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""" |
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Functions for data cleaning. |
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:author: Andreas Kanz |
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""" |
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# Imports |
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import itertools |
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import numpy as np |
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import pandas as pd |
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import re |
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from sklearn.base import BaseEstimator, TransformerMixin |
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from typing import List, Optional, Union |
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from klib.describe import corr_mat |
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from klib.utils import ( |
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_diff_report, |
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_drop_duplicates, |
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_missing_vals, |
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_validate_input_bool, |
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_validate_input_range, |
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) |
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__all__ = [ |
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"clean_column_names", |
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"convert_datatypes", |
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"data_cleaning", |
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"drop_missing", |
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"mv_col_handling", |
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] |
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def optimize_ints(data: Union[pd.Series, pd.DataFrame]) -> pd.DataFrame: |
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data = pd.DataFrame(data).copy() |
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ints = data.select_dtypes(include=["int64"]).columns.tolist() |
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data[ints] = data[ints].apply(pd.to_numeric, downcast="integer") |
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return data |
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def optimize_floats(data: Union[pd.Series, pd.DataFrame]) -> pd.DataFrame: |
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data = pd.DataFrame(data).copy() |
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floats = data.select_dtypes(include=["float64"]).columns.tolist() |
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data[floats] = data[floats].apply(pd.to_numeric, downcast="float") |
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return data |
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def clean_column_names(data: pd.DataFrame, hints: bool = True) -> pd.DataFrame: |
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"""Clean the column names of the provided Pandas Dataframe and optionally \ |
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provides hints on duplicate and long column names. |
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Parameters |
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---------- |
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data : pd.DataFrame |
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Original Dataframe with columns to be cleaned |
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hints : bool, optional |
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Print out hints on column name duplication and colum name length, by default \ |
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True |
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Returns |
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------- |
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pd.DataFrame |
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Pandas DataFrame with cleaned column names |
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""" |
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_validate_input_bool(hints, "hints") |
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# Handle CamelCase |
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for i, col in enumerate(data.columns): |
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matches = re.findall(re.compile("[a-z][A-Z]"), col) |
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column = col |
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for match in matches: |
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column = column.replace(match, match[0] + "_" + match[1]) |
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data.rename(columns={data.columns[i]: column}, inplace=True) |
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data.columns = ( |
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data.columns.str.replace("\n", "_", regex=False) |
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.str.replace("(", "_", regex=False) |
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.str.replace(")", "_", regex=False) |
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.str.replace("'", "_", regex=False) |
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.str.replace('"', "_", regex=False) |
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.str.replace(".", "_", regex=False) |
