Exploratory Data Analysis

Preface

After you have acquired the data, you should do the following:

Diagnose data quality.
- If there is a problem with data quality,
- The data must be corrected or re-acquired.
Explore data to understand the data and find scenarios for performing the analysis.
Derive new variables or perform variable transformations.

The dlookr package makes these steps fast and easy:

Performs a data diagnosis or automatically generates a data diagnosis report.
Discover data in various ways, and automatically generate EDA(exploratory data analysis) report.
Impute missing values and outliers, resolve skewed data, and categorize continuous variables into categorical variables. And generates an automated report to support it.

This document introduces EDA(Exploratory Data Analysis) methods provided by the dlookr package. You will learn how to EDA of tbl_df data that inherits from data.frame and data.frame with functions provided by dlookr.

dlookr increases synergy with dplyr. Particularly in data exploration and data wrangling, it increases the efficiency of the tidyverse package group.

Supported data structures

Data diagnosis supports the following data structures.

data frame: data.frame class.
data table: tbl_df class.
table of DBMS: table of the DBMS through tbl_dbi.
- Use dplyr as the back-end interface for any DBI-compatible database.

datasets

To illustrate the primary use of EDA in the dlookr package, I use a Carseats dataset. Carseats in the ISLR package is a simulated data set containing sales of child car seats at 400 stores. This data is a data.frame created to predict sales volume.

str(Carseats)
'data.frame':   400 obs. of  11 variables:
 $ Sales      : num  9.5 11.22 10.06 7.4 4.15 ...
 $ CompPrice  : num  138 111 113 117 141 124 115 136 132 132 ...
 $ Income     : num  73 48 35 100 64 113 105 81 110 113 ...
 $ Advertising: num  11 16 10 4 3 13 0 15 0 0 ...
 $ Population : num  276 260 269 466 340 501 45 425 108 131 ...
 $ Price      : num  120 83 80 97 128 72 108 120 124 124 ...
 $ ShelveLoc  : Factor w/ 3 levels "Bad","Good","Medium": 1 2 3 3 1 1 3 2 3 3 ...
 $ Age        : num  42 65 59 55 38 78 71 67 76 76 ...
 $ Education  : num  17 10 12 14 13 16 15 10 10 17 ...
 $ Urban      : Factor w/ 2 levels "No","Yes": 2 2 2 2 2 1 2 2 1 1 ...
 $ US         : Factor w/ 2 levels "No","Yes": 2 2 2 2 1 2 1 2 1 2 ...

The contents of individual variables are as follows. (Refer to ISLR::Carseats Man page)

Sales
- Unit sales (in thousands) at each location
CompPrice
- Price charged by a competitor at each location
Income
- Community income level (in thousands of dollars)
Advertising
- Local advertising budget for company at each location (in thousands of dollars)
Population
- Population size in region (in thousands)
Price
- Price company charges for car seats at each site
ShelveLoc
- A factor with levels of Bad, Good, and Medium indicating the quality of the shelving location for the car seats at each site
Age
- Average age of the local population
Education
- Education level at each location
Urban
- A factor with levels No and Yes to indicate whether the store is in an urban or rural location
US
- A factor with levels No and Yes to indicate whether the store is in the US or not

When data analysis is performed, data containing missing values is frequently encountered. However, ‘Carseats’ is complete data without missing values. So the following script created the missing values and saved them as carseats.

carseats <- Carseats

suppressWarnings(RNGversion("3.5.0"))
set.seed(123)
carseats[sample(seq(NROW(carseats)), 20), "Income"] <- NA

suppressWarnings(RNGversion("3.5.0"))
set.seed(456)
carseats[sample(seq(NROW(carseats)), 10), "Urban"] <- NA

Exploratory Data Analysis

dlookr can help understand the distribution of data by calculating descriptive statistics of numerical data. In addition, the correlation between variables is identified, and a normality test is performed. It also identifies the relationship between target variables and independent variables.:

The following is a list of the EDA functions included in the dlookr package.:

describe() provides descriptive statistics for numerical data.
normality() and plot_normality() perform normalization and visualization of numerical data.
correlate() and plot.correlate() calculate the correlation coefficient between two numerical data and provide visualization.
target_by() defines the target variable, and relate() describes the relationship with the variables of interest corresponding to the target variable.
plot.relate() visualizes the relationship to the variable of interest corresponding to the destination variable.
eda_report() performs an exploratory data analysis and reports the results.

Univariate data EDA

Calculating descriptive statistics using `describe()`

describe() computes descriptive statistics for numerical data. Descriptive statistics help determine the distribution of numerical variables. Like the function of dplyr, the first argument is the tibble (or data frame). The second and subsequent arguments refer to variables within that data frame.

The variables of the tbl_df object returned by describe() are as follows.

n: number of observations excluding missing values
na: number of missing values
mean: arithmetic average
sd: standard deviation
se_mean: standard error mean. sd/sqrt(n)
IQR: interquartile range (Q3-Q1)
skewness: skewness
kurtosis: kurtosis
p25: Q1. 25% percentile
p50: median. 50% percentile
p75: Q3. 75% percentile
p01, p05, p10, p20, p30: 1%, 5%, 20%, 30% percentiles
p40, p60, p70, p80: 40%, 60%, 70%, 80% percentiles
p90, p95, p99, p100: 90%, 95%, 99%, 100% percentiles

