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Group

Analysis of Variance and

Covariance

Level : E2

Contents

Key concepts

Analysis of Variance

Analysis of Covariance

GLM Procedure

Analysis of Variance

ANOVA

used to uncover the main and interaction effects of categorical

independent variables (called "factors") on interval dependent

variable (s).

Example:

An experiment may measure weight change (the dependent variable) for men

and women who participated in two different weight-loss programs. The 4

cells of the design are formed by the 4 combinations of sex (men, women) and

program (A, B).

Example:

Let us have a situation where we have three means A, B and C. We want to test the

H0 : A = B = C

Against H1 : at least one of them is different than others.

Assumptions

The scale on which the dependent variable is measured has the properties of an equal interval

scale.

The k samples are independently and randomly drawn from the source population(s)

The k samples have approximately equal variances.

Main Effect

Interaction Effect

the effects of one factor differs according to the levels of another factor

The key statistic in ANOVA is the F-test of difference of group means, testing if the

means of the groups formed by values of the independent variable (or combinations of

values for multiple independent variables) are different enough not to have occurred by

chance.

complete enumeration rather than a sample, then any difference of means is "real."

However, when ANOVA is used for comparing two or more different samples, the real

means are unknown. The researcher wants to know if the difference in sample means is

enough to conclude the real means do in fact differ among two or more groups.

If the group means do not differ significantly then it is inferred that the independent

variable(s) did not have an effect on the dependent variable.

If the F test shows that overall the independent variable(s) is (are) related to the

dependent variable, then multiple comparison tests of significance are used to explore

just which values of the independent(s) have the most to do with the relationship.

Post-hoc Comparisons

If null hypothesis in ANOVA is rejected then go for the multiple comparison (Post-hoc Comparisons)

test.

Duncan

Dunnett

Bonferroni, Scheffe

Suppose we are testing the null hypothesis that the four sample means are equal

H0 : m1 = m 2 = m3 = m 4

H1 : m1 m 2 m3 m 4

this hypothesis is rejected.

The F test in ANOVA tells that at least one mean is not same to the other but it

does not specify which particular mean it is

One of the possible ways to detect which particular sample mean is different may to

conduct the following six tests-

Unbalanced Designs

If the sample sizes for the treatment combinations are not all equal.

confounding is the condition that the effects of two (or more) explanatory variables cannot be

distinguished from each other

Type II sum of square are the reduction in the SSE due to adding the effect to a model that contains all other

effects except effects that contains the effect being tested.

Type III SS are each adjusted for all other effects in the model

If our model does not contain any interaction term then both will lead to same output

For the highest order interaction term the two methods will always provide same estimate

If interaction can be safely ignored then Type II provides more powerful than that obtained from Type III to test

the significance of main effect

If there are not sufficient reasons to ignore interactions then we should use Type III. This is the default type in

most of the softwares for Statistical Analysis

SAS Implementation

class treat;

model weight = treat;

run;

PROC ANOVA takes into account the special structure of a balanced design, it is faster

and uses less storage than PROC GLM for balanced data, ), whereas the GLM

procedure can analyze both balanced and unbalanced data

The classification variable is specified in the CLASS statement

The MODEL statement names the dependent variables and independent effects

Example

title1 'Nitrogen Content

data Clover;

input Strain $ Nitrogen

datalines;

1 19.4

1 32.6

1

5 17.7 5

24.8

5

4 17.0 4 19.4

4

7 20.7 7 21.0

7

13 14.3 13 14.4

13

15 17.3 15 19.4

15

@@;

27.0

27.9

9.1

20.5

11.8

19.1

class strain;

model Nitrogen = Strain;

run;

1

5

4

7

13

15

32.1

25.2

11.9

18.8

11.6

16.9

1

5

4

7

13

15

33.0

24.3

15.8

18.6

14.2

20.8 ;

Source

DF Sum of Squares Mean Square

Model

5

847.046667

169.409333

Error

24

282.928000

11.788667

Corrected Total 29

1129.974667

F value Pr>F

14.37 <.0001

Nitrogen Mean

0.749616

17.26515

3.433463

19.88667

Source

DF

Anova SS

Mean Square F Value Pr > F

Strain

5

847.0466667

169.4093333 14.37

<.0001

The degrees of freedom (DF) column should be used to check the analysis

results. The model degrees of freedom for a one-way analysis of variance

are the number of levels minus 1; in this case, 6-1=5. The Corrected Total

degrees of freedom are always the total number of observations minus one;

in this case 30-1=29. The sum of Model and Error degrees of freedom

equal the Corrected Total.