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.str.replace("-", "_", regex=False) |
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.str.replace(r"[!?:;/]", "_", regex=True) |
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.str.replace("+", "_plus_", regex=False) |
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.str.replace("*", "_times_", regex=False) |
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.str.replace("<", "_smaller", regex=False) |
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.str.replace(">", "_larger_", regex=False) |
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.str.replace("=", "_equal_", regex=False) |
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.str.replace("ä", "ae", regex=False) |
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.str.replace("ö", "oe", regex=False) |
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.str.replace("ü", "ue", regex=False) |
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.str.replace("ß", "ss", regex=False) |
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.str.replace("%", "_percent_", regex=False) |
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.str.replace("$", "_dollar_", regex=False) |
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.str.replace("€", "_euro_", regex=False) |
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.str.replace("@", "_at_", regex=False) |
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.str.replace("#", "_hash_", regex=False) |
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.str.replace("&", "_and_", regex=False) |
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.str.replace(r"\s+", "_", regex=True) |
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.str.replace(r"_+", "_", regex=True) |
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.str.strip("_") |
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.str.lower() |
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) |
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dupl_idx = [i for i, x in enumerate(data.columns.duplicated()) if x] |
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if dupl_idx: |
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dupl_before = data.columns[dupl_idx].tolist() |
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data.columns = [ |
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col if col not in data.columns[:i] else col + "_" + str(i) |
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for i, col in enumerate(data.columns) |
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] |
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if hints: |
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print( |
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f"Duplicate column names detected! Columns with index {dupl_idx} and " |
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f"names {dupl_before}) have been renamed to " |
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f"{data.columns[dupl_idx].tolist()}." |
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) |
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long_col_names = [x for x in data.columns if len(x) > 25] |
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if long_col_names and hints: |
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print( |
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"Long column names detected (>25 characters). Consider renaming the " |
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f"following columns {long_col_names}." |
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) |
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return data |
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def convert_datatypes( |
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data: pd.DataFrame, |
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category: bool = True, |
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cat_threshold: float = 0.05, |
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cat_exclude: Optional[List[Union[str, int]]] = None, |
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) -> pd.DataFrame: |
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"""Convert columns to best possible dtypes using dtypes supporting pd.NA. |
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Temporarily not converting to integers due to an issue in pandas. This is expected \ |
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to be fixed in pandas 1.1. See https://github.com/pandas-dev/pandas/issues/33803 |
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Parameters |
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---------- |
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data : pd.DataFrame |
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2D dataset that can be coerced into Pandas DataFrame |
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category : bool, optional |
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Change dtypes of columns with dtype "object" to "category". Set threshold \ |
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using cat_threshold or exclude columns using cat_exclude, by default True |
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cat_threshold : float, optional |
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Ratio of unique values below which categories are inferred and column dtype is \ |