For example, describe() can compute the statistics of all numerical variables in carseats:

describe(carseats)
# A tibble: 8 × 26
  described_variables     n    na   mean    sd se_mean   IQR skewness kurtosis
  <chr>               <int> <int>  <dbl> <dbl>   <dbl> <dbl>    <dbl>    <dbl>
1 Sales                 400     0   7.50  2.82   0.141  3.93   0.186   -0.0809
2 CompPrice             400     0 125.   15.3    0.767 20     -0.0428   0.0417
3 Income                380    20  68.9  28.1    1.44  48.2    0.0449  -1.09  
4 Advertising           400     0   6.64  6.65   0.333 12      0.640   -0.545 
# ℹ 4 more rows
# ℹ 17 more variables: p00 <dbl>, p01 <dbl>, p05 <dbl>, p10 <dbl>, p20 <dbl>,
#   p25 <dbl>, p30 <dbl>, p40 <dbl>, p50 <dbl>, p60 <dbl>, p70 <dbl>,
#   p75 <dbl>, p80 <dbl>, p90 <dbl>, p95 <dbl>, p99 <dbl>, p100 <dbl>

skewness: The left-skewed distribution data, that is, the variables with significant positive skewness, should consider the log or sqrt transformations to follow the normal distribution. The variable Advertising seems to need to consider variable transformation.
mean and sd, se_mean: ThePopulation with a significant standard error of the mean(se_mean) has low representativeness of the arithmetic mean(mean). The standard deviation(sd) is much more significant than the arithmetic average.

The following explains the descriptive statistics only for a few selected variables.:

# Select columns by name
describe(carseats, Sales, CompPrice, Income)
# A tibble: 3 × 26
  described_variables     n    na   mean    sd se_mean   IQR skewness kurtosis
  <chr>               <int> <int>  <dbl> <dbl>   <dbl> <dbl>    <dbl>    <dbl>
1 Sales                 400     0   7.50  2.82   0.141  3.93   0.186   -0.0809
2 CompPrice             400     0 125.   15.3    0.767 20     -0.0428   0.0417
3 Income                380    20  68.9  28.1    1.44  48.2    0.0449  -1.09  
# ℹ 17 more variables: p00 <dbl>, p01 <dbl>, p05 <dbl>, p10 <dbl>, p20 <dbl>,
#   p25 <dbl>, p30 <dbl>, p40 <dbl>, p50 <dbl>, p60 <dbl>, p70 <dbl>,
#   p75 <dbl>, p80 <dbl>, p90 <dbl>, p95 <dbl>, p99 <dbl>, p100 <dbl>
# Select all columns between year and day (include)
describe(carseats, Sales:Income)
# A tibble: 3 × 26
  described_variables     n    na   mean    sd se_mean   IQR skewness kurtosis
  <chr>               <int> <int>  <dbl> <dbl>   <dbl> <dbl>    <dbl>    <dbl>
1 Sales                 400     0   7.50  2.82   0.141  3.93   0.186   -0.0809
2 CompPrice             400     0 125.   15.3    0.767 20     -0.0428   0.0417
3 Income                380    20  68.9  28.1    1.44  48.2    0.0449  -1.09  
# ℹ 17 more variables: p00 <dbl>, p01 <dbl>, p05 <dbl>, p10 <dbl>, p20 <dbl>,
#   p25 <dbl>, p30 <dbl>, p40 <dbl>, p50 <dbl>, p60 <dbl>, p70 <dbl>,
#   p75 <dbl>, p80 <dbl>, p90 <dbl>, p95 <dbl>, p99 <dbl>, p100 <dbl>
# Select all columns except those from year to day (exclude)
describe(carseats, -(Sales:Income))
# A tibble: 5 × 26
  described_variables     n    na   mean     sd se_mean   IQR skewness kurtosis
  <chr>               <int> <int>  <dbl>  <dbl>   <dbl> <dbl>    <dbl>    <dbl>
1 Advertising           400     0   6.64   6.65   0.333  12     0.640    -0.545
2 Population            400     0 265.   147.     7.37  260.   -0.0512   -1.20 
3 Price                 400     0 116.    23.7    1.18   31    -0.125     0.452
4 Age                   400     0  53.3   16.2    0.810  26.2  -0.0772   -1.13 
# ℹ 1 more row
# ℹ 17 more variables: p00 <dbl>, p01 <dbl>, p05 <dbl>, p10 <dbl>, p20 <dbl>,
#   p25 <dbl>, p30 <dbl>, p40 <dbl>, p50 <dbl>, p60 <dbl>, p70 <dbl>,
#   p75 <dbl>, p80 <dbl>, p90 <dbl>, p95 <dbl>, p99 <dbl>, p100 <dbl>

The describe() function can be sorted by left or right skewed size(skewness) using dplyr.:

carseats %>%
  describe() %>%
  select(described_variables, skewness, mean, p25, p50, p75) %>% 
  filter(!is.na(skewness)) %>% 
  arrange(desc(abs(skewness)))
# A tibble: 8 × 6
  described_variables skewness   mean    p25    p50    p75
  <chr>                  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>
1 Advertising           0.640    6.64   0      5     12   
2 Sales                 0.186    7.50   5.39   7.49   9.32
3 Price                -0.125  116.   100    117    131   
4 Age                  -0.0772  53.3   39.8   54.5   66   
# ℹ 4 more rows

The describe() function supports the group_by() function syntax of the dplyr package.

