Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Exploratory Data Analysis

Dr. Aijun ZhangSTAT3622 Data Visualization

12 September 2016

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Outline

1 Exploratory Data Analysis

2 Simple Base Graphics

3 Using Lattice Package

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

John Tukey

John Tukey (1915 – 2000)

Proposed “Exploratory Data Analysis”

Coined terms: Boxplot, Stem-and-Leafplot, ANOVA (Analysis of Variance)

Coined terms “Bit” and “Software”

Co-Developed Fast Fourier Transformalgorithm, Projection Pursuit, Jackknifeestimation

Famous quote: “The best thing aboutbeing a statistician is that you get to playin everyone’s backyard. ”

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

John Tukey

“The greatest value of a picture is when it forces us to notice whatwe never expected to see.”

John Tukey (1977)

Tables

Five-number summary

Scatter plot

Box-plot

Residual plot

Smoother

Stem-and-Leaf plot

Bag plot

Median Polish

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Example 1: Anscombe Dataset

x1 y1 x2 y2 x3 y3 x4 y41 10.00 8.04 10.00 9.14 10.00 7.46 8.00 6.582 8.00 6.95 8.00 8.14 8.00 6.77 8.00 5.763 13.00 7.58 13.00 8.74 13.00 12.74 8.00 7.714 9.00 8.81 9.00 8.77 9.00 7.11 8.00 8.845 11.00 8.33 11.00 9.26 11.00 7.81 8.00 8.476 14.00 9.96 14.00 8.10 14.00 8.84 8.00 7.047 6.00 7.24 6.00 6.13 6.00 6.08 8.00 5.258 4.00 4.26 4.00 3.10 4.00 5.39 19.00 12.509 12.00 10.84 12.00 9.13 12.00 8.15 8.00 5.56

10 7.00 4.82 7.00 7.26 7.00 6.42 8.00 7.9111 5.00 5.68 5.00 4.74 5.00 5.73 8.00 6.89

Mean 9.00 7.50 9.00 7.50 9.00 7.50 9.00 7.50Sd 3.32 2.03 3.32 2.03 3.32 2.03 3.32 2.03Cor 0.82 0.82 0.82 0.82

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Example 1: Anscombe Dataset

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Exploratory Data Analysis

The EDA is a statistical approach to make sense of data by using avariety of techniques (mostly graphical). It may help

Assess assumption about variables distribution

Identify relationship between variables

Extract important variables

Suggest use of appropriate models

Detect problems of collected data (e.g. outliers, missing data,measurement errors)

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Base Statistical Graphics

UnivariteHistogram, Stem-and-Leaf, Dot, Q-Q, Density plotsBoxplot, Box-and-whiskerBar, Pie, Polar, Waterfall charts

BivariateXYplot, Line, Area, Scatter, Bubble charts

Trivariate3D Scatter, Contour, Level/Heatmap, Surface plots

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Which Chart to Use?

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Which Chart to Use?

Indeed, experience matters!

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Outline

1 Exploratory Data Analysis

2 Simple Base Graphics

3 Using Lattice Package

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Iris Dataset

Let’s play with Iris data in RStudio. Refer to R markdown soucecodes and html output files (reproducible).

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Histogram

Options: title(.,main, xlab, ylab), hist(.,breaks, freq, col)figure layout by par(mfrow/mfcol = c(nr,nc))

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Histogram with Density Plot

Options: hist(.,freq=F); lines(density(.), lty, lwd,)

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Boxplot

Remarks: Outliers /∈ {Q1− 1.5IQR,Q3 + 1.5IQR}

Options: plotting x (vector), X (matrix) and x ∼ c (grouping)

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Plotting Categorical Variables

Ticks: data selection/subsetting; see UCLA R-site

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Relationship Between Variables

Tricks: mathematical annotations in plots; see plotmath.html

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Relationship Between Variables

Tricks: color indexing by unclass(DataX$Species)adding legend/text at different locations

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Pairwise Scatter Plots

Tricks: color indexing by unclass(DataX$Species)adding legend/text at different locations

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Pairwise Scatter Plots

Tricks: color indexing by unclass(DataX$Species)adding legend/text at different locations

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Outline

1 Exploratory Data Analysis

2 Simple Base Graphics

3 Using Lattice Package

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Lattice Package

Sarkar (2008; Springer)

Using trellis graphs for multivariate data

Multipanel conditioning and grouping

Elegant high-level data visualization

Covering most of statistical charts

Figures and Codes can be found athttp://lmdvr.r-forge.r-project.org/

Plot customization are not straightforward

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Univariate Distributions with Conditioning and Grouping

Refer to R Markdown for source codes/outputs (reproducible)

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Univariate Distributions with Conditioning and Grouping

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Univariate Distributions with Conditioning and Grouping

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Exploring Bivariate Relationships

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Trivariate Heatmap and 3D Plots

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Exploratory Data Analysis Simple Base Graphics Using Lattice Package

Trivariate Heatmap and 3D Plots

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