ANOVA example

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ANOVA example

© All Rights Reserved

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Mean , Variance 2, Proportion

Means, Variances, Proportions

1 vs. 2 12 vs. 22 1 vs. 2

Means, Variances, Proportions

1, , k 12, , k2 1, , k

CHAPTER 6

Statistical Inference & Hypothesis Testing

Mean , Variance 2, Proportion

Means, Variances, Proportions

1 vs. 2 12 vs. 22 1 vs. 2

Means, Variances, Proportions

1, , k 12, , k2 1, , k

Example: Y = $ Cost of a certain medical service

Assume Y is known to be normally distributed at each of k = 2 health care facilities (groups).

Hospital: Y1 ~ N(1, 1) Clinic: Y2 ~ N(2, 2)

Null Hypothesis H0: 1 = 2,

i.e., 1 2 = 0

(No difference exists.")

2-sided test at significance level = .05

Data: Sample 1 = {667, 653, 614, 612, 604}; n1 = 5 Sample 2 = {593, 525, 520}; n2 = 3

Analysis via T-test (if equivariance holds): Point estimates y = yi / n

NOTE:

Group Means y1 =

667 + 653 + 614 + 612 + 604

5 = 630 y2 = 593 + 525 + 520

3 = 546 y1 - y2 = 84 >0

Group 630)) 2 +K + (604 - 630 )2

(667 - 630 (593 - 546 2

+K + (520 - 546 2

= 1663 F =

= 2.11 < 4

Variances s1 =

2

5 -1 = 788.5 s2 2 = 546))

3-1

546)) 1663

788.5

2 2

Pooled 2

spooled = (5( n1--1)(1)n788.5

s1 + ()n+2 -(3

1)-s1)(

2 1663 )

= 1080 The pooled variance is a weighted average of the group

Variance 1 + n52+-32- 2 variances, using the degrees of freedom as the weights.

Example: Y = $ Cost of a certain medical service

Assume Y is known to be normally distributed at each of k = 2 health care facilities (groups).

Hospital: Y1 ~ N(1, 1) Clinic: Y2 ~ N(2, 2)

Null Hypothesis H0: 1 = 2,

i.e., 1 2 = 0

(No difference exists.")

2-sided test at significance level = .05

Data: Sample 1 = {667, 653, 614, 612, 604}; n1 = 5 Sample 2 = {593, 525, 520}; n2 = 3

Analysis via T-test (if equivariance holds): Point estimates y = yi / n

NOTE:

Group Means y1 =

667 + 653 + 614 + 612 + 604

5 = 630 y2 = 593 + 525 + 520

3 = 546 y1 - y2 = 84 >0

Group 630)) 2 +K + (604 - 630 )2

(667 - 630 (593 - 546 22

46 ) 22

+K + (520 - 5546)

Variances s1 =

2

5 -1 = 788.5 s2 2 = 546))

3-1 = 1663 F = 1663

788.5 = 2.11 < 4

s2 = SS/df SSErr = 6480

2 2

Pooled 2

spooled = (5( n1--1)(1)n788.

s1 +5()n+2 -(3

1)-s1)(

2 1663 )

= 1080 The pooled variance is a weighted average of the group

Variance 1 + n52+-32- 2 variances, using the degrees of freedom as the weights.

dfErr = 6

p-value ==2 P (Y1 - Y2 84) = 2 P ( T6 24 ) = 2 P T6 3.5

p-value 84 - 0

( )

Standard 11 1 1 > 2 * (1 - pt(3.5, 6)) Reject H0 at = .05

Error s.e.0 = s 2

1080 ++ = 24

pooled [1] 0.01282634 stat signif, Hosp > Clinic

5n1 3n2

R code:

> y1 = c(667, 653, 614, 612, 604)

> y2 = c(593, 525, 520)

>

> t.test(y1, y2, var.equal = T)

Formal Conclusion

Two Sample t-test

p-value < = .05

data: y1 and y2 Reject H0 at this level.

t = 3.5, df = 6, p-value = 0.01283

alternative hypothesis: true difference in means is not equal to 0

95 percent confidence interval:

25.27412 142.72588

sample estimates: Interpretation

mean of x mean of y

630 546 The samples provide evidence that the

difference between mean costs is (moderately)

statistically significant, at the 5% level, with

the hospital being higher than the clinic (by an

average of $84).

