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diff --git a/docs/data100_logo.png b/docs/data100_logo.png
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diff --git a/eda/eda.html b/docs/eda/eda.html
similarity index 80%
rename from eda/eda.html
rename to docs/eda/eda.html
index 6944abfb7..47fdd83f7 100644
--- a/eda/eda.html
+++ b/docs/eda/eda.html
@@ -686,7 +686,7 @@
force=False)
covid_file # a file path wrapper object
-
Using cached version that was downloaded (UTC): Mon Mar 18 21:13:08 2024
+
Using cached version that was downloaded (UTC): Fri Aug 25 09:57:25 2023
PosixPath('data/confirmed-cases.json')
@@ -718,7 +718,7 @@
!ls -lh {covid_file}!wc -l {covid_file}
-
-rw-r--r-- 1 Ishani staff 114K Mar 18 21:13 data/confirmed-cases.json
+
-rw-r--r-- 1 lillianweng staff 114K Aug 25 2023 data/confirmed-cases.json
1109 data/confirmed-cases.json
@@ -4130,14 +4130,8 @@
sns.displot(co2['Days']);plt.title("Distribution of days feature");# suppresses unneeded plotting output
-
-
/Users/Ishani/micromamba/lib/python3.9/site-packages/seaborn/axisgrid.py:118: UserWarning:
-
-The figure layout has changed to tight
-
-
-
+
In terms of data quality, a handful of months have averages based on measurements taken on fewer than half the days. In addition, there are nearly 200 missing values–that’s about 27% of the data!
@@ -4147,8 +4141,8 @@
Code
-
sns.scatterplot(x="Yr", y="Days", data=co2);
-plt.title("Day field by Year");# the ; suppresses output
+
sns.scatterplot(x="Yr", y="Days", data=co2);
+plt.title("Day field by Year");# the ; suppresses output
@@ -4172,23 +4166,17 @@
Code
-
# Histograms of average CO2 measurements
-sns.displot(co2['Avg']);
+
# Histograms of average CO2 measurements
+sns.displot(co2['Avg']);
-
-
/Users/Ishani/micromamba/lib/python3.9/site-packages/seaborn/axisgrid.py:118: UserWarning:
-
-The figure layout has changed to tight
-
-
-
+
The non-missing values are in the 300-400 range (a regular range of CO2 levels).
We also see that there are only a few missing Avg values (<1% of values). Let’s examine all of them:
-
co2[co2["Avg"] <0]
+
co2[co2["Avg"] <0]
@@ -4297,8 +4285,8 @@
Code
-
sns.lineplot(x='DecDate', y='Avg', data=co2)
-plt.title("CO2 Average By Month");
+
sns.lineplot(x='DecDate', y='Avg', data=co2)
+plt.title("CO2 Average By Month");
@@ -4309,9 +4297,9 @@
-
# 1. Drop missing values
-co2_drop = co2[co2['Avg'] >0]
-co2_drop.head()
+
# 1. Drop missing values
+co2_drop = co2[co2['Avg'] >0]
+co2_drop.head()
@@ -4387,9 +4375,9 @@
-
# 2. Replace NaN with -99.99
-co2_NA = co2.replace(-99.99, np.NaN)
-co2_NA.head()
+
# 2. Replace NaN with -99.99
+co2_NA = co2.replace(-99.99, np.NaN)
+co2_NA.head()
@@ -4473,10 +4461,10 @@
-
# 3. Use interpolated column which estimates missing Avg values
-co2_impute = co2.copy()
-co2_impute['Avg'] = co2['Int']
-co2_impute.head()
+
# 3. Use interpolated column which estimates missing Avg values
+co2_impute = co2.copy()
+co2_impute['Avg'] = co2['Int']
+co2_impute.head()
@@ -4556,30 +4544,30 @@
Code
-
# results of plotting data in 1958
-
-def line_and_points(data, ax, title):
-# assumes single year, hence Mo
- ax.plot('Mo', 'Avg', data=data)
- ax.scatter('Mo', 'Avg', data=data)
- ax.set_xlim(2, 13)
- ax.set_title(title)
- ax.set_xticks(np.arange(3, 13))
-
-def data_year(data, year):
-return data[data["Yr"] ==1958]
-
-# uses matplotlib subplots
-# you may see more next week; focus on output for now
-fig, axes = plt.subplots(ncols =3, figsize=(12, 4), sharey=True)
-
-year =1958
-line_and_points(data_year(co2_drop, year), axes[0], title="1. Drop Missing")
-line_and_points(data_year(co2_NA, year), axes[1], title="2. Missing Set to NaN")
-line_and_points(data_year(co2_impute, year), axes[2], title="3. Missing Interpolated")
-
-fig.suptitle(f"Monthly Averages for {year}")
-plt.tight_layout()
+
# results of plotting data in 1958
+
+def line_and_points(data, ax, title):
+# assumes single year, hence Mo
+ ax.plot('Mo', 'Avg', data=data)
+ ax.scatter('Mo', 'Avg', data=data)
+ ax.set_xlim(2, 13)
+ ax.set_title(title)
+ ax.set_xticks(np.arange(3, 13))
+
+def data_year(data, year):
+return data[data["Yr"] ==1958]
+
+# uses matplotlib subplots
+# you may see more next week; focus on output for now
+fig, axes = plt.subplots(ncols =3, figsize=(12, 4), sharey=True)
+
+year =1958
+line_and_points(data_year(co2_drop, year), axes[0], title="1. Drop Missing")
+line_and_points(data_year(co2_NA, year), axes[1], title="2. Missing Set to NaN")
+line_and_points(data_year(co2_impute, year), axes[2], title="3. Missing Interpolated")
+
+fig.suptitle(f"Monthly Averages for {year}")
+plt.tight_layout()
@@ -4595,8 +4583,8 @@
Code
-
sns.lineplot(x='DecDate', y='Avg', data=co2_impute)
-plt.title("CO2 Average By Month, Imputed");
+
sns.lineplot(x='DecDate', y='Avg', data=co2_impute)
+plt.title("CO2 Average By Month, Imputed");
@@ -4623,9 +4611,9 @@
Code
-
co2_year = co2_impute.groupby('Yr').mean()
-sns.lineplot(x='Yr', y='Avg', data=co2_year)
-plt.title("CO2 Average By Year");
+
co2_year = co2_impute.groupby('Yr').mean()
+sns.lineplot(x='Yr', y='Avg', data=co2_year)
+plt.title("CO2 Average By Year");
@@ -4966,1221 +4954,1221 @@
Source Code
-
---
-title: Data Cleaning and EDA
-execute:
- echo: true
-format:
- html:
- code-fold: true
- code-tools: true
- toc: true
- toc-title: Data Cleaning and EDA
- page-layout: full
- theme:
- - cosmo
- - cerulean
- callout-icon: false
-jupyter:
- jupytext:
- text_representation:
- extension: .qmd
- format_name: quarto
- format_version: '1.0'
- jupytext_version: 1.16.1
- kernelspec:
- display_name: Python 3 (ipykernel)
- language: python
- name: python3
----
-
-```{python}
-#| code-fold: true
-import numpy as np
-import pandas as pd
-
-import matplotlib.pyplot as plt
-import seaborn as sns
-#%matplotlib inline
-plt.rcParams['figure.figsize'] = (12, 9)
-
-sns.set()
-sns.set_context('talk')
-np.set_printoptions(threshold=20, precision=2, suppress=True)
-pd.set_option('display.max_rows', 30)
-pd.set_option('display.max_columns', None)
-pd.set_option('display.precision', 2)
-# This option stops scientific notation for pandas
-pd.set_option('display.float_format', '{:.2f}'.format)
-
-# Silence some spurious seaborn warnings
-import warnings
-warnings.filterwarnings("ignore", category=FutureWarning)
-```
-
-::: {.callout-note collapse="false"}
-## Learning Outcomes
-* Recognize common file formats
-* Categorize data by its variable type
-* Build awareness of issues with data faithfulness and develop targeted solutions
-:::
-
-In the past few lectures, we've learned that `pandas` is a toolkit to restructure, modify, and explore a dataset. What we haven't yet touched on is *how* to make these data transformation decisions. When we receive a new set of data from the "real world," how do we know what processing we should do to convert this data into a usable form?
-
-**Data cleaning**, also called **data wrangling**, is the process of transforming raw data to facilitate subsequent analysis. It is often used to address issues like:
-
-* Unclear structure or formatting
-* Missing or corrupted values
-* Unit conversions
-* ...and so on
-
-**Exploratory Data Analysis (EDA)** is the process of understanding a new dataset. It is an open-ended, informal analysis that involves familiarizing ourselves with the variables present in the data, discovering potential hypotheses, and identifying possible issues with the data. This last point can often motivate further data cleaning to address any problems with the dataset's format; because of this, EDA and data cleaning are often thought of as an "infinite loop," with each process driving the other.
-
-In this lecture, we will consider the key properties of data to consider when performing data cleaning and EDA. In doing so, we'll develop a "checklist" of sorts for you to consider when approaching a new dataset. Throughout this process, we'll build a deeper understanding of this early (but very important!) stage of the data science lifecycle.
-
-## Structure
-We often prefer rectangular data for data analysis. Rectangular structures are easy to manipulate and analyze. A key element of data cleaning is about transforming data to be more rectangular.
-
-There are two kinds of rectangular data: tables and matrices. Tables have named columns with different data types and are manipulated using data transformation languages. Matrices contain numeric data of the same type and are manipulated using linear algebra.
-
-### File Formats
-There are many file types for storing structured data: TSV, JSON, XML, ASCII, SAS, etc. We'll only cover CSV, TSV, and JSON in lecture, but you'll likely encounter other formats as you work with different datasets. Reading documentation is your best bet for understanding how to process the multitude of different file types.
-
-#### CSV
-CSVs, which stand for **Comma-Separated Values**, are a common tabular data format.
-In the past two `pandas` lectures, we briefly touched on the idea of file format: the way data is encoded in a file for storage. Specifically, our `elections` and `babynames` datasets were stored and loaded as CSVs:
-
-```{python}
-#| code-fold: false
-pd.read_csv("data/elections.csv").head(5)
-```
-
-To better understand the properties of a CSV, let's take a look at the first few rows of the raw data file to see what it looks like before being loaded into a `DataFrame`. We'll use the `repr()` function to return the raw string with its special characters:
-
-```{python}
-#| code-fold: false
-withopen("data/elections.csv", "r") as table:
- i =0
-for row in table:
-print(repr(row))
- i +=1
-if i >3:
-break
-```
-
-Each row, or **record**, in the data is delimited by a newline `\n`. Each column, or **field**, in the data is delimited by a comma `,` (hence, comma-separated!).
-
-#### TSV
-
-Another common file type is **TSV (Tab-Separated Values)**. In a TSV, records are still delimited by a newline `\n`, while fields are delimited by `\t` tab character.
-
-Let's check out the first few rows of the raw TSV file. Again, we'll use the `repr()` function so that `print` shows the special characters.
-
-```{python}
-#| code-fold: false
-withopen("data/elections.txt", "r") as table:
- i =0
-for row in table:
-print(repr(row))
- i +=1
-if i >3:
-break
-```
-
-TSVs can be loaded into `pandas` using `pd.read_csv`. We'll need to specify the **delimiter** with parameter` sep='\t'`[(documentation)](https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html).
-
-```{python}
-#| code-fold: false
-pd.read_csv("data/elections.txt", sep='\t').head(3)
-```
-
-An issue with CSVs and TSVs comes up whenever there are commas or tabs within the records. How does `pandas` differentiate between a comma delimiter vs. a comma within the field itself, for example `8,900`? To remedy this, check out the [`quotechar` parameter](https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html).
-
-#### JSON
-**JSON (JavaScript Object Notation)** files behave similarly to Python dictionaries. A raw JSON is shown below.
-
-```{python}
-#| code-fold: false
-withopen("data/elections.json", "r") as table:
- i =0
-for row in table:
-print(row)
- i +=1
-if i >8:
-break
-```
-
-JSON files can be loaded into `pandas` using `pd.read_json`.
-
-```{python}
-#| code-fold: false
-pd.read_json('data/elections.json').head(3)
-```
-
-##### EDA with JSON: Berkeley COVID-19 Data
-The City of Berkeley Open Data [website](https://data.cityofberkeley.info/Health/COVID-19-Confirmed-Cases/xn6j-b766) has a dataset with COVID-19 Confirmed Cases among Berkeley residents by date. Let's download the file and save it as a JSON (note the source URL file type is also a JSON). In the interest of reproducible data science, we will download the data programatically. We have defined some helper functions in the [`ds100_utils.py`](https://ds100.org/fa23/resources/assets/lectures/lec05/lec05-eda.html) file that we can reuse these helper functions in many different notebooks.
-
-```{python}
-#| code-fold: false
-from ds100_utils import fetch_and_cache
-
-covid_file = fetch_and_cache(
-"https://data.cityofberkeley.info/api/views/xn6j-b766/rows.json?accessType=DOWNLOAD",
-"confirmed-cases.json",
- force=False)
-covid_file # a file path wrapper object
-```
-
-###### File Size
-Let's start our analysis by getting a rough estimate of the size of the dataset to inform the tools we use to view the data. For relatively small datasets, we can use a text editor or spreadsheet. For larger datasets, more programmatic exploration or distributed computing tools may be more fitting. Here we will use `Python` tools to probe the file.
-
-Since there seem to be text files, let's investigate the number of lines, which often corresponds to the number of records
-
-```{python}
-#| code-fold: false
-import os
-
-print(covid_file, "is", os.path.getsize(covid_file) /1e6, "MB")
-
-withopen(covid_file, "r") as f:
-print(covid_file, "is", sum(1for l in f), "lines.")
-```
-
-###### Unix Commands
-As part of the EDA workflow, Unix commands can come in very handy. In fact, there's an entire book called ["Data Science at the Command Line"](https://datascienceatthecommandline.com/) that explores this idea in depth!
-In Jupyter/IPython, you can prefix lines with `!` to execute arbitrary Unix commands, and within those lines, you can refer to Python variables and expressions with the syntax `{expr}`.
-
-Here, we use the `ls` command to list files, using the `-lh` flags, which request "long format with information in human-readable form." We also use the `wc` command for "word count," but with the `-l` flag, which asks for line counts instead of words.
-
-These two give us the same information as the code above, albeit in a slightly different form:
-
-```{python}
-#| code-fold: false
-!ls -lh {covid_file}
-!wc -l {covid_file}
-```
-
-###### File Contents
-Let's explore the data format using `Python`.
-
-```{python}
-#| code-fold: false
-withopen(covid_file, "r") as f:
-for i, row inenumerate(f):
-print(repr(row)) # print raw strings
-if i >=4: break
-```
-
-We can use the `head` Unix command (which is where `pandas`' `head` method comes from!) to see the first few lines of the file:
-
-```{python}
-#| code-fold: false
-!head -5 {covid_file}
-```
-
-In order to load the JSON file into `pandas`, Let's first do some EDA with Oython's `json` package to understand the particular structure of this JSON file so that we can decide what (if anything) to load into `pandas`. Python has relatively good support for JSON data since it closely matches the internal python object model. In the following cell we import the entire JSON datafile into a python dictionary using the `json` package.
-
-```{python}
-#| code-fold: false
-import json
-
-withopen(covid_file, "rb") as f:
- covid_json = json.load(f)
-```
-
-The `covid_json` variable is now a dictionary encoding the data in the file:
-
-```{python}
-#| code-fold: false
-type(covid_json)
-```
-
-We can examine what keys are in the top level JSON object by listing out the keys.
-
-```{python}
-#| code-fold: false
-covid_json.keys()
-```
-
-**Observation**: The JSON dictionary contains a `meta` key which likely refers to metadata (data about the data). Metadata is often maintained with the data and can be a good source of additional information.
-
-
-We can investigate the metadata further by examining the keys associated with the metadata.
-
-```{python}
-#| code-fold: false
-covid_json['meta'].keys()
-```
-
-The `meta` key contains another dictionary called `view`. This likely refers to metadata about a particular "view" of some underlying database. We will learn more about views when we study SQL later in the class.
-
-```{python}
-#| code-fold: false
-covid_json['meta']['view'].keys()
-```
-
-Notice that this a nested/recursive data structure. As we dig deeper we reveal more and more keys and the corresponding data:
-
-```
-meta
-|-> data
- | ... (haven't explored yet)
-|-> view
- | -> id
- | -> name
- | -> attribution
- ...
- | -> description
- ...
- | -> columns
- ...
-```
-
-
-There is a key called description in the view sub dictionary. This likely contains a description of the data:
-
-```{python}
-#| code-fold: false
-print(covid_json['meta']['view']['description'])
-```
-
-###### Examining the Data Field for Records
-
-We can look at a few entries in the `data` field. This is what we'll load into `pandas`.
-
-```{python}
-#| code-fold: false
-for i inrange(3):
-print(f"{i:03} | {covid_json['data'][i]}")
-```
-
-Observations:
-* These look like equal-length records, so maybe `data` is a table!
-* But what do each of values in the record mean? Where can we find column headers?
-
-For that, we'll need the `columns` key in the metadata dictionary. This returns a list:
-
-```{python}
-#| code-fold: false
-type(covid_json['meta']['view']['columns'])
-```
-
-###### Summary of exploring the JSON file
-
-1. The above **metadata** tells us a lot about the columns in the data including column names, potential data anomalies, and a basic statistic.
-1. Because of its non-tabular structure, JSON makes it easier (than CSV) to create **self-documenting data**, meaning that information about the data is stored in the same file as the data.
-1. Self-documenting data can be helpful since it maintains its own description and these descriptions are more likely to be updated as data changes.
-
-###### Loading COVID Data into `pandas`
-Finally, let's load the data (not the metadata) into a `pandas``DataFrame`. In the following block of code we:
-
-1. Translate the JSON records into a `DataFrame`:
-
- * fields: `covid_json['meta']['view']['columns']`
- * records: `covid_json['data']`
-
-
-1. Remove columns that have no metadata description. This would be a bad idea in general, but here we remove these columns since the above analysis suggests they are unlikely to contain useful information.