The overall F test is significant (F=14.37, p<0.0001), indicating that the

model as a whole accounts for a significant portion of the variability in the

dependent variable. The F test for Strain is significant, indicating that some

contrast between the means for the different strains is different from zero.

Notice that the Model and Strain F tests are identical, since Strain is the

only term in the model.

The F test for Strain (F=14.37, p<0.0001) suggests that there are

differences among the bacterial strains, but it does not reveal any

information about the nature of the differences. Mean comparison methods

can be used to gather further information.

Analysis of Covariance

A combination of linear Regression and ANOVA.

dependent variable and we want to control that variable also the

we use ANCOVA at the place of ANOVA. That is, In experimental

designs, to control for factors which cannot be randomized but

which can be measured on an interval scale.

Example: In some study baseline values can be a variable which we

need to control to examine the significance of categorical

predictors.

When covariate scores are available we have information about

differences between treatment groups that existed before the

experiment was performed and we want to control for that.

Failure to do this often means that some portion of the effect of the predictor is

removed from the dependent when the covariate adjustment is calculated.

The rules like that for sum of squares etc remain as they were in the case of

ANOVA.

GLM Procedures

The general linear model (GLM) is a statistical

linear model. It may be written as

Y = XB + U

where Y is a matrix with series of multivariate measurements, X is a matrix that might be a design matrix,

B is a matrix containing parameters that are usually to be estimated and U is a matrix containing residuals

(i.e., errors or noise). The residual is usually assumed to follow a multivariate normal distribution. If the

residual is not a multivariate normal distribution, Generalized linear models may be used to relax

assumptions about Y and U.

The GLM procedure uses the method of least squares to fit general linear models.

GLM handles models relating one or several continuous dependent variables to one or several

independent variables. The independent variables may be either classification variables, which divide the

observations into discrete groups, or continuous variables.

Thus, the GLM procedure can be used for many different analyses, including

simple regression

multiple regression

response-surface models

weighted regression

polynomial regression

partial correlation

CLASS variables;

MODEL dependents = independents </options>;

MEANS effects </options>;

LSMEANS effects </ options>;

OUTPUT OUT = SAS data-set keyword = variable... ;

RUN;

QUIT;

PROC GLM handles models relating one or several continuous dependent variables

to one or several independent variables.

MEANS computes means of the dependent variable for each value of the specified

effect

LSMEANS produces means for the outcome variable, broken out by the variable

specified and adjusting for any other explanatory variables included on the MODEL

statement.

OUTPUT specifies an output data set that contains all variables from the input data

set and variables representing statistics from the analysis.

Example

data exp;

input A $ B $ Y @@;

datalines;

A1 B1 12 A1 B1 14

A1 B2 11 A1 B2 9

A2 B1 20 A2 B1 18

A2 B2 17

;

proc glm;

class A B;

model Y=A B A*B;

run;

Result

Analysis of Unbalanced 2-by-2 Factorial

The GLM Procedure

Dependent Variable: Y

Source

DF

Sum of Squares Mean Square F Value

Model

3

91.71428571

30.57142857

15.29

Error

3

6.00000000

2.00000000

Corrected Total 6

97.71428571

R-Square

0.938596

Source

A

B

A*B

Source

A

B

A*B

DF

1

1

1

DF

1

1

1

Coeff Var

9.801480

Pr > F

0.0253

Root MSE

Y Mean

1.414214

14.42857

Type I SS

Mean Square

F Value

Pr > F

80.04761905

80.04761905

40.02

0.0080

11.26666667

11.26666667

5.63

0.0982

0.40000000

0.40000000

0.20

0.6850

Type III SS

Mean Square

F Value

Pr > F

67.60000000

67.60000000

33.80

0.0101

10.00000000

10.00000000

5.00

0.1114

0.40000000

0.40000000

0.20

0.6850

Interpretation

The degrees of freedom may be used to check your data. The Model degrees of freedom for a 2 2