Alternate method ~

Main Idea: Among several (k 2) independent, equivariant,

normally-distributed treatment groups

Total Variability = Variability between groups + Variability within groups

Y1 Y2 Yk

kk

L

1

1 2

2

Null

H:

sis?

0

m1 = m2 = K = mk

pot he

Hy HA: At least one treatment mean i is

significantly different from the others.

Example: Y = $ Cost of a certain medical service

Assume Y is known to be normally distributed at each of k = 2 health care facilities (groups).

Hospital: Y1 ~ N(1, 1) Clinic: Y2 ~ N(2, 2)

Null Hypothesis H0: 1 = 2,

i.e., 1 2 = 0

(No difference exists.")

2-sided test at significance level = .05

Data: Sample 1 = {667, 653, 614, 612, 604}; n1 = 5 Sample 2 = {593, 525, 520}; n2 = 3

ANOVA F-test (if equivariance holds): Point estimates y = yi / n

NOTE:

Group Means y1 =

667 + 653 + 614 + 612 + 604

5 = 630 y2 = 593 + 525 + 520

3 = 546 y1 - y2 = 84 >0

5 (630) 3 (546)

Grand Mean

667 + 653 + 614 + 612 + 604 + 593 + 525 + 520

y= = 598.50

5+3

means, using the sample sizes as the weights.

Alternate method ~

Main Idea: Among several (k 2) independent, equivariant,

normally-distributed treatment groups

Total Variability = Variability between groups + Variability within groups

Y1 Y2 Yk

kk

L

1

1 2

2

H0: m1 = m2 = K = mk

significantly different from the others.

Example: Y = $ Cost of a certain medical service

Assume Y is known to be normally distributed at each of k = 2 health care facilities (groups).

Hospital: Y1 ~ N(1, 1) Clinic: Y2 ~ N(2, 2)

Null Hypothesis H0: 1 = 2,

i.e., 1 2 = 0

(No difference exists.")

2-sided test at significance level = .05

Data: Sample 1 = {667, 653, 614, 612, 604}; n1 = 5 Sample 2 = {593, 525, 520}; n2 = 3

ANOVA F-test (if equivariance holds): Point estimates y = yi / n

667 + 653 + 614 + 612 + 604 593 + 525 + 520

Group Means y1 = 5 = 630 y2 = 3 = 546

5(630) + 3(546)

Grand Mean y= = 598.50

5+3

Example: Y = $ Cost of a certain medical service

Assume Y is known to be normally distributed at each of k = 2 health care facilities (groups).

Hospital: Y1 ~ N(1, 1) Clinic: Y2 ~ N(2, 2)

Null Hypothesis H0: 1 = 2,

i.e., 1 2 = 0

(No difference exists.")

2-sided test at significance level = .05

Data: Sample 1 = {667, 653, 614, 612, 604}; n1 = 5 Sample 2 = {593, 525, 520}; n2 = 3

ANOVA F-test (if equivariance holds): Point estimates y = yi / n

667 + 653 + 614 + 612 + 604 593 + 525 + 520

Group Means y1 = 5 = 630 y2 = 3 = 546

5(630) + 3(546)

Grand Mean y= = 598.50

5+3

SSTot = (667 - 598.5) + (653 - 598.5) + (614 - 598.5) + (612 - 598.5) + (604 - 598.5)

2 2 2 2 2

Alternate method ~

Main Idea: Among several (k 2) independent, equivariant,

normally-distributed treatment groups

Total Variability = Variability between groups + Variability within groups

Y1 Y2 Yk

kk

L

1

1 2

2

H0: m1 = m2 = K = mk

How can we measure this? Imagine zero variability within groups

Alternate method ~

Main Idea: Among several (k 2) independent, equivariant,

normally-distributed treatment groups

Total Variability = Variability between groups + Variability within groups

Y1 Y2 Yk

kk

L

1

1 2

2

H0: m1 = m2 = K = mk

How can we measure this? Imagine zero variability within groups

Example: Y = $ Cost of a certain medical service

Assume Y is known to be normally distributed at each of k = 2 health care facilities (groups).