-
-1. Examine the `tail` of the table.
-
-```{python}
-#| code-fold: false
-# Load the data from JSON and assign column titles
-covid = pd.DataFrame(
- covid_json['data'],
- columns=[c['name'] for c in covid_json['meta']['view']['columns']])
-
-covid.tail()
-```
-
-### Primary and Foreign Keys
-
-Last time, we introduced `.merge` as the `pandas` method for joining multiple `DataFrame`s together. In our discussion of joins, we touched on the idea of using a "key" to determine what rows should be merged from each table. Let's take a moment to examine this idea more closely.
-
-The **primary key** is the column or set of columns in a table that *uniquely* determine the values of the remaining columns. It can be thought of as the unique identifier for each individual row in the table. For example, a table of Data 100 students might use each student's Cal ID as the primary key.
-
-```{python}
-#| echo: false
-pd.DataFrame({"Cal ID":[3034619471, 3035619472, 3025619473, 3046789372], \
-"Name":["Oski", "Ollie", "Orrie", "Ollie"], \
-"Major":["Data Science", "Computer Science", "Data Science", "Economics"]})
-```
-
-The **foreign key** is the column or set of columns in a table that reference primary keys in other tables. Knowing a dataset's foreign keys can be useful when assigning the `left_on` and `right_on` parameters of `.merge`. In the table of office hour tickets below, `"Cal ID"` is a foreign key referencing the previous table.
-
-```{python}
-#| echo: false
-pd.DataFrame({"OH Request":[1, 2, 3, 4], \
-"Cal ID":[3034619471, 3035619472, 3025619473, 3035619472], \
-"Question":["HW 2 Q1", "HW 2 Q3", "Lab 3 Q4", "HW 2 Q7"]})
-```
-
-### Variable Types
-
-Variables are columns. A variable is a measurement of a particular concept. Variables have two common properties: data type/storage type and variable type/feature type. The data type of a variable indicates how each variable value is stored in memory (integer, floating point, boolean, etc.) and affects which `pandas` functions are used. The variable type is a conceptualized measurement of information (and therefore indicates what values a variable can take on). Variable type is identified through expert knowledge, exploring the data itself, or consulting the data codebook. The variable type affects how one visualizes and inteprets the data. In this class, "variable types" are conceptual.
-
-After loading data into a file, it's a good idea to take the time to understand what pieces of information are encoded in the dataset. In particular, we want to identify what variable types are present in our data. Broadly speaking, we can categorize variables into one of two overarching types.
-
-**Quantitative variables** describe some numeric quantity or amount. We can divide quantitative data further into:
-
-* **Continuous quantitative variables**: numeric data that can be measured on a continuous scale to arbitrary precision. Continuous variables do not have a strict set of possible values – they can be recorded to any number of decimal places. For example, weights, GPA, or CO<sub>2</sub> concentrations.
-* **Discrete quantitative variables**: numeric data that can only take on a finite set of possible values. For example, someone's age or the number of siblings they have.
-
-**Qualitative variables**, also known as **categorical variables**, describe data that isn't measuring some quantity or amount. The sub-categories of categorical data are:
-
-* **Ordinal qualitative variables**: categories with ordered levels. Specifically, ordinal variables are those where the difference between levels has no consistent, quantifiable meaning. Some examples include levels of education (high school, undergrad, grad, etc.), income bracket (low, medium, high), or Yelp rating.
-* **Nominal qualitative variables**: categories with no specific order. For example, someone's political affiliation or Cal ID number.
-
-![Classification of variable types](images/variable.png)
-
-Note that many variables don't sit neatly in just one of these categories. Qualitative variables could have numeric levels, and conversely, quantitative variables could be stored as strings.
-
-## Granularity, Scope, and Temporality
-
-After understanding the structure of the dataset, the next task is to determine what exactly the data represents. We'll do so by considering the data's granularity, scope, and temporality.
-
-### Granularity
-The **granularity** of a dataset is what a single row represents. You can also think of it as the level of detail included in the data. To determine the data's granularity, ask: what does each row in the dataset represent? Fine-grained data contains a high level of detail, with a single row representing a small individual unit. For example, each record may represent one person. Coarse-grained data is encoded such that a single row represents a large individual unit – for example, each record may represent a group of people.
-
-### Scope
-The **scope** of a dataset is the subset of the population covered by the data. If we were investigating student performance in Data Science courses, a dataset with a narrow scope might encompass all students enrolled in Data 100 whereas a dataset with an expansive scope might encompass all students in California.
-
-### Temporality
-The **temporality** of a dataset describes the periodicity over which the data was collected as well as when the data was most recently collected or updated.
-
-Time and date fields of a dataset could represent a few things:
-
-1. when the "event" happened
-2. when the data was collected, or when it was entered into the system
-3. when the data was copied into the database
-
-To fully understand the temporality of the data, it also may be necessary to standardize time zones or inspect recurring time-based trends in the data (do patterns recur in 24-hour periods? Over the course of a month? Seasonally?). The convention for standardizing time is the Coordinated Universal Time (UTC), an international time standard measured at 0 degrees latitude that stays consistent throughout the year (no daylight savings). We can represent Berkeley's time zone, Pacific Standard Time (PST), as UTC-7 (with daylight savings).
-
-#### Temporality with `pandas`' `dt` accessors
-Let's briefly look at how we can use `pandas`' `dt` accessors to work with dates/times in a dataset using the dataset you'll see in Lab 3: the Berkeley PD Calls for Service dataset.
-
-```{python}
-#| code-fold: true
-calls = pd.read_csv("data/Berkeley_PD_-_Calls_for_Service.csv")
-calls.head()
-```
-
-Looks like there are three columns with dates/times: `EVENTDT`, `EVENTTM`, and `InDbDate`.
-
-Most likely, `EVENTDT` stands for the date when the event took place, `EVENTTM` stands for the time of day the event took place (in 24-hr format), and `InDbDate` is the date this call is recorded onto the database.
-
-If we check the data type of these columns, we will see they are stored as strings. We can convert them to `datetime` objects using pandas `to_datetime` function.
-
-```{python}
-#| code-fold: false
-calls["EVENTDT"] = pd.to_datetime(calls["EVENTDT"])
-calls.head()
-```
-
-Now, we can use the `dt` accessor on this column.
-
-We can get the month:
-
-```{python}
-#| code-fold: false
-calls["EVENTDT"].dt.month.head()
-```
-
-Which day of the week the date is on:
-
-```{python}
-#| code-fold: false
-calls["EVENTDT"].dt.dayofweek.head()
-```
-
-Check the mimimum values to see if there are any suspicious-looking, 70s dates:
-
-```{python}
-#| code-fold: false
-calls.sort_values("EVENTDT").head()
-```
-
-Doesn't look like it! We are good!
-
-
-We can also do many things with the `dt` accessor like switching time zones and converting time back to UNIX/POSIX time. Check out the documentation on [`.dt` accessor](https://pandas.pydata.org/docs/user_guide/basics.html#basics-dt-accessors) and [time series/date functionality](https://pandas.pydata.org/docs/user_guide/timeseries.html#).
-
-## Faithfulness
-
-At this stage in our data cleaning and EDA workflow, we've achieved quite a lot: we've identified how our data is structured, come to terms with what information it encodes, and gained insight as to how it was generated. Throughout this process, we should always recall the original intent of our work in Data Science – to use data to better understand and model the real world. To achieve this goal, we need to ensure that the data we use is faithful to reality; that is, that our data accurately captures the "real world."
-
-Data used in research or industry is often "messy" – there may be errors or inaccuracies that impact the faithfulness of the dataset. Signs that data may not be faithful include:
-
-* Unrealistic or "incorrect" values, such as negative counts, locations that don't exist, or dates set in the future
-* Violations of obvious dependencies, like an age that does not match a birthday
-* Clear signs that data was entered by hand, which can lead to spelling errors or fields that are incorrectly shifted
-* Signs of data falsification, such as fake email addresses or repeated use of the same names
-* Duplicated records or fields containing the same information
-* Truncated data, e.g. Microsoft Excel would limit the number of rows to 655536 and the number of columns to 255
-
-We often solve some of these more common issues in the following ways:
-
-* Spelling errors: apply corrections or drop records that aren't in a dictionary
-* Time zone inconsistencies: convert to a common time zone (e.g. UTC)
-* Duplicated records or fields: identify and eliminate duplicates (using primary keys)
-* Unspecified or inconsistent units: infer the units and check that values are in reasonable ranges in the data
-
-### Missing Values
-Another common issue encountered with real-world datasets is that of missing data. One strategy to resolve this is to simply drop any records with missing values from the dataset. This does, however, introduce the risk of inducing biases – it is possible that the missing or corrupt records may be systemically related to some feature of interest in the data. Another solution is to keep the data as `NaN` values.
-
-A third method to address missing data is to perform **imputation**: infer the missing values using other data available in the dataset. There is a wide variety of imputation techniques that can be implemented; some of the most common are listed below.
-
-* Average imputation: replace missing values with the average value for that field
-* Hot deck imputation: replace missing values with some random value
-* Regression imputation: develop a model to predict missing values and replace with the predicted value from the model.
-* Multiple imputation: replace missing values with multiple random values
-
-Regardless of the strategy used to deal with missing data, we should think carefully about *why* particular records or fields may be missing – this can help inform whether or not the absence of these values is significant or meaningful.
-
-## EDA Demo 1: Tuberculosis in the United States
-
-Now, let's walk through the data-cleaning and EDA workflow to see what can we learn about the presence of Tuberculosis in the United States!
-
-We will examine the data included in the [original CDC article](https://www.cdc.gov/mmwr/volumes/71/wr/mm7112a1.htm?s_cid=mm7112a1_w#T1_down) published in 2021.
-
-
-### CSVs and Field Names
-Suppose Table 1 was saved as a CSV file located in `data/cdc_tuberculosis.csv`.
-
-We can then explore the CSV (which is a text file, and does not contain binary-encoded data) in many ways:
-1. Using a text editor like emacs, vim, VSCode, etc.
-2. Opening the CSV directly in DataHub (read-only), Excel, Google Sheets, etc.
-3. The `Python` file object
-4. `pandas`, using `pd.read_csv()`
-
-To try out options 1 and 2, you can view or download the Tuberculosis from the [lecture demo notebook](https://data100.datahub.berkeley.edu/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2FDS-100%2Ffa23-student&urlpath=lab%2Ftree%2Ffa23-student%2Flecture%2Flec05%2Flec04-eda.ipynb&branch=main) under the `data` folder in the left hand menu. Notice how the CSV file is a type of **rectangular data (i.e., tabular data) stored as comma-separated values**.
-
-Next, let's try out option 3 using the `Python` file object. We'll look at the first four lines:
-
-```{python}
-#| code-fold: true
-withopen("data/cdc_tuberculosis.csv", "r") as f:
- i =0
-for row in f:
-print(row)
- i +=1
-if i >3:
-break
-```
-
-Whoa, why are there blank lines interspaced between the lines of the CSV?
-
-You may recall that all line breaks in text files are encoded as the special newline character `\n`. Python's `print()` prints each string (including the newline), and an additional newline on top of that.
-
-If you're curious, we can use the `repr()` function to return the raw string with all special characters:
-
-```{python}
-#| code-fold: true
-withopen("data/cdc_tuberculosis.csv", "r") as f:
- i =0
-for row in f:
-print(repr(row)) # print raw strings
- i +=1
-if i >3:
-break
-```
-
-Finally, let's try option 4 and use the tried-and-true Data 100 approach: `pandas`.
-
-```{python}
-#| code-fold: false
-tb_df = pd.read_csv("data/cdc_tuberculosis.csv")
-tb_df.head()
-```
-
-You may notice some strange things about this table: what's up with the "Unnamed" column names and the first row?
-
-Congratulations — you're ready to wrangle your data! Because of how things are stored, we'll need to clean the data a bit to name our columns better.
-
-A reasonable first step is to identify the row with the right header. The `pd.read_csv()` function ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html)) has the convenient `header` parameter that we can set to use the elements in row 1 as the appropriate columns:
-
-```{python}
-#| code-fold: false
-tb_df = pd.read_csv("data/cdc_tuberculosis.csv", header=1) # row index
-tb_df.head(5)
-```
-
-Wait...but now we can't differentiate betwen the "Number of TB cases" and "TB incidence" year columns. `pandas` has tried to make our lives easier by automatically adding ".1" to the latter columns, but this doesn't help us, as humans, understand the data.
-
-We can do this manually with `df.rename()` ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.rename.html?highlight=rename#pandas.DataFrame.rename)):
-
-```{python}
-#| code-fold: false
-rename_dict = {'2019': 'TB cases 2019',
-'2020': 'TB cases 2020',
-'2021': 'TB cases 2021',
-'2019.1': 'TB incidence 2019',
-'2020.1': 'TB incidence 2020',
-'2021.1': 'TB incidence 2021'}
-tb_df = tb_df.rename(columns=rename_dict)
-tb_df.head(5)
-```
-
-### Record Granularity
-
-You might already be wondering: what's up with that first record?
-
-Row 0 is what we call a **rollup record**, or summary record. It's often useful when displaying tables to humans. The **granularity** of record 0 (Totals) vs the rest of the records (States) is different.
-
-Okay, EDA step two. How was the rollup record aggregated?
-
-Let's check if Total TB cases is the sum of all state TB cases. If we sum over all rows, we should get **2x** the total cases in each of our TB cases by year (why do you think this is?).
-
-```{python}
-#| code-fold: true
-tb_df.sum(axis=0)
-```
-
-Whoa, what's going on with the TB cases in 2019, 2020, and 2021? Check out the column types:
-
-```{python}
-#| code-fold: true
-tb_df.dtypes
-```
-
-Since there are commas in the values for TB cases, the numbers are read as the `object` datatype, or **storage type** (close to the `Python` string datatype), so `pandas` is concatenating strings instead of adding integers (recall that Python can "sum", or concatenate, strings together: `"data" + "100"` evaluates to `"data100"`).
-
-
-Fortunately `read_csv` also has a `thousands` parameter ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html)):
-
-```{python}
-#| code-fold: false
-# improve readability: chaining method calls with outer parentheses/line breaks
-tb_df = (
- pd.read_csv("data/cdc_tuberculosis.csv", header=1, thousands=',')
- .rename(columns=rename_dict)
-)
-tb_df.head(5)
-```
-
-```{python}
-#| code-fold: false
-tb_df.sum()
-```
-
-The total TB cases look right. Phew!
-
-Let's just look at the records with **state-level granularity**:
-
-```{python}
-#| code-fold: true
-state_tb_df = tb_df[1:]
-state_tb_df.head(5)
-```
-
-### Gather Census Data
-
-U.S. Census population estimates [source](https://www.census.gov/data/tables/time-series/demo/popest/2010s-state-total.html) (2019), [source](https://www.census.gov/data/tables/time-series/demo/popest/2020s-state-total.html) (2020-2021).
-
-Running the below cells cleans the data.
-There are a few new methods here:
-* `df.convert_dtypes()` ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.convert_dtypes.html)) conveniently converts all float dtypes into ints and is out of scope for the class.
-* `df.drop_na()` ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.dropna.html)) will be explained in more detail next time.
-
-```{python}
-#| code-fold: true
-# 2010s census data
-census_2010s_df = pd.read_csv("data/nst-est2019-01.csv", header=3, thousands=",")
-census_2010s_df = (
- census_2010s_df
- .reset_index()
- .drop(columns=["index", "Census", "Estimates Base"])
- .rename(columns={"Unnamed: 0": "Geographic Area"})
- .convert_dtypes() # "smart" converting of columns, use at your own risk
- .dropna() # we'll introduce this next time
-)
-census_2010s_df['Geographic Area'] = census_2010s_df['Geographic Area'].str.strip('.')
-
-# with pd.option_context('display.min_rows', 30): # shows more rows
-# display(census_2010s_df)
-
-census_2010s_df.head(5)
-```
-
-Occasionally, you will want to modify code that you have imported. To reimport those modifications you can either use `python`'s `importlib` library:
-
-```python
-from importlib importreload
-reload(utils)
-```
-
-or use `iPython` magic which will intelligently import code when files change:
-
-```python
-%load_ext autoreload
-%autoreload 2
-```
-
-```{python}
-#| code-fold: true
-# census 2020s data
-census_2020s_df = pd.read_csv("data/NST-EST2022-POP.csv", header=3, thousands=",")
-census_2020s_df = (
- census_2020s_df
- .reset_index()
- .drop(columns=["index", "Unnamed: 1"])
- .rename(columns={"Unnamed: 0": "Geographic Area"})
- .convert_dtypes() # "smart" converting of columns, use at your own risk
- .dropna() # we'll introduce this next time
-)
-census_2020s_df['Geographic Area'] = census_2020s_df['Geographic Area'].str.strip('.')
-
-census_2020s_df.head(5)
-```
-
-### Joining Data (Merging `DataFrame`s)
-
-Time to `merge`! Here we use the `DataFrame` method `df1.merge(right=df2, ...)` on `DataFrame``df1` ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.merge.html)). Contrast this with the function `pd.merge(left=df1, right=df2, ...)` ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.merge.html?highlight=pandas%20merge#pandas.merge)). Feel free to use either.
-
-```{python}
-#| code-fold: false
-# merge TB DataFrame with two US census DataFrames
-tb_census_df = (
- tb_df
- .merge(right=census_2010s_df,
- left_on="U.S. jurisdiction", right_on="Geographic Area")
- .merge(right=census_2020s_df,
- left_on="U.S. jurisdiction", right_on="Geographic Area")
-)
-tb_census_df.head(5)
-```
-
-Having all of these columns is a little unwieldy. We could either drop the unneeded columns now, or just merge on smaller census `DataFrame`s. Let's do the latter.
