical_features)
+
+    numerical_features = input_set.drop(categorical_feature_colnames, axis=1)
+    
+    return pd.concat([numerical_features, categorical_features], axis=1)
+
+# %% [markdown]
+# ## Set script's parameters
+n_clusters = 3 # Number of clusters (could be regarded as a hyperparameter)
+n_sl = 3 # Number of largest/smallest accuracies (of particular CV) outputs
+
+# %% jupyter={"source_hidden": true}
+model_input = pd.read_csv("../data/intradaily_30_min_all_targets/input_JCQ_job_demand_mean.csv")
+index_columns = ["local_segment", "local_segment_label", "local_segment_start_datetime", "local_segment_end_datetime"]
+
+clust_col = model_input.set_index(index_columns).var().idxmax() # age is a col with the highest variance
+
+model_input.columns[list(model_input.columns).index('age'):-1]
+
+lime_cols = [col for col in model_input if col.startswith('limesurvey')]
+lime_cols
+lime_col = 'limesurvey_demand_control_ratio'
+clust_col = lime_col
+
+model_input[clust_col].describe()
+
+
+# %% jupyter={"source_hidden": true}
+
+# Filter-out outlier rows by clust_col 
+model_input = model_input[(np.abs(stats.zscore(model_input[clust_col])) < 3)]
+
+uniq = model_input[[clust_col, 'pid']].drop_duplicates().reset_index(drop=True)
+plt.bar(uniq['pid'], uniq[clust_col])
+
+# %% jupyter={"source_hidden": true}
+# Get clusters by cluster col & and merge the clusters to main df
+km = KMeans(n_clusters=n_clusters).fit_predict(uniq.set_index('pid'))
+np.unique(km, return_counts=True)
+uniq['cluster'] = km
+uniq
+
+model_input = model_input.merge(uniq[['pid', 'cluster']])   
+
+# %% jupyter={"source_hidden": true}
+model_input.set_index(index_columns, inplace=True)
+
+# %% jupyter={"source_hidden": true}
+# Create dict with classification ml models
+cm = ClassificationModels()
+cmodels = cm.get_cmodels()
+
+# %% jupyter={"source_hidden": true}
+for k in range(n_clusters):
+    model_input_subset = model_input[model_input["cluster"] == k].copy()
+    
+    # Takes 10th percentile and above 90th percentile as the test set -> the rest for the training set. Only two classes, seperated by z-score of 0.
+    model_input_subset['numerical_target'] = model_input_subset['target']
+    bins = [-10, 0, 10] # bins for z-scored targets
+    model_input_subset.loc[:, 'target'] = \
+        pd.cut(model_input_subset.loc[:, 'target'], bins=bins, labels=[0, 1], right=True)
+        
+    p15 = np.percentile(model_input_subset['numerical_target'], 15)
+    p85 = np.percentile(model_input_subset['numerical_target'], 85)
+    
+    # Treat categorical features
+    model_input_subset = treat_categorical_features(model_input_subset)
+    
+    # Split to train, validate, and test subsets
+    train_set = model_input_subset[(model_input_subset['numerical_target'] > p15) & (model_input_subset['numerical_target'] < p85)].drop(['numerical_target'], axis=1)
+    test_set = model_input_subset[(model_input_subset['numerical_target'] <= p15) | (model_input_subset['numerical_target'] >= p85)].drop(['numerical_target'], axis=1)
+
+    train_set['target'].value_counts()
+    test_set['target'].value_counts()
+    
+    train_x, train_y = train_set.drop(["target", "pid"], axis=1), train_set["target"]
+    
+    validate_x, test_x, validate_y, test_y = \
+        train_test_split(test_set.drop(["target", "pid"], axis=1), test_set["target"], test_size=0.50, random_state=42)
+    
+    # Impute missing values
+    imputer = SimpleImputer(missing_values=np.nan, strategy='median')
+
+    train_x = imputer.fit_transform(train_x)
+    validate_x = imputer.fit_transform(validate_x)
+    test_x = imputer.fit_transform(test_x)
+
+    for model_title, model in cmodels.items():
+        model['model'].fit(train_x, train_y)
+        y_pred = model['model'].predict(validate_x)
+        
+        acc = accuracy_score(validate_y, y_pred)
+        prec = precision_score(validate_y, y_pred)
+        rec = recall_score(validate_y, y_pred)
+        f1 = f1_score(validate_y, y_pred)
+        
+        print("\n-------------------------------------\n")
+        print("Current cluster:", k, end="\n")
+        print("Current model:", model_title, end="\n")
+        print("Acc", acc)
+        print("Precision", prec)
+        print("Recall", rec)
+        print("F1", f1)
+        
+        cmodels[model_title]['metrics'][0] += acc
+        cmodels[model_title]['metrics'][1] += prec
+        cmodels[model_title]['metrics'][2] += rec
+        cmodels[model_title]['metrics'][3] += f1
+
+# %% jupyter={"source_hidden": true}
+# Get overall results
+cm.get_total_models_scores(n_clusters=n_clusters)