factorial design with interaction are (ab-1), where a is the number of levels of A and b is the

number of levels of B; in this case, (22-1) = 3. The Corrected Total degrees of freedom are always

one less than the number of observations used in the analysis; in this case, 7-1=6.

The overall F test is significant (F=15.29, p=0.0253), indicating strong evidence that the means for

the four different AB cells are different. You can further analyze this difference by examining the

individual tests for each effect.

Four types of estimable functions of parameters are available for testing hypotheses in PROC GLM.

For data with no missing cells, the Type III and Type IV estimable functions are the same and test

the same hypotheses that would be tested if the data were balanced. Type I and Type III sums of

squares are typically not equal when the data are unbalanced; Type III sums of squares are

preferred in testing effects in unbalanced cases because they test a function of the underlying

parameters that is independent of the number of observations per treatment combination.

According to a significance level of 5% , the A*B interaction is not significant (F=0.20, p=0.6850).

This indicates that the effect of A does not depend on the level of B and vice versa. Therefore, the

tests for the individual effects are valid, showing a significant A effect (F=33.80, p=0.0101) but no

significant B effect (F=5.00, p=0.1114).

QUESTIONS ? ?

Key Concepts

Non-Parametric Tests

Kruskal - Wallis Test

Friedman Test

McNemar Test

Log - Rank Test

Parametric

These methods needs distributional

assumption from which samples are drawn.

Require a sufficiently large sample size.

Non Parametric

These methods needs no distributional assumption from which

samples are drawn i.e. to say it is Distribution Free Test.

It should be used when the sample size is small.

Introduction

Used to test the null hypothesis that two independent samples have identical

distribution functions against the alternative hypothesis that the two

distribution functions differ only with respect to mean or median i.e. to say

used to make inferences about population mean or median without requiring

the assumption of normality.

Used as an alternative to the two sample t-test when the normality

assumption is not satisfied.

Applied when the observations in a sample are ranks, that is, ordinal data

rather than direct measurements

Assumptions

Dependent variable is continuous, capable of producing measures carried out to the nth decimal

place.

Measures within the two samples have the properties of at least an ordinal scale of measurement, so

that it is meaningful to speak of "greater than," "less than," and "equal to."

Data can be ranked including tied rank values wherever appropriate. Ranks helps to focus only on the

ordinal relationships among the raw measures"greater than," "less than," and "equal to.

ANOVA), tests for location differences (options WILCOXON, MEDIAN,

SAVAGE, and VW), and performs empirical distribution function tests (option

EDF). Call is

BY variables ;

CLASS variable ;

EXACT <WILCOXON> < / computation-options > ;

FREQ variable ;

OUTPUT < OUT=SAS-data-set > < WILCOXON > ;

VAR variables ;

RUN;

Options are:

Task

Options

Description

DATA=

MISSING

Treats missing values of the CLASS variable as a

valid class level.

NOPRINT

Request analyses

WILCOXON

NPAR1WAY. If you omit the DATA= option, the

procedure uses the most recently created SAS

data set

Requests an analysis using Wilcoxon scores.

When there are two classification levels, or two

samples, this option produces the Wilcoxon ranksum test. For any number of classification levels,

this option produces the Kruskal- Wallis test.

Wilcoxon two- sample test and the SiegelTukey two-sample test

BY variables. When a BY statement appears, the procedure expects the input

data set to be sorted in order of the BY variables.

The CLASS variable identifies groups (or samples) in the data. The variable

can be character or numeric.

The FREQ statement names a numeric variable that provides a frequency for

each observation in the DATA= data set.