carseats %>%
  group_by(US) %>% 
  describe(Sales, Income) 
# A tibble: 4 × 27
  described_variables US        n    na  mean    sd se_mean   IQR skewness
  <chr>               <fct> <int> <int> <dbl> <dbl>   <dbl> <dbl>    <dbl>
1 Income              No      130    12 65.8  28.2    2.48  50      0.100 
2 Income              Yes     250     8 70.4  27.9    1.77  48      0.0199
3 Sales               No      142     0  6.82  2.60   0.218  3.44   0.323 
4 Sales               Yes     258     0  7.87  2.88   0.179  4.23   0.0760
# ℹ 18 more variables: kurtosis <dbl>, p00 <dbl>, p01 <dbl>, p05 <dbl>,
#   p10 <dbl>, p20 <dbl>, p25 <dbl>, p30 <dbl>, p40 <dbl>, p50 <dbl>,
#   p60 <dbl>, p70 <dbl>, p75 <dbl>, p80 <dbl>, p90 <dbl>, p95 <dbl>,
#   p99 <dbl>, p100 <dbl>

carseats %>%
  group_by(US, Urban) %>% 
  describe(Sales, Income) 
# A tibble: 12 × 28
  described_variables US    Urban     n    na  mean    sd se_mean   IQR skewness
  <chr>               <fct> <fct> <int> <int> <dbl> <dbl>   <dbl> <dbl>    <dbl>
1 Income              No    No       42     4  60.2  29.1    4.49  45.2   0.408 
2 Income              No    Yes      84     8  69.5  27.4    2.99  47    -0.0497
3 Income              No    <NA>      4     0  48.2  24.7   12.3   40.8  -0.0496
4 Income              Yes   No       65     4  70.5  29.9    3.70  48     0.0736
# ℹ 8 more rows
# ℹ 18 more variables: kurtosis <dbl>, p00 <dbl>, p01 <dbl>, p05 <dbl>,
#   p10 <dbl>, p20 <dbl>, p25 <dbl>, p30 <dbl>, p40 <dbl>, p50 <dbl>,
#   p60 <dbl>, p70 <dbl>, p75 <dbl>, p80 <dbl>, p90 <dbl>, p95 <dbl>,
#   p99 <dbl>, p100 <dbl>

Test of normality on numeric variables using `normality()`

normality() performs a normality test on numerical data. Shapiro-Wilk normality test is performed. When the number of observations exceeds 5000, it is tested after extracting 5000 samples by random simple sampling.

The variables of the tbl_df object returned by normality() are as follows.

statistic: Statistics of the Shapiro-Wilk test
p_value: p-value of the Shapiro-Wilk test
sample: Number of sample observations performed Shapiro-Wilk test

normality() performs the normality test for all numerical variables of carseats as follows.:

normality(carseats)
# A tibble: 8 × 4
  vars        statistic  p_value sample
  <chr>           <dbl>    <dbl>  <dbl>
1 Sales           0.995 2.54e- 1    400
2 CompPrice       0.998 9.77e- 1    400
3 Income          0.961 1.52e- 8    400
4 Advertising     0.874 1.49e-17    400
# ℹ 4 more rows

The following example performs a normality test on only a few selected variables.

# Select columns by name
normality(carseats, Sales, CompPrice, Income)
# A tibble: 3 × 4
  vars      statistic      p_value sample
  <chr>         <dbl>        <dbl>  <dbl>
1 Sales         0.995 0.254           400
2 CompPrice     0.998 0.977           400
3 Income        0.961 0.0000000152    400

# Select all columns between year and day (inclusive)
normality(carseats, Sales:Income)
# A tibble: 3 × 4
  vars      statistic      p_value sample
  <chr>         <dbl>        <dbl>  <dbl>
1 Sales         0.995 0.254           400
2 CompPrice     0.998 0.977           400
3 Income        0.961 0.0000000152    400

# Select all columns except those from year to day (inclusive)
normality(carseats, -(Sales:Income))
# A tibble: 5 × 4
  vars        statistic  p_value sample
  <chr>           <dbl>    <dbl>  <dbl>
1 Advertising     0.874 1.49e-17    400
2 Population      0.952 4.08e-10    400
3 Price           0.996 3.90e- 1    400
4 Age             0.957 1.86e- 9    400
# ℹ 1 more row

You can use dplyr to sort variables that do not follow a normal distribution in order of p_value:

library(dplyr)

carseats %>%
  normality() %>%
  filter(p_value <= 0.01) %>% 
  arrange(abs(p_value))
# A tibble: 5 × 4
  vars        statistic  p_value sample
  <chr>           <dbl>    <dbl>  <dbl>
1 Advertising     0.874 1.49e-17    400
2 Education       0.924 2.43e-13    400
3 Population      0.952 4.08e-10    400
4 Age             0.957 1.86e- 9    400
# ℹ 1 more row

In particular, the Advertising variable is considered to be the most out of the normal distribution

The normality() function supports the group_by() function syntax in the dplyr package.

carseats %>%
  group_by(ShelveLoc, US) %>%
  normality(Income) %>% 
  arrange(desc(p_value))
# A tibble: 6 × 6
  variable ShelveLoc US    statistic p_value sample
  <chr>    <fct>     <fct>     <dbl>   <dbl>  <dbl>
1 Income   Bad       No        0.969  0.470      34
2 Income   Bad       Yes       0.958  0.0343     62
3 Income   Good      No        0.902  0.0328     24
4 Income   Good      Yes       0.955  0.0296     61
# ℹ 2 more rows

The Income variable does not follow the normal distribution. However, where US is No and ShelveLoc is Good and Bad at the significance level 0.01, it follows the normal distribution.