Hospital: Y1 ~ N(1, 1) Clinic: Y2 ~ N(2, 2)

Null Hypothesis H0: 1 = 2,

i.e., 1 2 = 0

(No difference exists.")

2-sided test at significance level = .05

653, 614,

630, 612,

630, 604}; n1 = 5

630, Sample 2 = {593,

{546, 525,

546, 520};

546} n2 = 3

ANOVA F-test (if equivariance630 }

holds): Point estimates y = yi / n

667 + 653 + 614 + 612 + 604 593 + 525 + 520

Group Means y1 = 5 = 630 y2 = 3 = 546

5(630) + 3(546)

Grand Mean y= = 598.50

5+3

SSTot = (667 - 598.5) + (653 - 598.5) + (614 - 598.5) + (612 - 598.5) + (604 - 598.5)

2 2 2 2 2

SSTrt = 5 (630 - 598.5) 2 + 3 (546 - 598.5) 2 = 13230 dfTrt = (2) 1 =1

The

Alternate method ~

Main Idea: Among several (k 2) independent, equivariant,

normally-distributed treatment groups

Total Variability = Variability between groups + Variability within groups

Y1 Y2 Yk

kk

L

1

1 2

2

H0: m1 = m2 = K = mk

Example: Y = $ Cost of a certain medical service

Assume Y is known to be normally distributed at each of k = 2 health care facilities (groups).

Hospital: Y1 ~ N(1, 1) Clinic: Y2 ~ N(2, 2)

Null Hypothesis H0: 1 = 2,

i.e., 1 2 = 0

(No difference exists.")

2-sided test at significance level = .05

Data: Sample 1 = {667, 653, 614, 612, 604}; n1 = 5 Sample 2 = {593, 525, 520}; n2 = 3

ANOVA F-test (if equivariance holds): Point estimates y = yi / n

667 + 653 + 614 + 612 + 604 593 + 525 + 520

Group Means y1 = 5 = 630 y2 = 3 = 546

5(630) + 3(546)

Grand Mean y= = 598.50

5+3

SSTot = (667 - 598.5) + (653 - 598.5) + (614 - 598.5) + (612 - 598.5) + (604 - 598.5)

2 2 2 2 2

SSTrt = 5 (630 - 598.5) 2 + 3 (546 - 598.5) 2 = 13230 dfTrt = (2) 1 =1

Example: Y = $ Cost of a certain medical service

Assume Y is known to be normally distributed at each of k = 2 health care facilities (groups).

Hospital: Y1 ~ N(1, 1) Clinic: Y2 ~ N(2, 2)

Null Hypothesis H0: 1 = 2,

i.e., 1 2 = 0

(No difference exists.")

2-sided test at significance level = .05

Data: Sample 1 = {667, 653, 614, 612, 604}; n1 = 5 Sample 2 = {593, 525, 520}; n2 = 3

ANOVA F-test (if equivariance holds): Point estimates y = yi / n

667 + 653 + 614 + 612 + 604 593 + 525 + 520

Group Means y1 = 5 = 630 y2 = 3 = 546

5(630) + 3(546)

Grand Mean y= = 598.50

5+3

SSTot = (667 - 598.5) + (653 - 598.5) + (614 - 598.5) + (612 - 598.5) + (604 - 598.5)

2 2 2 2 2

SSTrt = 5 (630 - 598.5) 2 + 3 (546 - 598.5) 2 = 13230 dfTrt = (2) 1 =1

SSErr = (667 - 630) + (653 - 630) + (614 - 630) + (612 - 630) + (604 - 630)

2 2 2 2 2

Example: Y = $ Cost of a certain medical service

Assume Y is known to be normally distributed at each of k = 2 health care facilities (groups).

Hospital: Y1 ~ N(1, 1) Clinic: Y2 ~ N(2, 2)

Null Hypothesis H0: 1 = 2,

i.e., 1 2 = 0

(No difference exists.")