-
-```{python}
-#| code-fold: false
-# try merging again, but cleaner this time
-tb_census_df = (
- tb_df
- .merge(right=census_2010s_df[["Geographic Area", "2019"]],
- left_on="U.S. jurisdiction", right_on="Geographic Area")
- .drop(columns="Geographic Area")
- .merge(right=census_2020s_df[["Geographic Area", "2020", "2021"]],
- left_on="U.S. jurisdiction", right_on="Geographic Area")
- .drop(columns="Geographic Area")
-)
-tb_census_df.head(5)
-```
-
-### Reproducing Data: Compute Incidence
-
-Let's recompute incidence to make sure we know where the original CDC numbers came from.
-
-From the [CDC report](https://www.cdc.gov/mmwr/volumes/71/wr/mm7112a1.htm?s_cid=mm7112a1_w#T1_down): TB incidence is computed as “Cases per 100,000 persons using mid-year population estimates from the U.S. Census Bureau.”
-
-If we define a group as 100,000 people, then we can compute the TB incidence for a given state population as
-
-$$\text{TB incidence} = \frac{\text{TB cases in population}}{\text{groups in population}} = \frac{\text{TB cases in population}}{\text{population}/100000} $$
-
-$$= \frac{\text{TB cases in population}}{\text{population}} \times 100000$$
-
-Let's try this for 2019:
-
-```{python}
-#| code-fold: false
-tb_census_df["recompute incidence 2019"] = tb_census_df["TB cases 2019"]/tb_census_df["2019"]*100000
-tb_census_df.head(5)
-```
-
-Awesome!!!
-
-Let's use a for-loop and Python format strings to compute TB incidence for all years. Python f-strings are just used for the purposes of this demo, but they're handy to know when you explore data beyond this course ([documentation](https://docs.python.org/3/tutorial/inputoutput.html)).
-
-```{python}
-#| code-fold: false
-# recompute incidence for all years
-for year in [2019, 2020, 2021]:
- tb_census_df[f"recompute incidence {year}"] = tb_census_df[f"TB cases {year}"]/tb_census_df[f"{year}"]*100000
-tb_census_df.head(5)
-```
-
-These numbers look pretty close!!! There are a few errors in the hundredths place, particularly in 2021. It may be useful to further explore reasons behind this discrepancy.
-
-```{python}
-#| code-fold: false
-tb_census_df.describe()
-```
-
-### Bonus EDA: Reproducing the Reported Statistic
-
-
-**How do we reproduce that reported statistic in the original [CDC report](https://www.cdc.gov/mmwr/volumes/71/wr/mm7112a1.htm?s_cid=mm7112a1_w)?**
-
-> Reported TB incidence (cases per 100,000 persons) increased **9.4%**, from **2.2** during 2020 to **2.4** during 2021 but was lower than incidence during 2019 (2.7). Increases occurred among both U.S.-born and non–U.S.-born persons.
-
-This is TB incidence computed across the entire U.S. population! How do we reproduce this?
-* We need to reproduce the "Total" TB incidences in our rolled record.
-* But our current `tb_census_df` only has 51 entries (50 states plus Washington, D.C.). There is no rolled record.
-* What happened...?
-
-Let's get exploring!
-
-Before we keep exploring, we'll set all indexes to more meaningful values, instead of just numbers that pertain to some row at some point. This will make our cleaning slightly easier.
-
-```{python}
-#| code-fold: true
-tb_df = tb_df.set_index("U.S. jurisdiction")
-tb_df.head(5)
-```
-
-```{python}
-#| code-fold: false
-census_2010s_df = census_2010s_df.set_index("Geographic Area")
-census_2010s_df.head(5)
-```
-
-```{python}
-#| code-fold: false
-census_2020s_df = census_2020s_df.set_index("Geographic Area")
-census_2020s_df.head(5)
-```
-
-It turns out that our merge above only kept state records, even though our original `tb_df` had the "Total" rolled record:
-
-```{python}
-#| code-fold: false
-tb_df.head()
-```
-
-Recall that `merge` by default does an **inner** merge by default, meaning that it only preserves keys that are present in **both** `DataFrame`s.
-
-The rolled records in our census `DataFrame` have different `Geographic Area` fields, which was the key we merged on:
-
-```{python}
-#| code-fold: false
-census_2010s_df.head(5)
-```
-
-The Census `DataFrame` has several rolled records. The aggregate record we are looking for actually has the Geographic Area named "United States".
-
-One straightforward way to get the right merge is to rename the value itself. Because we now have the Geographic Area index, we'll use `df.rename()` ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.rename.html)):
-
-```{python}
-#| code-fold: false
-# rename rolled record for 2010s
-census_2010s_df.rename(index={'United States':'Total'}, inplace=True)
-census_2010s_df.head(5)
-```
-
-```{python}
-#| code-fold: false
-# same, but for 2020s rename rolled record
-census_2020s_df.rename(index={'United States':'Total'}, inplace=True)
-census_2020s_df.head(5)
-```
-
-<br/>
-
-Next let's rerun our merge. Note the different chaining, because we are now merging on indexes (`df.merge()`[documentation](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.merge.html)).
-
-```{python}
-#| code-fold: false
-tb_census_df = (
- tb_df
- .merge(right=census_2010s_df[["2019"]],
- left_index=True, right_index=True)
- .merge(right=census_2020s_df[["2020", "2021"]],
- left_index=True, right_index=True)
-)
-tb_census_df.head(5)
-```
-
-<br/>
-
-Finally, let's recompute our incidences:
-
-```{python}
-#| code-fold: false
-# recompute incidence for all years
-for year in [2019, 2020, 2021]:
- tb_census_df[f"recompute incidence {year}"] = tb_census_df[f"TB cases {year}"]/tb_census_df[f"{year}"]*100000
-tb_census_df.head(5)
-```
-
-We reproduced the total U.S. incidences correctly!
-
-We're almost there. Let's revisit the quote:
-
-> Reported TB incidence (cases per 100,000 persons) increased **9.4%**, from **2.2** during 2020 to **2.4** during 2021 but was lower than incidence during 2019 (2.7). Increases occurred among both U.S.-born and non–U.S.-born persons.
-
-Recall that percent change from $A$ to $B$ is computed as
-$\text{percent change} = \frac{B - A}{A} \times 100$.
-
-```{python}
-#| code-fold: false
-incidence_2020 = tb_census_df.loc['Total', 'recompute incidence 2020']
-incidence_2020
-```
-
-```{python}
-#| code-fold: false
-incidence_2021 = tb_census_df.loc['Total', 'recompute incidence 2021']
-incidence_2021
-```
-
-```{python}
-#| code-fold: false
-difference = (incidence_2021 - incidence_2020)/incidence_2020 *100
-difference
-```
-
-## EDA Demo 2: Mauna Loa CO<sub>2</sub> Data -- A Lesson in Data Faithfulness
-
-[Mauna Loa Observatory](https://gml.noaa.gov/ccgg/trends/data.html) has been monitoring CO<sub>2</sub> concentrations since 1958.
-
-```{python}
-#| code-fold: false
-co2_file ="data/co2_mm_mlo.txt"
-```
-
-Let's do some **EDA**!!
-
-### Reading this file into `Pandas`?
-Let's instead check out this `.txt` file. Some questions to keep in mind: Do we trust this file extension? What structure is it?
-
-Lines 71-78 (inclusive) are shown below:
-
- line number | file contents
-
- 71 | # decimal average interpolated trend #days
- 72 | # date (season corr)
- 73 | 1958 3 1958.208 315.71 315.71 314.62 -1
- 74 | 1958 4 1958.292 317.45 317.45 315.29 -1
- 75 | 1958 5 1958.375 317.50 317.50 314.71 -1
- 76 | 1958 6 1958.458 -99.99 317.10 314.85 -1
- 77 | 1958 7 1958.542 315.86 315.86 314.98 -1
- 78 | 1958 8 1958.625 314.93 314.93 315.94 -1
-
-
-Notice how:
-
-- The values are separated by white space, possibly tabs.
-- The data line up down the rows. For example, the month appears in 7th to 8th position of each line.
-- The 71st and 72nd lines in the file contain column headings split over two lines.
-
-We can use `read_csv` to read the data into a `pandas``DataFrame`, and we provide several arguments to specify that the separators are white space, there is no header (**we will set our own column names**), and to skip the first 72 rows of the file.
-
-```{python}
-#| code-fold: false
-co2 = pd.read_csv(
- co2_file, header =None, skiprows =72,
- sep =r'\s+'#delimiter for continuous whitespace (stay tuned for regex next lecture))
-)
-co2.head()
-```
-
-Congratulations! You've wrangled the data!
-
-<br/>
-
-...But our columns aren't named.
-**We need to do more EDA.**
-
-### Exploring Variable Feature Types
-
-The NOAA [webpage](https://gml.noaa.gov/ccgg/trends/) might have some useful tidbits (in this case it doesn't).
-
-Using this information, we'll rerun `pd.read_csv`, but this time with some **custom column names.**
-
-```{python}
-#| code-fold: false
-co2 = pd.read_csv(
- co2_file, header =None, skiprows =72,
- sep ='\s+', #regex for continuous whitespace (next lecture)
- names = ['Yr', 'Mo', 'DecDate', 'Avg', 'Int', 'Trend', 'Days']
-)
-co2.head()
-```
-
-### Visualizing CO<sub>2</sub>
-Scientific studies tend to have very clean data, right...? Let's jump right in and make a time series plot of CO<sub>2</sub> monthly averages.
-
-```{python}
-#| code-fold: true
-sns.lineplot(x='DecDate', y='Avg', data=co2);
-```
-
-The code above uses the `seaborn` plotting library (abbreviated `sns`). We will cover this in the Visualization lecture, but now you don't need to worry about how it works!
-
-Yikes! Plotting the data uncovered a problem. The sharp vertical lines suggest that we have some **missing values**. What happened here?
-
-```{python}
-#| code-fold: false
-co2.head()
-```
-
-```{python}
-#| code-fold: false
-co2.tail()
-```
-
-Some data have unusual values like -1 and -99.99.
-
-Let's check the description at the top of the file again.
-
-* -1 signifies a missing value for the number of days `Days` the equipment was in operation that month.
-* -99.99 denotes a missing monthly average `Avg`
-
-How can we fix this? First, let's explore other aspects of our data. Understanding our data will help us decide what to do with the missing values.
-
-<br/>
-
-
-### Sanity Checks: Reasoning about the data
-First, we consider the shape of the data. How many rows should we have?
-
-* If chronological order, we should have one record per month.
-* Data from March 1958 to August 2019.
-* We should have $ 12 \times (2019-1957) - 2 - 4 = 738 $ records.
-
-```{python}
-#| code-fold: false
-co2.shape
-```
-
-Nice!! The number of rows (i.e. records) match our expectations.
-
-
-Let's now check the quality of each feature.
-
-### Understanding Missing Value 1: `Days`
-`Days` is a time field, so let's analyze other time fields to see if there is an explanation for missing values of days of operation.
-
-Let's start with **months**, `Mo`.
-
-Are we missing any records? The number of months should have 62 or 61 instances (March 1957-August 2019).
-
-```{python}
-#| code-fold: false
-co2["Mo"].value_counts().sort_index()
-```
-
-As expected Jan, Feb, Sep, Oct, Nov, and Dec have 61 occurrences and the rest 62.
-
-<br/>
-
-Next let's explore **days** `Days` itself, which is the number of days that the measurement equipment worked.
-
-```{python}
-#| code-fold: true
-sns.displot(co2['Days']);
-plt.title("Distribution of days feature");# suppresses unneeded plotting output
-```
-
-In terms of data quality, a handful of months have averages based on measurements taken on fewer than half the days. In addition, there are nearly 200 missing values--**that's about 27% of the data**!
-
-<br/>
-
-Finally, let's check the last time feature, **year** `Yr`.
-
-Let's check to see if there is any connection between missing-ness and the year of the recording.
-
-```{python}
-#| code-fold: true
-sns.scatterplot(x="Yr", y="Days", data=co2);
-plt.title("Day field by Year");# the ; suppresses output
-```
-
-**Observations**:
-
-* All of the missing data are in the early years of operation.
-* It appears there may have been problems with equipment in the mid to late 80s.
-
-**Potential Next Steps**:
-
-* Confirm these explanations through documentation about the historical readings.
-* Maybe drop the earliest recordings? However, we would want to delay such action until after we have examined the time trends and assess whether there are any potential problems.
-
-<br/>
-
-### Understanding Missing Value 2: `Avg`
-Next, let's return to the -99.99 values in `Avg` to analyze the overall quality of the CO<sub>2</sub> measurements. We'll plot a histogram of the average CO<sub>2</sub> measurements
-
-```{python}
-#| code-fold: true
-# Histograms of average CO2 measurements
-sns.displot(co2['Avg']);
-```
-
-The non-missing values are in the 300-400 range (a regular range of CO<sub>2</sub> levels).
-
-We also see that there are only a few missing `Avg` values (**<1% of values**). Let's examine all of them:
-
-```{python}
-#| code-fold: false
-co2[co2["Avg"] <0]
-```
-
-There doesn't seem to be a pattern to these values, other than that most records also were missing `Days` data.
-
-### Drop, `NaN`, or Impute Missing `Avg` Data?
-
-How should we address the invalid `Avg` data?
-
-1. Drop records
-2. Set to NaN
-3. Impute using some strategy
-
-Remember we want to fix the following plot:
-
-```{python}
-#| code-fold: true
-sns.lineplot(x='DecDate', y='Avg', data=co2)
-plt.title("CO2 Average By Month");
-```
-
-Since we are plotting `Avg` vs `DecDate`, we should just focus on dealing with missing values for `Avg`.
-
-
-Let's consider a few options:
-1. Drop those records
-2. Replace -99.99 with NaN
-3. Substitute it with a likely value for the average CO<sub>2</sub>?
-
-What do you think are the pros and cons of each possible action?
-
-Let's examine each of these three options.
-
-```{python}
-#| code-fold: false
-# 1. Drop missing values
-co2_drop = co2[co2['Avg'] >0]
-co2_drop.head()
-```
-
-```{python}
-#| code-fold: false
-# 2. Replace NaN with -99.99
-co2_NA = co2.replace(-99.99, np.NaN)
-co2_NA.head()
-```
-
-We'll also use a third version of the data.
-
-First, we note that the dataset already comes with a **substitute value** for the -99.99.
-
-From the file description:
-
-> The `interpolated` column includes average values from the preceding column (`average`)
-and **interpolated values** where data are missing. Interpolated values are
-computed in two steps...
-
-The `Int` feature has values that exactly match those in `Avg`, except when `Avg` is -99.99, and then a **reasonable** estimate is used instead.
-
-So, the third version of our data will use the `Int` feature instead of `Avg`.
-
-```{python}
-#| code-fold: false
-# 3. Use interpolated column which estimates missing Avg values
-co2_impute = co2.copy()
-co2_impute['Avg'] = co2['Int']
-co2_impute.head()
-```
-
-What's a **reasonable** estimate?
-
-To answer this question, let's zoom in on a short time period, say the measurements in 1958 (where we know we have two missing values).
-
-```{python}
-#| code-fold: true
-# results of plotting data in 1958
-
-def line_and_points(data, ax, title):
-# assumes single year, hence Mo
- ax.plot('Mo', 'Avg', data=data)
- ax.scatter('Mo', 'Avg', data=data)
- ax.set_xlim(2, 13)
- ax.set_title(title)
- ax.set_xticks(np.arange(3, 13))
-
-def data_year(data, year):
-return data[data["Yr"] ==1958]
-
-# uses matplotlib subplots
-# you may see more next week; focus on output for now
-fig, axes = plt.subplots(ncols =3, figsize=(12, 4), sharey=True)
-
-year =1958
-line_and_points(data_year(co2_drop, year), axes[0], title="1. Drop Missing")
-line_and_points(data_year(co2_NA, year), axes[1], title="2. Missing Set to NaN")
-line_and_points(data_year(co2_impute, year), axes[2], title="3. Missing Interpolated")
-
-fig.suptitle(f"Monthly Averages for {year}")
-plt.tight_layout()
-```
-
-In the big picture since there are only 7 `Avg` values missing (**<1%** of 738 months), any of these approaches would work.
-
-However there is some appeal to **option C, Imputing**:
-
-* Shows seasonal trends for CO<sub>2</sub>
-* We are plotting all months in our data as a line plot
-
-
-Let's replot our original figure with option 3:
-
-```{python}
-#| code-fold: true
-sns.lineplot(x='DecDate', y='Avg', data=co2_impute)
-plt.title("CO2 Average By Month, Imputed");
-```
-
-Looks pretty close to what we see on the NOAA [website](https://gml.noaa.gov/ccgg/trends/)!
-
-### Presenting the Data: A Discussion on Data Granularity
-
-From the description:
-
-* Monthly measurements are averages of average day measurements.
-* The NOAA GML website has datasets for daily/hourly measurements too.
-
-The data you present depends on your research question.
-
-**How do CO<sub>2</sub> levels vary by season?**
-
-* You might want to keep average monthly data.
-
-**Are CO<sub>2</sub> levels rising over the past 50+ years, consistent with global warming predictions?**
-
-* You might be happier with a **coarser granularity** of average year data!
-
-```{python}
-#| code-fold: true
-co2_year = co2_impute.groupby('Yr').mean()
-sns.lineplot(x='Yr', y='Avg', data=co2_year)
-plt.title("CO2 Average By Year");
-```
-
-Indeed, we see a rise by nearly 100 ppm of CO<sub>2</sub> since Mauna Loa began recording in 1958.
-
-## Summary
-We went over a lot of content this lecture; let's summarize the most important points:
-
-### Dealing with Missing Values
-There are a few options we can take to deal with missing data:
-
-* Drop missing records
-* Keep `NaN` missing values
-* Impute using an interpolated column
-
-### EDA and Data Wrangling
-There are several ways to approach EDA and Data Wrangling:
-
-* Examine the **data and metadata**: what is the date, size, organization, and structure of the data?
-* Examine each **field/attribute/dimension** individually.
-* Examine pairs of related dimensions (e.g. breaking down grades by major).
-* Along the way, we can:
- * **Visualize** or summarize the data.
- * **Validate assumptions** about data and its collection process. Pay particular attention to when the data was collected.
- * Identify and **address anomalies**.
- * Apply data transformations and corrections (we'll cover this in the upcoming lecture).