The following example performs the normality test of log(Income) for each combination of ShelveLoc and US categorical variables to search for variables that follow the normal distribution.

carseats %>%
  mutate(log_income = log(Income)) %>%
  group_by(ShelveLoc, US) %>%
  normality(log_income) %>%
  filter(p_value > 0.01)
# A tibble: 1 × 6
  variable   ShelveLoc US    statistic p_value sample
  <chr>      <fct>     <fct>     <dbl>   <dbl>  <dbl>
1 log_income Bad       No        0.940  0.0737     34

Visualization of normality of numerical variables using `plot_normality()`

plot_normality() visualizes the normality of numeric data.

The information visualized by plot_normality() is as follows.:

Histogram of original data
Q-Q plot of original data
histogram of log transformed data
Histogram of square root transformed data

The data analysis often encounters numerical data that follows the power-law distribution. Since the numerical data that follows the power-law distribution is converted into a normal distribution by performing the log or sqrt transformation, so draw a histogram of the log and sqrt transformed data.

plot_normality() can also specify several variables like normality() function.

# Select columns by name
plot_normality(carseats, Sales, CompPrice)

The plot_normality() function also supports the group_by() function syntax in the dplyr package.

carseats %>%
  filter(ShelveLoc == "Good") %>%
  group_by(US) %>%
  plot_normality(Income)

EDA of bivariate data

Calculation of `correlation coefficient` using `correlate()`

correlate() calculates the correlation coefficient of all combinations of carseats numerical variables as follows:

correlate(carseats)
# A tibble: 56 × 3
  var1        var2  coef_corr
  <fct>       <fct>     <dbl>
1 CompPrice   Sales    0.0641
2 Income      Sales    0.151 
3 Advertising Sales    0.270 
4 Population  Sales    0.0505
# ℹ 52 more rows

The following example performs a normality test only on combinations that include several selected variables.

# Select columns by name
correlate(carseats, Sales, CompPrice, Income)
# A tibble: 21 × 3
  var1      var2      coef_corr
  <fct>     <fct>         <dbl>
1 CompPrice Sales        0.0641
2 Income    Sales        0.151 
3 Sales     CompPrice    0.0641
4 Income    CompPrice   -0.0761
# ℹ 17 more rows

# Select all columns between year and day (include)
correlate(carseats, Sales:Income)
# A tibble: 21 × 3
  var1      var2      coef_corr
  <fct>     <fct>         <dbl>
1 CompPrice Sales        0.0641
2 Income    Sales        0.151 
3 Sales     CompPrice    0.0641
4 Income    CompPrice   -0.0761
# ℹ 17 more rows

# Select all columns except those from year to day (exclude)
correlate(carseats, -(Sales:Income))
# A tibble: 35 × 3
  var1        var2  coef_corr
  <fct>       <fct>     <dbl>
1 Advertising Sales    0.270 
2 Population  Sales    0.0505
3 Price       Sales   -0.445 
4 Age         Sales   -0.232 
# ℹ 31 more rows

correlate() produces two pairs of variables. So the following example uses filter() to get the correlation coefficient for a pair of variable combinations:

carseats %>%
  correlate(Sales:Income) %>%
  filter(as.integer(var1) > as.integer(var2))
# A tibble: 3 × 3
  var1      var2      coef_corr
  <fct>     <fct>         <dbl>
1 CompPrice Sales        0.0641
2 Income    Sales        0.151 
3 Income    CompPrice   -0.0761

The correlate() also supports the group_by() function syntax in the dplyr package.

tab_corr <- carseats %>%
  filter(ShelveLoc == "Good") %>%
  group_by(Urban, US) %>%
  correlate(Sales) %>%
  filter(abs(coef_corr) > 0.5)

tab_corr
# A tibble: 10 × 5
  Urban US    var1  var2       coef_corr
  <fct> <fct> <fct> <fct>          <dbl>
1 No    No    Sales Population    -0.530
2 No    No    Sales Price         -0.838
3 No    Yes   Sales Price         -0.630
4 Yes   No    Sales Price         -0.833
# ℹ 6 more rows

Visualization of the correlation matrix using `plot.correlate()`

plot.correlate() visualizes the correlation matrix with correlate class.

carseats %>% 
  correlate() %>% 
  plot()

plot.correlate() can also specify multiple variables, like the correlate() function. The following visualize the correlation matrix, including several selected variables.

# Select columns by name
correlate(carseats, Sales, Price) %>% 
  plot()

The plot.correlate() function also supports the group_by() function syntax in the dplyr package.

carseats %>%
  filter(ShelveLoc == "Good") %>%
  group_by(Urban) %>%
  correlate() %>%
  plot()

EDA based on target variable

Definition of target variable

To perform EDA based on the target variable, you must create a target_by class object. target_by() creates a target_by class with an object inheriting data.frame or data.frame. target_by() is similar to group_by() in dplyr which creates grouped_df. The difference is that you specify only one variable.

The following is an example of specifying US as the target variable in carseats data.frame.:

categ <- target_by(carseats, US)

EDA when target variable is categorical variable

Let’s perform EDA when the target variable is categorical. When the categorical variable US is the target variable, we examine the relationship between the target variable and the predictor.

Cases where predictors are numeric variable

relate() shows the relationship between the target variable and the predictor. The following example shows the relationship between Sales and the target variable US. The predictor Sales is a numeric variable. In this case, the descriptive statistics are shown for each level of the target variable.

