Objectives

The objectives of this problem set is to orient you to a number of activities in R. And to conduct a thoughtful exercise in appreciating the importance of data visualization. For each question create a code chunk or text response that completes/answers the activity or question requested. Finally, upload a link to your file hosted on rpubs.com

Questions

  1. Anscombes quartet is a set of 4 \(x,y\) data sets that were published by Francis Anscombe in a 1973 paper Graphs in statistical analysis. For this first question load the anscombe data that is part of the library(datasets) in R. And assign that data to a new object called data.
library(datasets)
str(anscombe)
## 'data.frame':    11 obs. of  8 variables:
##  $ x1: num  10 8 13 9 11 14 6 4 12 7 ...
##  $ x2: num  10 8 13 9 11 14 6 4 12 7 ...
##  $ x3: num  10 8 13 9 11 14 6 4 12 7 ...
##  $ x4: num  8 8 8 8 8 8 8 19 8 8 ...
##  $ y1: num  8.04 6.95 7.58 8.81 8.33 ...
##  $ y2: num  9.14 8.14 8.74 8.77 9.26 8.1 6.13 3.1 9.13 7.26 ...
##  $ y3: num  7.46 6.77 12.74 7.11 7.81 ...
##  $ y4: num  6.58 5.76 7.71 8.84 8.47 7.04 5.25 12.5 5.56 7.91 ...
data <- anscombe
data
##    x1 x2 x3 x4    y1   y2    y3    y4
## 1  10 10 10  8  8.04 9.14  7.46  6.58
## 2   8  8  8  8  6.95 8.14  6.77  5.76
## 3  13 13 13  8  7.58 8.74 12.74  7.71
## 4   9  9  9  8  8.81 8.77  7.11  8.84
## 5  11 11 11  8  8.33 9.26  7.81  8.47
## 6  14 14 14  8  9.96 8.10  8.84  7.04
## 7   6  6  6  8  7.24 6.13  6.08  5.25
## 8   4  4  4 19  4.26 3.10  5.39 12.50
## 9  12 12 12  8 10.84 9.13  8.15  5.56
## 10  7  7  7  8  4.82 7.26  6.42  7.91
## 11  5  5  5  8  5.68 4.74  5.73  6.89
  1. Summarise the data by calculating the mean, variance, for each column and the correlation between each pair (eg. x1 and y1, x2 and y2, etc) (Hint: use the fBasics() package!)
install.packages("fBasics", repos = "http://cran.us.r-project.org")
## 
## The downloaded binary packages are in
##  /var/folders/_f/hk0n1w157s5bfmt2ykvxt1yh0000gn/T//RtmpabUpLk/downloaded_packages
library(fBasics)
## Loading required package: timeDate
## Warning: package 'timeDate' was built under R version 3.4.3
## Loading required package: timeSeries

Means of the columns can be computed using colMeans function on the data

colMeans(data)
##       x1       x2       x3       x4       y1       y2       y3       y4 
## 9.000000 9.000000 9.000000 9.000000 7.500909 7.500909 7.500000 7.500909

Variance of each column can be computed using colVar function on the data

colVars(data)
##        x1        x2        x3        x4        y1        y2        y3 
## 11.000000 11.000000 11.000000 11.000000  4.127269  4.127629  4.122620 
##        y4 
##  4.123249

Correlation of variable x1 with y1 using fBasics

x1<-data[,1]
x2<-data[,2]
x3<-data[,3]
x4<-data[,4]
y1<-data[,5]
y2<-data[,6]
y3<-data[,7]
y4<-data[,8]

correlationTest(x1,y1,method = c("pearson", "kendall", "spearman"))
## 
## Title:
##  Pearson's Correlation Test
## 
## Test Results:
##   PARAMETER:
##     Degrees of Freedom: 9
##   SAMPLE ESTIMATES:
##     Correlation: 0.8164
##   STATISTIC:
##     t: 4.2415
##   P VALUE:
##     Alternative Two-Sided: 0.00217 
##     Alternative      Less: 0.9989 
##     Alternative   Greater: 0.001085 
##   CONFIDENCE INTERVAL:
##     Two-Sided: 0.4244, 0.9507
##          Less: -1, 0.9388
##       Greater: 0.5113, 1
## 
## Description:
##  Wed Apr 11 07:32:50 2018

