Department of Statistics

COURSE STATS 330

Assignment 2, 2006

Instructions: Hand in your completed assignment to the Student Resource Centre by 4pm
on Thursday 17th August.

Note: You must show all R code used in your answers. Failure to do this will cost you
marks.

Question 1 [30 marks]

The file mammalsleep.txt contains data on 61 species of mammal. The variables in
the data set are

body: body weight in kg

brain: brain weight in g
nondream: slow wave ("nondreaming") sleep (hrs/day)
dream: paradoxical ("dreaming") sleep (hrs/day)
sleep: total sleep (hrs/day) (sum of dream and nondream)
lifespan: maximum life span (years)
gestation: gestation time (days)
predation: predation index (1-5) 1 = minimum (least likely to be
preyed upon) to 5 = maximum (most likely to be preyed upon)
exposure: sleep exposure index (1-5) 1 = least exposed (e.g.
animal sleeps in a well-protected den) 5 = most exposed
danger: overall danger index (1-5) (based on the above two indices and other
information) 1 = least danger (from other animals) 5 = most danger
(from other animals)
.
The data were gathered in a study to examine what factors are related to the sleep patterns
of mammals. See the article "Sleep in Mammals: Ecological and Constitutional
Correlates" Allison, T. and Cicchetti, D. (1976), Science, November 12, vol. 194, pp.
732-734. You can download a pdf copy of this article from the Library webpages.

a. Load the data into R and create a data frame. Make a pairs plot. Correct any obvious
typos in the data. [3 marks]

b. The three variables body, brain and lifespan have values that differ by orders
of magnitude. Do you think the relationships between these variables and the variable
sleep are linear? If we consider logged versions of these variables, would this
difficulty go away? Would another transformation be suitable? [3 marks]

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c. There are also many missing values in this data. When fitting regressions, the lm
function drops out any cases that have missing values in any of the variables involved
in the regression. However, this causes difficulties when we come to compare models,
as we do in part 4 of this question. What should we do? See tutorial sheet 2 for some
hints. Take the appropriate corrective action. [3 marks]

d. Fit a model to the data, using sleep as the response and taking into account suitable
transformations of the variables body, brain and lifespan. Comment on the quality of
the fit. [4 marks]

e. In their article, Allison and Cicchetti fitted a model with log body and danger as
explanatory variables, using nondream as response . Do these variables adequately
explain the variation in the variable sleep? (in other words, is the model with log
body and danger as explanatory variables an adequate model?) [3 marks]

f. It would seem that both the size of the animal, and the danger/risk aspect effect sleep.
Does adding other variables improve the model? Try the effect of variables log brain
and predation only I dont expect a full-scale model selection exercise. [4 marks]

g. Subject you chosen model to the usual diagnostic checks. Are there any high-leverage
observations or outliers? You should take your answer into Question 2 into account
when answering this. [6 marks]

h. The Okapi species did not have the variable sleep recorded in this data set. Use
your model to make a prediction of what the value of sleep is for this animal.
[4 marks]

Okapi

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 Question 2 [10 marks]
How can we tell if the largest residual in a regression is truly an outlier, or if it is just due to
chance? After all, one of the residuals must be the biggest! One way to answer this is the
following. If the model assumptions are satisfied (i.e. no outliers), we can think of the
studentised residuals as being (at least approximately) random samples from a standard
normal N(0,1) distribution. Suppose there are n residuals in a regression. We could simulate
a sample of size n from a standard normal, and select the largest residual. We could repeat
this say 10,000 times and examine the distribution of these 10,000 largest residuals. We
could then see if the largest residual in our regression was extreme in comparison to this
distribution. If it is, the observation is probably a genuine outlier.

Carry out this program for the final model you fitted in Question 1. What do you conclude?
[6 marks for R code, and display of results, 4 marks for comments]

Hint: We can interpret the largest residual as the one having largest absolute value. We
can calculate this for a normal sample of size n using the R statement

maxres = max(abs(rnorm(n)))

You can collect the results of doing this 10,000 times in a vector with 10,000 elements by
using a loop. Display the results as we did for the exchange rate data as we did in Lecture 2.
You may find consulting the R documentation for the functions rnorm, for, hist and
density useful.

Data for Assignment 2 (also in file mammalsleep.txt)

body brain nondream dream sleep lifespan gestation predation exposure danger
African.elephant 6654.000 5712.00 NA NA 3.3 38.6 645.0 3 5 3
African.giant.pouched.rat 1.000 6.60 6.3 2.0 8.3 4.5 42.0 3 1 3
Arctic.Fox 3.385 44.50 NA NA 12.5 14.0 60.0 1 1 1
Arctic.ground.squirrel 0.920 5.70 NA NA 16.5 NA 25.0 5 2 3
Asian.elephant 2547.000 4603.00 2.1 1.8 3.9 69.0 624.0 3 5 4
Baboon 10.550 179.50 9.1 0.7 9.8 27.0 180.0 4 4 4
Big.brown.bat 0.023 0.30 15.8 3.9 19.7 19.0 35.0 1 1 1
Brazilian.tapir 160.000 169.00 5.2 1.0 6.2 30.4 392.0 4 5 4
Cat 3.300 25.60 10.9 3.6 14.5 28.0 63.0 1 2 1
Chimpanzee 52.160 440.00 8.3 1.4 9.7 50.0 230.0 1 1 1
Chinchilla 0.425 6.40 11.0 1.5 12.5 7.0 112.0 5 4 4
Cow 465.000 423.00 3.2 0.7 3.9 30.0 281.0 5 5 5
Desert.hedgehog 0.550 2.40 7.6 2.7 10.3 NA NA 2 1 2
Donkey 187.100 419.00 NA NA 3.1 40.0 365.0 5 5 5
Eastern.American.mole 0.075 1.20 6.3 2.1 8.4 3.5 42.0 1 1 1
Echidna 3.000 25.00 8.6 0.0 8.6 50.0 28.0 2 2 2
European.hedgehog 0.785 3.50 6.6 4.1 10.7 6.0 42.0 2 2 2
Galago 0.200 5.00 9.5 1.2 10.7 10.4 120.0 2 2 2
Genet 1.410 17.50 4.8 1.3 6.1 34.0 NA 1 2 1
Giant.armadillo 60.000 81.00 12.0 6.1 18.1 7.0 NA 1 1 1