# If the variable of interest is a numerical variable
cat_num <- relate(categ, Sales)
cat_num
# A tibble: 3 × 27
  described_variables US        n    na  mean    sd se_mean   IQR skewness
  <chr>               <fct> <int> <int> <dbl> <dbl>   <dbl> <dbl>    <dbl>
1 Sales               No      142     0  6.82  2.60   0.218  3.44   0.323 
2 Sales               Yes     258     0  7.87  2.88   0.179  4.23   0.0760
3 Sales               total   400     0  7.50  2.82   0.141  3.93   0.186 
# ℹ 18 more variables: kurtosis <dbl>, p00 <dbl>, p01 <dbl>, p05 <dbl>,
#   p10 <dbl>, p20 <dbl>, p25 <dbl>, p30 <dbl>, p40 <dbl>, p50 <dbl>,
#   p60 <dbl>, p70 <dbl>, p75 <dbl>, p80 <dbl>, p90 <dbl>, p95 <dbl>,
#   p99 <dbl>, p100 <dbl>
summary(cat_num)
 described_variables     US          n               na         mean      
 Length:3            No   :1   Min.   :142.0   Min.   :0   Min.   :6.823  
 Class :character    Yes  :1   1st Qu.:200.0   1st Qu.:0   1st Qu.:7.160  
 Mode  :character    total:1   Median :258.0   Median :0   Median :7.496  
                               Mean   :266.7   Mean   :0   Mean   :7.395  
                               3rd Qu.:329.0   3rd Qu.:0   3rd Qu.:7.682  
                               Max.   :400.0   Max.   :0   Max.   :7.867  
       sd           se_mean            IQR           skewness      
 Min.   :2.603   Min.   :0.1412   Min.   :3.442   Min.   :0.07603  
 1st Qu.:2.713   1st Qu.:0.1602   1st Qu.:3.686   1st Qu.:0.13080  
 Median :2.824   Median :0.1791   Median :3.930   Median :0.18556  
 Mean   :2.768   Mean   :0.1796   Mean   :3.866   Mean   :0.19489  
 3rd Qu.:2.851   3rd Qu.:0.1988   3rd Qu.:4.077   3rd Qu.:0.25432  
 Max.   :2.877   Max.   :0.2184   Max.   :4.225   Max.   :0.32308  
    kurtosis             p00              p01              p05       
 Min.   :-0.32638   Min.   :0.0000   Min.   :0.4675   Min.   :3.147  
 1st Qu.:-0.20363   1st Qu.:0.0000   1st Qu.:0.6868   1st Qu.:3.148  
 Median :-0.08088   Median :0.0000   Median :0.9062   Median :3.149  
 Mean   : 0.13350   Mean   :0.1233   Mean   :1.0072   Mean   :3.183  
 3rd Qu.: 0.36344   3rd Qu.:0.1850   3rd Qu.:1.2771   3rd Qu.:3.200  
 Max.   : 0.80776   Max.   :0.3700   Max.   :1.6480   Max.   :3.252  
      p10             p20             p25             p30       
 Min.   :3.917   Min.   :4.754   Min.   :5.080   Min.   :5.306  
 1st Qu.:4.018   1st Qu.:4.910   1st Qu.:5.235   1st Qu.:5.587  
 Median :4.119   Median :5.066   Median :5.390   Median :5.867  
 Mean   :4.073   Mean   :5.051   Mean   :5.411   Mean   :5.775  
 3rd Qu.:4.152   3rd Qu.:5.199   3rd Qu.:5.576   3rd Qu.:6.010  
 Max.   :4.184   Max.   :5.332   Max.   :5.763   Max.   :6.153  
      p40             p50             p60             p70       
 Min.   :5.994   Min.   :6.660   Min.   :7.496   Min.   :7.957  
 1st Qu.:6.301   1st Qu.:7.075   1st Qu.:7.787   1st Qu.:8.386  
 Median :6.608   Median :7.490   Median :8.078   Median :8.815  
 Mean   :6.506   Mean   :7.313   Mean   :8.076   Mean   :8.740  
 3rd Qu.:6.762   3rd Qu.:7.640   3rd Qu.:8.366   3rd Qu.:9.132  
 Max.   :6.916   Max.   :7.790   Max.   :8.654   Max.   :9.449  
      p75             p80              p90              p95       
 Min.   :8.523   Min.   : 8.772   Min.   : 9.349   Min.   :11.28  
 1st Qu.:8.921   1st Qu.: 9.265   1st Qu.:10.325   1st Qu.:11.86  
 Median :9.320   Median : 9.758   Median :11.300   Median :12.44  
 Mean   :9.277   Mean   : 9.665   Mean   :10.795   Mean   :12.08  
 3rd Qu.:9.654   3rd Qu.:10.111   3rd Qu.:11.518   3rd Qu.:12.49  
 Max.   :9.988   Max.   :10.464   Max.   :11.736   Max.   :12.54  
      p99             p100      
 Min.   :13.64   Min.   :14.90  
 1st Qu.:13.78   1st Qu.:15.59  
 Median :13.91   Median :16.27  
 Mean   :13.86   Mean   :15.81  
 3rd Qu.:13.97   3rd Qu.:16.27  
 Max.   :14.03   Max.   :16.27

plot() visualizes the relate class object created by relate() as the relationship between the target and predictor variables. The relationship between US and Sales is visualized by a density plot.

plot(cat_num)

Cases where predictors are categorical variable

The following example shows the relationship between ShelveLoc and the target variable US. The predictor variable ShelveLoc is categorical. This case illustrates the contingency table of two variables. The summary() function performs an independence test on the contingency table.