Correlation of variable x2 with y2 using fBasics

correlationTest(x2,y2,method = c("pearson", "kendall", "spearman"))
## 
## Title:
##  Pearson's Correlation Test
## 
## Test Results:
##   PARAMETER:
##     Degrees of Freedom: 9
##   SAMPLE ESTIMATES:
##     Correlation: 0.8162
##   STATISTIC:
##     t: 4.2386
##   P VALUE:
##     Alternative Two-Sided: 0.002179 
##     Alternative      Less: 0.9989 
##     Alternative   Greater: 0.001089 
##   CONFIDENCE INTERVAL:
##     Two-Sided: 0.4239, 0.9506
##          Less: -1, 0.9387
##       Greater: 0.5109, 1
## 
## Description:
##  Wed Apr 11 07:32:50 2018

Correlation of variable x3 with y3 using fBasics

correlationTest(x3,y3,method = c("pearson", "kendall", "spearman"))
## 
## Title:
##  Pearson's Correlation Test
## 
## Test Results:
##   PARAMETER:
##     Degrees of Freedom: 9
##   SAMPLE ESTIMATES:
##     Correlation: 0.8163
##   STATISTIC:
##     t: 4.2394
##   P VALUE:
##     Alternative Two-Sided: 0.002176 
##     Alternative      Less: 0.9989 
##     Alternative   Greater: 0.001088 
##   CONFIDENCE INTERVAL:
##     Two-Sided: 0.4241, 0.9507
##          Less: -1, 0.9387
##       Greater: 0.511, 1
## 
## Description:
##  Wed Apr 11 07:32:50 2018

Correlation of variable x4 with y4 using fBasics

correlationTest(x4,y4,method = c("pearson", "kendall", "spearman"))
## 
## Title:
##  Pearson's Correlation Test
## 
## Test Results:
##   PARAMETER:
##     Degrees of Freedom: 9
##   SAMPLE ESTIMATES:
##     Correlation: 0.8165
##   STATISTIC:
##     t: 4.243
##   P VALUE:
##     Alternative Two-Sided: 0.002165 
##     Alternative      Less: 0.9989 
##     Alternative   Greater: 0.001082 
##   CONFIDENCE INTERVAL:
##     Two-Sided: 0.4246, 0.9507
##          Less: -1, 0.9388
##       Greater: 0.5115, 1
## 
## Description:
##  Wed Apr 11 07:32:50 2018
  1. Create scatter plots for each \(x, y\) pair of data.

Scatterplot of x1 with y1

plot(x1,y1,main="Figure 1",xlab="x1",ylab="y1")

Scatterplot of x2 with y2

plot(x2,y2,main="Figure 2",xlab="x2",ylab="y2")

Scatterplot of x3 with y3

plot(x3,y3,main="Figure 3",xlab="x3",ylab="y3")

Scatterplot of x4 with y4

plot(x4,y4,main="Figure 4",xlab="x4",ylab="y4")

  1. Now change the symbols on the scatter plots to solid circles and plot them together as a 4 panel graphic

Scatter Plots as a panel with pch=19 for solid circles

par(mfrow = c(2,2))
plot(x1,y1, main = "Figure 1", pch = 19)
plot(x2,y2,main = "Figure 2", pch = 19)
plot(x3,y3, main = "Figure 3", pch = 19)
plot(x4,y4, main = "Figure 4", pch = 19)