- * **Record everything you do!** Developing in Jupyter Notebook promotes *reproducibility* of your own work!
+
---
+title: Data Cleaning and EDA
+execute:
+ echo: true
+format:
+ html:
+ code-fold: true
+ code-tools: true
+ toc: true
+ toc-title: Data Cleaning and EDA
+ page-layout: full
+ theme:
+ - cosmo
+ - cerulean
+ callout-icon: false
+jupyter:
+ jupytext:
+ text_representation:
+ extension: .qmd
+ format_name: quarto
+ format_version: '1.0'
+ jupytext_version: 1.16.1
+ kernelspec:
+ display_name: Python 3 (ipykernel)
+ language: python
+ name: python3
+---
+
+```{python}
+#| code-fold: true
+import numpy as np
+import pandas as pd
+
+import matplotlib.pyplot as plt
+import seaborn as sns
+#%matplotlib inline
+plt.rcParams['figure.figsize'] = (12, 9)
+
+sns.set()
+sns.set_context('talk')
+np.set_printoptions(threshold=20, precision=2, suppress=True)
+pd.set_option('display.max_rows', 30)
+pd.set_option('display.max_columns', None)
+pd.set_option('display.precision', 2)
+# This option stops scientific notation for pandas
+pd.set_option('display.float_format', '{:.2f}'.format)
+
+# Silence some spurious seaborn warnings
+import warnings
+warnings.filterwarnings("ignore", category=FutureWarning)
+```
+
+::: {.callout-note collapse="false"}
+## Learning Outcomes
+* Recognize common file formats
+* Categorize data by its variable type
+* Build awareness of issues with data faithfulness and develop targeted solutions
+:::
+
+In the past few lectures, we've learned that `pandas` is a toolkit to restructure, modify, and explore a dataset. What we haven't yet touched on is *how* to make these data transformation decisions. When we receive a new set of data from the "real world," how do we know what processing we should do to convert this data into a usable form?
+
+**Data cleaning**, also called **data wrangling**, is the process of transforming raw data to facilitate subsequent analysis. It is often used to address issues like:
+
+* Unclear structure or formatting
+* Missing or corrupted values
+* Unit conversions
+* ...and so on
+
+**Exploratory Data Analysis (EDA)** is the process of understanding a new dataset. It is an open-ended, informal analysis that involves familiarizing ourselves with the variables present in the data, discovering potential hypotheses, and identifying possible issues with the data. This last point can often motivate further data cleaning to address any problems with the dataset's format; because of this, EDA and data cleaning are often thought of as an "infinite loop," with each process driving the other.
+
+In this lecture, we will consider the key properties of data to consider when performing data cleaning and EDA. In doing so, we'll develop a "checklist" of sorts for you to consider when approaching a new dataset. Throughout this process, we'll build a deeper understanding of this early (but very important!) stage of the data science lifecycle.
+
+## Structure
+We often prefer rectangular data for data analysis. Rectangular structures are easy to manipulate and analyze. A key element of data cleaning is about transforming data to be more rectangular.
+
+There are two kinds of rectangular data: tables and matrices. Tables have named columns with different data types and are manipulated using data transformation languages. Matrices contain numeric data of the same type and are manipulated using linear algebra.
+
+### File Formats
+There are many file types for storing structured data: TSV, JSON, XML, ASCII, SAS, etc. We'll only cover CSV, TSV, and JSON in lecture, but you'll likely encounter other formats as you work with different datasets. Reading documentation is your best bet for understanding how to process the multitude of different file types.
+
+#### CSV
+CSVs, which stand for **Comma-Separated Values**, are a common tabular data format.
+In the past two `pandas` lectures, we briefly touched on the idea of file format: the way data is encoded in a file for storage. Specifically, our `elections` and `babynames` datasets were stored and loaded as CSVs:
+
+```{python}
+#| code-fold: false
+pd.read_csv("data/elections.csv").head(5)
+```
+
+To better understand the properties of a CSV, let's take a look at the first few rows of the raw data file to see what it looks like before being loaded into a `DataFrame`. We'll use the `repr()` function to return the raw string with its special characters:
+
+```{python}
+#| code-fold: false
+withopen("data/elections.csv", "r") as table:
+ i =0
+for row in table:
+print(repr(row))
+ i +=1
+if i >3:
+break
+```
+
+Each row, or **record**, in the data is delimited by a newline `\n`. Each column, or **field**, in the data is delimited by a comma `,` (hence, comma-separated!).
+
+#### TSV
+
+Another common file type is **TSV (Tab-Separated Values)**. In a TSV, records are still delimited by a newline `\n`, while fields are delimited by `\t` tab character.
+
+Let's check out the first few rows of the raw TSV file. Again, we'll use the `repr()` function so that `print` shows the special characters.
+
+```{python}
+#| code-fold: false
+withopen("data/elections.txt", "r") as table:
+ i =0
+for row in table:
+print(repr(row))
+ i +=1
+if i >3:
+break
+```
+
+TSVs can be loaded into `pandas` using `pd.read_csv`. We'll need to specify the **delimiter** with parameter` sep='\t'`[(documentation)](https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html).
+
+```{python}
+#| code-fold: false
+pd.read_csv("data/elections.txt", sep='\t').head(3)
+```
+
+An issue with CSVs and TSVs comes up whenever there are commas or tabs within the records. How does `pandas` differentiate between a comma delimiter vs. a comma within the field itself, for example `8,900`? To remedy this, check out the [`quotechar` parameter](https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html).
+
+#### JSON
+**JSON (JavaScript Object Notation)** files behave similarly to Python dictionaries. A raw JSON is shown below.
+
+```{python}
+#| code-fold: false
+withopen("data/elections.json", "r") as table:
+ i =0
+for row in table:
+print(row)
+ i +=1
+if i >8:
+break
+```
+
+JSON files can be loaded into `pandas` using `pd.read_json`.
+
+```{python}
+#| code-fold: false
+pd.read_json('data/elections.json').head(3)
+```
+
+##### EDA with JSON: Berkeley COVID-19 Data
+The City of Berkeley Open Data [website](https://data.cityofberkeley.info/Health/COVID-19-Confirmed-Cases/xn6j-b766) has a dataset with COVID-19 Confirmed Cases among Berkeley residents by date. Let's download the file and save it as a JSON (note the source URL file type is also a JSON). In the interest of reproducible data science, we will download the data programatically. We have defined some helper functions in the [`ds100_utils.py`](https://ds100.org/fa23/resources/assets/lectures/lec05/lec05-eda.html) file that we can reuse these helper functions in many different notebooks.
+
+```{python}
+#| code-fold: false
+from ds100_utils import fetch_and_cache
+
+covid_file = fetch_and_cache(
+"https://data.cityofberkeley.info/api/views/xn6j-b766/rows.json?accessType=DOWNLOAD",
+"confirmed-cases.json",
+ force=False)
+covid_file # a file path wrapper object
+```
+
+###### File Size
+Let's start our analysis by getting a rough estimate of the size of the dataset to inform the tools we use to view the data. For relatively small datasets, we can use a text editor or spreadsheet. For larger datasets, more programmatic exploration or distributed computing tools may be more fitting. Here we will use `Python` tools to probe the file.
+
+Since there seem to be text files, let's investigate the number of lines, which often corresponds to the number of records
+
+```{python}
+#| code-fold: false
+import os
+
+print(covid_file, "is", os.path.getsize(covid_file) /1e6, "MB")
+
+withopen(covid_file, "r") as f:
+print(covid_file, "is", sum(1for l in f), "lines.")
+```
+
+###### Unix Commands
+As part of the EDA workflow, Unix commands can come in very handy. In fact, there's an entire book called ["Data Science at the Command Line"](https://datascienceatthecommandline.com/) that explores this idea in depth!
+In Jupyter/IPython, you can prefix lines with `!` to execute arbitrary Unix commands, and within those lines, you can refer to Python variables and expressions with the syntax `{expr}`.
+
+Here, we use the `ls` command to list files, using the `-lh` flags, which request "long format with information in human-readable form." We also use the `wc` command for "word count," but with the `-l` flag, which asks for line counts instead of words.
+
+These two give us the same information as the code above, albeit in a slightly different form:
+
+```{python}
+#| code-fold: false
+!ls -lh {covid_file}
+!wc -l {covid_file}
+```
+
+###### File Contents
+Let's explore the data format using `Python`.
+
+```{python}
+#| code-fold: false
+withopen(covid_file, "r") as f:
+for i, row inenumerate(f):
+print(repr(row)) # print raw strings
+if i >=4: break
+```
+
+We can use the `head` Unix command (which is where `pandas`' `head` method comes from!) to see the first few lines of the file:
+
+```{python}
+#| code-fold: false
+!head -5 {covid_file}
+```
+
+In order to load the JSON file into `pandas`, Let's first do some EDA with Oython's `json` package to understand the particular structure of this JSON file so that we can decide what (if anything) to load into `pandas`. Python has relatively good support for JSON data since it closely matches the internal python object model. In the following cell we import the entire JSON datafile into a python dictionary using the `json` package.
+
+```{python}
+#| code-fold: false
+import json
+
+withopen(covid_file, "rb") as f:
+ covid_json = json.load(f)
+```
+
+The `covid_json` variable is now a dictionary encoding the data in the file:
+
+```{python}
+#| code-fold: false
+type(covid_json)
+```
+
+We can examine what keys are in the top level JSON object by listing out the keys.
+
+```{python}
+#| code-fold: false
+covid_json.keys()
+```
+
+**Observation**: The JSON dictionary contains a `meta` key which likely refers to metadata (data about the data). Metadata is often maintained with the data and can be a good source of additional information.
+
+
+We can investigate the metadata further by examining the keys associated with the metadata.
+
+```{python}
+#| code-fold: false
+covid_json['meta'].keys()
+```
+
+The `meta` key contains another dictionary called `view`. This likely refers to metadata about a particular "view" of some underlying database. We will learn more about views when we study SQL later in the class.
+
+```{python}
+#| code-fold: false
+covid_json['meta']['view'].keys()
+```
+
+Notice that this a nested/recursive data structure. As we dig deeper we reveal more and more keys and the corresponding data:
+
+```
+meta
+|-> data
+ | ... (haven't explored yet)
+|-> view
+ | -> id
+ | -> name
+ | -> attribution
+ ...
+ | -> description
+ ...
+ | -> columns
+ ...
+```
+
+
+There is a key called description in the view sub dictionary. This likely contains a description of the data:
+
+```{python}
+#| code-fold: false
+print(covid_json['meta']['view']['description'])
+```
+
+###### Examining the Data Field for Records
+
+We can look at a few entries in the `data` field. This is what we'll load into `pandas`.
+
+```{python}
+#| code-fold: false
+for i inrange(3):
+print(f"{i:03} | {covid_json['data'][i]}")
+```
+
+Observations:
+* These look like equal-length records, so maybe `data` is a table!
+* But what do each of values in the record mean? Where can we find column headers?
+
+For that, we'll need the `columns` key in the metadata dictionary. This returns a list:
+
+```{python}
+#| code-fold: false
+type(covid_json['meta']['view']['columns'])
+```
+
+###### Summary of exploring the JSON file
+
+1. The above **metadata** tells us a lot about the columns in the data including column names, potential data anomalies, and a basic statistic.
+1. Because of its non-tabular structure, JSON makes it easier (than CSV) to create **self-documenting data**, meaning that information about the data is stored in the same file as the data.
+1. Self-documenting data can be helpful since it maintains its own description and these descriptions are more likely to be updated as data changes.
+
+###### Loading COVID Data into `pandas`
+Finally, let's load the data (not the metadata) into a `pandas``DataFrame`. In the following block of code we:
+
+1. Translate the JSON records into a `DataFrame`:
+
+ * fields: `covid_json['meta']['view']['columns']`
+ * records: `covid_json['data']`
+
+
+1. Remove columns that have no metadata description. This would be a bad idea in general, but here we remove these columns since the above analysis suggests they are unlikely to contain useful information.
+
+1. Examine the `tail` of the table.
+
+```{python}
+#| code-fold: false
+# Load the data from JSON and assign column titles
+covid = pd.DataFrame(
+ covid_json['data'],
+ columns=[c['name'] for c in covid_json['meta']['view']['columns']])
+
+covid.tail()
+```
+
+### Primary and Foreign Keys
+
+Last time, we introduced `.merge` as the `pandas` method for joining multiple `DataFrame`s together. In our discussion of joins, we touched on the idea of using a "key" to determine what rows should be merged from each table. Let's take a moment to examine this idea more closely.
+
+The **primary key** is the column or set of columns in a table that *uniquely* determine the values of the remaining columns. It can be thought of as the unique identifier for each individual row in the table. For example, a table of Data 100 students might use each student's Cal ID as the primary key.
+
+```{python}
+#| echo: false
+pd.DataFrame({"Cal ID":[3034619471, 3035619472, 3025619473, 3046789372], \
+"Name":["Oski", "Ollie", "Orrie", "Ollie"], \
+"Major":["Data Science", "Computer Science", "Data Science", "Economics"]})
+```
+
+The **foreign key** is the column or set of columns in a table that reference primary keys in other tables. Knowing a dataset's foreign keys can be useful when assigning the `left_on` and `right_on` parameters of `.merge`. In the table of office hour tickets below, `"Cal ID"` is a foreign key referencing the previous table.
+
+```{python}
+#| echo: false
+pd.DataFrame({"OH Request":[1, 2, 3, 4], \
+"Cal ID":[3034619471, 3035619472, 3025619473, 3035619472], \
+"Question":["HW 2 Q1", "HW 2 Q3", "Lab 3 Q4", "HW 2 Q7"]})
+```
+
+### Variable Types
+
+Variables are columns. A variable is a measurement of a particular concept. Variables have two common properties: data type/storage type and variable type/feature type. The data type of a variable indicates how each variable value is stored in memory (integer, floating point, boolean, etc.) and affects which `pandas` functions are used. The variable type is a conceptualized measurement of information (and therefore indicates what values a variable can take on). Variable type is identified through expert knowledge, exploring the data itself, or consulting the data codebook. The variable type affects how one visualizes and inteprets the data. In this class, "variable types" are conceptual.
+
+After loading data into a file, it's a good idea to take the time to understand what pieces of information are encoded in the dataset. In particular, we want to identify what variable types are present in our data. Broadly speaking, we can categorize variables into one of two overarching types.
+
+**Quantitative variables** describe some numeric quantity or amount. We can divide quantitative data further into:
+
+* **Continuous quantitative variables**: numeric data that can be measured on a continuous scale to arbitrary precision. Continuous variables do not have a strict set of possible values – they can be recorded to any number of decimal places. For example, weights, GPA, or CO<sub>2</sub> concentrations.
+* **Discrete quantitative variables**: numeric data that can only take on a finite set of possible values. For example, someone's age or the number of siblings they have.
+
+**Qualitative variables**, also known as **categorical variables**, describe data that isn't measuring some quantity or amount. The sub-categories of categorical data are:
+
+* **Ordinal qualitative variables**: categories with ordered levels. Specifically, ordinal variables are those where the difference between levels has no consistent, quantifiable meaning. Some examples include levels of education (high school, undergrad, grad, etc.), income bracket (low, medium, high), or Yelp rating.
+* **Nominal qualitative variables**: categories with no specific order. For example, someone's political affiliation or Cal ID number.
+
+![Classification of variable types](images/variable.png)
+
+Note that many variables don't sit neatly in just one of these categories. Qualitative variables could have numeric levels, and conversely, quantitative variables could be stored as strings.
+
+## Granularity, Scope, and Temporality
+
+After understanding the structure of the dataset, the next task is to determine what exactly the data represents. We'll do so by considering the data's granularity, scope, and temporality.
+
+### Granularity
+The **granularity** of a dataset is what a single row represents. You can also think of it as the level of detail included in the data. To determine the data's granularity, ask: what does each row in the dataset represent? Fine-grained data contains a high level of detail, with a single row representing a small individual unit. For example, each record may represent one person. Coarse-grained data is encoded such that a single row represents a large individual unit – for example, each record may represent a group of people.
+
+### Scope
+The **scope** of a dataset is the subset of the population covered by the data. If we were investigating student performance in Data Science courses, a dataset with a narrow scope might encompass all students enrolled in Data 100 whereas a dataset with an expansive scope might encompass all students in California.
+
+### Temporality
+The **temporality** of a dataset describes the periodicity over which the data was collected as well as when the data was most recently collected or updated.
+
+Time and date fields of a dataset could represent a few things:
+
+1. when the "event" happened
+2. when the data was collected, or when it was entered into the system
+3. when the data was copied into the database
+
+To fully understand the temporality of the data, it also may be necessary to standardize time zones or inspect recurring time-based trends in the data (do patterns recur in 24-hour periods? Over the course of a month? Seasonally?). The convention for standardizing time is the Coordinated Universal Time (UTC), an international time standard measured at 0 degrees latitude that stays consistent throughout the year (no daylight savings). We can represent Berkeley's time zone, Pacific Standard Time (PST), as UTC-7 (with daylight savings).
+
+#### Temporality with `pandas`' `dt` accessors
+Let's briefly look at how we can use `pandas`' `dt` accessors to work with dates/times in a dataset using the dataset you'll see in Lab 3: the Berkeley PD Calls for Service dataset.
+
+```{python}
+#| code-fold: true
+calls = pd.read_csv("data/Berkeley_PD_-_Calls_for_Service.csv")
+calls.head()
+```
+
+Looks like there are three columns with dates/times: `EVENTDT`, `EVENTTM`, and `InDbDate`.
+
+Most likely, `EVENTDT` stands for the date when the event took place, `EVENTTM` stands for the time of day the event took place (in 24-hr format), and `InDbDate` is the date this call is recorded onto the database.
+
+If we check the data type of these columns, we will see they are stored as strings. We can convert them to `datetime` objects using pandas `to_datetime` function.
+
+```{python}
+#| code-fold: false
+calls["EVENTDT"] = pd.to_datetime(calls["EVENTDT"])
+calls.head()
+```
+
+Now, we can use the `dt` accessor on this column.