exploration/ml_pipeline_regression.py

@@ -0,0 +1,355 @@
+# ---
+# jupyter:
+#   jupytext:
+#     formats: ipynb,py:percent
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.13.0
+#   kernelspec:
+#     display_name: straw2analysis
+#     language: python
+#     name: straw2analysis
+# ---
+
+# %% jupyter={"source_hidden": true}
+# %matplotlib inline
+import datetime
+import importlib
+import os
+import sys
+
+import numpy as np
+import matplotlib.pyplot as plt
+import pandas as pd
+import seaborn as sns
+import yaml
+from pyprojroot import here
+from sklearn import linear_model, svm, kernel_ridge, gaussian_process
+from sklearn.model_selection import LeaveOneGroupOut, cross_val_score, cross_validate
+from sklearn.metrics import mean_squared_error, r2_score
+from sklearn.impute import SimpleImputer
+from sklearn.dummy import DummyRegressor
+import xgboost as xg
+from IPython.core.interactiveshell import InteractiveShell
+InteractiveShell.ast_node_interactivity = "all"
+
+nb_dir = os.path.split(os.getcwd())[0]
+if nb_dir not in sys.path:
+    sys.path.append(nb_dir)
+
+import machine_learning.features_sensor
+import machine_learning.labels
+import machine_learning.model
+
+# %% [markdown]
+# # RAPIDS models
+
+# %% [markdown]
+# ## PANAS negative affect
+
+# %% jupyter={"source_hidden": true}
+model_input = pd.read_csv("../data/intradaily_30_min_all_targets/input_JCQ_job_demand_mean.csv")
+
+# %% jupyter={"source_hidden": true}
+index_columns = ["local_segment", "local_segment_label", "local_segment_start_datetime", "local_segment_end_datetime"]
+#if "pid" in model_input.columns:
+#    index_columns.append("pid")
+model_input.set_index(index_columns, inplace=True)
+
+cv_method = 'half_logo' # logo, half_logo, 5kfold
+if cv_method == 'logo':
+    data_x, data_y, data_groups = model_input.drop(["target", "pid"], axis=1), model_input["target"], model_input["pid"]
+else:
+    model_input['pid_index'] = model_input.groupby('pid').cumcount()
+    model_input['pid_count'] = model_input.groupby('pid')['pid'].transform('count')
+
+    model_input["pid_index"] = (model_input['pid_index'] / model_input['pid_count'] + 1).round()
+    model_input["pid_half"] = model_input["pid"] + "_" +  model_input["pid_index"].astype(int).astype(str)
+
+    data_x, data_y, data_groups = model_input.drop(["target", "pid", "pid_index", "pid_half"], axis=1), model_input["target"], model_input["pid_half"]
+
+# %% jupyter={"source_hidden": true}
+categorical_feature_colnames = ["gender", "startlanguage"]
+additional_categorical_features = [col for col in data_x.columns if "mostcommonactivity" in col or "homelabel" in col]
+categorical_feature_colnames += additional_categorical_features
+
+# %% jupyter={"source_hidden": true}
+categorical_features = data_x[categorical_feature_colnames].copy()
+
+# %% jupyter={"source_hidden": true}
+mode_categorical_features = categorical_features.mode().iloc[0]
+
+# %% jupyter={"source_hidden": true}
+# fillna with mode
+categorical_features = categorical_features.fillna(mode_categorical_features)
+
+# %% jupyter={"source_hidden": true}
+# one-hot encoding
+categorical_features = categorical_features.apply(lambda col: col.astype("category"))
+if not categorical_features.empty:
+    categorical_features = pd.get_dummies(categorical_features)
+
+# %% jupyter={"source_hidden": true}
+numerical_features = data_x.drop(categorical_feature_colnames, axis=1)
+
+# %% jupyter={"source_hidden": true}
+train_x = pd.concat([numerical_features, categorical_features], axis=1)
+
+# %% jupyter={"source_hidden": true}
+train_x.dtypes
+
+# %% jupyter={"source_hidden": true}
+logo = LeaveOneGroupOut()
+logo.get_n_splits(
+    train_x,
+    data_y,
+    groups=data_groups,
+)
+
+# Defaults to 5 k folds in cross_validate method
+if cv_method != 'logo' and cv_method != 'half_logo':
+    logo = None
+
+# %% jupyter={"source_hidden": true}
+sum(data_y.isna())
+
+# %% [markdown]
+# ### Baseline: Dummy Regression (mean)
+dummy_regr = DummyRegressor(strategy="mean")
+
+# %% jupyter={"source_hidden": true}
+imputer = SimpleImputer(missing_values=np.nan, strategy='mean')
+
+# %% jupyter={"source_hidden": true}
+dummy_regressor = cross_validate(
+    dummy_regr,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.median(dummy_regressor['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.median(dummy_regressor['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.median(dummy_regressor['test_neg_root_mean_squared_error']))
+print("R2", np.median(dummy_regressor['test_r2']))
+
+# %% [markdown]
+# ### Linear Regression
+
+# %% jupyter={"source_hidden": true}
+lin_reg_rapids = linear_model.LinearRegression()
+# %% jupyter={"source_hidden": true}
+imputer = SimpleImputer(missing_values=np.nan, strategy='mean')
+
+# %% jupyter={"source_hidden": true}
+lin_reg_scores = cross_validate(
+    lin_reg_rapids,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.median(lin_reg_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.median(lin_reg_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.median(lin_reg_scores['test_neg_root_mean_squared_error']))
+print("R2", np.median(lin_reg_scores['test_r2']))
+
+# %% [markdown]
+# ### XGBRegressor Linear Regression
+# %% jupyter={"source_hidden": true}
+xgb_r = xg.XGBRegressor(objective ='reg:squarederror', n_estimators = 10)
+# %% jupyter={"source_hidden": true}
+imputer = SimpleImputer(missing_values=np.nan, strategy='mean')
+
+# %% jupyter={"source_hidden": true}
+xgb_reg_scores = cross_validate(
+    xgb_r,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.median(xgb_reg_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.median(xgb_reg_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.median(xgb_reg_scores['test_neg_root_mean_squared_error']))
+print("R2", np.median(xgb_reg_scores['test_r2']))
+
+# %% [markdown]
+# ### XGBRegressor Pseudo Huber Error Regression
+# %% jupyter={"source_hidden": true}
+xgb_psuedo_huber_r = xg.XGBRegressor(objective ='reg:pseudohubererror', n_estimators = 10)
+# %% jupyter={"source_hidden": true}
+imputer = SimpleImputer(missing_values=np.nan, strategy='mean')
+
+# %% jupyter={"source_hidden": true}
+xgb_psuedo_huber_reg_scores = cross_validate(
+    xgb_psuedo_huber_r,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.median(xgb_psuedo_huber_reg_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.median(xgb_psuedo_huber_reg_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.median(xgb_psuedo_huber_reg_scores['test_neg_root_mean_squared_error']))
+print("R2", np.median(xgb_psuedo_huber_reg_scores['test_r2']))
+
+# %% [markdown]
+# ### Ridge regression
+
+# %% jupyter={"source_hidden": true}
+ridge_reg = linear_model.Ridge(alpha=.5)
+
+# %% tags=[] jupyter={"source_hidden": true}
+ridge_reg_scores = cross_validate(
+    ridge_reg,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.median(ridge_reg_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.median(ridge_reg_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.median(ridge_reg_scores['test_neg_root_mean_squared_error']))
+print("R2", np.median(ridge_reg_scores['test_r2']))
+
+# %% [markdown]
+# ### Lasso
+
+# %% jupyter={"source_hidden": true}
+lasso_reg = linear_model.Lasso(alpha=0.1)
+
+# %% jupyter={"source_hidden": true}
+lasso_reg_score = cross_validate(
+    lasso_reg,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.median(lasso_reg_score['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.median(lasso_reg_score['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.median(lasso_reg_score['test_neg_root_mean_squared_error']))
+print("R2", np.median(lasso_reg_score['test_r2']))
+
+# %% [markdown]
+# ### Bayesian Ridge
+
+# %% jupyter={"source_hidden": true}
+bayesian_ridge_reg = linear_model.BayesianRidge()
+
+# %% jupyter={"source_hidden": true}
+bayesian_ridge_reg_score = cross_validate(
+    bayesian_ridge_reg,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.median(bayesian_ridge_reg_score['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.median(bayesian_ridge_reg_score['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.median(bayesian_ridge_reg_score['test_neg_root_mean_squared_error']))
+print("R2", np.median(bayesian_ridge_reg_score['test_r2']))
+
+# %% [markdown]
+# ### RANSAC (outlier robust regression)
+
+# %% jupyter={"source_hidden": true}
+ransac_reg = linear_model.RANSACRegressor()
+
+# %% jupyter={"source_hidden": true}
+ransac_reg_scores = cross_validate(
+    ransac_reg,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.median(ransac_reg_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.median(ransac_reg_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.median(ransac_reg_scores['test_neg_root_mean_squared_error']))
+print("R2", np.median(ransac_reg_scores['test_r2']))
+
+# %% [markdown]
+# ### Support vector regression
+
+# %% jupyter={"source_hidden": true}
+svr = svm.SVR()
+
+# %% jupyter={"source_hidden": true}
+svr_scores = cross_validate(
+    svr,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.median(svr_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.median(svr_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.median(svr_scores['test_neg_root_mean_squared_error']))
+print("R2", np.median(svr_scores['test_r2']))
+
+# %% [markdown]
+# ### Kernel Ridge regression
+
+# %% jupyter={"source_hidden": true}
+kridge = kernel_ridge.KernelRidge()
+
+# %% jupyter={"source_hidden": true}
+kridge_scores = cross_validate(
+    kridge,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.median(kridge_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.median(kridge_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.median(kridge_scores['test_neg_root_mean_squared_error']))
+print("R2", np.median(kridge_scores['test_r2']))
+
+# %% [markdown]
+# ### Gaussian Process Regression
+
+# %% jupyter={"source_hidden": true}
+gpr = gaussian_process.GaussianProcessRegressor()
+
+# %% jupyter={"source_hidden": true}
+
+gpr_scores = cross_validate(
+    gpr,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.median(gpr_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.median(gpr_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.median(gpr_scores['test_neg_root_mean_squared_error']))
+print("R2", np.median(gpr_scores['test_r2']))
+
+# %%