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changed to categorical, by default 0.05 |
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cat_exclude : Optional[List[Union[str, int]]], optional |
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List of columns to exclude from categorical conversion, by default None |
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Returns |
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------- |
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pd.DataFrame |
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Pandas DataFrame with converted Datatypes |
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""" |
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# Validate Inputs |
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_validate_input_bool(category, "Category") |
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_validate_input_range(cat_threshold, "cat_threshold", 0, 1) |
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cat_exclude = [] if cat_exclude is None else cat_exclude.copy() |
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data = pd.DataFrame(data).copy() |
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for col in data.columns: |
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unique_vals_ratio = data[col].nunique(dropna=False) / data.shape[0] |
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if ( |
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category |
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and unique_vals_ratio < cat_threshold |
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and col not in cat_exclude |
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and data[col].dtype == "object" |
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): |
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data[col] = data[col].astype("category") |
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data[col] = data[col].convert_dtypes( |
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infer_objects=True, |
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convert_string=True, |
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convert_integer=False, |
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convert_boolean=True, |
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) |
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data = optimize_ints(data) |
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data = optimize_floats(data) |
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return data |
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187
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def drop_missing( |
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data: pd.DataFrame, |
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drop_threshold_cols: float = 1, |
190
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drop_threshold_rows: float = 1, |
191
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col_exclude: Optional[List[str]] = None, |
192
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) -> pd.DataFrame: |
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"""Drop completely empty columns and rows by default and optionally provides \ |
194
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flexibility to loosen restrictions to drop additional non-empty columns and \ |
195
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rows based on the fraction of NA-values. |
196
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197
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Parameters |
198
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---------- |
199
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data : pd.DataFrame |
200
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2D dataset that can be coerced into Pandas DataFrame |
201
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drop_threshold_cols : float, optional |
202
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Drop columns with NA-ratio equal to or above the specified threshold, by \ |
203
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default 1 |
204
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drop_threshold_rows : float, optional |
205
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Drop rows with NA-ratio equal to or above the specified threshold, by default 1 |
206
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col_exclude : Optional[List[str]], optional |
207
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Specify a list of columns to exclude from dropping. The excluded columns do \ |
208
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not affect the drop thresholds, by default None |
209
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210
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Returns |
211
|
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------- |
212
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pd.DataFrame |
213
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Pandas DataFrame without any empty columns or rows |
214
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215
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Notes |
216
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----- |
217
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Columns are dropped first |
218
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""" |
219
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# Validate Inputs |
220
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1 |