+
+We can get the month:
+
+```{python}
+#| code-fold: false
+calls["EVENTDT"].dt.month.head()
+```
+
+Which day of the week the date is on:
+
+```{python}
+#| code-fold: false
+calls["EVENTDT"].dt.dayofweek.head()
+```
+
+Check the mimimum values to see if there are any suspicious-looking, 70s dates:
+
+```{python}
+#| code-fold: false
+calls.sort_values("EVENTDT").head()
+```
+
+Doesn't look like it! We are good!
+
+
+We can also do many things with the `dt` accessor like switching time zones and converting time back to UNIX/POSIX time. Check out the documentation on [`.dt` accessor](https://pandas.pydata.org/docs/user_guide/basics.html#basics-dt-accessors) and [time series/date functionality](https://pandas.pydata.org/docs/user_guide/timeseries.html#).
+
+## Faithfulness
+
+At this stage in our data cleaning and EDA workflow, we've achieved quite a lot: we've identified how our data is structured, come to terms with what information it encodes, and gained insight as to how it was generated. Throughout this process, we should always recall the original intent of our work in Data Science – to use data to better understand and model the real world. To achieve this goal, we need to ensure that the data we use is faithful to reality; that is, that our data accurately captures the "real world."
+
+Data used in research or industry is often "messy" – there may be errors or inaccuracies that impact the faithfulness of the dataset. Signs that data may not be faithful include:
+
+* Unrealistic or "incorrect" values, such as negative counts, locations that don't exist, or dates set in the future
+* Violations of obvious dependencies, like an age that does not match a birthday
+* Clear signs that data was entered by hand, which can lead to spelling errors or fields that are incorrectly shifted
+* Signs of data falsification, such as fake email addresses or repeated use of the same names
+* Duplicated records or fields containing the same information
+* Truncated data, e.g. Microsoft Excel would limit the number of rows to 655536 and the number of columns to 255
+
+We often solve some of these more common issues in the following ways:
+
+* Spelling errors: apply corrections or drop records that aren't in a dictionary
+* Time zone inconsistencies: convert to a common time zone (e.g. UTC)
+* Duplicated records or fields: identify and eliminate duplicates (using primary keys)
+* Unspecified or inconsistent units: infer the units and check that values are in reasonable ranges in the data
+
+### Missing Values
+Another common issue encountered with real-world datasets is that of missing data. One strategy to resolve this is to simply drop any records with missing values from the dataset. This does, however, introduce the risk of inducing biases – it is possible that the missing or corrupt records may be systemically related to some feature of interest in the data. Another solution is to keep the data as `NaN` values.
+
+A third method to address missing data is to perform **imputation**: infer the missing values using other data available in the dataset. There is a wide variety of imputation techniques that can be implemented; some of the most common are listed below.
+
+* Average imputation: replace missing values with the average value for that field
+* Hot deck imputation: replace missing values with some random value
+* Regression imputation: develop a model to predict missing values and replace with the predicted value from the model.
+* Multiple imputation: replace missing values with multiple random values
+
+Regardless of the strategy used to deal with missing data, we should think carefully about *why* particular records or fields may be missing – this can help inform whether or not the absence of these values is significant or meaningful.
+
+## EDA Demo 1: Tuberculosis in the United States
+
+Now, let's walk through the data-cleaning and EDA workflow to see what can we learn about the presence of Tuberculosis in the United States!
+
+We will examine the data included in the [original CDC article](https://www.cdc.gov/mmwr/volumes/71/wr/mm7112a1.htm?s_cid=mm7112a1_w#T1_down) published in 2021.
+
+
+### CSVs and Field Names
+Suppose Table 1 was saved as a CSV file located in `data/cdc_tuberculosis.csv`.
+
+We can then explore the CSV (which is a text file, and does not contain binary-encoded data) in many ways:
+1. Using a text editor like emacs, vim, VSCode, etc.
+2. Opening the CSV directly in DataHub (read-only), Excel, Google Sheets, etc.
+3. The `Python` file object
+4. `pandas`, using `pd.read_csv()`
+
+To try out options 1 and 2, you can view or download the Tuberculosis from the [lecture demo notebook](https://data100.datahub.berkeley.edu/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2FDS-100%2Ffa23-student&urlpath=lab%2Ftree%2Ffa23-student%2Flecture%2Flec05%2Flec04-eda.ipynb&branch=main) under the `data` folder in the left hand menu. Notice how the CSV file is a type of **rectangular data (i.e., tabular data) stored as comma-separated values**.
+
+Next, let's try out option 3 using the `Python` file object. We'll look at the first four lines:
+
+```{python}
+#| code-fold: true
+withopen("data/cdc_tuberculosis.csv", "r") as f:
+ i =0
+for row in f:
+print(row)
+ i +=1
+if i >3:
+break
+```
+
+Whoa, why are there blank lines interspaced between the lines of the CSV?
+
+You may recall that all line breaks in text files are encoded as the special newline character `\n`. Python's `print()` prints each string (including the newline), and an additional newline on top of that.
+
+If you're curious, we can use the `repr()` function to return the raw string with all special characters:
+
+```{python}
+#| code-fold: true
+withopen("data/cdc_tuberculosis.csv", "r") as f:
+ i =0
+for row in f:
+print(repr(row)) # print raw strings
+ i +=1
+if i >3:
+break
+```
+
+Finally, let's try option 4 and use the tried-and-true Data 100 approach: `pandas`.
+
+```{python}
+#| code-fold: false
+tb_df = pd.read_csv("data/cdc_tuberculosis.csv")
+tb_df.head()
+```
+
+You may notice some strange things about this table: what's up with the "Unnamed" column names and the first row?
+
+Congratulations — you're ready to wrangle your data! Because of how things are stored, we'll need to clean the data a bit to name our columns better.
+
+A reasonable first step is to identify the row with the right header. The `pd.read_csv()` function ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html)) has the convenient `header` parameter that we can set to use the elements in row 1 as the appropriate columns:
+
+```{python}
+#| code-fold: false
+tb_df = pd.read_csv("data/cdc_tuberculosis.csv", header=1) # row index
+tb_df.head(5)
+```
+
+Wait...but now we can't differentiate betwen the "Number of TB cases" and "TB incidence" year columns. `pandas` has tried to make our lives easier by automatically adding ".1" to the latter columns, but this doesn't help us, as humans, understand the data.
+
+We can do this manually with `df.rename()` ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.rename.html?highlight=rename#pandas.DataFrame.rename)):
+
+```{python}
+#| code-fold: false
+rename_dict = {'2019': 'TB cases 2019',
+'2020': 'TB cases 2020',
+'2021': 'TB cases 2021',
+'2019.1': 'TB incidence 2019',
+'2020.1': 'TB incidence 2020',
+'2021.1': 'TB incidence 2021'}
+tb_df = tb_df.rename(columns=rename_dict)
+tb_df.head(5)
+```
+
+### Record Granularity
+
+You might already be wondering: what's up with that first record?
+
+Row 0 is what we call a **rollup record**, or summary record. It's often useful when displaying tables to humans. The **granularity** of record 0 (Totals) vs the rest of the records (States) is different.
+
+Okay, EDA step two. How was the rollup record aggregated?
+
+Let's check if Total TB cases is the sum of all state TB cases. If we sum over all rows, we should get **2x** the total cases in each of our TB cases by year (why do you think this is?).
+
+```{python}
+#| code-fold: true
+tb_df.sum(axis=0)
+```
+
+Whoa, what's going on with the TB cases in 2019, 2020, and 2021? Check out the column types:
+
+```{python}
+#| code-fold: true
+tb_df.dtypes
+```
+
+Since there are commas in the values for TB cases, the numbers are read as the `object` datatype, or **storage type** (close to the `Python` string datatype), so `pandas` is concatenating strings instead of adding integers (recall that Python can "sum", or concatenate, strings together: `"data" + "100"` evaluates to `"data100"`).
+
+
+Fortunately `read_csv` also has a `thousands` parameter ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html)):
+
+```{python}
+#| code-fold: false
+# improve readability: chaining method calls with outer parentheses/line breaks
+tb_df = (
+ pd.read_csv("data/cdc_tuberculosis.csv", header=1, thousands=',')
+ .rename(columns=rename_dict)
+)
+tb_df.head(5)
+```
+
+```{python}
+#| code-fold: false
+tb_df.sum()
+```
+
+The total TB cases look right. Phew!
+
+Let's just look at the records with **state-level granularity**:
+
+```{python}
+#| code-fold: true
+state_tb_df = tb_df[1:]
+state_tb_df.head(5)
+```
+
+### Gather Census Data
+
+U.S. Census population estimates [source](https://www.census.gov/data/tables/time-series/demo/popest/2010s-state-total.html) (2019), [source](https://www.census.gov/data/tables/time-series/demo/popest/2020s-state-total.html) (2020-2021).
+
+Running the below cells cleans the data.
+There are a few new methods here:
+* `df.convert_dtypes()` ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.convert_dtypes.html)) conveniently converts all float dtypes into ints and is out of scope for the class.
+* `df.drop_na()` ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.dropna.html)) will be explained in more detail next time.
+
+```{python}
+#| code-fold: true
+# 2010s census data
+census_2010s_df = pd.read_csv("data/nst-est2019-01.csv", header=3, thousands=",")
+census_2010s_df = (
+ census_2010s_df
+ .reset_index()
+ .drop(columns=["index", "Census", "Estimates Base"])
+ .rename(columns={"Unnamed: 0": "Geographic Area"})
+ .convert_dtypes() # "smart" converting of columns, use at your own risk
+ .dropna() # we'll introduce this next time
+)
+census_2010s_df['Geographic Area'] = census_2010s_df['Geographic Area'].str.strip('.')
+
+# with pd.option_context('display.min_rows', 30): # shows more rows
+# display(census_2010s_df)
+
+census_2010s_df.head(5)
+```
+
+Occasionally, you will want to modify code that you have imported. To reimport those modifications you can either use `python`'s `importlib` library:
+
+```python
+from importlib importreload
+reload(utils)
+```
+
+or use `iPython` magic which will intelligently import code when files change:
+
+```python
+%load_ext autoreload
+%autoreload 2
+```
+
+```{python}
+#| code-fold: true
+# census 2020s data
+census_2020s_df = pd.read_csv("data/NST-EST2022-POP.csv", header=3, thousands=",")
+census_2020s_df = (
+ census_2020s_df
+ .reset_index()
+ .drop(columns=["index", "Unnamed: 1"])
+ .rename(columns={"Unnamed: 0": "Geographic Area"})
+ .convert_dtypes() # "smart" converting of columns, use at your own risk
+ .dropna() # we'll introduce this next time
+)
+census_2020s_df['Geographic Area'] = census_2020s_df['Geographic Area'].str.strip('.')
+
+census_2020s_df.head(5)
+```
+
+### Joining Data (Merging `DataFrame`s)
+
+Time to `merge`! Here we use the `DataFrame` method `df1.merge(right=df2, ...)` on `DataFrame``df1` ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.merge.html)). Contrast this with the function `pd.merge(left=df1, right=df2, ...)` ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.merge.html?highlight=pandas%20merge#pandas.merge)). Feel free to use either.
+
+```{python}
+#| code-fold: false
+# merge TB DataFrame with two US census DataFrames
+tb_census_df = (
+ tb_df
+ .merge(right=census_2010s_df,
+ left_on="U.S. jurisdiction", right_on="Geographic Area")
+ .merge(right=census_2020s_df,
+ left_on="U.S. jurisdiction", right_on="Geographic Area")
+)
+tb_census_df.head(5)
+```
+
+Having all of these columns is a little unwieldy. We could either drop the unneeded columns now, or just merge on smaller census `DataFrame`s. Let's do the latter.
+
+```{python}
+#| code-fold: false
+# try merging again, but cleaner this time
+tb_census_df = (
+ tb_df
+ .merge(right=census_2010s_df[["Geographic Area", "2019"]],
+ left_on="U.S. jurisdiction", right_on="Geographic Area")
+ .drop(columns="Geographic Area")
+ .merge(right=census_2020s_df[["Geographic Area", "2020", "2021"]],
+ left_on="U.S. jurisdiction", right_on="Geographic Area")
+ .drop(columns="Geographic Area")
+)
+tb_census_df.head(5)
+```
+
+### Reproducing Data: Compute Incidence
+
+Let's recompute incidence to make sure we know where the original CDC numbers came from.
+
+From the [CDC report](https://www.cdc.gov/mmwr/volumes/71/wr/mm7112a1.htm?s_cid=mm7112a1_w#T1_down): TB incidence is computed as “Cases per 100,000 persons using mid-year population estimates from the U.S. Census Bureau.”
+
+If we define a group as 100,000 people, then we can compute the TB incidence for a given state population as
+
+$$\text{TB incidence} = \frac{\text{TB cases in population}}{\text{groups in population}} = \frac{\text{TB cases in population}}{\text{population}/100000} $$
+
+$$= \frac{\text{TB cases in population}}{\text{population}} \times 100000$$
+
+Let's try this for 2019:
+
+```{python}
+#| code-fold: false
+tb_census_df["recompute incidence 2019"] = tb_census_df["TB cases 2019"]/tb_census_df["2019"]*100000
+tb_census_df.head(5)
+```
+
+Awesome!!!
+
+Let's use a for-loop and Python format strings to compute TB incidence for all years. Python f-strings are just used for the purposes of this demo, but they're handy to know when you explore data beyond this course ([documentation](https://docs.python.org/3/tutorial/inputoutput.html)).
+
+```{python}
+#| code-fold: false
+# recompute incidence for all years
+for year in [2019, 2020, 2021]:
+ tb_census_df[f"recompute incidence {year}"] = tb_census_df[f"TB cases {year}"]/tb_census_df[f"{year}"]*100000
+tb_census_df.head(5)
+```
+
+These numbers look pretty close!!! There are a few errors in the hundredths place, particularly in 2021. It may be useful to further explore reasons behind this discrepancy.
+
+```{python}
+#| code-fold: false
+tb_census_df.describe()
+```
+
+### Bonus EDA: Reproducing the Reported Statistic
+
+
+**How do we reproduce that reported statistic in the original [CDC report](https://www.cdc.gov/mmwr/volumes/71/wr/mm7112a1.htm?s_cid=mm7112a1_w)?**
+
+> Reported TB incidence (cases per 100,000 persons) increased **9.4%**, from **2.2** during 2020 to **2.4** during 2021 but was lower than incidence during 2019 (2.7). Increases occurred among both U.S.-born and non–U.S.-born persons.
+
+This is TB incidence computed across the entire U.S. population! How do we reproduce this?
+* We need to reproduce the "Total" TB incidences in our rolled record.
+* But our current `tb_census_df` only has 51 entries (50 states plus Washington, D.C.). There is no rolled record.
+* What happened...?
+
+Let's get exploring!
+
+Before we keep exploring, we'll set all indexes to more meaningful values, instead of just numbers that pertain to some row at some point. This will make our cleaning slightly easier.
+
+```{python}
+#| code-fold: true
+tb_df = tb_df.set_index("U.S. jurisdiction")
+tb_df.head(5)
+```
+
+```{python}
+#| code-fold: false
+census_2010s_df = census_2010s_df.set_index("Geographic Area")
+census_2010s_df.head(5)
+```
+
+```{python}
+#| code-fold: false
+census_2020s_df = census_2020s_df.set_index("Geographic Area")
+census_2020s_df.head(5)
+```
+
+It turns out that our merge above only kept state records, even though our original `tb_df` had the "Total" rolled record:
+
+```{python}
+#| code-fold: false
+tb_df.head()
+```
+
+Recall that `merge` by default does an **inner** merge by default, meaning that it only preserves keys that are present in **both** `DataFrame`s.
+
+The rolled records in our census `DataFrame` have different `Geographic Area` fields, which was the key we merged on:
+
+```{python}
+#| code-fold: false
+census_2010s_df.head(5)
+```
+
+The Census `DataFrame` has several rolled records. The aggregate record we are looking for actually has the Geographic Area named "United States".
+
+One straightforward way to get the right merge is to rename the value itself. Because we now have the Geographic Area index, we'll use `df.rename()` ([documentation](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.rename.html)):
+
+```{python}
+#| code-fold: false
+# rename rolled record for 2010s
+census_2010s_df.rename(index={'United States':'Total'}, inplace=True)
+census_2010s_df.head(5)
+```
+
+```{python}
+#| code-fold: false
+# same, but for 2020s rename rolled record
+census_2020s_df.rename(index={'United States':'Total'}, inplace=True)
+census_2020s_df.head(5)
+```
+
+<br/>
+
+Next let's rerun our merge. Note the different chaining, because we are now merging on indexes (`df.merge()`[documentation](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.merge.html)).
+
+```{python}
+#| code-fold: false
+tb_census_df = (
+ tb_df
+ .merge(right=census_2010s_df[["2019"]],
+ left_index=True, right_index=True)
+ .merge(right=census_2020s_df[["2020", "2021"]],
+ left_index=True, right_index=True)
+)
+tb_census_df.head(5)
+```
+
+<br/>
+
+Finally, let's recompute our incidences:
+
+```{python}
+#| code-fold: false
+# recompute incidence for all years
+for year in [2019, 2020, 2021]:
+ tb_census_df[f"recompute incidence {year}"] = tb_census_df[f"TB cases {year}"]/tb_census_df[f"{year}"]*100000
+tb_census_df.head(5)
+```
+
+We reproduced the total U.S. incidences correctly!
+
+We're almost there. Let's revisit the quote:
+
+> Reported TB incidence (cases per 100,000 persons) increased **9.4%**, from **2.2** during 2020 to **2.4** during 2021 but was lower than incidence during 2019 (2.7). Increases occurred among both U.S.-born and non–U.S.-born persons.
+
+Recall that percent change from $A$ to $B$ is computed as
+$\text{percent change} = \frac{B - A}{A} \times 100$.
