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and Hypothesis Testing (II)

bheavlin@stat.stanford.edu

Statistics

Way Too

No Data Some Data Much Data

Inferential Descriptive

Probability Statistics Statistics

distributions testing

topics

• comparing proportions

• paired vs two-sample (again)

• sample size calculations

• hypothesis testing

• power transformations

• the other two-sample test

• the k-sample problem

even odd

column column total

yields 40 28 68

no yield 60 72 132

total 100 100 00

have different test heads

Three measures

2. risk reduction 40/100 – 28/100 = 0.12

3. relative risk (72/100)/(60/100)= 1.20

4. odds ratio (40/60)/(28/72) = 1.71

Stat 110 bheavlin@stat.stanford.edu

Terms for Comparing Two Probabilities

Risk reduction:

• Rate1 – Rate2 (good≡bad)

Relative risk:

• Rate1 / Rate2 (bad, usually)

Odds:

• Rate / (1– Rate) (good≡bad)

Odds ratio:

• ratio of two odds (good≡bad)

• [Rate1/(1– Rate1)]/[Rate2/(1– Rate2)]

Stat 110 bheavlin@stat.stanford.edu

… comparing probabilities

Index Pluses Minuses

Risk •simplest •awkward to model

reduction •aids cost-benefit analyses •additive model less

physical

(delta) •smaller sample sizes

•… extrapolation {A} and Pr{not A}

•requires prospective data

•larger sample sizes

•can use with retrospective risk

datasets, rare events •harder to explain

•simple formula for std err

… comparing New Old

#fail a b

probabilities #pass c d

total nN nO

Which Index Estimate Standard Error2

Risk pN – pO pN (1–pN)/nN + pO(1–pO)/nO

Reduction

Risk

Loge Odds Loge( ad / cd ) = pN (1–pO) 1/a + 1/b + 1/c + 1/d

Ratio (1–pN ) pO

Example confidence intervals

estimate error limit limit

risk reduction 0.12 0.066 -0.129 0.253

(log RR) 0.182 0.103 -0.023 0.388

(log OR) 0.539 0.302 -0.065 .14

odds ratios and “recommend indices”

notation:

attrition

Pr{“Y”(0)} = this year's RI = 1–Pr{“N”(0)”} “yes”

Pr{“Y”(-1)} = last year's RI = 1–Pr{“N”(-1)”}

Pr{“Y”(0)|“Y”(-1)}

= this year's retention rate

Pr{“Y”(0)|“N”(-1)} re-enlistment “no”

= this year's re-enlistment rate

Pr{“N”(0)|“Y”(-1)}

= this year's de-enlistment rate

= 1–Pr{“Y”(0)|“Y”(-1)} = 1-retention rate equilibrium RI/(1-RI)

Pr{“Y”(0)|“N”(-1)}

conversion rates Pr{“N”(0)|“Y”(-1)}

Pr{“Y”(0)|“N”(-1)} and Pr{“N”(0)|“Y”(-1)}

Stat 110 bheavlin@stat.stanford.edu

Schredder-Schredder chess match

Intel=L Intel=W

AMD=W Draw AMD=L

AMD white 16 44 11 Intel black

AMD black 11 40 19 ntel white

AMD white odds = 16:11 AMD vs Intel effects, ignores

AMD black odds = 11:19 any sample size imbalances.

= Intel white odds vs

AMD odds = 27:30 log(AMD white odds)+

log(Intel white odds),

White odds = 35:22

which implicitly does so adjust

Stat 110 bheavlin@stat.stanford.edu

confidence intervals for odds

White odds = 35:22 = 1.59 AMD white odds ×

ln(35/22)= 0.464 Intel white odds

1/35=0.0286 1/22=0.0455 = (16/11) ×(19/11)

s.e.=[0.0286+0.0455]1/2 Log odds “ratio”=0.921

=0.272 s.e.=[1/16+1/11+1/19+1/11]1/2

0.464 ± 2×0.272 =[0.297]1/2 = 0.5449

=(–0.080,1.008) log-odds 0.921 ±2×0.5449

(0.923,2.741) as odds =(–0.169,1.089) as log odds

OR (0.845,2.97) as odds

sample sizes from confidence intervals

• any difference in yield?

• standard error for the difference in means

= σd(n) = σ(1/no + 1/n+)1/2

= σ(2/n)1/2, where no=n+= n.