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_validate_input_range(drop_threshold_cols, "drop_threshold_cols", 0, 1) |
221
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1 |
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_validate_input_range(drop_threshold_rows, "drop_threshold_rows", 0, 1) |
222
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223
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col_exclude = [] if col_exclude is None else col_exclude.copy() |
224
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1 |
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data_exclude = data[col_exclude] |
225
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226
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1 |
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data = pd.DataFrame(data).copy() |
227
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228
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1 |
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data_dropped = data.drop(columns=col_exclude, errors="ignore") |
229
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1 |
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data_dropped = data_dropped.drop( |
230
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columns=data_dropped.loc[ |
231
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:, _missing_vals(data)["mv_cols_ratio"] > drop_threshold_cols |
232
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].columns |
233
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).dropna(axis=1, how="all") |
234
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235
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1 |
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data = pd.concat([data_dropped, data_exclude], axis=1) |
236
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|
237
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1 |
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return data.drop( |
238
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index=data.loc[ |
239
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_missing_vals(data)["mv_rows_ratio"] > drop_threshold_rows, : |
240
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].index |
241
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).dropna(axis=0, how="all") |
242
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243
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|
244
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1 |
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def data_cleaning( |
245
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data: pd.DataFrame, |
246
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drop_threshold_cols: float = 0.9, |
247
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drop_threshold_rows: float = 0.9, |
248
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drop_duplicates: bool = True, |
249
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convert_dtypes: bool = True, |
250
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col_exclude: Optional[List[str]] = None, |
251
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category: bool = True, |
252
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cat_threshold: float = 0.03, |
253
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cat_exclude: Optional[List[Union[str, int]]] = None, |
254
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clean_col_names: bool = True, |
255
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show: str = "changes", |
256
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) -> pd.DataFrame: |
257
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"""Perform initial data cleaning tasks on a dataset, such as dropping single \ |
258
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valued and empty rows, empty columns as well as optimizing the datatypes. |
259
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|
260
|
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Parameters |
261
|
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---------- |
262
|
|
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data : pd.DataFrame |
263
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|
2D dataset that can be coerced into Pandas DataFrame |
264
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drop_threshold_cols : float, optional |
265
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Drop columns with NA-ratio equal to or above the specified threshold, by \ |
266
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default 0.9 |
267
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drop_threshold_rows : float, optional |
268
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Drop rows with NA-ratio equal to or above the specified threshold, by \ |
269
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default 0.9 |
270
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drop_duplicates : bool, optional |
271
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Drop duplicate rows, keeping the first occurence. This step comes after the \ |
272
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dropping of missing values, by default True |
273
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convert_dtypes : bool, optional |
274
|
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Convert dtypes using pd.convert_dtypes(), by default True |
275
|
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col_exclude : Optional[List[str]], optional |