+
+```{python}
+#| code-fold: false
+incidence_2020 = tb_census_df.loc['Total', 'recompute incidence 2020']
+incidence_2020
+```
+
+```{python}
+#| code-fold: false
+incidence_2021 = tb_census_df.loc['Total', 'recompute incidence 2021']
+incidence_2021
+```
+
+```{python}
+#| code-fold: false
+difference = (incidence_2021 - incidence_2020)/incidence_2020 *100
+difference
+```
+
+## EDA Demo 2: Mauna Loa CO<sub>2</sub> Data -- A Lesson in Data Faithfulness
+
+[Mauna Loa Observatory](https://gml.noaa.gov/ccgg/trends/data.html) has been monitoring CO<sub>2</sub> concentrations since 1958.
+
+```{python}
+#| code-fold: false
+co2_file ="data/co2_mm_mlo.txt"
+```
+
+Let's do some **EDA**!!
+
+### Reading this file into `Pandas`?
+Let's instead check out this `.txt` file. Some questions to keep in mind: Do we trust this file extension? What structure is it?
+
+Lines 71-78 (inclusive) are shown below:
+
+ line number | file contents
+
+ 71 | # decimal average interpolated trend #days
+ 72 | # date (season corr)
+ 73 | 1958 3 1958.208 315.71 315.71 314.62 -1
+ 74 | 1958 4 1958.292 317.45 317.45 315.29 -1
+ 75 | 1958 5 1958.375 317.50 317.50 314.71 -1
+ 76 | 1958 6 1958.458 -99.99 317.10 314.85 -1
+ 77 | 1958 7 1958.542 315.86 315.86 314.98 -1
+ 78 | 1958 8 1958.625 314.93 314.93 315.94 -1
+
+
+Notice how:
+
+- The values are separated by white space, possibly tabs.
+- The data line up down the rows. For example, the month appears in 7th to 8th position of each line.
+- The 71st and 72nd lines in the file contain column headings split over two lines.
+
+We can use `read_csv` to read the data into a `pandas``DataFrame`, and we provide several arguments to specify that the separators are white space, there is no header (**we will set our own column names**), and to skip the first 72 rows of the file.
+
+```{python}
+#| code-fold: false
+co2 = pd.read_csv(
+ co2_file, header =None, skiprows =72,
+ sep =r'\s+'#delimiter for continuous whitespace (stay tuned for regex next lecture))
+)
+co2.head()
+```
+
+Congratulations! You've wrangled the data!
+
+<br/>
+
+...But our columns aren't named.
+**We need to do more EDA.**
+
+### Exploring Variable Feature Types
+
+The NOAA [webpage](https://gml.noaa.gov/ccgg/trends/) might have some useful tidbits (in this case it doesn't).
+
+Using this information, we'll rerun `pd.read_csv`, but this time with some **custom column names.**
+
+```{python}
+#| code-fold: false
+co2 = pd.read_csv(
+ co2_file, header =None, skiprows =72,
+ sep ='\s+', #regex for continuous whitespace (next lecture)
+ names = ['Yr', 'Mo', 'DecDate', 'Avg', 'Int', 'Trend', 'Days']
+)
+co2.head()
+```
+
+### Visualizing CO<sub>2</sub>
+Scientific studies tend to have very clean data, right...? Let's jump right in and make a time series plot of CO<sub>2</sub> monthly averages.
+
+```{python}
+#| code-fold: true
+sns.lineplot(x='DecDate', y='Avg', data=co2);
+```
+
+The code above uses the `seaborn` plotting library (abbreviated `sns`). We will cover this in the Visualization lecture, but now you don't need to worry about how it works!
+
+Yikes! Plotting the data uncovered a problem. The sharp vertical lines suggest that we have some **missing values**. What happened here?
+
+```{python}
+#| code-fold: false
+co2.head()
+```
+
+```{python}
+#| code-fold: false
+co2.tail()
+```
+
+Some data have unusual values like -1 and -99.99.
+
+Let's check the description at the top of the file again.
+
+* -1 signifies a missing value for the number of days `Days` the equipment was in operation that month.
+* -99.99 denotes a missing monthly average `Avg`
+
+How can we fix this? First, let's explore other aspects of our data. Understanding our data will help us decide what to do with the missing values.
+
+<br/>
+
+
+### Sanity Checks: Reasoning about the data
+First, we consider the shape of the data. How many rows should we have?
+
+* If chronological order, we should have one record per month.
+* Data from March 1958 to August 2019.
+* We should have $ 12 \times (2019-1957) - 2 - 4 = 738 $ records.
+
+```{python}
+#| code-fold: false
+co2.shape
+```
+
+Nice!! The number of rows (i.e. records) match our expectations.
+
+
+Let's now check the quality of each feature.
+
+### Understanding Missing Value 1: `Days`
+`Days` is a time field, so let's analyze other time fields to see if there is an explanation for missing values of days of operation.
+
+Let's start with **months**, `Mo`.
+
+Are we missing any records? The number of months should have 62 or 61 instances (March 1957-August 2019).
+
+```{python}
+#| code-fold: false
+co2["Mo"].value_counts().sort_index()
+```
+
+As expected Jan, Feb, Sep, Oct, Nov, and Dec have 61 occurrences and the rest 62.
+
+<br/>
+
+Next let's explore **days** `Days` itself, which is the number of days that the measurement equipment worked.
+
+```{python}
+#| code-fold: true
+sns.displot(co2['Days']);
+plt.title("Distribution of days feature");# suppresses unneeded plotting output
+```
+
+In terms of data quality, a handful of months have averages based on measurements taken on fewer than half the days. In addition, there are nearly 200 missing values--**that's about 27% of the data**!
+
+<br/>
+
+Finally, let's check the last time feature, **year** `Yr`.
+
+Let's check to see if there is any connection between missing-ness and the year of the recording.
+
+```{python}
+#| code-fold: true
+sns.scatterplot(x="Yr", y="Days", data=co2);
+plt.title("Day field by Year");# the ; suppresses output
+```
+
+**Observations**:
+
+* All of the missing data are in the early years of operation.
+* It appears there may have been problems with equipment in the mid to late 80s.
+
+**Potential Next Steps**:
+
+* Confirm these explanations through documentation about the historical readings.
+* Maybe drop the earliest recordings? However, we would want to delay such action until after we have examined the time trends and assess whether there are any potential problems.
+
+<br/>
+
+### Understanding Missing Value 2: `Avg`
+Next, let's return to the -99.99 values in `Avg` to analyze the overall quality of the CO<sub>2</sub> measurements. We'll plot a histogram of the average CO<sub>2</sub> measurements
+
+```{python}
+#| code-fold: true
+# Histograms of average CO2 measurements
+sns.displot(co2['Avg']);
+```
+
+The non-missing values are in the 300-400 range (a regular range of CO<sub>2</sub> levels).
+
+We also see that there are only a few missing `Avg` values (**<1% of values**). Let's examine all of them:
+
+```{python}
+#| code-fold: false
+co2[co2["Avg"] <0]
+```
+
+There doesn't seem to be a pattern to these values, other than that most records also were missing `Days` data.
+
+### Drop, `NaN`, or Impute Missing `Avg` Data?
+
+How should we address the invalid `Avg` data?
+
+1. Drop records
+2. Set to NaN
+3. Impute using some strategy
+
+Remember we want to fix the following plot:
+
+```{python}
+#| code-fold: true
+sns.lineplot(x='DecDate', y='Avg', data=co2)
+plt.title("CO2 Average By Month");
+```
+
+Since we are plotting `Avg` vs `DecDate`, we should just focus on dealing with missing values for `Avg`.
+
+
+Let's consider a few options:
+1. Drop those records
+2. Replace -99.99 with NaN
+3. Substitute it with a likely value for the average CO<sub>2</sub>?
+
+What do you think are the pros and cons of each possible action?
+
+Let's examine each of these three options.
+
+```{python}
+#| code-fold: false
+# 1. Drop missing values
+co2_drop = co2[co2['Avg'] >0]
+co2_drop.head()
+```
+
+```{python}
+#| code-fold: false
+# 2. Replace NaN with -99.99
+co2_NA = co2.replace(-99.99, np.NaN)
+co2_NA.head()
+```
+
+We'll also use a third version of the data.
+
+First, we note that the dataset already comes with a **substitute value** for the -99.99.
+
+From the file description:
+
+> The `interpolated` column includes average values from the preceding column (`average`)
+and **interpolated values** where data are missing. Interpolated values are
+computed in two steps...
+
+The `Int` feature has values that exactly match those in `Avg`, except when `Avg` is -99.99, and then a **reasonable** estimate is used instead.
+
+So, the third version of our data will use the `Int` feature instead of `Avg`.
+
+```{python}
+#| code-fold: false
+# 3. Use interpolated column which estimates missing Avg values
+co2_impute = co2.copy()
+co2_impute['Avg'] = co2['Int']
+co2_impute.head()
+```
+
+What's a **reasonable** estimate?
+
+To answer this question, let's zoom in on a short time period, say the measurements in 1958 (where we know we have two missing values).
+
+```{python}
+#| code-fold: true
+# results of plotting data in 1958
+
+def line_and_points(data, ax, title):
+# assumes single year, hence Mo
+ ax.plot('Mo', 'Avg', data=data)
+ ax.scatter('Mo', 'Avg', data=data)
+ ax.set_xlim(2, 13)
+ ax.set_title(title)
+ ax.set_xticks(np.arange(3, 13))
+
+def data_year(data, year):
+return data[data["Yr"] ==1958]
+
+# uses matplotlib subplots
+# you may see more next week; focus on output for now
+fig, axes = plt.subplots(ncols =3, figsize=(12, 4), sharey=True)
+
+year =1958
+line_and_points(data_year(co2_drop, year), axes[0], title="1. Drop Missing")
+line_and_points(data_year(co2_NA, year), axes[1], title="2. Missing Set to NaN")
+line_and_points(data_year(co2_impute, year), axes[2], title="3. Missing Interpolated")
+
+fig.suptitle(f"Monthly Averages for {year}")
+plt.tight_layout()
+```
+
+In the big picture since there are only 7 `Avg` values missing (**<1%** of 738 months), any of these approaches would work.
+
+However there is some appeal to **option C, Imputing**:
+
+* Shows seasonal trends for CO<sub>2</sub>
+* We are plotting all months in our data as a line plot
+
+
+Let's replot our original figure with option 3:
+
+```{python}
+#| code-fold: true
+sns.lineplot(x='DecDate', y='Avg', data=co2_impute)
+plt.title("CO2 Average By Month, Imputed");
+```
+
+Looks pretty close to what we see on the NOAA [website](https://gml.noaa.gov/ccgg/trends/)!
+
+### Presenting the Data: A Discussion on Data Granularity
+
+From the description:
+
+* Monthly measurements are averages of average day measurements.
+* The NOAA GML website has datasets for daily/hourly measurements too.
+
+The data you present depends on your research question.
+
+**How do CO<sub>2</sub> levels vary by season?**
+
+* You might want to keep average monthly data.
+
+**Are CO<sub>2</sub> levels rising over the past 50+ years, consistent with global warming predictions?**
+
+* You might be happier with a **coarser granularity** of average year data!
+
+```{python}
+#| code-fold: true
+co2_year = co2_impute.groupby('Yr').mean()
+sns.lineplot(x='Yr', y='Avg', data=co2_year)
+plt.title("CO2 Average By Year");
+```
+
+Indeed, we see a rise by nearly 100 ppm of CO<sub>2</sub> since Mauna Loa began recording in 1958.
+
+## Summary
+We went over a lot of content this lecture; let's summarize the most important points:
+
+### Dealing with Missing Values
+There are a few options we can take to deal with missing data:
+
+* Drop missing records
+* Keep `NaN` missing values
+* Impute using an interpolated column
+
+### EDA and Data Wrangling
+There are several ways to approach EDA and Data Wrangling:
+
+* Examine the **data and metadata**: what is the date, size, organization, and structure of the data?
+* Examine each **field/attribute/dimension** individually.
+* Examine pairs of related dimensions (e.g. breaking down grades by major).
+* Along the way, we can:
+ * **Visualize** or summarize the data.
+ * **Validate assumptions** about data and its collection process. Pay particular attention to when the data was collected.
+ * Identify and **address anomalies**.
+ * Apply data transformations and corrections (we'll cover this in the upcoming lecture).
+ * **Record everything you do!** Developing in Jupyter Notebook promotes *reproducibility* of your own work!
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diff --git a/feature_engineering/feature_engineering.html b/docs/feature_engineering/feature_engineering.html
similarity index 99%
rename from feature_engineering/feature_engineering.html
rename to docs/feature_engineering/feature_engineering.html
index ddd15067c..0dce32e25 100644
--- a/feature_engineering/feature_engineering.html
+++ b/docs/feature_engineering/feature_engineering.html
@@ -752,7 +752,7 @@
print(f"MSE of model with (hp^2) feature: {np.mean((Y-hp2_model_predictions)**2)}")
-
MSE of model with (hp^2) feature: 18.984768907617223
+
MSE of model with (hp^2) feature: 18.984768907617216
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index 1589ea599..6c0d68abc 100644
--- a/gradient_descent/gradient_descent.html
+++ b/docs/gradient_descent/gradient_descent.html
@@ -106,7 +106,7 @@
require.undef("plotly");
requirejs.config({
paths: {
- 'plotly': ['https://cdn.plot.ly/plotly-2.25.2.min']
+ 'plotly': ['https://cdn.plot.ly/plotly-2.12.1.min']
}
});
require(['plotly'], function(Plotly) {
@@ -591,7 +591,7 @@
my_model.fit(X, Y)
-
LinearRegression()
In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook. On GitHub, the HTML representation is unable to render, please try loading this page with nbviewer.org.
LinearRegression()
+
LinearRegression()
In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook. On GitHub, the HTML representation is unable to render, please try loading this page with nbviewer.org.
LinearRegression()
Notice that we use double brackets to extract this column. Why double brackets instead of just single brackets? The .fit method, by default, expects to receive 2-dimensional data – some kind of data that includes both rows and columns. Writing penguins["flipper_length_mm"] would return a 1D Series, causing sklearn to error. We avoid this by writing penguins[["flipper_length_mm"]] to produce a 2D DataFrame.
@@ -642,7 +642,7 @@
print(f"The RMSE of the model is {np.sqrt(np.mean((Y-Y_hat_two_features)**2))}")
-
The RMSE of the model is 0.9881331104079044
+
The RMSE of the model is 0.9881331104079045
We can also see that we obtain the same predictions using sklearn as we did when applying the ordinary least squares formula before!
Perform data cleaning and text manipulation in SQL
+
Join data across tables
+
+
+
+
+
In this lecture, we’ll continue our work from last time to introduce some advanced SQL syntax.
+
First, let’s load in the basic_examples.db database.
+
+
+Code
+
# Load the SQL Alchemy Python library and DuckDB
+import sqlalchemy
+import duckdb
+
+
+
+
# Load %%sql cell magic
+%load_ext sql
+
+
+
# Connect to the database
+%sql duckdb:///data/basic_examples.db --alias basic
+
+
+
21.1 Aggregating with GROUP BY
+
At this point, we’ve seen that SQL offers much of the same functionality that was given to us by pandas. We can extract data from a table, filter it, and reorder it to suit our needs.
+
In pandas, much of our analysis work relied heavily on being able to use .groupby() to aggregate across the rows of our dataset. SQL’s answer to this task is the (very conveniently named) GROUP BY clause. While the outputs of GROUP BY are similar to those of .groupby() —— in both cases, we obtain an output table where some column has been used for grouping —— the syntax and logic used to group data in SQL are fairly different to the pandas implementation.
+
To illustrate GROUP BY, we will consider the Dish table from our database.
+
+
%%sql
+SELECT *
+FROM Dish;
+
+
* duckdb:///data/basic_examples.db
+Done.
+
+
+
+
+
+
name
+
type
+
cost
+
+
+
+
+
+
+
+
Notice that there are multiple dishes of the same type. What if we wanted to find the total costs of dishes of a certain type? To accomplish this, we would write the following code.
+
+
%%sql
+SELECT type, SUM(cost)
+FROM Dish
+GROUP BY type;
+
+
* duckdb:///data/basic_examples.db
+Done.
+
+
+
+
+
+
type
+
sum("cost")
+
+
+
+
+
+
+
+
What is going on here? The statement GROUP BY type tells SQL to group the data based on the value contained in the type column (whether a record is an appetizer, entree, or dessert). SUM(cost) sums up the costs of dishes in each type and displays the result in the output table.
+
You may be wondering: why does SUM(cost) come before the command to GROUP BY type? Don’t we need to form groups before we can count the number of entries in each? Remember that SQL is a declarative programming language —— a SQL programmer simply states what end result they would like to see, and leaves the task of figuring out how to obtain this result to SQL itself. This means that SQL queries sometimes don’t follow what a reader sees as a “logical” sequence of thought. Instead, SQL requires that we follow its set order of operations when constructing queries. So long as we follow this order, SQL will handle the underlying logic.
+
In practical terms: our goal with this query was to output the total costs of each type. To communicate this to SQL, we say that we want to SELECT the SUMmed cost values for each type group.
+
There are many aggregation functions that can be used to aggregate the data contained in each group. Some common examples are:
+
+
COUNT: count the number of rows associated with each group
+
MIN: find the minimum value of each group
+
MAX: find the maximum value of each group
+
SUM: sum across all records in each group
+
AVG: find the average value of each group
+
+
We can easily compute multiple aggregations all at once (a task that was very tricky in pandas).
To count the number of rows associated with each group, we use the COUNT keyword. Calling COUNT(*) will compute the total number of rows in each group, including rows with null values. Its pandas equivalent is .groupby().size().
+
Recall the Dragon table from the previous lecture:
+
+
%%sql
+SELECT * FROM Dragon;
+
+
* duckdb:///data/basic_examples.db
+Done.
+
+
+
+
+
+
name
+
year
+
cute
+
+
+
+
+
+
+
+
Notice that COUNT(*) and COUNT(cute) result in different outputs.
+
+
%%sql
+SELECT year, COUNT(*)
+FROM Dragon
+GROUP BY year;
+
+
* duckdb:///data/basic_examples.db
+Done.