2-sided test at significance level = .05

Data: Sample 1 = {667, 653, 614, 612, 604}; n1 = 5 Sample 2 = {593, 525, 520}; n2 = 3

Analysis via T-test (if equivariance holds): Point estimates y = yi / n

NOTE:

Group Means y1 =

667 + 653 + 614 + 612 + 604

5 = 630 y2 = 593 + 525 + 520

3 = 546 y1 - y2 = 84 >0

Group 630)) 2 +K + (604

(667 - 630 (604 - 630 )2 (593 - 546 22

46 ) 22

+K + (520 - 5546)

Variances s1 =

2

5 -1 = 788.5 s2 2 = 546))

3-1 = 1663 F = 1663

788.5 = 2.11 < 4

s2 = SS/df SS1 SS2

2 2

Pooled 2

spooled = (5( n1--1)(1)n788.5

s1 + ()n+2 -(3

1)-s1)(

2 1663 )

= 1080 The pooled variance is a weighted average of the group

Variance 1 + n52+-32- 2 variances, using the degrees of freedom as the weights.

LL

RECA

Example: Y = $ Cost of a certain medical service

Assume Y is known to be normally distributed at each of k = 2 health care facilities (groups).

Hospital: Y1 ~ N(1, 1) Clinic: Y2 ~ N(2, 2)

Null Hypothesis H0: 1 = 2,

i.e., 1 2 = 0

(No difference exists.")

2-sided test at significance level = .05

Data: Sample 1 = {667, 653, 614, 612, 604}; n1 = 5 Sample 2 = {593, 525, 520}; n2 = 3

Analysis via T-test (if equivariance holds): Point estimates y = yi / n

NOTE:

Group Means y1 =

667 + 653 + 614 + 612 + 604

5 = 630 y2 = 593 + 525 + 520

3 = 546 y1 - y2 = 84 >0

Group 630)) 2 +K + (604

(667 - 630 (604 - 630 )2 (593 - 546 22

46 ) 22

+K + (520 - 5546)

Variances s1 =

2

5 -1 = 788.5 s2 2 = 546))

3-1 = 1663 F = 1663

788.5 = 2.11 < 4

s2 = SS/df SSErr = 6480

2 2

Pooled 2

spooled = (5( n1--1)(1)n788.5

s1 + ()n+2 -(3

1)-s1)(

2 1663 )

= 1080 The pooled variance is a weighted average of the group

Variance 1 + n52+-32- 2 variances, using the degrees of freedom as the weights.

dfErr = 6

LL

RECA

Example: Y = $ Cost of a certain medical service

Assume Y is known to be normally distributed at each of k = 2 health care facilities (groups).

Hospital: Y1 ~ N(1, 1) Clinic: Y2 ~ N(2, 2)

Null Hypothesis H0: 1 = 2,

i.e., 1 2 = 0

(No difference exists.")

2-sided test at significance level = .05

ANOVA F-test (if equivariance holds): Point estimates y = yi / n

667 + 653 + 614 + 612 + 604 593 + 525 + 520

Group Means y1 = 5 = 630 y2 = 3 = 546

5(630) + 3(546)

Grand Mean y= = 598.50

5+3

SSTot = (667 - 598.5) + (653 - 598.5) + (614 - 598.5) + (612 - 598.5) + (604 - 598.5)

2 2 2 2 2

SSTrt = 5 (630 - 598.5) 2 + 3 (546 - 598.5) 2 = 13230 dfTrt = (2) 1 =1

SSErr = (667 - 630) + (653 - 630) + (614 - 630) + (612 - 630) + (604 - 630)

2 2 2 2 2

Example: Y = $ Cost of a certain medical service

Assume Y is known to be normally distributed at each of k = 2 health care facilities (groups).

Hospital: Y1 ~ N(1, 1) Clinic: Y2 ~ N(2, 2)

Null Hypothesis H0: 1 = 2,

i.e., 1 2 = 0

(No difference exists.")