276
|
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Specify a list of columns to exclude from dropping, by default None |
277
|
|
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category : bool, optional |
278
|
|
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Enable changing dtypes of "object" columns to "category". Set threshold using \ |
279
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cat_threshold. Requires convert_dtypes=True, by default True |
280
|
|
|
cat_threshold : float, optional |
281
|
|
|
Ratio of unique values below which categories are inferred and column dtype is \ |
282
|
|
|
changed to categorical, by default 0.03 |
283
|
|
|
cat_exclude : Optional[List[str]], optional |
284
|
|
|
List of columns to exclude from categorical conversion, by default None |
285
|
|
|
clean_column_names: bool, optional |
286
|
|
|
Cleans the column names and provides hints on duplicate and long names, by \ |
287
|
|
|
default True |
288
|
|
|
show : str, optional |
289
|
|
|
{"all", "changes", None}, by default "changes" |
290
|
|
|
Specify verbosity of the output: |
291
|
|
|
|
292
|
|
|
* "all": Print information about the data before and after cleaning as \ |
293
|
|
|
well as information about changes and memory usage (deep). Please be \ |
294
|
|
|
aware, that this can slow down the function by quite a bit. |
295
|
|
|
* "changes": Print out differences in the data before and after cleaning. |
296
|
|
|
* None: No information about the data and the data cleaning is printed. |
297
|
|
|
|
298
|
|
|
Returns |
299
|
|
|
------- |
300
|
|
|
pd.DataFrame |
301
|
|
|
Cleaned Pandas DataFrame |
302
|
|
|
|
303
|
|
|
See Also |
304
|
|
|
-------- |
305
|
|
|
convert_datatypes: Convert columns to best possible dtypes. |
306
|
|
|
drop_missing : Flexibly drop columns and rows. |
307
|
|
|
_memory_usage: Gives the total memory usage in megabytes. |
308
|
|
|
_missing_vals: Metrics about missing values in the dataset. |
309
|
|
|
|
310
|
|
|
Notes |
311
|
|
|
----- |
312
|
|
|
The category dtype is not grouped in the summary, unless it contains exactly the \ |
313
|
|
|
same categories. |
314
|
|
|
""" |
315
|
|
|
# Validate Inputs |
316
|
1 |
|
_validate_input_range(drop_threshold_cols, "drop_threshold_cols", 0, 1) |
317
|
1 |
|
_validate_input_range(drop_threshold_rows, "drop_threshold_rows", 0, 1) |
318
|
1 |
|
_validate_input_bool(drop_duplicates, "drop_duplicates") |
319
|
1 |
|
_validate_input_bool(convert_dtypes, "convert_datatypes") |
320
|
1 |
|
_validate_input_bool(category, "category") |
321
|
1 |
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_validate_input_range(cat_threshold, "cat_threshold", 0, 1) |
322
|
|
|
|
323
|
1 |
|
data = pd.DataFrame(data).copy() |
324
|
1 |
|
data_cleaned = drop_missing( |
325
|
|
|
data, drop_threshold_cols, drop_threshold_rows, col_exclude=col_exclude |
326
|
|
|
) |
327
|
|
|
|
328
|
1 |
|
if clean_col_names: |
329
|
1 |
|
data_cleaned = clean_column_names(data_cleaned) |
330
|
|
|
|
331
|
1 |
|
single_val_cols = data_cleaned.columns[ |
332
|
|
|
data_cleaned.nunique(dropna=False) == 1 |
333
|
|
|
].tolist() |
334
|
1 |
|
data_cleaned = data_cleaned.drop(columns=single_val_cols) |
335
|
|
|
|
336
|
1 |
|
dupl_rows = None |
337
|
|
|
|
338
|
1 |
|
if drop_duplicates: |
339
|
1 |
|
data_cleaned, dupl_rows = _drop_duplicates(data_cleaned) |
340
|
1 |
|
if convert_dtypes: |
341
|
1 |
|
data_cleaned = convert_datatypes( |
342
|
|
|
data_cleaned, |
343
|
|
|
category=category, |
344
|
|
|
cat_threshold=cat_threshold, |
345
|
|
|
cat_exclude=cat_exclude, |
346
|
|
|
) |
347
|
|
|
|
348
|
1 |
|
_diff_report( |
349
|
|
|
data, |
350
|
|
|
data_cleaned, |
351
|
|
|
dupl_rows=dupl_rows, |
352
|
|
|
single_val_cols=single_val_cols, |
353
|
|
|
show=show, |
354
|
|
|
) |
355
|
|
|
|
356
|
1 |
|
return data_cleaned |
357
|
|
|
|
358
|
|
|
|
359
|
1 |
|
class DataCleaner(BaseEstimator, TransformerMixin): |
360
|
|
|
"""Wrapper for data_cleaning(). Allows data_cleaning() to be put into a pipeline \ |
361
|
|
|
with similar functions (e.g. using MVColHandler() or SubsetPooler()). |
362
|
|
|
|
363
|
|
|
Parameters |
364
|
|
|
---------- |
365
|
|
|
drop_threshold_cols: float, default 0.9 |
366
|
|
|
Drop columns with NA-ratio equal to or above the specified threshold. |
367
|
|
|
drop_threshold_rows: float, default 0.9 |
368
|
|
|
Drop rows with NA-ratio equal to or above the specified threshold. |
369
|
|
|
drop_duplicates: bool, default True |
370
|
|
|
Drop duplicate rows, keeping the first occurence. This step comes after the \ |
371
|
|
|
dropping of missing values. |
372
|
|
|
convert_dtypes: bool, default True |
373
|
|
|
Convert dtypes using pd.convert_dtypes(). |
374
|
|
|
col_exclude: list, default None |
375
|
|
|
Specify a list of columns to exclude from dropping. |
376
|
|
|
category: bool, default True |
377
|
|
|
Change dtypes of columns to "category". Set threshold using cat_threshold. \ |
378
|
|
|
Requires convert_dtypes=True |
379
|
|
|
cat_threshold: float, default 0.03 |
380
|
|
|
Ratio of unique values below which categories are inferred and column dtype is \ |
381
|
|
|
changed to categorical. |
382
|
|
|
cat_exclude: list, default None |
383
|
|
|
List of columns to exclude from categorical conversion. |
384
|
|
|
clean_column_names: bool, optional |
385
|
|
|
Cleans the column names and provides hints on duplicate and long names, by \ |
386
|
|
|
default True |
387
|
|
|
show: str, optional |
388
|
|
|
{"all", "changes", None}, by default "changes" |
389
|
|
|
Specify verbosity of the output: |
390
|
|
|