+
+
+
+
+
+
year
+
count_star()
+
+
+
+
+
+
+
+
+
%%sql
+SELECT year, COUNT(cute)
+FROM Dragon
+GROUP BY year;
+
+
* duckdb:///data/basic_examples.db
+Done.
+
+
+
+
+
+
year
+
count(cute)
+
+
+
+
+
+
+
+
With this definition of GROUP BY in hand, let’s update our SQL order of operations. Remember: every SQL query must list clauses in this order.
+
SELECT <column expression list>
+FROM <table>
+[WHERE <predicate>]
+[GROUP BY <column list>]
+[ORDER BY <column list>]
+[LIMIT <number of rows>]
+[OFFSET <number of rows>];
+
Note that we can use the AS keyword to rename columns during the selection process and that column expressions may include aggregation functions (MAX, MIN, etc.).
+
+
+
21.2 Filtering Groups
+
Now, what if we only want groups that meet a certain condition? HAVING filters groups by applying some condition across all rows in each group. We interpret it as a way to keep only the groups HAVING some condition. Note the difference between WHERE and HAVING: we use WHERE to filter rows, whereas we use HAVING to filter groups. WHERE precedes HAVING in terms of how SQL executes a query.
+
Let’s take a look at the Dish table to see how we can use HAVING. Say we want to group dishes with a cost greater than 4 by type and only keep groups where the max cost is less than 10.
+
+
%%sql
+SELECT type, COUNT(*)
+FROM Dish
+WHERE cost >4
+GROUP BY type
+HAVING MAX(cost) <10;
+
+
* duckdb:///data/basic_examples.db
+Done.
+
+
+
+
+
+
type
+
count_star()
+
+
+
+
+
+
+
+
Here, we first use WHERE to filter for rows with a cost greater than 4. We then group our values by type before applying the HAVING operator. With HAVING, we can filter our groups based on if the max cost is less than 10.
+
+
+
21.3 Summary: SQL
+
With this definition of GROUP BY and HAVING in hand, let’s update our SQL order of operations. Remember: every SQL query must list clauses in this order.
+
SELECT <column expression list>
+FROM <table>
+[WHERE <predicate>]
+[GROUP BY <column list>]
+[ORDER BY <column list>]
+[LIMIT <number of rows>]
+[OFFSET <number of rows>];
+
Note that we can use the AS keyword to rename columns during the selection process and that column expressions may include aggregation functions (MAX, MIN, etc.).
+
+
+
21.4 EDA in SQL
+
In the last lecture, we mostly worked under the assumption that our data had already been cleaned. However, as we saw in our first pass through the data science lifecycle, we’re very unlikely to be given data that is free of formatting issues. With this in mind, we’ll want to learn how to clean and transform data in SQL.
+
Our typical workflow when working with “big data” is:
+
+
Use SQL to query data from a database
+
Use Python (with pandas) to analyze this data in detail
+
+
We can, however, still perform simple data cleaning and re-structuring using SQL directly. To do so, we’ll use the Title table from the imdb_duck database, which contains information about movies and actors.
* duckdb:///data/basic_examples.db
+(duckdb.duckdb.ParserException) Parser Error: syntax error at or near "imdb_engine"
+[SQL: imdb_engine]
+(Background on this error at: https://sqlalche.me/e/20/f405)
+
+
+
Since we’ll be working with the Title table, let’s take a quick look at what it contains.
+
+
%%sql imdb
+
+SELECT *
+FROM Title
+WHERE primaryTitle IN ('Ginny & Georgia', 'What If...?', 'Succession', 'Veep', 'Tenet')
+LIMIT 10;
+
+
* duckdb:///data/basic_examples.db
+(duckdb.duckdb.ParserException) Parser Error: syntax error at or near "imdb"
+[SQL: imdb
+
+SELECT *
+FROM Title
+WHERE primaryTitle IN ('Ginny & Georgia', 'What If...?', 'Succession', 'Veep', 'Tenet')
+LIMIT 10;]
+(Background on this error at: https://sqlalche.me/e/20/f405)
+
+
+
+
21.4.1 Matching Text using LIKE
+
One common task we encountered in our first look at EDA was needing to match string data. For example, we might want to remove entries beginning with the same prefix as part of the data cleaning process.
+
In SQL, we use the LIKE operator to (you guessed it) look for strings that are like a given string pattern.
+
+
%%sql
+SELECT titleType, primaryTitle
+FROM Title
+WHERE primaryTitle LIKE 'Star Wars: Episode I - The Phantom Menace'
+
+
* duckdb:///data/basic_examples.db
+(duckdb.duckdb.CatalogException) Catalog Error: Table with name Title does not exist!
+Did you mean "temp.information_schema.tables"?
+LINE 2: FROM Title
+ ^
+[SQL: SELECT titleType, primaryTitle
+FROM Title
+WHERE primaryTitle LIKE 'Star Wars: Episode I - The Phantom Menace']
+(Background on this error at: https://sqlalche.me/e/20/f405)
+
+
+
What if we wanted to find all Star Wars movies? % is the wildcard operator, it means “look for any character, any number of times”. This makes it helpful for identifying strings that are similar to our desired pattern, even when we don’t know the full text of what we aim to extract.
+
+
%%sql
+SELECT titleType, primaryTitle
+FROM Title
+WHERE primaryTitle LIKE '%Star Wars%'
+LIMIT 10;
+
+
* duckdb:///data/basic_examples.db
+(duckdb.duckdb.CatalogException) Catalog Error: Table with name Title does not exist!
+Did you mean "temp.information_schema.tables"?
+LINE 2: FROM Title
+ ^
+[SQL: SELECT titleType, primaryTitle
+FROM Title
+WHERE primaryTitle LIKE '%Star Wars%'
+LIMIT 10;]
+(Background on this error at: https://sqlalche.me/e/20/f405)
+
+
+
Alternatively, we can use RegEx! DuckDB and most real DBMSs allow for this. Note that here, we have to use the SIMILAR TO operater rather than LIKE.
+
+
%%sql
+SELECT titleType, primaryTitle
+FROM Title
+WHERE primaryTitle SIMILAR TO '.*Star Wars*.'
+LIMIT 10;
+
+
* duckdb:///data/basic_examples.db
+(duckdb.duckdb.CatalogException) Catalog Error: Table with name Title does not exist!
+Did you mean "temp.information_schema.tables"?
+LINE 2: FROM Title
+ ^
+[SQL: SELECT titleType, primaryTitle
+FROM Title
+WHERE primaryTitle SIMILAR TO '.*Star Wars*.'
+LIMIT 10;]
+(Background on this error at: https://sqlalche.me/e/20/f405)
+
+
+
+
+
21.4.2CASTing Data Types
+
A common data cleaning task is converting data to the correct variable type. The CAST keyword is used to generate a new output column. Each entry in this output column is the result of converting the data in an existing column to a new data type. For example, we may wish to convert numeric data stored as a string to an integer.
+
+
%%sql
+SELECT primaryTitle, CAST(runtimeMinutes AS INT)
+FROM Title;
+
+
* duckdb:///data/basic_examples.db
+(duckdb.duckdb.CatalogException) Catalog Error: Table with name Title does not exist!
+Did you mean "temp.information_schema.tables"?
+LINE 2: FROM Title;
+ ^
+[SQL: SELECT primaryTitle, CAST(runtimeMinutes AS INT)
+FROM Title;]
+(Background on this error at: https://sqlalche.me/e/20/f405)
+
+
+
We use CAST when SELECTing colunns for our output table. In the example above, we want to SELECT the columns of integer year and runtime data that is created by the CAST.
+
SQL will automatically name a new column according to the command used to SELECT it, which can lead to unwieldy column names. We can rename the CASTed column using the AS keyword.
+
+
%%sql
+SELECT primaryTitle AS title, CAST(runtimeMinutes AS INT) AS minutes, CAST(startYear AS INT) AS year
+FROM Title
+LIMIT 5;
+
+
* duckdb:///data/basic_examples.db
+(duckdb.duckdb.CatalogException) Catalog Error: Table with name Title does not exist!
+Did you mean "temp.information_schema.tables"?
+LINE 2: FROM Title
+ ^
+[SQL: SELECT primaryTitle AS title, CAST(runtimeMinutes AS INT) AS minutes, CAST(startYear AS INT) AS year
+FROM Title
+LIMIT 5;]
+(Background on this error at: https://sqlalche.me/e/20/f405)
+
+
+
+
+
21.4.3 Using Conditional Statements with CASE
+
When working with pandas, we often ran into situations where we wanted to generate new columns using some form of conditional statement. For example, say we wanted to describe a film title as “old,” “mid-aged,” or “new,” depending on the year of its release.
+
In SQL, conditional operations are performed using a CASE clause. Conceptually, CASE behaves much like the CAST operation: it creates a new column that we can then SELECT to appear in the output. The syntax for a CASE clause is as follows:
+
CASE WHEN <condition> THEN <value>
+ WHEN <other condition> THEN <other value>
+ ...
+ ELSE <yet another value>
+ END
+
Scanning through the skeleton code above, you can see that the logic is similar to that of an if statement in Python. The conditional statement is first opened by calling CASE. Each new condition is specified by WHEN, with THEN indicating what value should be filled if the condition is met. ELSE specifies the value that should be filled if no other conditions are met. Lastly, END indicates the end of the conditional statement; once END has been called, SQL will continue evaluating the query as usual.
+
Let’s see this in action. In the example below, we give the new column created by the CASE statement the name movie_age.
+
+
%%sql
+/* If a movie was filmed before 1950, it is"old"
+Otherwise, if a movie was filmed before 2000, it is"mid-aged"
+Else, a movie is"new"*/
+
+SELECT titleType, startYear,
+CASE WHEN startYear <1950 THEN 'old'
+ WHEN startYear <2000 THEN 'mid-aged'
+ ELSE 'new'
+ END AS movie_age
+FROM Title;
+
+
* duckdb:///data/basic_examples.db
+(duckdb.duckdb.CatalogException) Catalog Error: Table with name Title does not exist!
+Did you mean "temp.information_schema.tables"?
+LINE 10: FROM Title;
+ ^
+[SQL: /* If a movie was filmed before 1950, it is "old"
+Otherwise, if a movie was filmed before 2000, it is "mid-aged"
+Else, a movie is "new" */
+
+SELECT titleType, startYear,
+CASE WHEN startYear < 1950 THEN 'old'
+ WHEN startYear < 2000 THEN 'mid-aged'
+ ELSE 'new'
+ END AS movie_age
+FROM Title;]
+(Background on this error at: https://sqlalche.me/e/20/f405)
+
+
+
+
+
+
21.5JOINing Tables
+
At this point, we’re well-versed in using SQL as a tool to clean, manipulate, and transform data in a table. Notice that this sentence referred to one table, specifically. What happens if the data we need is distributed across multiple tables? This is an important consideration when using SQL —— recall that we first introduced SQL as a language to query from databases. Databases often store data in a multidimensional structure. In other words, information is stored across several tables, with each table containing a small subset of all the data housed by the database.
+
A common way of organizing a database is by using a star schema. A star schema is composed of two types of tables. A fact table is the central table of the database —— it contains the information needed to link entries across several dimension tables, which contain more detailed information about the data.
+
Say we were working with a database about boba offerings in Berkeley. The dimension tables of the database might contain information about tea varieties and boba toppings. The fact table would be used to link this information across the various dimension tables.
+
+
+
+
If we explicitly mark the relationships between tables, we start to see the star-like structure of the star schema.
+
+
+
+
To join data across multiple tables, we’ll use the (creatively named) JOIN keyword. We’ll make things easier for now by first considering the simpler cats dataset, which consists of the tables s and t.
+
+
+
+
To perform a join, we amend the FROM clause. You can think of this as saying, “SELECT my data FROM tables that have been JOINed together.”
+
Remember: SQL does not consider newlines or whitespace when interpreting queries. The indentation given in the example below is to help improve readability. If you wish, you can write code that does not follow this formatting.
We also need to specify what column from each table should be used to determine matching entries. By defining these keys, we provide SQL with the information it needs to pair rows of data together.
+
The most commonly used type of SQL JOIN is the inner join. It turns out you’re already familiar with what an inner join does, and how it works – this is the type of join we’ve been using in pandas all along! In an inner join, we combine every row in our first table with its matching entry in the second table. If a row from either table does not have a match in the other table, it is omitted from the output.
+
+
+
+
In a cross join, all possible combinations of rows appear in the output table, regardless of whether or not rows share a matching key. Because all rows are joined, even if there is no matching key, it is not necessary to specify what keys to consider in an ON statement. A cross join is also known as a cartesian product.
+
+
+
+
Conceptually, we can interpret an inner join as a cross join, followed by removing all rows that do not share a matching key. Notice that the output of the inner join above contains all rows of the cross join example that contain a single color across the entire row.
+
In a left outer join, all rows in the left table are kept in the output table. If a row in the right table shares a match with the left table, this row will be kept; otherwise, the rows in the right table are omitted from the output. We can fill in any missing values with NULL.
+
+
+
+
A right outer join keeps all rows in the right table. Rows in the left table are only kept if they share a match in the right table. Again, we can fill in any missing values with NULL.
+
+
+
+
In a full outer join, all rows that have a match between the two tables are joined together. If a row has no match in the second table, then the values of the columns for that second table are filled with NULL. In other words, a full outer join performs an inner join while still keeping rows that have no match in the other table. This is best understood visually:
+
+
+
+
We have kept the same output achieved using an inner join, with the addition of partially null rows for entries in s and t that had no match in the second table.
+
+
21.5.1 Aliasing in JOINs
+
When joining tables, we often create aliases for table names (similarly to what we did with column names in the last lecture). We do this as it is typically easier to refer to aliases, especially when we are working with long table names. We can even reference columns using aliased table names!
+
Let’s say we want to determine the average rating of various movies. We’ll need to JOIN the Title and Rating tables and can create aliases for both tables.
+
+
%%sql
+
+SELECT primaryTitle, averageRating
+FROM Title AS T INNER JOIN Rating AS R
+ON T.tconst = R.tconst;
+
+
* duckdb:///data/basic_examples.db
+(duckdb.duckdb.CatalogException) Catalog Error: Table with name Title does not exist!
+Did you mean "temp.information_schema.tables"?
+LINE 2: FROM Title AS T INNER JOIN Rating AS R
+ ^
+[SQL: SELECT primaryTitle, averageRating
+FROM Title AS T INNER JOIN Rating AS R
+ON T.tconst = R.tconst;]
+(Background on this error at: https://sqlalche.me/e/20/f405)
+
+
+
Note that the AS is actually optional! We can create aliases for our tables even without it, but we usually include it for clarity.
+
+
%%sql
+
+SELECT primaryTitle, averageRating
+FROM Title T INNER JOIN Rating R
+ON T.tconst = R.tconst;
+
+
* duckdb:///data/basic_examples.db
+(duckdb.duckdb.CatalogException) Catalog Error: Table with name Title does not exist!
+Did you mean "temp.information_schema.tables"?
+LINE 2: FROM Title T INNER JOIN Rating R
+ ^
+[SQL: SELECT primaryTitle, averageRating
+FROM Title T INNER JOIN Rating R
+ON T.tconst = R.tconst;]
+(Background on this error at: https://sqlalche.me/e/20/f405)
+
+
+
+
+
21.5.2 Common Table Expressions
+
For more sophisticated data problems, the queries can become very complex. Common table expressions (CTEs) allow us to break down these complex queries into more manageable parts. To do so, we create temporary tables corresponding to different aspects of the problem and then reference them in the final query:
+
WITH
+table_name1 AS (
+ SELECT ...
+),
+table_name2 AS (
+ SELECT ...
+)
+SELECT ...
+FROM
+table_name1,
+table_name2, ...
+
Let’s say we want to identify the top 10 action movies that are highly rated (with an average rating greater than 7) and popular (having more than 5000 votes), along with the primary actors who are the most popular. We can use CTEs to break this query down into separate problems. Initially, we can filter to find good action movies and prolific actors separately. This way, in our final join, we only need to change the order.
+
+
%%sql
+WITH
+good_action_movies AS (
+ SELECT *
+ FROM Title T JOIN Rating R ON T.tconst = R.tconst
+ WHERE genres LIKE '%Action%' AND averageRating >7 AND numVotes >5000
+),
+prolific_actors AS (
+ SELECT N.nconst, primaryName, COUNT(*) as numRoles
+ FROM Name N JOIN Principal P ON N.nconst = P.nconst
+ WHERE category ='actor'
+ GROUP BY N.nconst, primaryName
+)
+SELECT primaryTitle, primaryName, numRoles, ROUND(averageRating) AS rating
+FROM good_action_movies m, prolific_actors a, principal p
+WHERE p.tconst = m.tconst AND p.nconst = a.nconst
+ORDER BY rating DESC, numRoles DESC
+LIMIT 10;
+
+
* duckdb:///data/basic_examples.db
+(duckdb.duckdb.CatalogException) Catalog Error: Table with name Title does not exist!
+Did you mean "temp.information_schema.tables"?
+LINE 4: F...
+ ^
+[SQL: WITH
+good_action_movies AS (
+ SELECT *
+ FROM Title T JOIN Rating R ON T.tconst = R.tconst
+ WHERE genres LIKE '%Action%' AND averageRating > 7 AND numVotes > 5000
+),
+prolific_actors AS (
+ SELECT N.nconst, primaryName, COUNT(*) as numRoles
+ FROM Name N JOIN Principal P ON N.nconst = P.nconst
+ WHERE category = 'actor'
+ GROUP BY N.nconst, primaryName
+)
+SELECT primaryTitle, primaryName, numRoles, ROUND(averageRating) AS rating
+FROM good_action_movies m, prolific_actors a, principal p
+WHERE p.tconst = m.tconst AND p.nconst = a.nconst
+ORDER BY rating DESC, numRoles DESC
+LIMIT 10;]
+(Background on this error at: https://sqlalche.me/e/20/f405)
---
+title: SQL II
+execute:
+ echo: true
+format:
+ html:
+ code-fold: false
+ code-tools: true
+ toc: true
+ toc-title: SQL II
+ page-layout: full
+ theme:
+ - cosmo
+ - cerulean
+ callout-icon: false
+jupyter:
+ jupytext:
+ text_representation:
+ extension: .qmd
+ format_name: quarto
+ format_version: '1.0'
+ jupytext_version: 1.16.1
+ kernelspec:
+ display_name: Python 3 (ipykernel)
+ language: python
+ name: python3
+---
+
+::: {.callout-note collapse="false"}
+## Learning Outcomes
+* Perform aggregations using `GROUP BY`
+* Introduce the ability to filter groups
+* Perform data cleaning and text manipulation in SQL
+* Join data across tables
+:::
+
+In this lecture, we'll continue our work from last time to introduce some advanced SQL syntax.
