# HIDDEN
# Clear previously defined variables
%reset -f

import os
os.chdir(os.path.expanduser('~/notebooks/04'))

# HIDDEN
import warnings
# Ignore numpy dtype warnings. These warnings are caused by an interaction
# between numpy and Cython and can be safely ignored.
# Reference: https://stackoverflow.com/a/40846742
warnings.filterwarnings("ignore", message="numpy.dtype size changed")
warnings.filterwarnings("ignore", message="numpy.ufunc size changed")

import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
%matplotlib inline
import ipywidgets as widgets
from ipywidgets import interact, interactive, fixed, interact_manual
import nbinteract as nbi

sns.set()
sns.set_context('talk')
np.set_printoptions(threshold=20, precision=2, suppress=True)
pd.options.display.max_rows = 7
pd.options.display.max_columns = 8
pd.set_option('precision', 2)
# This option stops scientific notation for pandas
# pd.set_option('display.float_format', '{:.2f}'.format)

# HIDDEN
def df_interact(df, nrows=7, ncols=7):
'''
Outputs sliders that show rows and columns of df
'''
def peek(row=0, col=0):
return df.iloc[row:row + nrows, col:col + ncols]

row_arg = (0, len(df), nrows) if len(df) > nrows else fixed(0)
col_arg = ((0, len(df.columns), ncols)
if len(df.columns) > ncols else fixed(0))

interact(peek, row=row_arg, col=col_arg)
print('({} rows, {} columns) total'.format(df.shape[0], df.shape[1]))

# HIDDEN
babies_small = pd.read_csv('data/babies23.data', delimiter='\s+')[['wt', 'race', 'ed']]


## Data Types¶

We often begin exploratory data analysis by examining the types of data that occur in a table. Although there are multiple ways of categorizing data types, in this book we discuss three broad types of data:

1. Nominal data, which represents categories that do not have a natural ordering. For example: political party affiliation (Democrat, Republican, Other), sex (male, female, other), and computer operating system (Windows, MacOS, Linux).
2. Ordinal data, which represents ordered categories. For example: T-shirt sizes (small, medium, large), Likert-scale responses (disagree, neutral, agree), and level of education (high school, college, graduate school). Ordinal and nominal data are considered subtypes of categorical data.
3. Numerical data, which represents amounts or quantities. For example: heights, prices, and distances.

We refer to these types as statistical data types, or simply data types.

Computational vs. Statistical Data Types

pandas assigns each column of a DataFrame a computational data type that represents how the data are stored in the computer's memory. It is essential to remember that the statistical data type can differ from the computational data type.

For example, consider the table below which records weights of babies at birth, race of the mother, and educational level of the mother.

babies_small

wt race ed
0 120 8 5
1 113 0 5
2 128 0 2
... ... ... ...
1233 130 1 2
1234 125 0 4
1235 117 0 4

1236 rows × 3 columns

Every column of this DataFrame has a numeric computational data type. In this case, the int64 type signifies that each column contains integers.

babies_small.dtypes

wt      int64
race    int64
ed      int64
dtype: object

However, it does not make sense to work with all three columns as if they have a numeric statistical data type. In order to understand the dataset's data types, we almost always need to consult the dataset's data dictionary. A data dictionary is a document included with the data that describes what each column in the data records. For example, the data dictionary for this dataset states the following:

wt -  birth weight in ounces (999 unknown)
race - mother's race 0-5=white 6=mex 7=black 8=asian 9=mixed 99=unknown
ed - mother's education 0= less than 8th grade,
4=HS+some college 5= College graduate, 6&7 Trade school HS unclear, 9=unknown

Although the wt, race, and ed columns are stored as integers in pandas, the race column contains nominal data and ed contains ordinal data.

In fact, we must exercise caution even with the wt column. Computing the average birth weight by taking the average of the wt column will not give an accurate result because unknown values are recorded as 999. If left as is, the unknown values will cause our average to be higher than it should be.

The Importance of Data Types

Data types guide further data analysis by specifying the operations, visualizations, and models we can meaningfully apply to values in the data. For example, the magnitudes of differences between numerical data are meaningful while the magnitudes of differences between ordinal data are not. This means that for the babies_small DataFrame the mean baby birth weight has meaning but not the "mean" educational level.

pandas will not complain if we attempt to compute the mean of the values in the educational level column:

# Don't use this value in actual data analysis
babies_small['ed'].mean()

2.9215210355987056

This quantity, however, provides no useful information. We could have easily replaced the values in the ed column with their string descriptions — for example, we can replace 0's with 'less than 8th grade', 1's with '8th-12th grade', and so on. We would not say that the "mean" of these strings contains much value. We would not say the same with the mean of the numeric values either.

