### -------------------------------------------------------------------------###
### NMSA407 - Linear Regression ###
### Winter Term 2021/2022 | Online ###
### ###
### EXERCISE #1 Review ###
### -------------------------------------------------------------------------###
### There will be one R script (analogous to this one) available for each week
### of the term. Each script is split into three separate parts:
### i) Teaching material; ii) Individual work; and iii) Additional material.
###
### i) The first part - the teaching material - will be walked through in detail
### during the exercise classes.
### ii) The second part - the individual work - is meant for student's specific
### interests. Going through the R code in this part is not an obligation but it
### is highly recommended.
### iii) Finally, the last part - the additional material - can be used to
### enrich specific knowledge and to get some deeper insight into some specific
### steps of the first part of the script.
### -------------------------------------------------------------------------###
### Block 1: TEACHING MATERIAL ###
### -------------------------------------------------------------------------###
### If you use your personal computer an additional package mffSM is needed
### The package is not available at CRAN but, from can be downloaded from
### the official course website
### https://www2.karlin.mff.cuni.cz/~komarek/vyuka/2021_22/nmsa407-2021.html
### Use the following command for the instalation:
### 1) find the working directory of R using
# getwd()
### 2) download either the .zip or the tar.gz file of the package mffSM
### to the working directory
### 3) run
# install.packages("mffSM_1.1.zip", repos = NULL)
### or
# install.packages("mffSM_1.1.tar.gz", repos = NULL)
library("mffSM")
help(package="mffSM")
### data
data(Cars2004nh, package = "mffSM")
dim(Cars2004nh)
str(Cars2004nh)
head(Cars2004nh)
summary(Cars2004nh)
### Excluding cars where the consumption is missing.
Cars2004nh <- Cars2004nh[!is.na(Cars2004nh$consumption),]
### Creating a working subsample
set.seed(201617)
idx <- c(sample((1:nrow(Cars2004nh))[Cars2004nh$ftype=="personal"], size=100),
sample((1:nrow(Cars2004nh))[Cars2004nh$ftype!="personal"], size=120))
Cars2004nh <- Cars2004nh[idx,]
### Deriving some additional variables
### fdrive2: factor which distinguishes whether the drive is
### front or other (rear or 4x4)
Cars2004nh <- transform(Cars2004nh, fdrive2 = factor(1*(fdrive == "front") +
2*(fdrive != "front"), labels = c("front", "other")))
with(Cars2004nh, table(fdrive, fdrive2))
### cons10: 0/1 variable which is 1 if consumption <= 10 l/100 km, 0 otherwise
### fcons10: factor No/Yes derived from cons10 (0 -> No, 1 -> Yes)
Cars2004nh <- transform(Cars2004nh, cons10 = 1 * (consumption <= 10),
fcons10 = factor(1 * (consumption <= 10), labels = c("No", "Yes")))
summary(Cars2004nh)
### 1. TWO SAMPLE PROBLEM (continuous variable vs. binary variable):
### Does the consumption depend on the drive
### (distinguishing only two categories: front and other)?
### Exloratory part: Boxplot - usually the most useful plot for this problem
### What could be used instead?
plot(consumption ~ fdrive2, data = Cars2004nh, col = rainbow_hcl(2))
### Sample characteristics
with(Cars2004nh, tapply(consumption, fdrive2, summary))
with(Cars2004nh, tapply(consumption, fdrive2, sd, na.rm = TRUE))
X = subset(Cars2004nh, fdrive2 == "front")$consumption
Y = subset(Cars2004nh, fdrive2 == "other")$consumption
### Formal statistical test(s)
### | What is the underlying model in each test? | What are the assumptions?
### Standard two-sample t-test (assuming equal variances)
t.test(consumption ~ fdrive2, data = Cars2004nh, var.equal = TRUE)
mean(X) - mean(Y)
### Welch two-sample t-test (not assuming equal variances)
t.test(consumption ~ fdrive2, data = Cars2004nh)
### Wilcoxon two-sample rank test
wilcox.test(consumption ~ fdrive2, data = Cars2004nh, conf.int = TRUE)
median(X) - median(Y)
XYdiff = outer(X,Y,FUN="-")
median(XYdiff)
### Kolmogorov-Smirnov test
ks.test(subset(Cars2004nh, fdrive2 == "front")$consumption,
subset(Cars2004nh, fdrive2 == "other")$consumption, data = Cars2004nh)
plot(ecdf(X),main="ECDF")
plot(ecdf(Y),col=2,add=TRUE)