  1. Now fit a linear model to each data set using the lm() function.
linear_model1<-lm(y1~x1)
linear_model2<-lm(y2~x2)
linear_model3<-lm(y3~x3)
linear_model4<-lm(y4~x4)
summary(linear_model1)
## 
## Call:
## lm(formula = y1 ~ x1)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -1.92127 -0.45577 -0.04136  0.70941  1.83882 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)   
## (Intercept)   3.0001     1.1247   2.667  0.02573 * 
## x1            0.5001     0.1179   4.241  0.00217 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 1.237 on 9 degrees of freedom
## Multiple R-squared:  0.6665, Adjusted R-squared:  0.6295 
## F-statistic: 17.99 on 1 and 9 DF,  p-value: 0.00217
summary(linear_model2)
## 
## Call:
## lm(formula = y2 ~ x2)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -1.9009 -0.7609  0.1291  0.9491  1.2691 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)   
## (Intercept)    3.001      1.125   2.667  0.02576 * 
## x2             0.500      0.118   4.239  0.00218 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 1.237 on 9 degrees of freedom
## Multiple R-squared:  0.6662, Adjusted R-squared:  0.6292 
## F-statistic: 17.97 on 1 and 9 DF,  p-value: 0.002179
summary(linear_model3)
## 
## Call:
## lm(formula = y3 ~ x3)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -1.1586 -0.6146 -0.2303  0.1540  3.2411 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)   
## (Intercept)   3.0025     1.1245   2.670  0.02562 * 
## x3            0.4997     0.1179   4.239  0.00218 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 1.236 on 9 degrees of freedom
## Multiple R-squared:  0.6663, Adjusted R-squared:  0.6292 
## F-statistic: 17.97 on 1 and 9 DF,  p-value: 0.002176
summary(linear_model4)
## 
## Call:
## lm(formula = y4 ~ x4)
## 
## Residuals:
##    Min     1Q Median     3Q    Max 
## -1.751 -0.831  0.000  0.809  1.839 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)   
## (Intercept)   3.0017     1.1239   2.671  0.02559 * 
## x4            0.4999     0.1178   4.243  0.00216 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 1.236 on 9 degrees of freedom
## Multiple R-squared:  0.6667, Adjusted R-squared:  0.6297 
## F-statistic:    18 on 1 and 9 DF,  p-value: 0.002165
par(mfrow = c(2,2))
plot(linear_model1)

plot(linear_model2)

plot(linear_model3)

plot(linear_model4)
## Warning: not plotting observations with leverage one:
##   8

## Warning: not plotting observations with leverage one:
##   8

  1. Now combine the last two tasks. Create a four panel scatter plot matrix that has both the data points and the regression lines. (hint: the model objects will carry over chunks!)
par(mfrow=c(2,2))
plot(x1,y1,main="Figure 1",xlab="x1",ylab="y1",pch=19)
abline(linear_model1)
plot(x2,y2,main="Figure 2",xlab="x2",ylab="y2",pch=19)
abline(linear_model2)
plot(x3,y3,main="Figure 3",xlab="x3",ylab="y3",pch=19)
abline(linear_model3)
plot(x4,y4,main="Figure 4",xlab="x4",ylab="y4",pch=19)
abline(linear_model4)

  1. Now compare the model fits for each model object.
anova(linear_model1)

Analysis of Variance Table

Response: y1 Df Sum Sq Mean Sq F value Pr(>F)
x1 1 27.510 27.5100 17.99 0.00217 ** Residuals 9 13.763 1.5292
— Signif. codes: 0 ‘’ 0.001 ’’ 0.01 ’’ 0.05 ‘.’ 0.1 ‘’ 1

anova(linear_model2)

Analysis of Variance Table

Response: y2 Df Sum Sq Mean Sq F value Pr(>F)
x2 1 27.500 27.5000 17.966 0.002179 ** Residuals 9 13.776 1.5307
— Signif. codes: 0 ‘’ 0.001 ’’ 0.01 ’’ 0.05 ‘.’ 0.1 ‘’ 1

anova(linear_model3)

Analysis of Variance Table

Response: y3 Df Sum Sq Mean Sq F value Pr(>F)
x3 1 27.470 27.4700 17.972 0.002176 ** Residuals 9 13.756 1.5285
— Signif. codes: 0 ‘’ 0.001 ’’ 0.01 ’’ 0.05 ‘.’ 0.1 ‘’ 1

anova(linear_model4)

Analysis of Variance Table

Response: y4 Df Sum Sq Mean Sq F value Pr(>F)
x4 1 27.490 27.4900 18.003 0.002165 ** Residuals 9 13.742 1.5269
— Signif. codes: 0 ‘’ 0.001 ’’ 0.01 ’’ 0.05 ‘.’ 0.1 ‘’ 1

  1. In text, summarize the lesson of Anscombe’s Quartet and what it says about the value of data visualization.

The Anscombe’s Quartet is basically made up of four data sets that have the same statistical properties such as mean, variance, linear regression etc., however, when this data is visualised, the data is very different. This concludes that quantitative summary statistics is not entirely able to show comparison, instead qualitative visualisation of the data provides a better picture. This means data can not be truly understood with statistical analyses, it should be supplemented with visualisation. Statistics summary is important for analyzing huge datasets, however alone it is not sufficient.