Although the value differences of ordinal data are not meaningful, the direction of the difference has meaning. For example, we could say a mother with ed=5 (college graduate) has a greater education level than a mother with ed=2 (high school graduate).

Nominal data, in comparison, do not provide meaning in the direction of the differences. A mother with race=6 (Mexican) and a mother with race=7 (Black) simply have different races.

### Example: Maternal Smoking and Infant Health¶

The Child Health and Development Studies (CHDS) organization conducts long-term research on how health and disease are passed on between generations (http://www.chdstudies.org/about_us/index.php).

In one notable study, the CHDS collected comprehensive data on all pregnancies between 1960 and 1967 for women using the Kaiser Foundation Health Plan in the San Francisco-East Bay area. Although the CHDS typically requires submitting a request to access its data, a subset of the data on pregnancies is available online through the Stat Labs website (link). We have downloaded and read the data into a pandas DataFrame below.

babies = pd.read_csv('data/babies.data', delimiter='\s+')
babies

bwt gestation parity age height weight smoke
0 120 284 0 27 62 100 0
1 113 282 0 33 64 135 0
2 128 279 0 28 64 115 1
... ... ... ... ... ... ... ...
1233 130 291 0 30 65 150 1
1234 125 281 1 21 65 110 0
1235 117 297 0 38 65 129 0

1236 rows × 7 columns

To understand the data types of the columns, we refer to the data dictionary. We have copied the data dictionary from the Stat Labs website into this page for convenience:

 Variable Description bwt Birth weight in ounces (999 unknown) gestation Length of pregnancy in days (999 unknown) parity 0= first born, 9=unknown age mother's age in years height mother's height in inches (99 unknown) weight Mother's prepregnancy weight in pounds (999 unknown) smoke Smoking status of mother   0=not now, 1=yes now, 9=unknown

Although the data dictionary does not explicitly specify the data types, we can clearly see that some columns contain nominal data even though all data values appear as numbers in the table. Based on the descriptions of the columns alone, we would likely treat the parity and smoke columns as nominal data and the remaining columns as numerical.

We hope that the data dictionary provides all necessary information about each column; it is nonetheless useful to double-check our hope by examining the data themselves. For example, it will not always be clear whether a column that records ages contains age values (21, 30, 41) or age ranges (21-29, 30-40, 41+).

The babies DataFrame appears to exclusively contain integer values:

babies

bwt gestation parity age height weight smoke
0 120 284 0 27 62 100 0
1 113 282 0 33 64 135 0
2 128 279 0 28 64 115 1
... ... ... ... ... ... ... ...
1233 130 291 0 30 65 150 1
1234 125 281 1 21 65 110 0
1235 117 297 0 38 65 129 0

1236 rows × 7 columns

To peek at a column's values, we can use the series.value_counts() method which counts the number of times each value appears.

# Displays the ages (left) and their counts (right)
babies['age'].value_counts()

23    93
26    90
24    86
..
45     1
44     1
15     1
Name: age, Length: 31, dtype: int64

We can see that many of the mothers in the dataset were between 24 and 26 years old. In addition, we do not see any fractional ages (e.g. 24.5), suggesting that the age column contains integers.

By default, pandas restricts its output to only show a few values at once. To see more possible values, we can ask pandas to display more rows, though the output can be verbose if there are many rows to display.

from IPython.display import display

# Within this block, display up to 10 rows. To display more rows,
# change the 10 in the code below to a higher number.
with pd.option_context('display.max_rows', 10):
display(babies['age'].value_counts())

23    93
26    90
24    86
27    85
22    79
..
42     4
99     2
45     1
44     1
15     1
Name: age, Length: 31, dtype: int64

After double checking the values within the rest of the columns in the DataFrame in a similar way, we label each column with the following data types based on the data dictionary and examination of the data values.

Variable Description Data Type
bwt Birth weight in ounces (999 unknown) Numerical
gestation Length of pregnancy in days (999 unknown) Numerical
parity 0= first born, 9=unknown Nominal
age mother's age in years Numerical
height mother's height in inches (99 unknown) Numerical
weight Mother's prepregnancy weight in pounds (999 unknown) Numerical
smoke Smoking status of mother (0=not now, 1=yes now, 9=unknown) Nominal

### Example: San Francisco Restaurant Health Violations¶

The city of San Francisco, California periodically inspects restaurants for health code violations. At each inspection, the restaurant receives a score from 0 to 100 based on the number and types of violations recorded. The restuarants, scores, and violations are publicly available on the DataSF website (link); the dataset contains all inspections from January 2016 and onward.