# If the variable of interest is a categorical variable
cat_cat <- relate(categ, ShelveLoc)
cat_cat
     ShelveLoc
US    Bad Good Medium
  No   34   24     84
  Yes  62   61    135
summary(cat_cat)
Call: xtabs(formula = formula_str, data = data, addNA = TRUE)
Number of cases in table: 400 
Number of factors: 2 
Test for independence of all factors:
    Chisq = 2.7397, df = 2, p-value = 0.2541

plot() visualizes the relationship between the target variable and the predictor. A mosaics plot represents the relationship between US and ShelveLoc.

plot(cat_cat)

EDA when target variable is numerical variable

Let’s perform EDA when the target variable is numeric. When the numeric variable Sales is the target variable, we examine the relationship between the target variable and the predictor.

# If the variable of interest is a numerical variable
num <- target_by(carseats, Sales)

Cases where predictors are numeric variable

The following example shows the relationship between Price and the target variable Sales. The predictor variable Price is numeric. In this case, it shows the result of a simple linear model of the target ~ predictor formula. The summary() function expresses the details of the model.

# If the variable of interest is a numerical variable
num_num <- relate(num, Price)
num_num

Call:
lm(formula = formula_str, data = data)

Coefficients:
(Intercept)        Price  
   13.64192     -0.05307  
summary(num_num)

Call:
lm(formula = formula_str, data = data)

Residuals:
    Min      1Q  Median      3Q     Max 
-6.5224 -1.8442 -0.1459  1.6503  7.5108 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)    
(Intercept) 13.641915   0.632812  21.558   <2e-16 ***
Price       -0.053073   0.005354  -9.912   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 2.532 on 398 degrees of freedom
Multiple R-squared:  0.198, Adjusted R-squared:  0.196 
F-statistic: 98.25 on 1 and 398 DF,  p-value: < 2.2e-16

plot() visualizes the relationship between the target and predictor variables. The relationship between Sales and Price is pictured with a scatter plot. The figure on the left shows the scatter plot of Sales and Price and the confidence interval of the regression line and regression line. The figure on the right shows the relationship between the original data and the predicted values of the linear model as a scatter plot. If there is a linear relationship between the two variables, the scatter plot of the observations converges on the red diagonal line.

plot(num_num)

The scatter plot of the data with many observations is output as overlapping points. This makes it difficult to judge the relationship between the two variables. It also takes a long time to perform the visualization. In this case, the above problem can be solved by hexabin plot.

In plot(), the hex_thres argument provides a basis for drawing hexabin plot. If the number of observations is greater than hex_thres, draw a hexabin plot.

The following example visualizes the hexabin plot rather than the scatter plot by specifying 350 for the hex_thres argument. This is because the number of observations is 400.

plot(num_num, hex_thres = 350)

Cases where predictors are categorical variable

The following example shows the relationship between ShelveLoc and the target variable Sales. The predictor ShelveLoc is a categorical variable and displays the result of a one-way ANOVA of the target ~ predictor relationship. The results are expressed in terms of ANOVA. The summary() function shows the regression coefficients for each level of the predictor. In other words, it shows detailed information about the simple regression analysis of the target ~ predictor relationship.

# If the variable of interest is a categorical variable
num_cat <- relate(num, ShelveLoc)
num_cat
Analysis of Variance Table

Response: Sales
           Df Sum Sq Mean Sq F value    Pr(>F)    
ShelveLoc   2 1009.5  504.77   92.23 < 2.2e-16 ***
Residuals 397 2172.7    5.47                      
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
summary(num_cat)

Call:
lm(formula = formula(formula_str), data = data)

Residuals:
    Min      1Q  Median      3Q     Max 
-7.3066 -1.6282 -0.0416  1.5666  6.1471 

Coefficients:
                Estimate Std. Error t value Pr(>|t|)    
(Intercept)       5.5229     0.2388  23.131  < 2e-16 ***
ShelveLocGood     4.6911     0.3484  13.464  < 2e-16 ***
ShelveLocMedium   1.7837     0.2864   6.229  1.2e-09 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 2.339 on 397 degrees of freedom
Multiple R-squared:  0.3172,    Adjusted R-squared:  0.3138 
F-statistic: 92.23 on 2 and 397 DF,  p-value: < 2.2e-16

plot() visualizes the relationship between the target variable and the predictor. A box plot represents the relationship between Sales and ShelveLoc.

plot(num_cat)

Automated report

dlookr provides two automated EDA reports:

Web page-based dynamic reports can perform in-depth analysis through visualization and statistical tables.
Static reports generated as PDF files or HTML files can be archived as the output of data analysis.

Create a dynamic report using `eda_web_report()`

eda_web_report() creates a dynamic report for objects inherited from data.frame(tbl_df, tbl, etc) or data.frame.

Contents of dynamic web report

The contents of the report are as follows.:

Overview
- Data Structures
- Data Types
- Job Informations
Univariate Analysis
- Descriptive Statistics
- Normality Test
Bivariate Analysis
- Compare Numerical Variables
- Compare Categorical Variables
Multivariate Analysis
- Correlation Analysis
  - Correlation Matrix
  - Correlation Plot
Target based Analysis
- Grouped Numerical Variables
- Grouped Categorical Variables
- Grouped Correlation

Some arguments for dynamic web report

eda_web_report() generates various reports with the following arguments.

target
- target variable
output_file
- name of the generated file.
output_dir
- name of the directory to generate report file.
title
- title of the report.
subtitle
- subtitle of the report.
author
- author of the report.
title_color
- color of title.
logo_img
- name of the logo image file on the top left.
create_date
- The date on which the report is generated.
theme
- name of theme for report. Support “orange” and “blue”.
sample_percent
- Sample percent of data for performing EDA.