• with approx 95% confidence interval

d ± 2σd(n)

Stat 110 bheavlin@stat.stanford.edu

sample sizes (solution)

solve for n:

Δ = (d+2σd(n))–(d–2σd(n)) = 4σd(n) = 4×σ(2/n)1/2 or

Δ2 = 16×σ2×(2/n) = 32σ2/n

n = 32σ2/Δ2

e.g. Δ= σ, n = 32 per group

sample sizes (one-sample version)

When: process monitoring, paired data

Suppose we know σd.

• standard error for the mean difference = σd / n1/2

• with approx 95% confidence interval d ± 2σd / n1/2

• Δ = (d+2σd /√n )–(d–2σd/√n) = 4σd/√n or

• n = 16σd2/Δ2

e.g. Δ= 2σd, n = 16σ2/(2σ)2= 4 pairs

e.g.

Stat 110

Δ= σd, n = 16σ /σ

2 2

=16 pairs

bheavlin@stat.stanford.edu

The price of two-sample testing

problem requires twice the number of

observations. This is because the value of its

control group is random.

2. In addition, the cost of a pair is usually less that

of two unrelated observations.

3. Finally, when pairing is feasible, it is reasonable

for σd < σx . When pairing is at random, σd = σx√2,

and the one-sample test is burdened by the loss

of degrees of freedom.

Stat 110 bheavlin@stat.stanford.edu

Hypothesis testing

parameter is “uninteresting, unremarkable,

default, null=zero.”

2. alternative hypothesis which is implicitly

accepted if the null hypothesis is rejected. The

alternative hypothesis is usually not unique.

3. test statistic computed from observed sample.

4. rejection region which defines values of the test

statistic that would reject the null hypothesis.

e.g. one-sample mean, σ known

Null hypothesis Ho : Δ=0.

Alternative HΔ : Δ=ΔA.

Test statistic z = d / (σ/n1/2) = d×n1/2/σ

Rejection region: z > 1.645

0.4

0.3

0.2

0.1

-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6

standard normal z

Stat 110 bheavlin@stat.stanford.edu

…p-value version

Null hypothesis Ho : Δ=0.

Alternative HΔ : Δ=ΔA.

Test statistic z = d / (σ/n1/2) = d × n1/2/σ

One-sided p-value:

0.4

0.2

= P( d /(σ/n )> zpv |Δ=0)

1/2

0.1

= 1– Φ(d /(σ/n1/2)) 0

-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6

=StatΦ(–d×n

110

1/2

/σ) standard normal z

bheavlin@stat.stanford.edu

…two-tailed p-value

Null hypothesis Ho : Δ=0.

Alternative HΔ : Δ=ΔA.

Test statistic z = d / (σ/n1/2) = d × n1/2/σ

Two-sided p-value:

p2-value = P(|zobs| > zpv | Ho ) 0.4

=1–[Φ(|d|/(σ/n1/2))–Φ(-|d|/(σ/n1/2))] 0.2

= 2×Φ(-|d|×n1/2/σ) 0.1

= 2×p1-value 0

-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6

standard normal z

Stat 110 bheavlin@stat.stanford.edu

one-sample mean, σ unknown, p-value

Null hypothesis Ho : Δ=0.

Alternative HΔ : Δ=ΔA.

Test statistic t = d / (s/n1/2) = d × n1/2/s

Rejection region: |t| > tdf=n-1 (α/2)

0.4

0.3

Two-sided p-value:

0.2

p2-value = P(|tobs|>tpv |Ho )

0.1

= P( |d|/(s/n1/2)> tpv|Δ=0) 0

= 2×T(–|d|×n1/2/s, df=n-1) -6 -5 -4 -3 -2 -1 0

t(df=4)