### 2. MORE SAMPLE PROBLEM
### (continuous variable vs. categorical variable with more than two categories)
### Does the consumption depend on the drive (distinguishing front/rear/4x4)?
### Boxplots
plot(consumption ~ fdrive, data = Cars2004nh, col = rainbow_hcl(3))
with(Cars2004nh, tapply(consumption, fdrive, summary))
with(Cars2004nh, tapply(consumption, fdrive, sd, na.rm = TRUE))
### Formal statistical test(s)
### | What is the underlying model in each test? | What are the assumptions?
### Standard ANOVA
summary(aov(consumption ~ fdrive, data = Cars2004nh))
### ANOVA without assuming equal variances
oneway.test(consumption ~ fdrive, data = Cars2004nh)
### Kruskal-Wallis Rank Sum Test
kruskal.test(consumption ~ fdrive, data = Cars2004nh)
### Alternatively: the same test statistics as in the standard ANOVA above
summary(m0<-lm(consumption~fdrive,data=Cars2004nh))
anova(m0)
oneway.test(consumption ~ fdrive, data = Cars2004nh,var.equal=TRUE)
X = subset(Cars2004nh, fdrive == "front")$consumption
Y = subset(Cars2004nh, fdrive == "rear")$consumption
Z = subset(Cars2004nh, fdrive == "4x4")$consumption
nX = length(X)
nY = length(Y)
nZ = length(Z)
mX = mean(X)
mY = mean(Y)
mZ = mean(Z)
m = mean(c(X,Y,Z))
nX*(m - mX)^2+nY*(m-mY)^2+nZ*(m-mZ)^2
sum((X - mX)^2)+sum((Y-mY)^2)+sum((Z-mZ)^2)
sum((c(X,Y,Z)-m)^2)
nX+nY+nZ
### 3. CONDITIONAL MEAN / REGRESSION
### (continuous variable vs. continuous variable):
### Does the consumption depend on the length?
### Exploratory part: boxplots are not a reasonable choice here - why?
plot(consumption ~ length, data = Cars2004nh, col = "red3", bg = "orange",
pch = 23)
### Histograms
par(mfrow = c(1, 2))
hist(Cars2004nh$consumption, prob = TRUE, main = "", col = "seagreen",
xlab = "Consumption [l/100 km]")
hist(Cars2004nh$length, prob = TRUE, main = "", col = "seagreen",
xlab = "Length [cm]")
par(mfrow = c(1, 1))
with(Cars2004nh, cor(consumption, length))
with(Cars2004nh, cor(consumption, length, use = "complete.obs"))
with(Cars2004nh, cor(consumption, length, method = "spearman",
use = "complete.obs"))
### Formal statistical test(s)
### | What is the underlying model in each test? | What are the assumptions?
with(Cars2004nh, cor.test(consumption, length))
with(Cars2004nh, cor.test(consumption, length, method = "spearman"))
### Is there any link between the test on a row "length"
### in the output from summary(m1) and any of the previous two tests?
m1 <- lm(consumption ~ length, data = Cars2004nh)
summary(m1)
X = Cars2004nh$length
Y = Cars2004nh$consumption
I = (!is.na(X)) & (!is.na(Y))
X = X[I]
Y = Y[I]
n = length(X)
### point estimates of regression coefficients
(b<-sum((X-mean(X))*(Y-mean(Y)))/sum((X-mean(X))^2))
(a = mean(Y) - mean(X)*b)
### in matrix notation
Xm = cbind(1,X)
solve(t(Xm)%*%Xm)%*%t(Xm)%*%matrix(Y,ncol=1)
### residuals and the estimate of residual variance
r = Y - (a+b*X)
summary(r)
(sig = sqrt(sum(r^2)/(n-2)))
n - 2
### standard deviations
sqrt(sig^2*solve(t(Xm)%*%Xm))
### multiple R^2
cor(X,Y)^2
### Is there any link of the above output to the lines in the plot below?
### When does the correlations coefficient equal to the slope parameter?
plot(consumption ~ length, data = Cars2004nh, col = "red3", bg = "orange",
pch = 23)
abline(m1, col = "blue", lwd = 2)
abline(h = mean(Cars2004nh$consumption, na.rm = TRUE), col = "darkgreen",
lwd = 2)
X = X/sd(X)
Y = Y/sd(Y)
summary(lm(Y~X))
cor(X,Y)
X = X - mean(X)
Y = Y - mean(Y)
summary(m2<-lm(Y~X))
cor(X,Y)
plot(Y~X, col = "red3", bg = "orange", pch = 23)
abline(m2, col = "blue", lwd = 2)
abline(h = mean(Y), col = "darkgreen", lwd = 2)