exploration/ml_pipeline_stress_event_cleaned.py

@@ -0,0 +1,358 @@
+# ---
+# jupyter:
+#   jupytext:
+#     formats: ipynb,py:percent
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.13.0
+#   kernelspec:
+#     display_name: straw2analysis
+#     language: python
+#     name: straw2analysis
+# ---
+
+# %% jupyter={"source_hidden": true}
+# %matplotlib inline
+import datetime
+import importlib
+import os
+import sys
+
+import numpy as np
+import matplotlib.pyplot as plt
+import pandas as pd
+import seaborn as sns
+import yaml
+from pyprojroot import here
+from sklearn import linear_model, svm, kernel_ridge, gaussian_process
+from sklearn.model_selection import LeaveOneGroupOut, LeavePGroupsOut, cross_val_score, cross_validate
+from sklearn.metrics import mean_squared_error, r2_score
+from sklearn.impute import SimpleImputer
+from sklearn.dummy import DummyRegressor
+import xgboost as xg
+from IPython.core.interactiveshell import InteractiveShell
+InteractiveShell.ast_node_interactivity = "all"
+
+nb_dir = os.path.split(os.getcwd())[0]
+if nb_dir not in sys.path:
+    sys.path.append(nb_dir)
+
+import machine_learning.features_sensor
+import machine_learning.labels
+import machine_learning.model
+
+# %% [markdown]
+# # RAPIDS models
+
+# %% [markdown]
+# ## PANAS negative affect
+
+# %% jupyter={"source_hidden": true}
+model_input = pd.read_csv("../data/stressfulness_event/input_appraisal_stressfulness_event_mean.csv")
+
+# %% jupyter={"source_hidden": true}
+
+index_columns = ["local_segment", "local_segment_label", "local_segment_start_datetime", "local_segment_end_datetime"]
+
+model_input.set_index(index_columns, inplace=True)
+
+cv_method = 'half_logo'
+if cv_method == 'logo':
+    data_x, data_y, data_groups = model_input.drop(["target", "pid"], axis=1), model_input["target"], model_input["pid"]
+else:
+
+    model_input[(model_input['pid'] == "p037") | (model_input['pid'] == "p064") | (model_input['pid'] == "p092")]
+
+    model_input['pid_index'] = model_input.groupby('pid').cumcount()
+    model_input['pid_count'] = model_input.groupby('pid')['pid'].transform('count')
+
+    model_input["pid_index"] = (model_input['pid_index'] / model_input['pid_count'] + 1).round()
+    model_input["pid_half"] = model_input["pid"] + "_" +  model_input["pid_index"].astype(int).astype(str)
+
+    data_x, data_y, data_groups = model_input.drop(["target", "pid", "pid_index", "pid_half"], axis=1), model_input["target"], model_input["pid_half"]
+
+# %% jupyter={"source_hidden": true}
+categorical_feature_colnames = ["gender", "startlanguage"]
+additional_categorical_features = [col for col in data_x.columns if "mostcommonactivity" in col or "homelabel" in col]
+categorical_feature_colnames += additional_categorical_features
+
+# %% jupyter={"source_hidden": true}
+categorical_features = data_x[categorical_feature_colnames].copy()
+
+# %% jupyter={"source_hidden": true}
+mode_categorical_features = categorical_features.mode().iloc[0]
+
+# %% jupyter={"source_hidden": true}
+# fillna with mode
+categorical_features = categorical_features.fillna(mode_categorical_features)
+
+# %% jupyter={"source_hidden": true}
+# one-hot encoding
+categorical_features = categorical_features.apply(lambda col: col.astype("category"))
+if not categorical_features.empty:
+    categorical_features = pd.get_dummies(categorical_features)
+
+# %% jupyter={"source_hidden": true}
+numerical_features = data_x.drop(categorical_feature_colnames, axis=1)
+
+# %% jupyter={"source_hidden": true}
+train_x = pd.concat([numerical_features, categorical_features], axis=1)
+
+# %% jupyter={"source_hidden": true}
+train_x.dtypes
+
+# %% jupyter={"source_hidden": true}
+logo = LeaveOneGroupOut()
+logo.get_n_splits(
+    train_x,
+    data_y,
+    groups=data_groups,
+)
+
+# Defaults to 5 k folds in cross_validate method
+if cv_method != 'logo' and cv_method != 'half_logo':
+    logo = None
+
+# %% jupyter={"source_hidden": true}
+sum(data_y.isna())
+
+# %% [markdown]
+# ### Baseline: Dummy Regression (mean)
+dummy_regr = DummyRegressor(strategy="mean")
+
+# %% jupyter={"source_hidden": true}
+imputer = SimpleImputer(missing_values=np.nan, strategy='mean')
+
+# %% jupyter={"source_hidden": true}
+lin_reg_scores = cross_validate(
+    dummy_regr,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.nanmedian(lin_reg_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.nanmedian(lin_reg_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.nanmedian(lin_reg_scores['test_neg_root_mean_squared_error']))
+print("R2", np.nanmedian(lin_reg_scores['test_r2']))
+
+# %% [markdown]
+# ### Linear Regression
+
+# %% jupyter={"source_hidden": true}
+lin_reg_rapids = linear_model.LinearRegression()
+# %% jupyter={"source_hidden": true}
+imputer = SimpleImputer(missing_values=np.nan, strategy='mean')
+
+# %% jupyter={"source_hidden": true}
+lin_reg_scores = cross_validate(
+    lin_reg_rapids,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.nanmedian(lin_reg_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.nanmedian(lin_reg_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.nanmedian(lin_reg_scores['test_neg_root_mean_squared_error']))
+print("R2", np.nanmedian(lin_reg_scores['test_r2']))
+
+# %% [markdown]
+# ### XGBRegressor Linear Regression
+# %% jupyter={"source_hidden": true}
+xgb_r = xg.XGBRegressor(objective ='reg:squarederror', n_estimators = 10)
+# %% jupyter={"source_hidden": true}
+imputer = SimpleImputer(missing_values=np.nan, strategy='mean')
+
+# %% jupyter={"source_hidden": true}
+xgb_reg_scores = cross_validate(
+    xgb_r,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.nanmedian(xgb_reg_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.nanmedian(xgb_reg_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.nanmedian(xgb_reg_scores['test_neg_root_mean_squared_error']))
+print("R2", np.nanmedian(xgb_reg_scores['test_r2']))
+
+# %% [markdown]
+# ### XGBRegressor Pseudo Huber Error Regression
+# %% jupyter={"source_hidden": true}
+xgb_psuedo_huber_r = xg.XGBRegressor(objective ='reg:pseudohubererror', n_estimators = 10)
+# %% jupyter={"source_hidden": true}
+imputer = SimpleImputer(missing_values=np.nan, strategy='mean')
+
+# %% jupyter={"source_hidden": true}
+xgb_psuedo_huber_reg_scores = cross_validate(
+    xgb_psuedo_huber_r,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.nanmedian(xgb_psuedo_huber_reg_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.nanmedian(xgb_psuedo_huber_reg_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.nanmedian(xgb_psuedo_huber_reg_scores['test_neg_root_mean_squared_error']))
+print("R2", np.nanmedian(xgb_psuedo_huber_reg_scores['test_r2']))
+
+# %% [markdown]
+# ### Ridge regression
+
+# %% jupyter={"source_hidden": true}
+ridge_reg = linear_model.Ridge(alpha=.5)
+
+# %% tags=[] jupyter={"source_hidden": true}
+ridge_reg_scores = cross_validate(
+    ridge_reg,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.nanmedian(ridge_reg_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.nanmedian(ridge_reg_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.nanmedian(ridge_reg_scores['test_neg_root_mean_squared_error']))
+print("R2", np.nanmedian(ridge_reg_scores['test_r2']))
+
+# %% [markdown]
+# ### Lasso
+
+# %% jupyter={"source_hidden": true}
+lasso_reg = linear_model.Lasso(alpha=0.1)
+
+# %% jupyter={"source_hidden": true}
+lasso_reg_score = cross_validate(
+    lasso_reg,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.nanmedian(lasso_reg_score['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.nanmedian(lasso_reg_score['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.nanmedian(lasso_reg_score['test_neg_root_mean_squared_error']))
+print("R2", np.nanmedian(lasso_reg_score['test_r2']))
+
+# %% [markdown]
+# ### Bayesian Ridge
+
+# %% jupyter={"source_hidden": true}
+bayesian_ridge_reg = linear_model.BayesianRidge()
+
+# %% jupyter={"source_hidden": true}
+bayesian_ridge_reg_score = cross_validate(
+    bayesian_ridge_reg,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.nanmedian(bayesian_ridge_reg_score['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.nanmedian(bayesian_ridge_reg_score['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.nanmedian(bayesian_ridge_reg_score['test_neg_root_mean_squared_error']))
+print("R2", np.nanmedian(bayesian_ridge_reg_score['test_r2']))
+
+# %% [markdown]
+# ### RANSAC (outlier robust regression)
+
+# %% jupyter={"source_hidden": true}
+ransac_reg = linear_model.RANSACRegressor()
+
+# %% jupyter={"source_hidden": true}
+ransac_reg_scores = cross_validate(
+    ransac_reg,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.nanmedian(ransac_reg_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.nanmedian(ransac_reg_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.nanmedian(ransac_reg_scores['test_neg_root_mean_squared_error']))
+print("R2", np.nanmedian(ransac_reg_scores['test_r2']))
+
+# %% [markdown]
+# ### Support vector regression
+
+# %% jupyter={"source_hidden": true}
+svr = svm.SVR()
+
+# %% jupyter={"source_hidden": true}
+svr_scores = cross_validate(
+    svr,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.nanmedian(svr_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.nanmedian(svr_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.nanmedian(svr_scores['test_neg_root_mean_squared_error']))
+print("R2", np.nanmedian(svr_scores['test_r2']))
+
+# %% [markdown]
+# ### Kernel Ridge regression
+
+# %% jupyter={"source_hidden": true}
+kridge = kernel_ridge.KernelRidge()
+
+# %% jupyter={"source_hidden": true}
+kridge_scores = cross_validate(
+    kridge,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.nanmedian(kridge_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.nanmedian(kridge_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.nanmedian(kridge_scores['test_neg_root_mean_squared_error']))
+print("R2", np.nanmedian(kridge_scores['test_r2']))
+
+# %% [markdown]
+# ### Gaussian Process Regression
+
+# %% jupyter={"source_hidden": true}
+gpr = gaussian_process.GaussianProcessRegressor()
+
+# %% jupyter={"source_hidden": true}
+
+gpr_scores = cross_validate(
+    gpr,
+    X=imputer.fit_transform(train_x),
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.nanmedian(gpr_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.nanmedian(gpr_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.nanmedian(gpr_scores['test_neg_root_mean_squared_error']))
+print("R2", np.nanmedian(gpr_scores['test_r2']))
+
+# %%