+
+First, let's load in the `basic_examples.db` database.
+
+```{python}
+#| code-fold: true
+# Load the SQL Alchemy Python library and DuckDB
+import sqlalchemy
+import duckdb
+```
+
+```{python}
+#| vscode: {languageId: python}
+# Load %%sql cell magic
+%load_ext sql
+```
+
+```{python}
+#| vscode: {languageId: python}
+# Connect to the database
+%sql duckdb:///data/basic_examples.db --alias basic
+```
+
+## Aggregating with `GROUP BY`
+
+At this point, we've seen that SQL offers much of the same functionality that was given to us by `pandas`. We can extract data from a table, filter it, and reorder it to suit our needs.
+
+In `pandas`, much of our analysis work relied heavily on being able to use `.groupby()` to aggregate across the rows of our dataset. SQL's answer to this task is the (very conveniently named) `GROUP BY` clause. While the outputs of `GROUP BY` are similar to those of `.groupby()` —— in both cases, we obtain an output table where some column has been used for grouping —— the syntax and logic used to group data in SQL are fairly different to the `pandas` implementation.
+
+To illustrate `GROUP BY`, we will consider the `Dish` table from our database.
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+SELECT *
+FROM Dish;
+```
+
+Notice that there are multiple dishes of the same `type`. What if we wanted to find the total costs of dishes of a certain `type`? To accomplish this, we would write the following code.
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+SELECT type, SUM(cost)
+FROM Dish
+GROUP BY type;
+```
+
+What is going on here? The statement `GROUP BY type` tells SQL to group the data based on the value contained in the `type` column (whether a record is an appetizer, entree, or dessert). `SUM(cost)` sums up the costs of dishes in each `type` and displays the result in the output table.
+
+You may be wondering: why does `SUM(cost)` come before the command to `GROUP BY type`? Don't we need to form groups before we can count the number of entries in each? Remember that SQL is a *declarative* programming language —— a SQL programmer simply states what end result they would like to see, and leaves the task of figuring out *how* to obtain this result to SQL itself. This means that SQL queries sometimes don't follow what a reader sees as a "logical" sequence of thought. Instead, SQL requires that we follow its set order of operations when constructing queries. So long as we follow this order, SQL will handle the underlying logic.
+
+In practical terms: our goal with this query was to output the total `cost`s of each `type`. To communicate this to SQL, we say that we want to `SELECT` the `SUM`med `cost` values for each `type` group.
+
+There are many aggregation functions that can be used to aggregate the data contained in each group. Some common examples are:
+
+* `COUNT`: count the number of rows associated with each group
+* `MIN`: find the minimum value of each group
+* `MAX`: find the maximum value of each group
+* `SUM`: sum across all records in each group
+* `AVG`: find the average value of each group
+
+We can easily compute multiple aggregations all at once (a task that was very tricky in `pandas`).
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+SELECT type, SUM(cost), MIN(cost), MAX(name)
+FROM Dish
+GROUP BY type;
+```
+
+To count the number of rows associated with each group, we use the `COUNT` keyword. Calling `COUNT(*)` will compute the total number of rows in each group, including rows with null values. Its `pandas` equivalent is `.groupby().size()`.
+
+Recall the `Dragon` table from the previous lecture:
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+SELECT * FROM Dragon;
+```
+
+Notice that `COUNT(*)` and `COUNT(cute)` result in different outputs.
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+SELECT year, COUNT(*)
+FROM Dragon
+GROUP BY year;
+```
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+SELECT year, COUNT(cute)
+FROM Dragon
+GROUP BY year;
+```
+
+With this definition of `GROUP BY` in hand, let's update our SQL order of operations. Remember: *every* SQL query must list clauses in this order.
+
+ SELECT <column expression list>
+ FROM <table>
+ [WHERE <predicate>]
+ [GROUP BY <column list>]
+ [ORDER BY <column list>]
+ [LIMIT <number of rows>]
+ [OFFSET <number of rows>];
+
+Note that we can use the `AS` keyword to rename columns during the selection process and that column expressions may include aggregation functions (`MAX`, `MIN`, etc.).
+
+## Filtering Groups
+
+Now, what if we only want groups that meet a certain condition? `HAVING` filters groups by applying some condition across all rows in each group. We interpret it as a way to keep only the groups `HAVING` some condition. Note the difference between `WHERE` and `HAVING`: we use `WHERE` to filter rows, whereas we use `HAVING` to filter *groups*. `WHERE` precedes `HAVING` in terms of how SQL executes a query.
+
+Let's take a look at the `Dish` table to see how we can use `HAVING`. Say we want to group dishes with a cost greater than 4 by `type` and only keep groups where the max cost is less than 10.
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+SELECT type, COUNT(*)
+FROM Dish
+WHERE cost >4
+GROUP BY type
+HAVING MAX(cost) <10;
+```
+
+Here, we first use `WHERE` to filter for rows with a cost greater than 4. We then group our values by `type` before applying the `HAVING` operator. With `HAVING`, we can filter our groups based on if the max cost is less than 10.
+
+## Summary: SQL
+With this definition of `GROUP BY` and `HAVING` in hand, let's update our SQL order of operations. Remember: *every* SQL query must list clauses in this order.
+
+ SELECT <column expression list>
+ FROM <table>
+ [WHERE <predicate>]
+ [GROUP BY <column list>]
+ [ORDER BY <column list>]
+ [LIMIT <number of rows>]
+ [OFFSET <number of rows>];
+
+Note that we can use the `AS` keyword to rename columns during the selection process and that column expressions may include aggregation functions (`MAX`, `MIN`, etc.).
+
+## EDA in SQL
+In the last lecture, we mostly worked under the assumption that our data had already been cleaned. However, as we saw in our first pass through the data science lifecycle, we're very unlikely to be given data that is free of formatting issues. With this in mind, we'll want to learn how to clean and transform data in SQL.
+
+Our typical workflow when working with "big data" is:
+
+1. Use SQL to query data from a database
+2. Use Python (with `pandas`) to analyze this data in detail
+
+We can, however, still perform simple data cleaning and re-structuring using SQL directly. To do so, we'll use the `Title` table from the `imdb_duck` database, which contains information about movies and actors.
+
+Let's load in the `imdb_duck` database.
+
+```{python}
+#| vscode: {languageId: python}
+import os
+if os.path.exists("/home/jovyan/shared/sql/imdb_duck.db"):
+ imdbpath ="duckdb:////home/jovyan/shared/sql/imdb_duck.db"
+elif os.path.exists("data/imdb_duck.db"):
+ imdbpath ="duckdb:///data/imdb_duck.db"
+else:
+import gdown
+ url ='https://drive.google.com/uc?id=10tKOHGLt9QoOgq5Ii-FhxpB9lDSQgl1O'
+ output_path ='data/imdb_duck.db'
+ gdown.download(url, output_path, quiet=False)
+ imdbpath ="duckdb:///data/imdb_duck.db"
+print(imdbpath)
+```
+
+```{python}
+#| vscode: {languageId: python}
+from sqlalchemy import create_engine
+imdb_engine = create_engine(imdbpath, connect_args={'read_only': True})
+%sql imdb_engine --alias imdb
+```
+
+Since we'll be working with the `Title` table, let's take a quick look at what it contains.
+
+```{python}
+#| vscode: {languageId: python}
+%%sql imdb
+
+SELECT *
+FROM Title
+WHERE primaryTitle IN ('Ginny & Georgia', 'What If...?', 'Succession', 'Veep', 'Tenet')
+LIMIT 10;
+```
+
+### Matching Text using `LIKE`
+
+One common task we encountered in our first look at EDA was needing to match string data. For example, we might want to remove entries beginning with the same prefix as part of the data cleaning process.
+
+In SQL, we use the `LIKE` operator to (you guessed it) look for strings that are *like* a given string pattern.
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+SELECT titleType, primaryTitle
+FROM Title
+WHERE primaryTitle LIKE 'Star Wars: Episode I - The Phantom Menace'
+```
+
+What if we wanted to find *all* Star Wars movies? `%` is the wildcard operator, it means "look for any character, any number of times". This makes it helpful for identifying strings that are similar to our desired pattern, even when we don't know the full text of what we aim to extract.
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+SELECT titleType, primaryTitle
+FROM Title
+WHERE primaryTitle LIKE '%Star Wars%'
+LIMIT 10;
+```
+
+Alternatively, we can use RegEx! DuckDB and most real DBMSs allow for this. Note that here, we have to use the `SIMILAR TO` operater rather than `LIKE`.
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+SELECT titleType, primaryTitle
+FROM Title
+WHERE primaryTitle SIMILAR TO '.*Star Wars*.'
+LIMIT 10;
+```
+
+### `CAST`ing Data Types
+
+A common data cleaning task is converting data to the correct variable type. The `CAST` keyword is used to generate a new output column. Each entry in this output column is the result of converting the data in an existing column to a new data type. For example, we may wish to convert numeric data stored as a string to an integer.
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+SELECT primaryTitle, CAST(runtimeMinutes AS INT)
+FROM Title;
+```
+
+We use `CAST` when `SELECT`ing colunns for our output table. In the example above, we want to `SELECT` the columns of integer year and runtime data that is created by the `CAST`.
+
+SQL will automatically name a new column according to the command used to `SELECT` it, which can lead to unwieldy column names. We can rename the `CAST`ed column using the `AS` keyword.
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+SELECT primaryTitle AS title, CAST(runtimeMinutes AS INT) AS minutes, CAST(startYear AS INT) AS year
+FROM Title
+LIMIT 5;
+```
+
+### Using Conditional Statements with `CASE`
+
+When working with `pandas`, we often ran into situations where we wanted to generate new columns using some form of conditional statement. For example, say we wanted to describe a film title as "old," "mid-aged," or "new," depending on the year of its release.
+
+In SQL, conditional operations are performed using a `CASE` clause. Conceptually, `CASE` behaves much like the `CAST` operation: it creates a new column that we can then `SELECT` to appear in the output. The syntax for a `CASE` clause is as follows:
+
+ CASE WHEN <condition> THEN <value>
+ WHEN <other condition> THEN <other value>
+ ...
+ ELSE <yet another value>
+ END
+
+Scanning through the skeleton code above, you can see that the logic is similar to that of an `if` statement in Python. The conditional statement is first opened by calling `CASE`. Each new condition is specified by `WHEN`, with `THEN` indicating what value should be filled if the condition is met. `ELSE` specifies the value that should be filled if no other conditions are met. Lastly, `END` indicates the end of the conditional statement; once `END` has been called, SQL will continue evaluating the query as usual.
+
+Let's see this in action. In the example below, we give the new column created by the `CASE` statement the name `movie_age`.
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+/* If a movie was filmed before 1950, it is"old"
+Otherwise, if a movie was filmed before 2000, it is"mid-aged"
+Else, a movie is"new"*/
+
+SELECT titleType, startYear,
+CASE WHEN startYear <1950 THEN 'old'
+ WHEN startYear <2000 THEN 'mid-aged'
+ ELSE 'new'
+ END AS movie_age
+FROM Title;
+```
+
+## `JOIN`ing Tables
+
+At this point, we're well-versed in using SQL as a tool to clean, manipulate, and transform data in a table. Notice that this sentence referred to one *table*, specifically. What happens if the data we need is distributed across multiple tables? This is an important consideration when using SQL —— recall that we first introduced SQL as a language to query from databases. Databases often store data in a multidimensional structure. In other words, information is stored across several tables, with each table containing a small subset of all the data housed by the database.
+
+A common way of organizing a database is by using a **star schema**. A star schema is composed of two types of tables. A **fact table** is the central table of the database —— it contains the information needed to link entries across several **dimension tables**, which contain more detailed information about the data.
+
+Say we were working with a database about boba offerings in Berkeley. The dimension tables of the database might contain information about tea varieties and boba toppings. The fact table would be used to link this information across the various dimension tables.
+
+<divstyle="text-align: center;">
+<imgsrc="images/multidimensional.png"alt='multidimensional'width='850'>
+</div>
+
+If we explicitly mark the relationships between tables, we start to see the star-like structure of the star schema.
+
+<divstyle="text-align: center;">
+<imgsrc="images/star.png"alt='star'width='650'>
+</div>
+
+To join data across multiple tables, we'll use the (creatively named) `JOIN` keyword. We'll make things easier for now by first considering the simpler `cats` dataset, which consists of the tables `s` and `t`.
+
+<divstyle="text-align: center;">
+<imgsrc="images/cats.png"alt='cats'width='500'>
+</div>
+
+To perform a join, we amend the `FROM` clause. You can think of this as saying, "`SELECT` my data `FROM` tables that have been `JOIN`ed together."
+
+Remember: SQL does not consider newlines or whitespace when interpreting queries. The indentation given in the example below is to help improve readability. If you wish, you can write code that does not follow this formatting.
+
+ SELECT <column list>
+ FROM table_1
+ JOIN table_2
+ ON key_1 = key_2;
+
+We also need to specify what column from each table should be used to determine matching entries. By defining these keys, we provide SQL with the information it needs to pair rows of data together.
+
+
+The most commonly used type of SQL `JOIN` is the **inner join**. It turns out you're already familiar with what an inner join does, and how it works – this is the type of join we've been using in `pandas` all along! In an inner join, we combine every row in our first table with its matching entry in the second table. If a row from either table does not have a match in the other table, it is omitted from the output.
+
+<divstyle="text-align: center;">
+<imgsrc="images/inner.png"alt='inner'width='800'>
+</div>
+
+In a **cross join**, *all* possible combinations of rows appear in the output table, regardless of whether or not rows share a matching key. Because all rows are joined, even if there is no matching key, it is not necessary to specify what keys to consider in an `ON` statement. A cross join is also known as a cartesian product.
+
+<divstyle="text-align: center;">
+<imgsrc="images/cross.png"alt='cross'width='800'>
+</div>
+
+Conceptually, we can interpret an inner join as a cross join, followed by removing all rows that do not share a matching key. Notice that the output of the inner join above contains all rows of the cross join example that contain a single color across the entire row.
+
+In a **left outer join**, *all* rows in the left table are kept in the output table. If a row in the right table shares a match with the left table, this row will be kept; otherwise, the rows in the right table are omitted from the output. We can fill in any missing values with `NULL`.
+
+<divstyle="text-align: center;">
+<imgsrc="images/left.png"alt='left'width='800'>
+</div>
+
+A **right outer join** keeps all rows in the right table. Rows in the left table are only kept if they share a match in the right table. Again, we can fill in any missing values with `NULL`.
+
+<divstyle="text-align: center;">
+<imgsrc="images/right.png"alt='right'width='800'>
+</div>
+
+In a **full outer join**, all rows that have a match between the two tables are joined together. If a row has no match in the second table, then the values of the columns for that second table are filled with `NULL`. In other words, a full outer join performs an inner join *while still keeping* rows that have no match in the other table. This is best understood visually:
+
+<divstyle="text-align: center;">
+<imgsrc="images/full.png"alt='full'width='800'>
+</div>
+
+We have kept the same output achieved using an inner join, with the addition of partially null rows for entries in `s` and `t` that had no match in the second table.
+
+### Aliasing in `JOIN`s
+
+When joining tables, we often create aliases for table names (similarly to what we did with column names in the last lecture). We do this as it is typically easier to refer to aliases, especially when we are working with long table names. We can even reference columns using aliased table names!
+
+Let's say we want to determine the average rating of various movies. We'll need to `JOIN` the `Title` and `Rating` tables and can create aliases for both tables.
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+
+SELECT primaryTitle, averageRating
+FROM Title AS T INNER JOIN Rating AS R
+ON T.tconst = R.tconst;
+```
+
+Note that the `AS` is actually optional! We can create aliases for our tables even without it, but we usually include it for clarity.
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+
+SELECT primaryTitle, averageRating
+FROM Title T INNER JOIN Rating R
+ON T.tconst = R.tconst;
+```
+
+### Common Table Expressions
+
+For more sophisticated data problems, the queries can become very complex. Common table expressions (CTEs) allow us to break down these complex queries into more manageable parts. To do so, we create temporary tables corresponding to different aspects of the problem and then reference them in the final query:
+
+ WITH
+ table_name1 AS (
+ SELECT ...
+ ),
+ table_name2 AS (
+ SELECT ...
+ )
+ SELECT ...
+ FROM
+ table_name1,
+ table_name2, ...
+
+Let's say we want to identify the top 10 action movies that are highly rated (with an average rating greater than 7) and popular (having more than 5000 votes), along with the primary actors who are the most popular. We can use CTEs to break this query down into separate problems. Initially, we can filter to find good action movies and prolific actors separately. This way, in our final join, we only need to change the order.
+
+```{python}
+#| vscode: {languageId: python}
+%%sql
+WITH
+good_action_movies AS (
+ SELECT *
+ FROM Title T JOIN Rating R ON T.tconst = R.tconst
+ WHERE genres LIKE '%Action%' AND averageRating >7 AND numVotes >5000
+),
+prolific_actors AS (
+ SELECT N.nconst, primaryName, COUNT(*) as numRoles
+ FROM Name N JOIN Principal P ON N.nconst = P.nconst
+ WHERE category ='actor'
+ GROUP BY N.nconst, primaryName
+)
+SELECT primaryTitle, primaryName, numRoles, ROUND(averageRating) AS rating
+FROM good_action_movies m, prolific_actors a, principal p
+WHERE p.tconst = m.tconst AND p.nconst = a.nconst
+ORDER BY rating DESC, numRoles DESC
+LIMIT 10;
+```
+