The following script creates an EDA report for the data.frame class object, heartfailure.

heartfailure %>%
  eda_web_report(target = "death_event", subtitle = "heartfailure", 
                 output_dir = "./", output_file = "EDA.html", theme = "blue")

Screenshot of dynamic report

The dynamic contents of the report are shown in the following figure.:

The part of the report

Create a EDA report using `eda_paged_report()`

eda_paged_report() creates a static report for an object inherited from data.frame(tbl_df, tbl, etc) or data.frame.

Contents of static paged report

The contents of the report are as follows.:

Overview
- Data Structures
- Job Informations
Univariate Analysis
- Descriptive Statistics
  - Numerical Variables
  - Categorical Variables
- Normality Test
Bivariate Analysis
- Compare Numerical Variables
- Compare Categorical Variables
Multivariate Analysis
- Correlation Analysis
  - Correlation Coefficient Matrix
  - Correlation Plot
Target based Analysis
- Grouped Numerical Variables
- Grouped Categorical Variables
- Grouped Correlation

Some arguments for static paged report

eda_paged_report() generates various reports with the following arguments.

target
- target variable
output_format
- report output type. Choose either “pdf” or “html”.
output_file
- name of the generated file.
output_dir
- name of the directory to generate the report file.
title
- title of the report.
subtitle
- subtitle of the report.
abstract_title
- abstract of the report
author
- author of the report.
title_color
- color of title.
subtitle_color
- color of subtitle.
logo_img
- the name of the logo image file is on the top left.
cover_img
- name of cover image file on center.
create_date
- The date on which the report is generated.
theme
- name of the theme for the report. Support “orange” and “blue”.
sample_percent
- Sample percent of data for performing EDA.

The following script creates an EDA report for the data.frame class object, heartfailure.

heartfailure %>%
  eda_paged_report(target = "death_event", subtitle = "heartfailure", 
                   output_dir = "./", output_file = "EDA.pdf", theme = "blue")

Screenshot of static report

The cover of the report is shown in the following figure.:

The part of the report

The contents of the report are shown in the following figure.:

The dynamic contents of the report

Exploratory data analysis for tables in DBMS

EDA function for a table of DBMS supports In-database mode that performs SQL operations on the DBMS side. If the data size is large, using In-database mode is faster.

It is challenging to obtain anomalies or to implement the sampling-based algorithm in SQL of DBMS. So, some functions do not yet support In-database mode. In this case, it is performed in In-memory mode, where table data is brought to the R side and calculated. In this case, if the data size is large, the execution speed may be slow. It supports the collect_size argument, allowing you to import the specified number of data samples into R.

In-database support functions
- none
In-database not support functions
- normality()
- plot_normality()
- correlate()
- plot.correlate()
- describe()
- eda_web_report()
- eda_paged_report()

Preparing table data

Copy the carseats data frame to the SQLite DBMS and create it as a table named TB_CARSEATS. Mysql/MariaDB, PostgreSQL, Oracle DBMS, and other DBMS are also available for your environment.

library(dplyr)

carseats <- Carseats
carseats[sample(seq(NROW(carseats)), 20), "Income"] <- NA
carseats[sample(seq(NROW(carseats)), 5), "Urban"] <- NA

# connect DBMS
con_sqlite <- DBI::dbConnect(RSQLite::SQLite(), ":memory:")

# copy carseats to the DBMS with a table named TB_CARSEATS
copy_to(con_sqlite, carseats, name = "TB_CARSEATS", overwrite = TRUE)

Calculating descriptive statistics of numerical column of table in the DBMS

Use dplyr::tbl() to create a tbl_dbi object, then use it as a data frame object. The data argument of all EDA functions is specified as a tbl_dbi object instead of a data frame object.

# Positive values select variables
con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
  describe(Sales, CompPrice, Income)

# Negative values to drop variables, and In-memory mode and collect size is 200
con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
  describe(-Sales, -CompPrice, -Income, collect_size = 200)

# Find the statistic of all numerical variables by 'ShelveLoc' and 'US',
# and extract only those with the 'ShelveLoc' variable level as "Good".
con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
  group_by(ShelveLoc, US) %>%
  describe() %>%
  filter(ShelveLoc == "Good")

# extract only those with 'Urban' variable level is "Yes",
# and find 'Sales' statistics by 'ShelveLoc' and 'US'
con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
  filter(Urban == "Yes") %>%
  group_by(ShelveLoc, US) %>%
  describe(Sales)

Test of normality on numeric columns using in the DBMS

# Test all numerical variables by 'ShelveLoc' and 'US',
# and extract only those with the 'ShelveLoc' variable level is "Good".
con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
 group_by(ShelveLoc, US) %>%
 normality() %>%
 filter(ShelveLoc == "Good")

# extract only those with 'Urban' variable level is "Yes",
# and test 'Sales' by 'ShelveLoc' and 'US'
con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
 filter(Urban == "Yes") %>%
 group_by(ShelveLoc, US) %>%
 normality(Sales)

# Test log(Income) variables by 'ShelveLoc' and 'US',
# and extract only p.value greater than 0.01.

# SQLite extension functions for log transformation
RSQLite::initExtension(con_sqlite)

con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
 mutate(log_income = log(Income)) %>%
 group_by(ShelveLoc, US) %>%
 normality(log_income) %>%
 filter(p_value > 0.01)

Normalization visualization of numerical column in the DBMS

# Extract only those with the 'ShelveLoc' variable level is "Good",
# and plot 'Income' by 'US'
# The result is the same as the data.frame, but not displayed here. Reference above in document.
con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
  filter(ShelveLoc == "Good") %>%
  group_by(US) %>%
  plot_normality(Income)