features/timezone.py

@@ -0,0 +1,30 @@
+from collections.abc import Collection
+
+import pandas as pd
+
+from config.models import Participant, Timezone
+from setup import db_engine, session
+
+
+def get_timezone_data(usernames: Collection) -> pd.DataFrame:
+    """
+    Read the data from the proximity sensor table and return it in a dataframe.
+
+    Parameters
+    ----------
+    usernames: Collection
+        A list of usernames to put into the WHERE condition.
+
+    Returns
+    -------
+    df_proximity: pd.DataFrame
+        A dataframe of proximity data.
+    """
+    query_timezone = (
+        session.query(Timezone, Participant.username)
+        .filter(Participant.id == Timezone.participant_id)
+        .filter(Participant.username.in_(usernames))
+    )
+    with db_engine.connect() as connection:
+        df_timezone = pd.read_sql(query_timezone.statement, connection)
+    return df_timezone

images/dag_calls_nokia_example.svg

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+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<!-- Generated by graphviz version 2.43.0 (0)
+ -->
+<!-- Title: snakemake_dag Pages: 1 -->
+<svg width="548pt" height="625pt"
+ viewBox="0.00 0.00 548.00 625.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 621)">
+<title>snakemake_dag</title>
+<polygon fill="white" stroke="transparent" points="-4,4 -4,-621 544,-621 544,4 -4,4"/>
+<!-- 0 -->
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+<text text-anchor="middle" x="187" y="-15.5" font-family="sans" font-size="10.00">all</text>
+</g>
+<!-- 1 -->
+<g id="node2" class="node">
+<title>1</title>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M100,-617C100,-617 12,-617 12,-617 6,-617 0,-611 0,-605 0,-605 0,-588 0,-588 0,-582 6,-576 12,-576 12,-576 100,-576 100,-576 106,-576 112,-582 112,-588 112,-588 112,-605 112,-605 112,-611 106,-617 100,-617"/>
+<text text-anchor="middle" x="56" y="-605" font-family="sans" font-size="10.00">pull_phone_data</text>
+<text text-anchor="middle" x="56" y="-594" font-family="sans" font-size="10.00">pid: nokia_0000003</text>
+<text text-anchor="middle" x="56" y="-583" font-family="sans" font-size="10.00">sensor: calls</text>
+</g>
+<!-- 1&#45;&gt;0 -->
+<g id="edge1" class="edge">
+<title>1&#45;&gt;0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M47.83,-575.78C37.21,-548.32 20,-496.76 20,-451 20,-451 20,-451 20,-161 20,-114.96 38.83,-102.85 73,-72 95.21,-51.94 126.33,-38.17 150.45,-29.7"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="151.61,-33 159.97,-26.5 149.38,-26.37 151.61,-33"/>
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+<!-- 2 -->
+<g id="node3" class="node">
+<title>2</title>
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+<text text-anchor="middle" x="92" y="-519.5" font-family="sans" font-size="10.00">calls_episodes</text>
+</g>
+<!-- 1&#45;&gt;2 -->
+<g id="edge9" class="edge">
+<title>1&#45;&gt;2</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M65.84,-575.69C69.87,-567.56 74.6,-558.03 78.92,-549.33"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="82.09,-550.83 83.4,-540.32 75.82,-547.72 82.09,-550.83"/>
+</g>
+<!-- 2&#45;&gt;0 -->
+<g id="edge2" class="edge">
+<title>2&#45;&gt;0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M85.12,-503.83C75.18,-477.44 58,-425.14 58,-379 58,-379 58,-379 58,-161 58,-105.34 112.96,-61.84 151.14,-38.34"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="153.16,-41.21 159.96,-33.08 149.58,-35.2 153.16,-41.21"/>
+</g>
+<!-- 3 -->
+<g id="node4" class="node">
+<title>3</title>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M187.5,-468C187.5,-468 98.5,-468 98.5,-468 92.5,-468 86.5,-462 86.5,-456 86.5,-456 86.5,-444 86.5,-444 86.5,-438 92.5,-432 98.5,-432 98.5,-432 187.5,-432 187.5,-432 193.5,-432 199.5,-438 199.5,-444 199.5,-444 199.5,-456 199.5,-456 199.5,-462 193.5,-468 187.5,-468"/>
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+<text text-anchor="middle" x="143" y="-442" font-family="sans" font-size="10.00">sensor: phone_calls</text>
+</g>
+<!-- 2&#45;&gt;3 -->
+<g id="edge10" class="edge">
+<title>2&#45;&gt;3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M104.61,-503.7C110.6,-495.47 117.88,-485.48 124.48,-476.42"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="127.48,-478.25 130.54,-468.1 121.82,-474.13 127.48,-478.25"/>
+</g>
+<!-- 3&#45;&gt;0 -->
+<g id="edge3" class="edge">
+<title>3&#45;&gt;0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M140.43,-432C136.64,-405.4 130,-352.3 130,-307 130,-307 130,-307 130,-161 130,-117.8 153,-72.19 169.78,-44.66"/>
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+<!-- 4 -->
+<g id="node5" class="node">
+<title>4</title>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M357.5,-396C357.5,-396 194.5,-396 194.5,-396 188.5,-396 182.5,-390 182.5,-384 182.5,-384 182.5,-372 182.5,-372 182.5,-366 188.5,-360 194.5,-360 194.5,-360 357.5,-360 357.5,-360 363.5,-360 369.5,-366 369.5,-372 369.5,-372 369.5,-384 369.5,-384 369.5,-390 363.5,-396 357.5,-396"/>
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+</g>
+<!-- 3&#45;&gt;4 -->
+<g id="edge11" class="edge">
+<title>3&#45;&gt;4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M175.54,-431.88C193.25,-422.55 215.35,-410.92 234.32,-400.94"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="236.12,-403.94 243.34,-396.19 232.86,-397.75 236.12,-403.94"/>
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+<!-- 4&#45;&gt;0 -->
+<g id="edge4" class="edge">
+<title>4&#45;&gt;0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M250.68,-359.83C218.76,-335.92 168,-289.36 168,-235 168,-235 168,-235 168,-161 168,-120.86 175.55,-74.9 181.13,-46.4"/>
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+<g id="node9" class="node">
+<title>8</title>
+<path fill="none" stroke="#68d856" stroke-width="2" d="M353.5,-324C353.5,-324 248.5,-324 248.5,-324 242.5,-324 236.5,-318 236.5,-312 236.5,-312 236.5,-300 236.5,-300 236.5,-294 242.5,-288 248.5,-288 248.5,-288 353.5,-288 353.5,-288 359.5,-288 365.5,-294 365.5,-300 365.5,-300 365.5,-312 365.5,-312 365.5,-318 359.5,-324 353.5,-324"/>
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+<text text-anchor="middle" x="301" y="-298" font-family="sans" font-size="10.00">provider_key: rapids</text>
+</g>
+<!-- 4&#45;&gt;8 -->
+<g id="edge15" class="edge">
+<title>4&#45;&gt;8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M282.18,-359.7C285,-351.81 288.39,-342.3 291.52,-333.55"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="294.82,-334.7 294.89,-324.1 288.23,-332.34 294.82,-334.7"/>