### 4. CONTINGENCY TABLE (categorical covariate vs. categorical covariate)
### Does the fact that the car is economical (in the U.S. sense ->
### consumption<=10) depend on the drive (distinguishing only front and other)?
### Exploratory part
plot(fcons10 ~ fdrive2, data = Cars2004nh, col = diverge_hcl(2))
(TAB2 <- with(Cars2004nh, table(fdrive2, fcons10)))
round(prop.table(TAB2, margin = 1), 2)
### Formal statistical test(s)
### | What is the underlying model in each test? | What are the assumptions?
chisq.test(TAB2) # Using continuity correction to be more conservative
chisq.test(TAB2, correct = FALSE); # Not using continuity correction
# Expected observed counts under the null hypothesis
print(chisq.test(TAB2)$expected)
(T = chisq.test(TAB2,correct=FALSE))
n = sum(TAB2) # number of observations
R = rowSums(TAB2)/n # observed proportion in rows
C = colSums(TAB2)/n # observed proportion in columns
R%*%t(C)*n # expected counts under independence
(T$observed - T$expected)/sqrt(T$expected) # residuals
T$residuals
(ts<-sum(T$res^2)) # test statistic
pchisq(ts,df=1,lower.tail=FALSE) # p-value
### Are the tests below different from those above (with the same p-value)?
### What else can now be learned from the output?
### Can you reconstruct the test statistics in the test below?
(x <- TAB2[, "Yes"])
(n <- apply(TAB2, 1, sum))
prop.test(x, n)
prop.test(x, n, correct = FALSE)
p2 = x/n # proportion estimates in groups
p = sum(x)/sum(n) # common proportion estimate
(ts<-(diff(p2)/sqrt(p*(1-p)*sum(1/n)))^2) # test statistic
pchisq(ts,df=1,lower.tail=FALSE)
### What is tested here?
prop.test(x, n, alternative = "greater")
### QUESTIONS:
### Would it be possible to find out whether the proportion of economical cars
### among those with the front drive is by more than 40 percentage points higher
### than the proportion of economical cars among those with the other drive?
### Even if it is not possible to get a p-value by just one call to a function,
### is it at least possible to decide on a 5% significance level?
### For completeness, there is one case which was not discussed in this script.
### What about the relationship between some categorical covariate and
### continuous covariates, in the sense that we intend to predict the value of
### a categorical covariate based on the observed value of a
### continuous covariate? Can you guess some usefull ideas/hints?
### Such a relationship is commonly investigated in practice, and a very broad
### class of so-called generalized linear models is used to formally assess this
### type of a relationship. Generalized linear models are more advanced models.
### They are closely discussed in the course
### "NMST 432 - Advanced Regression Models".
### -------------------------------------------------------------------------###
### Block 2: INDIVIDUAL WORK ###
### -------------------------------------------------------------------------###
### 1. Two-sample problem:
### Verify the assumptions for each two-sample test used in part 1
### For instance, a formal test for equal variances in two groups
(ts<-var(subset(Cars2004nh, fdrive2 == "front")$consumption)/
var(subset(Cars2004nh, fdrive2 == "other")$consumption))
(df1<-length(subset(Cars2004nh, fdrive2 == "front")$consumption-1))
(df2<-length(subset(Cars2004nh, fdrive2 == "other")$consumption-1))
p<-pf(ts,df1=df1-1,df2=df2-1)
2*(min(p,1-p))
### Alternatively:
var.test(subset(Cars2004nh, fdrive2 == "front")$consumption,
subset(Cars2004nh, fdrive2 == "other")$consumption)
### 2. More-sample problem:
### - instead of using three group specific means, consider a reformulation by
### using the conditional mean given the groups
### - what is the analogy with the regression formulation
### 3. Regression
### the linear function used in the model m1:
a <- m1$coeff[1] # intercept
b <- m1$coeff[2] # slope
y <- function(a, b, x){return(a + b * x)} ### two parameters
plot(consumption ~ length, data = Cars2004nh)
abline(m1, col = "black")