* "all": Print information about the data before and after cleaning as \ |
391
|
|
|
well as information about changes and memory usage (deep). Please be \ |
392
|
|
|
aware, that this can slow down the function by quite a bit. |
393
|
|
|
* "changes": Print out differences in the data before and after cleaning. |
394
|
|
|
* None: No information about the data and the data cleaning is printed. |
395
|
|
|
|
396
|
|
|
Returns |
397
|
|
|
------- |
398
|
|
|
data_cleaned: Pandas DataFrame |
399
|
|
|
""" |
400
|
|
|
|
401
|
1 |
|
def __init__( |
402
|
|
|
self, |
403
|
|
|
drop_threshold_cols: float = 0.9, |
404
|
|
|
drop_threshold_rows: float = 0.9, |
405
|
|
|
drop_duplicates: bool = True, |
406
|
|
|
convert_dtypes: bool = True, |
407
|
|
|
col_exclude: Optional[List[str]] = None, |
408
|
|
|
category: bool = True, |
409
|
|
|
cat_threshold: float = 0.03, |
410
|
|
|
cat_exclude: Optional[List[Union[str, int]]] = None, |
411
|
|
|
clean_col_names: bool = True, |
412
|
|
|
show: str = "changes", |
413
|
|
|
): |
414
|
|
|
self.drop_threshold_cols = drop_threshold_cols |
415
|
|
|
self.drop_threshold_rows = drop_threshold_rows |
416
|
|
|
self.drop_duplicates = drop_duplicates |
417
|
|
|
self.convert_dtypes = convert_dtypes |
418
|
|
|
self.col_exclude = col_exclude |
419
|
|
|
self.category = category |
420
|
|
|
self.cat_threshold = cat_threshold |
421
|
|
|
self.cat_exclude = cat_exclude |
422
|
|
|
self.clean_col_names = clean_col_names |
423
|
|
|
self.show = show |
424
|
|
|
|
425
|
1 |
|
def fit(self, data, target=None): |
426
|
|
|
return self |
427
|
|
|
|
428
|
1 |
|
def transform(self, data, target=None): |
429
|
|
|
return data_cleaning( |
430
|
|
|
data, |
431
|
|
|
drop_threshold_cols=self.drop_threshold_cols, |
432
|
|
|
drop_threshold_rows=self.drop_threshold_rows, |
433
|
|
|
drop_duplicates=self.drop_duplicates, |
434
|
|
|
convert_dtypes=self.convert_dtypes, |
435
|
|
|
col_exclude=self.col_exclude, |
436
|
|
|
category=self.category, |
437
|
|
|
cat_threshold=self.cat_threshold, |
438
|
|
|
cat_exclude=self.cat_exclude, |
439
|
|
|
clean_col_names=self.clean_col_names, |
440
|
|
|
show=self.show, |
441
|
|
|
) |
442
|
|
|
|
443
|
|
|
|
444
|
1 |
|
def mv_col_handling( |
445
|
|
|
data: pd.DataFrame, |
446
|
|
|
target: Optional[Union[str, pd.Series, List]] = None, |
447
|
|
|
mv_threshold: float = 0.1, |
448
|
|
|
corr_thresh_features: float = 0.5, |
449
|
|
|
corr_thresh_target: float = 0.3, |
450
|
|
|
return_details: bool = False, |
451
|
|
|
) -> pd.DataFrame: |
452
|
|
|
"""Convert columns with a high ratio of missing values into binary features and \ |
453
|
|
|
eventually drops them based on their correlation with other features and the \ |
454
|
|
|
target variable. |
455
|
|
|
|
456
|
|
|
This function follows a three step process: |
457
|
|
|
- 1) Identify features with a high ratio of missing values (above 'mv_threshold'). |
458
|
|
|
- 2) Identify high correlations of these features among themselves and with \ |
459
|
|
|
other features in the dataset (above 'corr_thresh_features'). |
460
|
|
|
- 3) Features with high ratio of missing values and high correlation among each \ |
461
|
|
|
other are dropped unless they correlate reasonably well with the target \ |
462
|
|
|
variable (above 'corr_thresh_target'). |
463
|
|
|
|
464
|
|
|
Note: If no target is provided, the process exits after step two and drops columns \ |
465
|
|
|
identified up to this point. |
466
|
|
|
|
467
|
|
|
Parameters |
468
|
|
|
---------- |
469
|
|
|
data : pd.DataFrame |
470
|
|
|
2D dataset that can be coerced into Pandas DataFrame |
471
|
|
|
target : Optional[Union[str, pd.Series, List]], optional |
472
|
|
|
Specify target for correlation. I.e. label column to generate only the \ |
473
|
|
|
correlations between each feature and the label, by default None |
474
|
|
|
mv_threshold : float, optional |
475
|
|
|
Value between 0 <= threshold <= 1. Features with a missing-value-ratio larger \ |
476
|
|
|
than mv_threshold are candidates for dropping and undergo further analysis, by \ |
477
|
|
|
default 0.1 |
478
|
|
|
corr_thresh_features : float, optional |
479
|
|
|
Value between 0 <= threshold <= 1. Maximum correlation a previously identified \ |
480
|
|
|
features (with a high mv-ratio) is allowed to have with another feature. If \ |
481
|
|
|
this threshold is overstepped, the feature undergoes further analysis, by \ |
482
|
|
|
default 0.5 |
483
|
|
|
corr_thresh_target : float, optional |
484
|
|
|
Value between 0 <= threshold <= 1. Minimum required correlation of a remaining \ |
485
|
|
|
feature (i.e. feature with a high mv-ratio and high correlation to another \ |
486
|
|
|
existing feature) with the target. If this threshold is not met the feature is \ |
487
|
|
|
ultimately dropped, by default 0.3 |
488
|
|
|
return_details : bool, optional |
489
|
|
|
Provdies flexibility to return intermediary results, by default False |
490
|
|
|
|
491
|
|
|
Returns |
492
|
|
|
------- |
493
|
|
|
pd.DataFrame |
494
|
|
|
Updated Pandas DataFrame |
495
|
|
|
|
496
|
|
|
optional: |
497
|
|
|
cols_mv: Columns with missing values included in the analysis |
498
|
|
|
drop_cols: List of dropped columns |
499
|
|
|
""" |
500
|
|
|
# Validate Inputs |
501
|
|
|
_validate_input_range(mv_threshold, "mv_threshold", 0, 1) |
502
|
|
|
_validate_input_range(corr_thresh_features, "corr_thresh_features", 0, 1) |
503
|
|
|
_validate_input_range(corr_thresh_target, "corr_thresh_target", 0, 1) |
504
|
|
|
|
505
|
|
|
data = pd.DataFrame(data).copy() |
506
|
|
|
data_local = data.copy() |
507
|
|
|