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Giraffe 529.000 680.00 NA 0.3 NA 28.0 400.0 5 5 5
Goat 27.660 115.00 3.3 0.5 3.8 20.0 148.0 5 5 5
Golden.hamster 0.120 1.00 11.0 3.4 14.4 3.9 16.0 3 1 2
Gorilla 207.000 406.00 NA NA 12.0 39.3 252.0 1 4 1
Gray.seal 85.000 325.00 4.7 1.5 6.2 41.0 310.0 1 3 1
Gray.wolf 36.330 119.50 NA NA 13.0 16.2 63.0 1 1 1
Ground.squirrel 0.101 4.00 10.4 3.4 13.8 9.0 28.0 5 1 3
Guinea.pig 1.040 5.50 7.4 0.8 8.2 7.6 68.0 5 3 4
Horse 521.000 655.00 2.1 0.8 2.9 46.0 336.0 5 5 5
Jaguar 100.000 157.00 NA NA 10.8 22.4 100.0 1 1 1
Kangaroo 35.000 56.00 NA NA NA 16.3 33.0 3 5 4
Lesser.short-
tailed.shrew 0.005 0.14 7.7 1.4 9.1 2.6 21.5 5 2 4
Little.brown.bat 0.010 0.25 17.9 2.0 19.9 24.0 50.0 1 1 1
Man 62.000 1320.00 6.1 1.9 8.0 100.0 267.0 1 1 1
Mole.rat 0.122 3.00 8.2 2.4 10.6 NA 30.0 2 1 1
Mountain.beaver 1.350 8.10 8.4 2.8 11.2 NA 45.0 3 1 3
Mouse 0.023 0.40 11.9 1.3 13.2 3.2 19.0 4 1 3
Musk.shrew 0.048 0.33 10.8 2.0 12.8 2.0 30.0 4 1 3
N.American.opossum 1.700 6.30 13.8 5.6 19.4 5.0 12.0 2 1 1
Nine-banded.armadillo 3.500 10.80 14.3 3.1 17.4 6.5 120.0 2 1 1
Okapi 250.000 490.00 NA 1.0 NA 23.6 440.0 5 5 5
Owl.monkey 0.480 15.50 15.2 1.8 17.0 12.0 140.0 2 2 2
Patas.monkey 10.000 115.00 10.0 0.9 10.9 20.2 170.0 4 4 4
Phanlanger 1.620 11.40 11.9 1.8 13.7 13.0 17.0 2 1 2
Pig 192.000 180.00 6.5 1.9 8.4 27.0 115.0 4 4 4
Rabbit 2.500 12.10 7.5 0.9 8.4 18.0 31.0 5 5 5
Raccoon 4.288 39.20 NA NA 12.5 13.7 63.0 2 2 2
Rat 0.280 1.90 10.6 2.6 13.2 4.7 21.0 3 1 3
Red.fox 4.235 50.40 7.4 2.4 9.8 9.8 52.0 1 1 1
Rhesus.monkey 6.800 179.00 8.4 1.2 9.6 29.0 164.0 2 3 2
Rock.hyrax.Hetero 0.750 12.30 5.7 0.9 6.6 7.0 225.0 2 2 2
Rock.hyrax.Procavia 3.600 21.00 4.9 0.5 5.4 6.0 225.0 3 2 3
Roe.deer 14.830 98.20 NA NA 2.6 17.0 150.0 5 5 5
Sheep 55.500 175.00 3.2 0.6 3.8 20.0 151.0 5 5 5
Slow.loris 1.400 12.50 NA NA 11.0 12.7 90.0 2 2 2
Star.nosed.mole 0.060 1.00 8.1 2.2 10.3 3.5 NA 3 1 2
Tenrec 0.900 2.60 11.0 2.3 13.3 4.5 60.0 2 1 2
Tree.hyrax 2.000 12.30 4.9 0.5 5.4 7.5 200.0 3 1 3
Tree.shrew 0.104 2.50 13.2 2.6 15.8 2.3 46.0 3 2 2
Vervet 4.190 58.00 9.7 0.6 10.3 24.0 210.0 4 3 4
Water.opossum 3.500 3.90 12.8 6.6 19.4 3.0 14.0 2 1 1
Yellow-bellied.marmot 4.050 17.00 NA NA NA 13.0 38.0 3 1 1