We have loaded a subset of the data into the scores DataFrame below.

scores = pd.read_csv('data/SFRestaurants.csv')
scores

0 All stars Donuts 86.0 Unclean or degraded floors walls or ceilings Low Risk
1 Soo Fong Restaurant 92.0 Wiping cloths not clean or properly stored or ... Low Risk
2 Dar Bar Pakistani/Indian Cusine 86.0 Moderate risk vermin infestation Moderate Risk
... ... ... ... ...
52795 USA Power Market 71.0 Unclean hands or improper use of gloves High Risk
52796 Thai Cottage Restaurant 81.0 Inadequate and inaccessible handwashing facili... Moderate Risk
52797 St Mary's Cathedral/Convention Center 90.0 Inadequate and inaccessible handwashing facili... Moderate Risk

52798 rows × 4 columns

For this dataset, we are fortunate enough to have a data dictionary that provides some information on the data types:

Field Name Data Type Description
inspection_score number Calculated inspection score, 0-100
violation_description string One line description of the violation.
risk_category string (No description provided.)

However, we see that the data dictionary describes computational data types rather than statistical data types — for example, it uses string rather than distinguishing between nominal and ordinal data types. In addition, the risk_category column does not have a description.

Text Data is not Always Nominal Data

The violation_description column provides a description of the violation. However, it is unclear from the data dictionary alone if we should treat the column's value as nominal data. The violation_description column might contain unstructured text, or free-form text entered in by hand. Unstructured text often originates from open-ended natural language data sources, such as newspaper articles, Google search queries, and free-response survey questions.

We typically do not treat free-form text as nominal data — nominal data typically record a fixed number of categories while unstructured text does not. Thus, we should check the contents of the violation_description column to determine whether it contains unstructured text data or nominal data.

If the violation_description column contains unstructured text, we would expect that few of its values repeat often because there are many ways to record the same violation: unclean floors, dirty floors, floor needs cleaning, and so on. On the other hand, if the violation_description column contains data selected from a pre-specified list, many of the values should repeat.

We indeed find that the column contains many repeat entries:

with pd.option_context('display.max_rows', 14):
display(scores['violation_description'].value_counts())

Unclean or degraded floors walls or ceilings                          3668
Unapproved or unmaintained equipment or utensils                      2704
Inadequate and inaccessible handwashing facilities                    2653
Moderate risk food holding temperature                                2588
Inadequately cleaned or sanitized food contact surfaces               2467
Wiping cloths not clean or properly stored or inadequate sanitizer    2121
Foods not protected from contamination                                1929
...
Discharge from employee nose mouth or eye                                6
Noncompliance with Gulf Coast oyster regulation                          5
Mobile food facility stored in unapproved location                       4
Mobile food facility with unapproved operating conditions                3
Unreported or unrestricted ill employee with communicable disease        1
Noncompliance with Cottage Food Operation                                1
Mobile food facility HCD insignia unavailable                            1
Name: violation_description, Length: 67, dtype: int64

This leads us to believe that the values in the violation_description column were selected from a list of possible violations. Thus, we treat the violation_description column as if it contains nominal data.

Investigating a Missing Description

Although the risk_category column was not described in the data dictionary, we can examine the column's contents to infer its meaning. First, we find that the column only has three unique values:

scores['risk_category'].value_counts()

Low Risk         19694
Moderate Risk    14712
High Risk         5686
Name: risk_category, dtype: int64

We might sense that these values describe the severity of the violation. We can check this intuition by examining violations for each value in the risk_category column.

def risk_counts(risk):
return (scores.loc[scores['risk_category'] == risk,
'violation_description']

risk_counts('High Risk')

High risk food holding temperature             1619
Unclean or unsanitary food contact surfaces    1197
Improper cooling methods                        823
Unclean hands or improper use of gloves         755
High risk vermin infestation                    712
Name: violation_description, dtype: int64
risk_counts('Moderate Risk')

Inadequate and inaccessible handwashing facilities         2653
Moderate risk food holding temperature                     2588
Inadequately cleaned or sanitized food contact surfaces    2467
Foods not protected from contamination                     1929
Moderate risk vermin infestation                           1814
Name: violation_description, dtype: int64
risk_counts('Low Risk')

Unclean or degraded floors walls or ceilings                          3668
Unapproved or unmaintained equipment or utensils                      2704
Wiping cloths not clean or properly stored or inadequate sanitizer    2121
Improper food storage                                                 1817
Unclean nonfood contact surfaces                                      1440
Name: violation_description, dtype: int64

At a cursory glance, the violation categories are divided into each risk level. In addition, the High Risk violations seem more likely to cause illness than the Low Risk violations. Presumably a restaurant with High risk vermin infestation would be less sanitary than a restaurant with Unclean nonfood contact surfaces.

Because of this, we decide that the risk_category column contains ordinal data describing the risk level of each violation (Low Risk < Moderate Risk < High Risk).

A Revised Data Dictionary

After investigating the remaining columns of the scores DataFrame, we arrive at the following revised data dictionary that we can use for further analysis:

Field Name Data Type Description