2-sided test at significance level = .05

ANOVA F-test (if equivariance holds): Point estimates y = yi / n

667 + 653 + 614 + 612 + 604 593 + 525 + 520

Group Means y1 = 5 = 630 y2 = 3 = 546

5(630) + 3(546)

Grand Mean y= = 598.50

5+3

SSTot = (667 - 598.5) + (653 - 598.5) + (614 - 598.5) + (612 - 598.5) + (604 - 598.5)

2 2 2 2 2

SSTrt = 5 (630 - 598.5) 2 + 3 (546 - 598.5) 2 = 13230 dfTrt = (2) 1 =1

SSTot = SSTrt + SSErr dfTot = dfTrt + dfErr

SSTot = SSTrt + SSErr dfTot = dfTrt + dfErr

Tot

Err

Trt

SS MSTrt

MS = F=

ANOVA Table df MSErr

( between )

= s 2

(=s 2

within )

Total 7 19710 Note:

2

This is also spooled .

SSTot = SSTrt + SSErr dfTot = dfTrt + dfErr

SSTot = SSTrt + SSErr dfTot = dfTrt + dfErr

Tot

Err

Trt

SS MSTrt

MS = F=

ANOVA Table df MSErr

( between )

= s 2

12.25 ????

Error 6 6480 1080

(=s 2

within )

Total 7 19710 Note:

2

This is also spooled .

H0: = 2

1

2 2

H A : 12 2 2

SS1 2 SS 2

s =

2

1 s2 =

df1 df 2

Test Statistic

s12

F= 2

s2

Sampling Distribution =?

SSTot = SSTrt + SSErr dfTot = dfTrt + dfErr

Tot

Err

Trt

SS MSTrt

MS = F=

ANOVA Table F1,6 df MSErr

( between )

= s 2

12.25

p-value

Error 6 6480 1080

(=s 2

within )

Total 7 19710 Note: |

2

This is also spooled . 12.25

5.99

SSTot = SSTrt + SSErr dfTot = dfTrt + dfErr

Tot

Err

Trt

SS MSTrt

MS = F=

ANOVA Table F1,6 df MSErr

( between )

= s 2

12.25

p-value

Error 6 6480 1080

(=s 2

within ) = .05

Total 7 19710 |

Note: |

2

5.99 This is also spooled . 12.25

SSTot = SSTrt + SSErr dfTot = dfTrt + dfErr

Tot

Err

Trt

SS MSTrt

MS = F=

ANOVA Table df MSErr

( between )

= s 2

12.25 p < .05

(on F1, 6 )

Error 6 6480 1080

(=s 2

within )

Total 7 19710 Note:

2

This is also spooled .

SSTot = SSTrt + SSErr dfTot = dfTrt + dfErr

Tot

Err

Trt

SS MSTrt

MS = F=

ANOVA Table df MSErr

( between )

= s 2

12.25 .01282634

(on F1, 6 )

Error 6 6480 1080

(=s 2

within )

Total 7 19710 Note:

2

This is also spooled .

SSTot = SSTrt + SSErr dfTot = dfTrt + dfErr

Tot

Err

Trt

SS MSTrt

MS = F=

ANOVA Table df MSErr

( between )

= s 2

12.25 .01282634

(on F1, 6 )

Error 6 6480 1080

(=s 2

within )

Total 7 19710

13230

Thus, the treatment accounts for 19710 = 67.1% of the total variability in the response Y.

R code:

# ANOVA FOR UNBALANCED DESIGN

> y1 = c(667, 653, 614, 612, 604)

> y2 = c(593, 525, 520)

>

> Data = data.frame(

+ Y = c(y1, y2),

+ X = factor(rep(c("y1", "y2"), times = c(length(y1),

length(y2))))

+ )

>

> var.test(Y ~ X, data = Data) # EQUIVARIANCE?

data: Y by X

F = 0.4741, num df = 4, denom df = 2,

p-value = 0.4738

alternative hypothesis: true ratio of variances is not equal to 1

95 percent confidence interval:

0.01208057 5.04920249

sample estimates:

ratio of variances

0.4741431

R code:

# ANOVA FOR UNBALANCED DESIGN

> anova(out)

Response: Y

Df Sum Sq Mean Sq F value Pr(>F)

X 1 13230 13230 12.25 0.01283 *

Residuals 6 6480 1080

---

Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1

p-value is the same using either method (.01283), since the sample is unchanged!