mv_ratios = _missing_vals(data_local)["mv_cols_ratio"] |
508
|
|
|
cols_mv = mv_ratios[mv_ratios > mv_threshold].index.tolist() |
509
|
|
|
data_local[cols_mv] = ( |
510
|
|
|
data_local[cols_mv].applymap(lambda x: 1 if not pd.isnull(x) else x).fillna(0) |
511
|
|
|
) |
512
|
|
|
|
513
|
|
|
high_corr_features = [] |
514
|
|
|
data_temp = data_local.copy() |
515
|
|
|
for col in cols_mv: |
516
|
|
|
corrmat = corr_mat(data_temp, colored=False) |
517
|
|
|
if abs(corrmat[col]).nlargest(2)[1] > corr_thresh_features: |
518
|
|
|
high_corr_features.append(col) |
519
|
|
|
data_temp = data_temp.drop(columns=[col]) |
520
|
|
|
|
521
|
|
|
drop_cols = [] |
522
|
|
|
if target is None: |
523
|
|
|
data = data.drop(columns=high_corr_features) |
524
|
|
|
else: |
525
|
|
|
corrs = corr_mat(data_local, target=target, colored=False).loc[ |
526
|
|
|
high_corr_features |
527
|
|
|
] |
528
|
|
|
drop_cols = corrs.loc[abs(corrs.iloc[:, 0]) < corr_thresh_target].index.tolist() |
529
|
|
|
data = data.drop(columns=drop_cols) |
530
|
|
|
|
531
|
|
|
if return_details: |
532
|
|
|
return data, cols_mv, drop_cols |
533
|
|
|
|
534
|
|
|
return data |
535
|
|
|
|
536
|
|
|
|
537
|
1 |
|
class MVColHandler(BaseEstimator, TransformerMixin): |
538
|
|
|
"""Wrapper for mv_col_handling(). Allows mv_col_handling() to be put into a \ |
539
|
|
|
pipeline with similar functions (e.g. using DataCleaner() or SubsetPooler()). |
540
|
|
|
|
541
|
|
|
Parameters |
542
|
|
|
---------- |
543
|
|
|
target: string, list, np.array or pd.Series, default None |
544
|
|
|
Specify target for correlation. E.g. label column to generate only the \ |
545
|
|
|
correlations between each feature and the label. |
546
|
|
|
mv_threshold: float, default 0.1 |
547
|
|
|
Value between 0 <= threshold <= 1. Features with a missing-value-ratio larger \ |
548
|
|
|
than mv_threshold are candidates for dropping and undergo further analysis. |
549
|
|
|
corr_thresh_features: float, default 0.6 |
550
|
|
|
Value between 0 <= threshold <= 1. Maximum correlation a previously identified \ |
551
|
|
|
features with a high mv-ratio is allowed to have with another feature. If this \ |
552
|
|
|
threshold is overstepped, the feature undergoes further analysis. |
553
|
|
|
corr_thresh_target: float, default 0.3 |
554
|
|
|
Value between 0 <= threshold <= 1. Minimum required correlation of a remaining \ |
555
|
|
|
feature (i.e. feature with a high mv-ratio and high correlation to another \ |
556
|
|
|
existing feature) with the target. If this threshold is not met the feature is \ |
557
|
|
|
ultimately dropped. |
558
|
|
|
return_details: bool, default True |
559
|
|
|
Provdies flexibility to return intermediary results. |
560
|
|
|
|
561
|
|
|
Returns |
562
|
|
|
------- |
563
|
|
|
data: Updated Pandas DataFrame |
564
|
|
|
""" |
565
|
|
|
|
566
|
1 |
|
def __init__( |
567
|
|
|
self, |
568
|
|
|
target: Optional[Union[str, pd.Series, List]] = None, |
569
|
|
|
mv_threshold: float = 0.1, |
570
|
|
|
corr_thresh_features: float = 0.6, |
571
|
|
|
corr_thresh_target: float = 0.3, |
572
|
|
|
return_details: bool = True, |
573
|
|
|
): |
574
|
|
|
self.target = target |
575
|
|
|
self.mv_threshold = mv_threshold |
576
|
|
|
self.corr_thresh_features = corr_thresh_features |
577
|
|
|
self.corr_thresh_target = corr_thresh_target |
578
|
|
|
self.return_details = return_details |
579
|
|
|
|
580
|
1 |
|
def fit(self, data, target=None): |
581
|
|
|
return self |
582
|
|
|
|
583
|
1 |
|
def transform(self, data, target=None): |
584
|
|
|
data, cols_mv, dropped_cols = mv_col_handling( |
585
|
|
|
data, |
586
|
|
|
target=self.target, |
587
|
|
|
mv_threshold=self.mv_threshold, |
588
|
|
|
corr_thresh_features=self.corr_thresh_features, |
589
|
|
|
corr_thresh_target=self.corr_thresh_target, |
590
|
|
|
return_details=self.return_details, |
591
|
|
|
) |
592
|
|
|
|
593
|
|
|
print(f"\nFeatures with MV-ratio > {self.mv_threshold}: {len(cols_mv)}") |
594
|
|
|
print("Features dropped:", len(dropped_cols), dropped_cols) |
595
|
|
|
|
596
|
|
|
return data |
597
|
|
|
|
598
|
|
|
|
599
|
1 |
|
def pool_duplicate_subsets( |
600
|
|
|
data: pd.DataFrame, |
601
|
|
|
col_dupl_thresh: float = 0.2, |
602
|
|
|
subset_thresh: float = 0.2, |
603
|
|
|
min_col_pool: int = 3, |
604
|
|
|
exclude: Optional[List[str]] = None, |
605
|
|
|
return_details=False, |
606
|
|
|
) -> pd.DataFrame: |
607
|
|
|
"""Check for duplicates in subsets of columns and pools them. This can reduce \ |
608
|
|
|
the number of columns in the data without loosing much information. Suitable \ |
609
|
|
|
columns are combined to subsets and tested for duplicates. In case sufficient \ |
610
|
|
|
duplicates can be found, the respective columns are aggregated into a \ |
611
|
|
|
"pooled_var" column. Identical numbers in the "pooled_var" column indicate \ |
612
|
|
|
identical information in the respective rows. |
613
|
|
|
|
614
|
|
|
Note: It is advised to exclude features that provide sufficient informational \ |
615
|
|
|
content by themselves as well as the target column by using the "exclude" \ |
616
|
|
|
setting. |
617
|
|
|
|
618
|
|
|
Parameters |
619
|
|
|
---------- |
620
|
|
|
data : pd.DataFrame |
621
|
|
|
2D dataset that can be coerced into Pandas DataFrame |
622
|
|
|
col_dupl_thresh : float, optional |
623
|
|
|
Columns with a ratio of duplicates higher than "col_dupl_thresh" are \ |
624
|
|
|
considered in the further analysis. Columns with a lower ratio are not \ |
625
|
|
|
considered for pooling, by default 0.2 |
626
|
|
|
subset_thresh : float, optional |
627
|
|
|
The first subset with a duplicate threshold higher than "subset_thresh" is \ |