### compare with
x <- Cars2004nh$length
lines(y(a, b, x) ~ x, col = "red", lwd = 2)
### what if we use a different function now:
y <- function(a,b,c,x){return(a * (x == "front") + b * (x == "rear") +
c * (x == "4x4"))} ### three parameters
summary(m1 <- lm(consumption ~ -1 + fdrive, data = Cars2004nh))
(gmeans <- with(Cars2004nh, tapply(consumption, fdrive, mean)))
boxplot(consumption ~ fdrive, data = Cars2004nh, col = rainbow_hcl(3))
points(consumption[fdrive == "front"] ~
runif(length(consumption[fdrive == "front"] ), 0.5, 1.5),
data = Cars2004nh, pch = 21, bg = "red", cex = 0.8)
points(consumption[fdrive == "rear"] ~
runif(length(consumption[fdrive == "rear"] ), 1.5, 2.5),
data = Cars2004nh, pch = 21, bg = "green", cex = 0.8)
points(consumption[fdrive == "4x4"] ~
runif(length(consumption[fdrive == "4x4"] ), 2.5, 3.5),
data = Cars2004nh, pch = 21, bg = "blue", cex = 0.8)
### sample means in three groups
lines(rep(gmeans[1],2) ~ c(0.5, 1.5), lwd = 4, col = "red")
lines(rep(gmeans[2],2) ~ c(1.5, 2.5), lwd = 4, col = "green")
lines(rep(gmeans[3],2) ~ c(2.5, 3.5), lwd = 4, col = "blue")
a <- m1$coeff[1]
b <- m1$coeff[2]
c <- m1$coeff[3]
### group means by the regression model
points(y(a,b,c, fdrive) ~ fdrive, data = Cars2004nh, pch = 22, bg = "black",
cex = 2)
### -------------------------------------------------------------------------###
### Block 3: ADDITIONAL MATERIAL ###
### -------------------------------------------------------------------------###
### More complex insight into the underlying data...
### Visual assessment of normality of the two samples
COL2 <- rainbow_hcl(2)
X = subset(Cars2004nh, fdrive2 == "front")$consumption
Y = subset(Cars2004nh, fdrive2 == "other")$consumption
par(mfrow = c(1, 2))
hist(X, prob = TRUE, main = "Front", col = COL2[1],
xlab = "Consumption [l/100 km]")
curve(dnorm(x,mean=mean(X),sd=sd(X)),add=TRUE,col=2,lwd=2)
hist(Y, prob = TRUE, main = "Other", col = COL2[2],
xlab = "Consumption [l/100 km]")
curve(dnorm(x,mean=mean(Y),sd=sd(Y)),add=TRUE,col=2,lwd=2)
par(mfrow = c(1, 1))
### How would you vizualize the sample means and medians which are tested in
### the two-sample problems?
### For practical purposes one sided alternative can be tested instead.
### Which alternative makes more sense? What exactly do we test here?
t.test(consumption ~ fdrive2, data = Cars2004nh, alternative = "less", mu = -2)
t.test(consumption ~ fdrive2, data = Cars2004nh, alternative = "less", mu = -2,
var.equal = TRUE)
wilcox.test(consumption ~ fdrive2, data = Cars2004nh, alternative = "less",
mu = -2, conf.int = TRUE)
### Reconstruct the test statistics and the corresponding p-values.
### Contingency tables for general categorical covariates
### Does the fact that the car is economical (in the U.S. sense ->
### consumption<=10) depend on the drive (while distinguishing front/rear/4x4)?
plot(fcons10 ~ fdrive, data = Cars2004nh, col = diverge_hcl(2))
(TAB3 <- with(Cars2004nh, table(fdrive, fcons10)))
prop.table(TAB3, margin = 1)
### What are we testing by the following test?
### What is the model behind this test?
### Does the model seem to be good enough to be useful?
### Which artefacts of the model might be relatively safely ignored and why?
### What is the conclusion?
chisq.test(TAB3)
print(chisq.test(TAB3)$expected)
print(chisq.test(TAB3)$residuals)
print(chisq.test(TAB3)$stdres)
### Does the drive (front/rear/4x4) depend
### on the type of the car (personal/wagon/SUV/pickup/sport/minivan)?
plot(fdrive ~ ftype, data = Cars2004nh, col = diverge_hcl(3))
(TAB4 <- with(Cars2004nh, table(ftype, fdrive)))
prop.table(TAB4, margin = 1)
### What are we testing by the following test?
### What is the model behind this test?
### Does the model seem to be good enough to be useful?
### Which artefacts of the model might be relatively safely ignored and why?
### What is the conclusion?
chisq.test(TAB4)
print(chisq.test(TAB4)$expected)
### Why did we get the warning message? What can be done about it?