1 2 3 4 5 6

Example: overetch yield experiment

1 clearout 01-12 75 68 7

2 clearout 01-12 45 61 -16

3 clearout 01-12 81 79 2

4 clearout 01-12 78 87 -9

5 clearout 01-12 57 77 20

mean = –7.20 t = d √n / s

stdev = 11.52 = –7.2×√5 / 11.52 = –1.40

t(df=4,0.975)=2.776 p-value = 0.117

Stat 110 bheavlin@stat.stanford.edu

Wafer position sequence effects

120

How to adjust

for this effect 100

in the 1st 12

80

vs 2nd 12 split

experiment? 60

zig-zag

even-vs-odd

40 early effect

wafer

20

effect

0

0 5 10 15 20 25

wafer processing sequence

Stat 110 bheavlin@stat.stanford.edu

20 concurrent unsplit lots

lot split 01-12 13-24 lot split 01-12 13-24

6 no splits 62.5 58.8 17 no splits 66.7 72.9

7 no splits 50.5 30.6 18 no splits 75.4 68.6

8 no splits 72.5 71.6 19 no splits 78.3 81.4

9 no splits 86.0 73.8 20 no splits 75.5 77.8

10 no splits 68.6 59.3 21 no splits 84.0 73.6

11 no splits 76.6 78.2 22 no splits 79.6 78.5

12 no splits 55.6 44.3 23 no splits 77.9 74.7

13 no splits 64.6 71.3 24 no splits 64.8 61.7

14 no splits 73.5 77.5 25 no splits 69.6 70.2

15 no splits 81.3 77.7 26 no splits 70.7 71.4

16 no splits 66.0 3.1

Stat 110 bheavlin@stat.stanford.edu

Adjusting for the wafer position bias

delta

-30 -20 -10 0 10 20

clearout

df 24

no splits

pooled stdev .96

t = –10.69 / [7.96×(1/5+1/24)1/2]

= –2.70 with df=24

two-sided p-value = 0.0126

Stat 110 bheavlin@stat.stanford.edu

Two errors

Type I error is the probability that, given the null

hypothesis is true, of the statistical procedure

rejecting the null hypothesis.

probability that, given the truly truly

alternative hypothesis is delta=0 delta≠0

true, of not rejecting the we say 1–α β=

null hypothesis. Type II "delta=0” type II

error is a strong function

of the particular we say α= 1–β =

alternative. "delta≠0” type I power

Stat 110 bheavlin@stat.stanford.edu

IF … THEN power(Δ)

1.0

0.9

0.8

0.7

0.6

0.4

0.3

the probability of a 0.2

0.0

-1 0 1 2 3

the probability of a

significant result = 1–β(ΔA)

one-sample mean…

power(ΔA)

1.0

0.9

Null Ho : Δ=0. Alt HΔ : Δ=ΔA. 0.8

0.7

statistic z = d /(σ/n ) = d×n

1/2 1/2

/σ 0.6

0.5

0.3

0.2

P( z > 1.645 | Δ=0 ) = α = 0.05 0.1

0.0

-1 0 1 2 3

power(ΔA) = 1–β

ΔA

= P( z > zα | Δ=ΔA ) = P( d×n /σ > zα |Δ=ΔA)

1/2

= P((d – ΔA )×n1/2/σ + ΔAn1/2/σ > zα | Δ= ΔA)

= P( z + ΔAn1/2/σ > zα )=P( z > zα–ΔAn1/2/σ )

= Φ( –zα + ΔAn1/2/σ )

Stat 110 bheavlin@stat.stanford.edu

connection to hypothesis tests:

• When the confidence interval contains zero, then

the conventional null hypothesis that the

population parameter is zero cannot be rejected

(at the given confidence level=1–significance).

• Confidence intervals consist of those null

hypotheses that cannot be rejected (at the given

confidence level=1–significance).

• Confidence intervals have sufficient information

to determine whether the null hypothesis is to be

rejected.

one-sample mean…

0.4

0.3 Δ=0 zα

power(ΔA) = 1– β 0.2

0.1

= P( z >zα–ΔA×n /σ )

1/2

0

so 0.4

0.3

Δ√n/σ =1

z1–β = zα – ΔA×n1/2/σ or 0.2

0.1

–zβ = zα – ΔA×n1/2/σ or 0

0.4

ΔA×n /σ = zα + zβ

1/2

or 0.3 Δ√n/σ =2

0.2

n 1/2

= ( zα + zβ ) ×σ / ΔA 0.1

0

n = ( zα + zβ )2×σ2/ ΔA2

-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6

Two sample version:

Guenther’s refinement:

2

n = 2[zα/2 + zβ]2 σ2/(μ1─μ0)2 + zα/2/4

Comparison of Sample Size Calculations

(Two-Sample Problem)

power=0.5 power=0.9

non- non-

alpha Δ/σ n* Guenther central n* Guenther central

0.05 0.25 122.93 123.89 123.88 336.24 337.2 337.2

0.05 0.5 30.73 31.69 31.71 84.06 85.02 85.03

0.05 0.75 13.66 14.62 14.67 37.06 38.32 38.34

0.05 1 7.68 8.64 8.73 21.01 21.98 22.02

0.05 1.25 4.92 5.88 6.02 13.45 14.41 14.48

0.05 1.5 3.41 4.37 4.57 9.34 10.3 10.4

0.05 1.75 1.92 2.88 3.17 5.25 6.21 .39

Examples:

Yield: standard process 100 dpw

“new” process 110 dpw?