The VAR statement names the response or dependent variables to be analyzed. These

variables must be numeric. If the VAR statement is omitted, the procedure analyzes all

numeric variables in the data set except for the CLASS variable, the FREQ variable,

and the BY variables.

Computation-Options are:

Options

Description

ALPHA= value

specifies the level of the confidence limits for Monte Carlo p-value

estimates. The value of the ALPHA= option must be between 0 and 1,

and the default is 0.01 which produces produces 99% confidence limits

for the Monte Carlo estimates.

MAXTIME=value

specifies the maximum clock time (in seconds) that PROC NPAR1WAY

can use to compute an exact p-value. If the procedure does not complete

the computation within the specified time, the computation terminates.

MC

p-value computation. Monte Carlo estimation can be useful for large

problems that require a great amount of time and memory for exact

computations

N=n

specifies the number of samples for Monte Carlo estimation. The value of

the N= option must be a positive integer, and the default is 10,000

samples. Larger values of n produce more precise estimates of exact pvalues.

POINT

SEED=number

specifies the initial seed for random number generation for Monte Carlo

estimation. The value of the SEED= option must be an integer.

Examples

Global Evaluations of drug A & drug B in back pain: In a treatment it was found that patients

with low back pain experienced a decrease in pain after 6 to 8 weeks of daily treatment. So, a

study was conducted to determine whether this phenomenon is a drug related response or

coincidental. For this patients were asked to provide a global rating of their pain, relative to

baseline, on the following scale

Introduction

Used to compare population location parameters among two or more groups based on independent

samples.

Used to test the null hypothesis that all populations have identical distribution functions against the

alternative hypothesis that at least two of the samples differ only with respect to location .

Assumptions

Example :

Comparison of three groups of people on the basis of percent error: A study

comparing three group of people senior staff, junior staff and residents were

conducted. They were studied on daily basis and data was collected on the basis of

percent error made by them in their work.

Friedman Test

Introduction

Models the ratings of n judges (rows) on k treatments (column).

Generalization of sign test and spearman rank correlation test as it reduces to

sign test if there are two columns and reduces to spearman rank correlation

test if there are two rows.

Also called two-way analysis on ranks as is used for two=way repeated

measures analysis of variance by ranks.

Used to test null hypothesis that treatment effects have identical effects

against the alternative hypothesis that at least one treatment is different from

at least one other treatment.

Assumptions

n rows are mutually independent. (i.e. results within one row do not affect the results within other

rows)

SAS Implementation

Proc freq with cmh2 option in table statement.

Friedman Test

Syntax

BY variables ;

EXACT statistic-options < / computation-options > ;

OUTPUT < OUT=SAS-data-set > options ;

TABLES requests < / options > ;

Run;

Where

BY

calculates separate frequency or crosstabulation tables for each BY group.

EXACT requests exact tests for specified statistics.

OUTPUT

creates an output data set that contains specified statistics.

TABLES specifies frequency or crosstabulation tables and requests tests and measures of

association.

TEST requests asymptotic tests for measures of association and agreement.

WEIGHT

identifies a variable with values that weight each observation.

Friedman Test

Options

AGREE

McNemar's test for 2 2 tables, simple kappa coefficient, and weighted kappa

coefficient

BINOMIAL

binomial proportion test for one-way tables

CHISQ

chi-square goodness-of-fit test for one-way tables; Pearson chi-square, likelihoodratio chi-square, and Mantel-Haenszel chi-square tests for two-way tables

COMOR

confidence limits for the common odds ratio for h 2 2 tables; common odds ratio

test

FISHER

Fisher's exact test

JT

Jonckheere-Terpstra test

KAPPA

test for the simple kappa coefficient

LRCHI

likelihood-ratio chi-square test

MCNEM

McNemar's test

MEASURES tests for the Pearson correlation and the Spearman correlation, and the odds ratio

confidence limits for 2 2 tables

MHCHI

Mantel-Haenszel chi-square test OR confidence limits for the odds ratio for 2 2

tables

PCHI

Pearson chi-square test

PCORR

test for the Pearson correlation coefficient

SCORR

test for the Spearman correlation coefficient

TREND

Cochran-Armitage test for trend

WTKAP

test for the weighted kappa coefficient

Options

AGREE

McNemar's test for 2 2 tables, simple kappa coefficient, and weighted kappa

coefficient

BINOMIAL

binomial proportion test for one-way tables

CHISQ

chi-square goodness-of-fit test for one-way tables; Pearson chi-square, likelihoodratio chi-square, and Mantel-Haenszel chi-square tests for two-way tables