+</g>
+<!-- 5 -->
+<g id="node6" class="node">
+<title>5</title>
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+<text text-anchor="middle" x="420" y="-453" font-family="sans" font-size="10.00">process_time_segments</text>
+<text text-anchor="middle" x="420" y="-442" font-family="sans" font-size="10.00">pid: nokia_0000003</text>
+</g>
+<!-- 5&#45;&gt;4 -->
+<g id="edge12" class="edge">
+<title>5&#45;&gt;4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M384.77,-431.88C365.42,-422.47 341.23,-410.71 320.57,-400.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="321.89,-397.41 311.36,-396.19 318.83,-403.71 321.89,-397.41"/>
+</g>
+<!-- 5&#45;&gt;8 -->
+<g id="edge16" class="edge">
+<title>5&#45;&gt;8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M415.13,-431.72C409.07,-412.57 397.25,-381.55 379,-360 369.03,-348.23 355.82,-337.94 343.12,-329.64"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="344.79,-326.55 334.45,-324.21 341.08,-332.49 344.79,-326.55"/>
+</g>
+<!-- 6 -->
+<g id="node7" class="node">
+<title>6</title>
+<path fill="none" stroke="#d86656" stroke-width="2" stroke-dasharray="5,2" d="M322.5,-468C322.5,-468 229.5,-468 229.5,-468 223.5,-468 217.5,-462 217.5,-456 217.5,-456 217.5,-444 217.5,-444 217.5,-438 223.5,-432 229.5,-432 229.5,-432 322.5,-432 322.5,-432 328.5,-432 334.5,-438 334.5,-444 334.5,-444 334.5,-456 334.5,-456 334.5,-462 328.5,-468 322.5,-468"/>
+<text text-anchor="middle" x="276" y="-447.5" font-family="sans" font-size="10.00">prepare_tzcodes_file</text>
+</g>
+<!-- 6&#45;&gt;4 -->
+<g id="edge13" class="edge">
+<title>6&#45;&gt;4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M276,-431.7C276,-423.98 276,-414.71 276,-406.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="279.5,-406.1 276,-396.1 272.5,-406.1 279.5,-406.1"/>
+</g>
+<!-- 7 -->
+<g id="node8" class="node">
+<title>7</title>
+<path fill="none" stroke="#56d86b" stroke-width="2" stroke-dasharray="5,2" d="M370,-540C370,-540 182,-540 182,-540 176,-540 170,-534 170,-528 170,-528 170,-516 170,-516 170,-510 176,-504 182,-504 182,-504 370,-504 370,-504 376,-504 382,-510 382,-516 382,-516 382,-528 382,-528 382,-534 376,-540 370,-540"/>
+<text text-anchor="middle" x="276" y="-519.5" font-family="sans" font-size="10.00">query_usernames_device_empatica_ids</text>
+</g>
+<!-- 7&#45;&gt;6 -->
+<g id="edge14" class="edge">
+<title>7&#45;&gt;6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M276,-503.7C276,-495.98 276,-486.71 276,-478.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="279.5,-478.1 276,-468.1 272.5,-478.1 279.5,-478.1"/>
+</g>
+<!-- 8&#45;&gt;0 -->
+<g id="edge5" class="edge">
+<title>8&#45;&gt;0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M264.63,-287.8C250.06,-279.08 234.51,-267.11 225,-252 184.07,-186.97 182.71,-92.23 184.91,-46.17"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="188.41,-46.26 185.49,-36.07 181.42,-45.85 188.41,-46.26"/>
+</g>
+<!-- 9 -->
+<g id="node10" class="node">
+<title>9</title>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M382,-252C382,-252 246,-252 246,-252 240,-252 234,-246 234,-240 234,-240 234,-228 234,-228 234,-222 240,-216 246,-216 246,-216 382,-216 382,-216 388,-216 394,-222 394,-228 394,-228 394,-240 394,-240 394,-246 388,-252 382,-252"/>
+<text text-anchor="middle" x="314" y="-237" font-family="sans" font-size="10.00">join_features_from_providers</text>
+<text text-anchor="middle" x="314" y="-226" font-family="sans" font-size="10.00">sensor_key: phone_calls</text>
+</g>
+<!-- 8&#45;&gt;9 -->
+<g id="edge17" class="edge">
+<title>8&#45;&gt;9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M304.21,-287.7C305.65,-279.98 307.37,-270.71 308.96,-262.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="312.44,-262.58 310.82,-252.1 305.56,-261.3 312.44,-262.58"/>
+</g>
+<!-- 9&#45;&gt;0 -->
+<g id="edge6" class="edge">
+<title>9&#45;&gt;0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M294.15,-215.87C283.81,-206.16 271.58,-193.31 263,-180 235.01,-136.57 243.3,-118.11 220,-72 215.36,-62.81 209.61,-53.14 204.23,-44.62"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="207.17,-42.72 198.81,-36.21 201.29,-46.51 207.17,-42.72"/>
+</g>
+<!-- 10 -->
+<g id="node11" class="node">
+<title>10</title>
+<path fill="none" stroke="#56d8d0" stroke-width="2" d="M526,-180C526,-180 284,-180 284,-180 278,-180 272,-174 272,-168 272,-168 272,-156 272,-156 272,-150 278,-144 284,-144 284,-144 526,-144 526,-144 532,-144 538,-150 538,-156 538,-156 538,-168 538,-168 538,-174 532,-180 526,-180"/>
+<text text-anchor="middle" x="405" y="-159.5" font-family="sans" font-size="10.00">merge_sensor_features_for_individual_participants</text>
+</g>
+<!-- 9&#45;&gt;10 -->
+<g id="edge18" class="edge">
+<title>9&#45;&gt;10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M336.49,-215.7C347.96,-206.88 362.06,-196.03 374.48,-186.47"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="376.97,-188.98 382.76,-180.1 372.7,-183.43 376.97,-188.98"/>
+</g>
+<!-- 10&#45;&gt;0 -->
+<g id="edge7" class="edge">
+<title>10&#45;&gt;0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M366.3,-143.85C346.21,-134.31 321.62,-121.63 301,-108 280.21,-94.25 277.55,-87.46 258,-72 245.35,-62 231.16,-51.3 218.81,-42.16"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="220.72,-39.22 210.59,-36.1 216.57,-44.85 220.72,-39.22"/>
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+<!-- 11 -->
+<g id="node12" class="node">
+<title>11</title>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M528,-108C528,-108 322,-108 322,-108 316,-108 310,-102 310,-96 310,-96 310,-84 310,-84 310,-78 316,-72 322,-72 322,-72 528,-72 528,-72 534,-72 540,-78 540,-84 540,-84 540,-96 540,-96 540,-102 534,-108 528,-108"/>
+<text text-anchor="middle" x="425" y="-87.5" font-family="sans" font-size="10.00">merge_sensor_features_for_all_participants</text>
+</g>
+<!-- 10&#45;&gt;11 -->
+<g id="edge19" class="edge">
+<title>10&#45;&gt;11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M409.94,-143.7C412.17,-135.9 414.85,-126.51 417.33,-117.83"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="420.73,-118.68 420.11,-108.1 414,-116.76 420.73,-118.68"/>
+</g>
+<!-- 11&#45;&gt;0 -->
+<g id="edge8" class="edge">
+<title>11&#45;&gt;0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M367.08,-71.97C322.5,-58.85 262.21,-41.12 223.96,-29.87"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="224.84,-26.48 214.26,-27.02 222.87,-33.2 224.84,-26.48"/>
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+</g>
+</svg>