Compute the correlation coefficient between two columns of the table in DBMS

# Correlation coefficient
# that eliminates redundant combination of variables
con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
  correlate() %>%
  filter(as.integer(var1) > as.integer(var2))

con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
  correlate(Sales, Price) %>%
  filter(as.integer(var1) > as.integer(var2))

# Compute the correlation coefficient of the Sales variable by 'ShelveLoc'
# and 'US' variables. And extract only those with absolute
# value of the correlation coefficient is more significant than 0.5
con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
  group_by(ShelveLoc, US) %>%
  correlate(Sales) %>%
  filter(abs(coef_corr) >= 0.5)

# Extract only those with the 'ShelveLoc' variable level is "Good",
# and compute the correlation coefficient of the 'Sales' variable
# by 'Urban' and 'US' variables.
# And the correlation coefficient is negative and smaller than 0.5
con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
  filter(ShelveLoc == "Good") %>%
  group_by(Urban, US) %>%
  correlate(Sales) %>%
  filter(coef_corr < 0) %>%
  filter(abs(coef_corr) > 0.5)

Visualize correlation plot of numerical columns in the DBMS

# Extract only those with 'ShelveLoc' variable level is "Good",
# and visualize correlation plot of 'Sales' variable by 'Urban'
# and 'US' variables.
# The result is the same as the data.frame, but not displayed here. Reference above in document.
con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
  filter(ShelveLoc == "Good") %>%
  group_by(Urban) %>%
  correlate() %>% 
  plot(Sales)

EDA based on target variable

The following is an EDA where the target column is a character, and the predictor column is a numeric type.

# If the target variable is a categorical variable
categ <- target_by(con_sqlite %>% tbl("TB_CARSEATS") , US)

# If the variable of interest is a numerical variable
cat_num <- relate(categ, Sales)
cat_num
summary(cat_num)

# The result is the same as the data.frame, but not displayed here. Reference above in document.
plot(cat_num)

Reporting the information of EDA for table of the DBMS

The following shows several examples of creating an EDA report for a DBMS table.

Using the collect_size argument, you can perform EDA with the corresponding number of sample data. If the number of data is huge, use collect_size.

# create a web report file. 
con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
  eda_web_report()
  
# create a pdf file. the file name is EDA.pdf, and the collect size is 350
con_sqlite %>% 
  tbl("TB_CARSEATS") %>% 
  eda_paged_report(collect_size = 350, output_file = "EDA.pdf")

Exploratory Data Analysis

Choonghyun Ryu

2024-02-06

Preface

Supported data structures

datasets

Exploratory Data Analysis

Univariate data EDA

Calculating descriptive statistics using `describe()`

Test of normality on numeric variables using `normality()`

Visualization of normality of numerical variables using `plot_normality()`

EDA of bivariate data

Calculation of `correlation coefficient` using `correlate()`

Visualization of the correlation matrix using `plot.correlate()`

EDA based on target variable

Definition of target variable

EDA when target variable is categorical variable

Cases where predictors are numeric variable

Cases where predictors are categorical variable

EDA when target variable is numerical variable

Cases where predictors are numeric variable

Cases where predictors are categorical variable

Automated report

Create a dynamic report using `eda_web_report()`

Contents of dynamic web report

Some arguments for dynamic web report

Screenshot of dynamic report

Create a EDA report using `eda_paged_report()`

Contents of static paged report

Some arguments for static paged report

Screenshot of static report

Exploratory data analysis for tables in DBMS

Preparing table data

Calculating descriptive statistics of numerical column of table in the DBMS

Test of normality on numeric columns using in the DBMS

Normalization visualization of numerical column in the DBMS

Compute the correlation coefficient between two columns of the table in DBMS

Visualize correlation plot of numerical columns in the DBMS

EDA based on target variable

Reporting the information of EDA for table of the DBMS

Exploratory Data Analysis

Choonghyun Ryu

2024-02-06

Preface

Supported data structures

datasets

Exploratory Data Analysis

Univariate data EDA

Calculating descriptive statistics using describe()

Test of normality on numeric variables using normality()

Visualization of normality of numerical variables using plot_normality()

EDA of bivariate data

Calculation of correlation coefficient using correlate()

Visualization of the correlation matrix using plot.correlate()

EDA based on target variable

Definition of target variable

EDA when target variable is categorical variable

Cases where predictors are numeric variable

Cases where predictors are categorical variable

EDA when target variable is numerical variable

Cases where predictors are numeric variable

Cases where predictors are categorical variable

Automated report

Create a dynamic report using eda_web_report()

Contents of dynamic web report

Some arguments for dynamic web report

Screenshot of dynamic report

Create a EDA report using eda_paged_report()

Contents of static paged report

Some arguments for static paged report

Screenshot of static report

Exploratory data analysis for tables in DBMS

Preparing table data

Calculating descriptive statistics of numerical column of table in the DBMS

Test of normality on numeric columns using in the DBMS

Normalization visualization of numerical column in the DBMS

Compute the correlation coefficient between two columns of the table in DBMS

Visualize correlation plot of numerical columns in the DBMS

EDA based on target variable

Reporting the information of EDA for table of the DBMS

Calculating descriptive statistics using `describe()`

Test of normality on numeric variables using `normality()`

Visualization of normality of numerical variables using `plot_normality()`

Calculation of `correlation coefficient` using `correlate()`

Visualization of the correlation matrix using `plot.correlate()`

Create a dynamic report using `eda_web_report()`

Create a EDA report using `eda_paged_report()`