COMOR

confidence limits for the common odds ratio for h 2 2 tables; common odds ratio

test

FISHER

Fisher's exact test

JT

Jonckheere-Terpstra test

KAPPA

test for the simple kappa coefficient

LRCHI

likelihood-ratio chi-square test

MCNEM

McNemar's test

MEASURES tests for the Pearson correlation and the Spearman correlation, and the odds ratio

confidence limits for 2 2 tables

MHCHI

Mantel-Haenszel chi-square test OR confidence limits for the odds ratio for 2 2

tables

PCHI

Pearson chi-square test

PCORR

test for the Pearson correlation coefficient

SCORR

test for the Spearman correlation coefficient

TREND

Cochran-Armitage test for trend

WTKAP

test for the weighted kappa coefficient

McNemar Test

Introduction

Determine whether the row and column marginal frequencies are equal or not.

Used when dichotomous outcomes are recorded twice for each patient under different conditions

(Eg different treatments or different measurement times).

Assumptions

Data consists of paired observations of labels (A,B).

Applied to 2x2 contingency tables with a dichotomous trait with matched pairs of subjects.

Used only when the conditions for the normal approximation apply.

SAS Implementation

Output gives Chi-Square p-value (two-tailed). One tailed can be obtained by

halving it.

Example

Comparing response rates (Eg. normal & abnormal of group of patients where data

are collected for pre and post study laboratory results) when patients are treated

under a particular drug say A. (Here, we need to test whether there is a change in

the pre - to - post - treatment rates of abnormalities.)

Suppose following program has been run where aim is to compare response

rates (yes/no) of case & control.

Log-Rank Test

Introduction

Used for comparing distributions of time until the occurrence of an event (Eg death, cure, failure,

relapse etc.) of interest occur among independent groups.

Used to test the null hypothesis that there is no difference between the populations in the

probability of an event at any time point.

Used when Wilcoxon test fails. (i.e. censoring condition is not satisfied)

Most likely to detect a difference between groups when the risk of an event is consistently greater

for one group than another.

Assumptions

Survival probabilities are the same for subjects recruited early and late in the study, and the events

happened at the times specified.

SAS Implementation

Proc lifetest

Output shows Chi-Square p-value.

PROC LIFETEST < options > ;

TIME variable < *censor(list) > ;

BY variables ;

FREQ variable ;

ID variables ;

STRATA variable < (list) > < ... variable < (list) > > ;

SURVIVAL options ;

TEST variables ;

Run;

variable is the name of the failure time variable that can be optionally followed

by an asterisk, the name of the censoring variable, and a parenthetical list of

values that correspond to right censoring. The censoring values should be

numeric, non missing values.

in groups defined by the BY variables.

The variable in the FREQ statement identifies a variable containing the frequency

of occurrence of each observation.

The ID variable values are used to label the observations of the product-limit

survival function estimates.

The STRATA statement indicates which variables determine strata levels for

the computations. The strata are formed according to the nonmissing values of

the designated strata variables.

Options available with STRATA statement

MISSING

used to allow missing values as a valid stratum level.

GROUP=variable specifies the variable whose formatted values identify the various

samples whose underlying survival curves are to be compared.

NODETAIL

suppresses the display of the rank statistics and the corresponding

covariance matrices for various strata.

NOTEST

suppresses the k-sample tests, stratified tests, and trend tests

TREND

computes the trend tests for testing the null hypothesis that the

k

population hazards rate are the same versus an ordered alternatives

TEST=(list)

enables you to select the weight functions for the k-sample tests,

stratified tests, or trend tests. You can specify a list containing one

or more of the following keywords

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