images/dag_participants_files.svg

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+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<!-- Generated by graphviz version 2.43.0 (0)
+ -->
+<!-- Title: snakemake_dag Pages: 1 -->
+<svg width="414pt" height="396pt"
+ viewBox="0.00 0.00 414.00 396.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 392)">
+<title>snakemake_dag</title>
+<polygon fill="white" stroke="transparent" points="-4,4 -4,-392 410,-392 410,4 -4,4"/>
+<!-- 0 -->
+<g id="node1" class="node">
+<title>0</title>
+<text text-anchor="start" x="81" y="-71.6" font-family="sans" font-weight="bold" font-size="18.00">create_participants_files</text>
+<text text-anchor="start" x="81" y="-47.8" font-family="sans" font-size="10.00"> </text>
+<text text-anchor="start" x="85" y="-47.8" font-family="sans" font-weight="bold" font-size="14.00">↪ input</text>
+<text text-anchor="start" x="143" y="-47.8" font-family="sans" font-size="10.00"> </text>
+<text text-anchor="start" x="81" y="-28" font-family="monospace" font-size="10.00">data/external/example_participants.csv</text>
+<text text-anchor="start" x="319" y="-10" font-family="sans" font-size="10.00"> &#160;</text>
+<polygon fill="#acd957" stroke="#acd957" points="75,-62 75,-62 333,-62 333,-62 75,-62"/>
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+<polygon fill="none" stroke="#acd957" stroke-width="2" points="74.5,-1 74.5,-91 331.5,-91 331.5,-1 74.5,-1"/>
+</g>
+<!-- 1 -->
+<g id="node2" class="node">
+<title>1</title>
+<text text-anchor="start" x="77" y="-221.6" font-family="sans" font-weight="bold" font-size="18.00">prepare_participants_csv</text>
+<text text-anchor="start" x="77" y="-197.8" font-family="sans" font-size="10.00"> </text>
+<text text-anchor="start" x="81" y="-197.8" font-family="sans" font-weight="bold" font-size="14.00">↪ input</text>
+<text text-anchor="start" x="139" y="-197.8" font-family="sans" font-size="10.00"> </text>
+<text text-anchor="start" x="77" y="-178" font-family="monospace" font-size="10.00">data/external/example_usernames.csv</text>
+<text text-anchor="start" x="251" y="-157.8" font-family="sans" font-size="10.00"> </text>
+<text text-anchor="start" x="255" y="-157.8" font-family="sans" font-weight="bold" font-size="14.00">output →</text>
+<text text-anchor="start" x="325" y="-157.8" font-family="sans" font-size="10.00"> </text>
+<text text-anchor="start" x="77" y="-138" font-family="monospace" font-size="10.00">data/external/example_participants.csv</text>
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+<polygon fill="none" stroke="#57d99e" stroke-width="2" points="71,-129 71,-241 335,-241 335,-129 71,-129"/>
+</g>
+<!-- 1&#45;&gt;0 -->
+<g id="edge1" class="edge">
+<title>1&#45;&gt;0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M203,-127.88C203,-119.48 203,-110.81 203,-102.42"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="206.5,-102.36 203,-92.36 199.5,-102.36 206.5,-102.36"/>
+</g>
+<!-- 2 -->
+<g id="node3" class="node">
+<title>2</title>
+<text text-anchor="start" x="7" y="-367.6" font-family="sans" font-weight="bold" font-size="18.00">query_usernames_device_empatica_ids</text>
+<text text-anchor="start" x="7" y="-346" font-family="sans" font-size="10.00"> &#160;</text>
+<text text-anchor="start" x="321" y="-325.8" font-family="sans" font-size="10.00"> </text>
+<text text-anchor="start" x="325" y="-325.8" font-family="sans" font-weight="bold" font-size="14.00">output →</text>
+<text text-anchor="start" x="395" y="-325.8" font-family="sans" font-size="10.00"> </text>
+<text text-anchor="start" x="7" y="-306" font-family="monospace" font-size="10.00">data/external/example_usernames.csv</text>
+<text text-anchor="start" x="7" y="-288" font-family="monospace" font-size="10.00">data/external/timezone.csv</text>
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+<!-- 2&#45;&gt;1 -->
+<g id="edge2" class="edge">
+<title>2&#45;&gt;1</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M203,-277.63C203,-269.45 203,-260.93 203,-252.53"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="206.5,-252.36 203,-242.36 199.5,-252.36 206.5,-252.36"/>
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+</g>
+</svg>

machine_learning/classification_models.py

@@ -0,0 +1,71 @@
+from sklearn.dummy import DummyClassifier
+from sklearn import linear_model, svm, naive_bayes, neighbors, tree, ensemble
+from lightgbm import LGBMClassifier
+import xgboost as xg 
+
+class ClassificationModels():
+    
+    def __init__(self):
+        self.cmodels = self.init_classification_models()
+        
+    def get_cmodels(self):
+        return self.cmodels
+
+    def init_classification_models(self):
+        cmodels = {
+            'dummy_classifier': {
+                'model': DummyClassifier(strategy="most_frequent"),
+                'metrics': [0, 0, 0, 0]
+            },
+            'logistic_regression': {
+                'model': linear_model.LogisticRegression(max_iter=1000),
+                'metrics': [0, 0, 0, 0]
+            },
+            'support_vector_machine': {
+                'model': svm.SVC(),
+                'metrics': [0, 0, 0, 0]
+            },
+            'gaussian_naive_bayes': {
+                'model': naive_bayes.GaussianNB(),
+                'metrics': [0, 0, 0, 0]
+            },
+            'stochastic_gradient_descent_classifier': {
+                'model': linear_model.SGDClassifier(),
+                'metrics': [0, 0, 0, 0]
+            },
+            'knn': {
+                'model': neighbors.KNeighborsClassifier(),
+                'metrics': [0, 0, 0, 0]
+            },
+            'decision_tree': {
+                'model': tree.DecisionTreeClassifier(),
+                'metrics': [0, 0, 0, 0]
+            },
+            'random_forest_classifier': {
+                'model': ensemble.RandomForestClassifier(),
+                'metrics': [0, 0, 0, 0]
+            },
+            'gradient_boosting_classifier': {
+                'model': ensemble.GradientBoostingClassifier(),
+                'metrics': [0, 0, 0, 0]
+            },
+            'lgbm_classifier': {
+                'model': LGBMClassifier(),
+                'metrics': [0, 0, 0, 0]
+            },
+            'XGBoost_classifier': {
+                'model': xg.sklearn.XGBClassifier(),
+                'metrics': [0, 0, 0, 0]
+            }
+        }
+        
+        return cmodels
+    
+    def get_total_models_scores(self, n_clusters=1):
+        for model_title, model in self.cmodels.items():
+            print("\n************************************\n")
+            print("Current model:", model_title, end="\n")
+            print("Acc:", model['metrics'][0]/n_clusters)
+            print("Precision:", model['metrics'][1]/n_clusters)
+            print("Recall:", model['metrics'][2]/n_clusters)
+            print("F1:", model['metrics'][3]/n_clusters)