628
|
|
|
chosen and aggregated. If no subset reaches the threshold, the algorithm \ |
629
|
|
|
continues with continuously smaller subsets until "min_col_pool" is reached, \ |
630
|
|
|
by default 0.2 |
631
|
|
|
min_col_pool : int, optional |
632
|
|
|
Minimum number of columns to pool. The algorithm attempts to combine as many \ |
633
|
|
|
columns as possible to suitable subsets and stops when "min_col_pool" is \ |
634
|
|
|
reached, by default 3 |
635
|
|
|
exclude : Optional[List[str]], optional |
636
|
|
|
List of column names to be excluded from the analysis. These columns are \ |
637
|
|
|
passed through without modification, by default None |
638
|
|
|
return_details : bool, optional |
639
|
|
|
Provdies flexibility to return intermediary results, by default False |
640
|
|
|
|
641
|
|
|
Returns |
642
|
|
|
------- |
643
|
|
|
pd.DataFrame |
644
|
|
|
DataFrame with low cardinality columns pooled |
645
|
|
|
|
646
|
|
|
optional: |
647
|
|
|
subset_cols: List of columns used as subset |
648
|
|
|
""" |
649
|
|
|
# Input validation |
650
|
1 |
|
_validate_input_range(col_dupl_thresh, "col_dupl_thresh", 0, 1) |
651
|
1 |
|
_validate_input_range(subset_thresh, "subset_thresh", 0, 1) |
652
|
1 |
|
_validate_input_range(min_col_pool, "min_col_pool", 0, data.shape[1]) |
653
|
|
|
|
654
|
1 |
|
excluded_cols = [] |
655
|
1 |
|
if exclude is not None: |
656
|
|
|
excluded_cols = data[exclude] |
657
|
|
|
data = data.drop(columns=exclude) |
658
|
|
|
|
659
|
1 |
|
subset_cols = [] |
660
|
1 |
|
for i in range(data.shape[1] + 1 - min_col_pool): |
661
|
|
|
# Consider only columns with lots of duplicates |
662
|
1 |
|
check_list = [ |
663
|
|
|
col |
664
|
|
|
for col in data.columns |
665
|
|
|
if data.duplicated(subset=col).mean() > col_dupl_thresh |
666
|
|
|
] |
667
|
|
|
|
668
|
|
|
# Identify all possible combinations for the current interation |
669
|
1 |
|
if check_list: |
670
|
1 |
|
combinations = itertools.combinations(check_list, len(check_list) - i) |
671
|
|
|
else: |
672
|
|
|
continue |
673
|
|
|
|
674
|
|
|
# Check subsets for all possible combinations |
675
|
1 |
|
ratios = [ |
676
|
|
|
*map(lambda comb: data.duplicated(subset=list(comb)).mean(), combinations) |
677
|
|
|
] |
678
|
1 |
|
max_idx = np.argmax(ratios) |
679
|
|
|
|
680
|
1 |
|
if max(ratios) > subset_thresh: |
681
|
|
|
# Get the best possible iterator and process the data |
682
|
1 |
|
best_subset = itertools.islice( |
683
|
|
|
itertools.combinations(check_list, len(check_list) - i), |
684
|
|
|
max_idx, |
685
|
|
|
max_idx + 1, |
686
|
|
|
) |
687
|
|
|
|
688
|
1 |
|
best_subset = data[list(list(best_subset)[0])] |
689
|
1 |
|
subset_cols = best_subset.columns.tolist() |
690
|
|
|
|
691
|
1 |
|
unique_subset = ( |
692
|
|
|
best_subset.drop_duplicates() |
693
|
|
|
.reset_index() |
694
|
|
|
.rename(columns={"index": "pooled_vars"}) |
695
|
|
|
) |
696
|
1 |
|
data = data.merge(unique_subset, how="left", on=subset_cols).drop( |
697
|
|
|
columns=subset_cols |
698
|
|
|
) |
699
|
1 |
|
data.index = pd.RangeIndex(len(data)) |
700
|
1 |
|
break |
701
|
|
|
|
702
|
1 |
|
data = pd.concat([data, pd.DataFrame(excluded_cols)], axis=1) |
703
|
|
|
|
704
|
1 |
|
if return_details: |
705
|
|
|
return data, subset_cols |
706
|
|
|
|
707
|
1 |
|
return data |
708
|
|
|
|
709
|
|
|
|
710
|
1 |
|
class SubsetPooler(BaseEstimator, TransformerMixin): |
711
|
|
|
"""Wrapper for pool_duplicate_subsets(). Allows pool_duplicate_subsets() to be \ |
712
|
|
|
put into a pipeline with similar functions (e.g. using DataCleaner() or \ |
713
|
|
|
MVColHandler()). |
714
|
|
|
|
715
|
|
|
Parameters |
716
|
|
|
---------- |
717
|
|
|
col_dupl_ratio: float, default 0.2 |
718
|
|
|
Columns with a ratio of duplicates higher than "col_dupl_ratio" are considered \ |
719
|
|
|
in the further analysis. Columns with a lower ratio are not considered for \ |
720
|
|
|
pooling. |
721
|
|
|
dupl_thresh: float, default 0.2 |
722
|
|
|
The first subset with a duplicate threshold higher than "dupl_thresh" is \ |
723
|
|
|
chosen and aggregated. If no subset reaches the threshold, the algorithm \ |
724
|
|
|
continues with continuously smaller subsets until "min_col_pool" is reached. |
725
|
|
|
min_col_pool: integer, default 3 |
726
|
|
|
Minimum number of columns to pool. The algorithm attempts to combine as many \ |
727
|
|
|
columns as possible to suitable subsets and stops when "min_col_pool" is \ |
728
|
|
|
reached. |
729
|
|
|
return_details: bool, default False |
730
|
|
|
Provdies flexibility to return intermediary results. |
731
|
|
|
|
732
|
|
|
Returns |
733
|
|
|
------- |
734
|
|
|
data: pd.DataFrame |
735
|
|
|
""" |
736
|
|
|
|
737
|
1 |
|
def __init__( |
738
|
|
|
self, |
739
|
|
|
col_dupl_thresh=0.2, |
740
|
|
|
subset_thresh=0.2, |
741
|
|
|
min_col_pool=3, |
742
|
|
|
return_details=True, |
743
|
|
|
): |
744
|
|
|
self.col_dupl_thresh = col_dupl_thresh |
745
|
|
|
self.subset_thresh = subset_thresh |
746
|
|
|
self.min_col_pool = min_col_pool |
747
|
|
|
self.return_details = return_details |
748
|
|
|
|
749
|
1 |
|
def fit(self, data, target=None): |
750
|
|
|
return self |
751
|
|
|
|
752
|
1 |
|
@staticmethod |
753
|
1 |
|
def transform(data, target=None): |
754
|
|
|
data, subset_cols = pool_duplicate_subsets( |
755
|
|
|
data, |
756
|
|
|
col_dupl_thresh=0.2, |
757
|
|
|
subset_thresh=0.2, |
758
|
|
|
min_col_pool=3, |
759
|
|
|
return_details=True, |
760
|
|
|
) |
761
|
|
|
|
762
|
|
|
print("Combined columns:", len(subset_cols), subset_cols) |
763
|
|
|
|
764
|
|
|
return data |
765
|
|
|
|