The square of the Tdf -score (3.5) is equal to the F1, df -score (12.25).

c 2

(Recall that the square of the Z-score is equal to the 1 -score.)

X1 X2 Xk

X1 X2 Xk

Suppose this ANOVA overall F-test

indicates that a significant difference

exists between one (or more) of the

treatment means, at = .05.

Y1 Y2 Yk

1

etc k

k

1 2

2

H0: m1 = m2 = K = mk

Idea: Test all possible pairwise comparisons, each via a two-sample t-test.

Example : Suppose there are k = 5 treatment groups.

(1, 2) (1, 3) (1, 4) (1, 5) (2, 3) (2, 4) (2, 5) (3, 4) (3,5) (4,5)

p = ... p = ... p = ... p = ... p = ... p = ... p = ... p = ... p = ... p = ...

5

There are = 10 such comparisons. PROBLEM???

2

SPURIOUSY1 Y2 Yk

SIGNIFICANCE!!!

1

etc k

k

1 2

2

H0: m1 = m2 = Ke = mk

p-valu

Idea: Test all possible pairwise comparisons, each via a two-sample t-test.

Example

= .05 : Suppose there are k = 5 treatment groups.

(1, 2) (1, 3) (1, 4) (1, 5) (2, 3) (2, 4) (2, 5) (3, 4) (3,5) (4,5)

p = ... p = ... p = ... p = ... p = ... p = ... p = ... p = ... p = ... p = ...

5

There are = 10 such comparisons. PROBLEM???

2

* = .05/10

Y1 Y2 Yk

1

etc k

k

1 2

2

H0: m1 = m2 = K = mk

Idea: Test all possible pairwise comparisons, each via a two-sample t-test.

Example : Suppose there are k = 5 treatment groups.

(1, 2) (1, 3) (1, 4) (1, 5) (2, 3) (2, 4) (2, 5) (3, 4) (3,5) (4,5)

p = ... p = ... p = ... p = ... p = ... p = ... p = ... p = ... p = ... p = ...

5

There are = 10 such comparisons. PROBLEM???

2

Make each comparison at level * = / 10.

Y1 Y2 Yk

1

etc k

k

1 2

2

H0: m1 = m2 = K = mk

Idea: Test all possible pairwise comparisons, each via a two-sample t-test.

Example : Suppose there are k = 5 treatment groups.

p = ... p = ... p = ... p = ... p = ... p = ... p = ... p = ... p = ... p = ...

5

There are = 10 such comparisons.

2

BONFERRONI

Make each comparison at level * = / 10. CORRECTION

Alternate method ~

Main Idea: Among several (k 2) independent, equivariant,

normally-distributed treatment groups

NS?

PTI O

SSU M

EL A

MOD

Y1 Y2 Yk

1

L kk

1 2

2

H0: m1 = m2 = K = mk

Alternate method ~

Main Idea: Among several (k 2) independent, equivariant,

normally-distributed treatment groups

6.2.2 (but this is very sensitive to normality assumption), or others.

If violated, can extend Welch Test for two means.

Y1 Y2 Yk

1

L kk

1 2

2

H0: m1 = m2 = K = mk

Alternate method ~

Main Idea: Among several (k 2) independent, equivariant,

normally-distributed treatment groups

If violated, use nonparametric Kruskal-Wallis Test.

Y1 Y2 Yk

1

L kk

1 2

2

H0: m1 = m2 = K = mk

Alternate method ~

Main Idea: Among several (k 2) independent, equivariant,

normally-distributed treatment groups

repeated measures, multiple factor levels within groups, etc.

Y1 Y2 Yk

1

L kk

1 2

2

H0: m1 = m2 = K = mk

Alternate method ~

Main Idea: Among several (k 2) independent, equivariant,

normally-distributed treatment groups

How to identify significant group(s)? Pairwise testing, with correction

(e.g., Bonferroni) for spurious significance.

Example: k = 5 groups result in 10 such tests, so let each * = / 10.

Y1 Y2 Yk

1

L kk

1 2

2

H0: m1 = m2 = K = mk

ssppuurrio

iou

ssiiggnniiffic uss

icaannccee

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