machine_learning/final_results/results_presentation.ipynb

@@ -0,0 +1,163 @@
+# %%
+import datetime
+import importlib
+import os
+import sys
+
+import numpy as np
+import matplotlib.pyplot as plt
+import pandas as pd
+import seaborn as sns
+import yaml
+from pyprojroot import here
+from sklearn import linear_model, svm, kernel_ridge, gaussian_process, ensemble
+from sklearn.model_selection import LeaveOneGroupOut, cross_val_score, cross_validate, cross_val_predict
+from sklearn.metrics import mean_squared_error, r2_score
+from sklearn.impute import SimpleImputer
+from sklearn.dummy import DummyRegressor
+from sklearn.decomposition import PCA
+from IPython.core.interactiveshell import InteractiveShell
+InteractiveShell.ast_node_interactivity = "all"
+
+nb_dir = os.path.split(os.getcwd())[0]
+if nb_dir not in sys.path:
+    sys.path.append(nb_dir)
+
+import machine_learning.helper
+
+# %%
+segment = "intradaily_30_min"
+target = "JCQ_job_demand"
+csv_name = "./data/" + segment + "_all_targets/input_" + target + "_mean.csv"
+#csv_name = "./data/daily_18_hours_all_targets/input_JCQ_job_demand_mean.csv"
+
+# %%
+data_x, data_y, data_groups = machine_learning.helper.prepare_model_input(csv_name)
+
+# %%
+data_y.head()
+
+# %%
+scores = machine_learning.helper.run_all_models(csv_name)
+
+
+# %% jupyter={"source_hidden": true}
+logo = LeaveOneGroupOut()
+logo.get_n_splits(
+    data_x,
+    data_y,
+    groups=data_groups,
+)
+
+# %% [markdown]
+# ### Baseline: Dummy Regression (mean)
+dummy_regr = DummyRegressor(strategy="mean")
+
+# %% jupyter={"source_hidden": true}
+lin_reg_scores = cross_validate(
+    dummy_regr,
+    X=data_x,
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.median(lin_reg_scores['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.median(lin_reg_scores['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.median(lin_reg_scores['test_neg_root_mean_squared_error']))
+print("R2", np.median(lin_reg_scores['test_r2']))
+
+##################
+# %%
+chosen_model = "Random Forest"
+rfr = ensemble.RandomForestRegressor(max_features=0.3, n_jobs=-1)
+rfr_score = cross_validate(
+    rfr,
+    X=data_x,
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Squared Error", np.median(rfr_score['test_neg_mean_squared_error']))
+print("Negative Mean Absolute Error", np.median(rfr_score['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.median(rfr_score['test_neg_root_mean_squared_error']))
+print("R2", np.median(rfr_score['test_r2']))
+
+# %%
+y_predicted = cross_val_predict(rfr, data_x, data_y, groups=data_groups, cv=logo)
+#########################
+# %%
+chosen_model = "Bayesian Ridge"
+bayesian_ridge_reg = linear_model.BayesianRidge()
+bayesian_ridge_reg_score = cross_validate(
+    bayesian_ridge_reg,
+    X=data_x,
+    y=data_y,
+    groups=data_groups,
+    cv=logo,
+    n_jobs=-1,
+    scoring=('r2', 'neg_mean_squared_error', 'neg_mean_absolute_error', 'neg_root_mean_squared_error')
+)
+print("Negative Mean Absolute Error", np.median(bayesian_ridge_reg_score['test_neg_mean_absolute_error']))
+print("Negative Root Mean Squared Error", np.median(bayesian_ridge_reg_score['test_neg_root_mean_squared_error']))
+print("R2", np.median(bayesian_ridge_reg_score['test_r2']))
+
+# %%
+y_predicted = cross_val_predict(bayesian_ridge_reg, data_x, data_y, groups=data_groups, cv=logo)
+
+# %%
+data_y = pd.DataFrame(pd.concat([data_y, data_groups], axis=1))
+data_y.rename(columns={"target": "y_true"}, inplace=True)
+data_y["y_predicted"] = y_predicted
+
+# %%
+data_y.head()
+
+# %%
+g1 = sns.relplot(data=data_y, x="y_true", y="y_predicted")
+#g1.set_axis_labels("true", "predicted")
+#g1.map(plt.axhline, y=0, color=".7", dashes=(2, 1), zorder=0)
+#g1.map(plt.axline, xy1=(0,0), slope=1)
+g1.set(title=",".join([segment, target, chosen_model]))
+display(g1)
+g1.savefig("_".join([segment, target, chosen_model, "_relplot.pdf"]))
+
+# %%
+data_y_long = pd.wide_to_long(
+    data_y.reset_index(),
+    i=["local_segment", "pid"],
+    j="value",
+    stubnames="y",
+    sep="_",
+    suffix=".+",
+)
+
+# %%
+data_y_long.head()
+# %%
+g2 = sns.displot(data_y_long, x="y", hue="value", binwidth=0.1, height=5, aspect=1.5)
+sns.move_legend(g2, "upper left", bbox_to_anchor=(.55, .45))
+g2.set(title=",".join([segment, target, chosen_model]))
+g2.savefig("_".join([segment, target, chosen_model, "hist.pdf"]))
+
+# %%
+pca = PCA(n_components=2)
+pca.fit(data_x)
+print(pca.explained_variance_ratio_)
+
+# %%
+data_x_pca = pca.fit_transform(data_x)
+data_pca = pd.DataFrame(pd.concat([data_y.reset_index()["y_true"], pd.DataFrame(data_x_pca, columns = {"pca_0", "pca_1"})], axis=1))
+
+# %%
+data_pca
+# %%
+
+g3 = sns.relplot(data = data_pca, x = "pca_0", y = "pca_1", hue = "y_true", palette = sns.color_palette("Spectral", as_cmap=True))
+g3.set(title=",".join([segment, target, chosen_model]) + "\n variance explained = " + str(round(sum(pca.explained_variance_ratio_), 2)))
+g3.savefig("_".join([segment, target, chosen_model, "_PCA.pdf"]))
+
+# %%

machine_learning/helper.py

@@ -1,6 +1,13 @@
 from pathlib import Path
+from sklearn import linear_model, svm, kernel_ridge, gaussian_process, ensemble
+from sklearn.model_selection import LeaveOneGroupOut, cross_val_score, cross_validate
+from sklearn.metrics import mean_squared_error, r2_score
+from sklearn.impute import SimpleImputer
+from sklearn.dummy import DummyRegressor
+from xgboost import XGBRegressor
 
 import pandas as pd
+import numpy as np
 
 
 def safe_outer_merge_on_index(left: pd.DataFrame, right: pd.DataFrame) -> pd.DataFrame:
@@ -55,3 +62,206 @@ def construct_full_path(folder: Path, filename_prefix: str, data_type: str) -> P
     export_filename = filename_prefix + "_" + data_type + ".csv"
     full_path = folder / export_filename
     return full_path
+
+def insert_row(df, row):
+    return pd.concat([df, pd.DataFrame([row], columns=df.columns)], ignore_index=True)
+
+def prepare_model_input(input_csv):
+
+    model_input = pd.read_csv(input_csv)
+
+    index_columns = ["local_segment", "local_segment_label", "local_segment_start_datetime", "local_segment_end_datetime"]
+    model_input.set_index(index_columns, inplace=True)
+
+    data_x, data_y, data_groups = model_input.drop(["target", "pid"], axis=1), model_input["target"], model_input["pid"]
+
+    categorical_feature_colnames = ["gender", "startlanguage", "limesurvey_demand_control_ratio_quartile"]
+    #TODO: check whether limesurvey_demand_control_ratio_quartile NaNs could be replaced meaningfully
+    #additional_categorical_features = [col for col in data_x.columns if "mostcommonactivity" in col or "homelabel" in col]
+    #TODO: check if mostcommonactivity is indeed a categorical features after aggregating
+    #categorical_feature_colnames += additional_categorical_features
+    categorical_features = data_x[categorical_feature_colnames].copy()
+    mode_categorical_features = categorical_features.mode().iloc[0]
+    # fillna with mode
+    categorical_features = categorical_features.fillna(mode_categorical_features)
+    # one-hot encoding
+    categorical_features = categorical_features.apply(lambda col: col.astype("category"))
+    if not categorical_features.empty:
+        categorical_features = pd.get_dummies(categorical_features)
+
+    numerical_features = data_x.drop(categorical_feature_colnames, axis=1)
+
+    train_x = pd.concat([numerical_features, categorical_features], axis=1)
+
+    return train_x, data_y, data_groups
+
+
+def run_all_models(input_csv):
+    # Prepare data
+    train_x, data_y, data_groups = prepare_model_input(input_csv)
+
+    # Prepare cross validation
+    logo = LeaveOneGroupOut()
+    logo.get_n_splits(
+        train_x,
+        data_y,
+        groups=data_groups,
+    )
+    scores = pd.DataFrame(columns=["method", "median", "max"])
+
+    # Validate models
+    lin_reg_rapids = linear_model.LinearRegression()
+    lin_reg_scores = cross_val_score(
+        lin_reg_rapids,
+        X=train_x,
+        y=data_y,
+        groups=data_groups,
+        cv=logo,
+        n_jobs=-1,
+        scoring='r2'
+    )
+    print("Linear regression:")
+    print(np.median(lin_reg_scores))
+    scores = insert_row(scores, ["Linear regression",np.median(lin_reg_scores),np.max(lin_reg_scores)])
+
+    ridge_reg = linear_model.Ridge(alpha=.5)
+    ridge_reg_scores = cross_val_score(
+        ridge_reg,
+        X=train_x,
+        y=data_y,
+        groups=data_groups,
+        cv=logo,
+        n_jobs=-1,
+        scoring="r2"
+    )
+    print("Ridge regression")
+    print(np.median(ridge_reg_scores))
+    scores = insert_row(scores, ["Ridge regression",np.median(ridge_reg_scores),np.max(ridge_reg_scores)])
+
+    lasso_reg = linear_model.Lasso(alpha=0.1)
+    lasso_reg_score = cross_val_score(
+        lasso_reg,
+        X=train_x,
+        y=data_y,
+        groups=data_groups,
+        cv=logo,
+        n_jobs=-1,
+        scoring="r2"
+    )
+    print("Lasso regression")
+    print(np.median(lasso_reg_score))
+    scores = insert_row(scores, ["Lasso regression",np.median(lasso_reg_score),np.max(lasso_reg_score)])
+
+    bayesian_ridge_reg = linear_model.BayesianRidge()
+    bayesian_ridge_reg_score = cross_val_score(
+        bayesian_ridge_reg,
+        X=train_x,
+        y=data_y,
+        groups=data_groups,
+        cv=logo,
+        n_jobs=-1,
+        scoring="r2"
+    )
+    print("Bayesian Ridge")
+    print(np.median(bayesian_ridge_reg_score))
+    scores = insert_row(scores, ["Bayesian Ridge",np.median(bayesian_ridge_reg_score),np.max(bayesian_ridge_reg_score)])
+
+    ransac_reg = linear_model.RANSACRegressor()
+    ransac_reg_score = cross_val_score(
+        ransac_reg,
+        X=train_x,
+        y=data_y,
+        groups=data_groups,
+        cv=logo,
+        n_jobs=-1,
+        scoring="r2"
+    )
+    print("RANSAC (outlier robust regression)")
+    print(np.median(ransac_reg_score))
+    scores = insert_row(scores, ["RANSAC",np.median(ransac_reg_score),np.max(ransac_reg_score)])
+
+    svr = svm.SVR()
+    svr_score = cross_val_score(
+        svr,
+        X=train_x,
+        y=data_y,
+        groups=data_groups,
+        cv=logo,
+        n_jobs=-1,
+        scoring="r2"
+    )
+    print("Support vector regression")
+    print(np.median(svr_score))
+    scores = insert_row(scores, ["Support vector regression",np.median(svr_score),np.max(svr_score)])
+
+    kridge = kernel_ridge.KernelRidge()
+    kridge_score = cross_val_score(
+        kridge,
+        X=train_x,
+        y=data_y,
+        groups=data_groups,
+        cv=logo,
+        n_jobs=-1,
+        scoring="r2"
+    )
+    print("Kernel Ridge regression")
+    print(np.median(kridge_score))
+    scores = insert_row(scores, ["Kernel Ridge regression",np.median(kridge_score),np.max(kridge_score)])
+
+    gpr = gaussian_process.GaussianProcessRegressor()
+    gpr_score = cross_val_score(
+        gpr,
+        X=train_x,
+        y=data_y,
+        groups=data_groups,
+        cv=logo,
+        n_jobs=-1,
+        scoring="r2"
+    )
+    print("Gaussian Process Regression")
+    print(np.median(gpr_score))
+    scores = insert_row(scores, ["Gaussian Process Regression",np.median(gpr_score),np.max(gpr_score)])
+
+    rfr = ensemble.RandomForestRegressor(max_features=0.3, n_jobs=-1)
+    rfr_score = cross_val_score(
+        rfr,
+        X=train_x,
+        y=data_y,
+        groups=data_groups,
+        cv=logo,
+        n_jobs=-1,
+        scoring="r2"
+    )
+    print("Random Forest Regression")
+    print(np.median(rfr_score))
+    scores = insert_row(scores, ["Random Forest Regression",np.median(rfr_score),np.max(rfr_score)])
+
+    xgb = XGBRegressor()
+    xgb_score = cross_val_score(
+        xgb,
+        X=train_x,
+        y=data_y,
+        groups=data_groups,
+        cv=logo,
+        n_jobs=-1,
+        scoring="r2"
+    )
+    print("XGBoost Regressor")
+    print(np.median(xgb_score))
+    scores = insert_row(scores, ["XGBoost Regressor",np.median(xgb_score),np.max(xgb_score)])
+
+    ada = ensemble.AdaBoostRegressor()
+    ada_score = cross_val_score(
+        ada,
+        X=train_x,
+        y=data_y,
+        groups=data_groups,
+        cv=logo,
+        n_jobs=-1,
+        scoring="r2"
+    )
+    print("ADA Boost Regressor")
+    print(np.median(ada_score))
+    scores = insert_row(scores, ["ADA Boost Regressor",np.median(ada_score),np.max(ada_score)])
+
+    return scores

participants/prepare_usernames_file.py

@@ -0,0 +1,69 @@
+import datetime
+import os
+import sys
+
+nb_dir = os.path.split(os.getcwd())[0]
+if nb_dir not in sys.path:
+    sys.path.append(nb_dir)
+
+import pandas as pd
+from features.timezone import get_timezone_data
+from pyprojroot import here
+
+import participants.query_db
+
+participants_inactive_usernames = participants.query_db.get_usernames(
+    tester=False,  # True participants are wanted.
+    active=False,  # They have all finished their participation.
+    collection_start=datetime.date.fromisoformat(
+        "2020-08-01"
+    ),  # This is the timeframe of the main study.
+    last_upload=datetime.date.fromisoformat("2021-09-01"),
+)
+
+participants_overview_si = pd.read_csv(
+    snakemake.params["baseline_folder"] + "Participants_overview_Slovenia.csv", sep=";"
+)
+participants_overview_be = pd.read_csv(
+    snakemake.params["baseline_folder"]+ "Participants_overview_Belgium.csv", sep=";"
+)
+
+participants_true_si = participants_overview_si[
+    participants_overview_si["Wristband_SerialNo"] != "DECLINED"
+]
+participants_true_be = participants_overview_be[
+    participants_overview_be["SmartphoneBrand+Generation"].str.slice(0, 3) != "Not"
+]
+
+# Concatenate participants from both countries.
+participants_usernames_empatica = pd.concat(
+    [participants_true_be, participants_true_si]
+)
+# Filter only the participants from the main study (queried from the database).
+participants_usernames_empatica = participants_usernames_empatica[
+    participants_usernames_empatica["Username"].isin(participants_inactive_usernames)
+]
+# Rename and select columns.
+participants_usernames_empatica = participants_usernames_empatica.rename(
+    columns={"Username": "label", "Wristband_SerialNo": "empatica_id"}
+)[["label", "empatica_id"]]
+# Adapt for csv export.
+participants_usernames_empatica["empatica_id"] = participants_usernames_empatica[
+    "empatica_id"
+].str.replace(",", ";")
+
+participants_usernames_empatica.to_csv(
+    snakemake.output["usernames_file"],
+    header=True,
+    index=False,
+    line_terminator="\n",
+)
+
+timezone_df = get_timezone_data(participants_inactive_usernames)
+
+timezone_df.to_csv(
+    snakemake.output["timezone_file"],
+    header=True,
+    index=False,
+    line_terminator="\n",
+)

rapids

@@ -0,0 +1 @@
+Subproject commit f78aa3e7b3567423b44045766b230cd60d557cb0

statistical_analysis/adherence.py

@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: percent
 #       format_version: '1.3'
-#       jupytext_version: 1.12.0
+#       jupytext_version: 1.13.0
 #   kernelspec:
 #     display_name: straw2analysis
 #     language: python
@@ -14,25 +14,7 @@
 # ---
 
 # %%
-# %matplotlib inline
-import datetime
-import os
-import sys
-
-import matplotlib.pyplot as plt
-import pandas as pd
-import seaborn as sns
-import statsmodels.api as sm
-import statsmodels.formula.api as smf
-
-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.esm import *
-
-# %%
-SAVE_FIGS = True
+SAVE_FIGS = False
 FIG_HEIGHT = 5
 FIG_ASPECT = 1.7
 FIG_COLOUR = "#28827C"