Δ=new-std 10 dpw

σ 25 dpw

“new” process 35, 40

Δ =new-std 5, 10

σ 6

Corporation Named

paired data

of Interest Competitor count

(binary): yeasayers => Yes Yes 798

Yes No 406

No Yes 95

naysayers => No No 220

total 519

We proceed conditionally: CoI vs NC odds = 406:95 = 4.27

Log odds 95% CI = 1.45 ± 2×0.114=(1.22,1.68)

Odds 95% CI = (3.40,5.36);

95 % CI Yes fraction = Odds/(1+Odds) = (0.773,0.843)

Stat 110 bheavlin@stat.stanford.edu

One-sample variance problem

Null hypothesis Ho : σ = σo

Alternative HA : σ > σo

Test statistic and ν s2 / σo2

rejection region > χ2(df=ν,0.95)

0.4

0.3

one-sided p-value:

p1-value 0.2

0.0

= 1– χ2Inv(df=ν, νs2/σo2 ) 0 1 2 3 4 5 6 7 8

Stat 110 bheavlin@stat.stanford.edu

Two-sample variance problem

Null hypothesis Ho : σ1 = σ2

Alternative HA : σ1 ≠ σ 2

Test statistic and s12 / s22

rejection region < F(ν1,ν2, 0.025) or

> F(ν1,ν2, 0.975)

two-sided p-value:

Label so that s1 > s2

p2-value

= 2×P( s12/s22 > F Inv(ν1,ν2,1–p2/2) | Ho)

= 2×F(ν1, ν2, s12/s22)

Stat 110 bheavlin@stat.stanford.edu

CPU times (reprise)

3 3 3

.99 .99

.99

2 2 2

.95 .95 .95

.90 .90 .90

1 1 1

.75 .75 .75

-1 -1 -1

.10 .10 .10

.05 .05 .05

-2 -2 -2

.01 .01 .01

-3 -3 -3

0 1 2 3 4 5 0 1 2 -6 -5 -4 -3 -2 -1 0 1 2 3

Stat 110 bheavlin@stat.stanford.edu

variability tracking with mean

0 5 10

raw

data group mean stdev

1.46 0.58 4.31 1.02 1 2.89 2.62

1.30 8.24 3.51 6.87 2 3.56 4.10

5.92 1.86 1.41 1.70 3 3.08 1.50

4 3.20 3.20

0.17 2.92 0.91 0.43 5 1.21 0.95

1.43 1.44 4.49 4.21 6 2.00 0.80

2.02 1.65 1.40 .40 7 2.27 1.94

8 2.01 .96

Stat 110 bheavlin@stat.stanford.edu

a few power transformations

5 1.25

4

1

stdev (linear)

stdev (sqrt)

3

0.75

2

0.5

1

linear sqrt

0 0.25

1.0 1.5 2.0 2.5 3.0 3.5 4.0 1 1.2 1.4 1.6 1.8

mean (linear) mean (sqrt)

2

stdev 1.75

1.5

stdev (log)

1.25

0.75

mean log

0.5

-0.5 0 .5 1 1.5

mean (log)

Stat 110 bheavlin@stat.stanford.edu

Why power transformations?

Theoretical reasons

• align physical relationships to (linear) statistical models.

Empirical reasons

• to reduce correlations of group variances to group

means.

• reduces the influence of large values without making

them into outliers

• reduces the skewness in right-skewed data (λ<1).

• resolve an ambiguity in scale, (e.g a rate vs its

reciprocal).

Preference order:

• λ = 0 (logs), 1/2 (square roots), -1 (inverses),

1/3 (cube roots~logs with zeros)

Stat 110 bheavlin@stat.stanford.edu

Box-Cox transformations

“poor man’s” Box-Cox

procedure

2. For each group, calculate

the mean, and the

standard devation.

3. Plot the log(stdev) vs log

(mean).

4. Estimate the slope, say r.

What are they? 5. The recommended

Response y → yλ power for transforming

Note: y → (yλ ─1)/ λ the raw data is 1–r,

@1 equals 0 with slope 1 (suitably rounded).

two examples

theoretical empirical Box-Cox

Suppose the standard 2.5

deviation is proportional 2

log stdev

1

0

Box-Cox plots log(σ(μ)) vs -0.5

log(μ): 0 .5 1 1.5 2

log mean

log(σ(μ))= 1×log(μ)+log(σo),

slope = 1.24

slope r is 1, 1–r=0, so

transform by taking logs 1–r = –0.24, suggests logs

of raw data. or reciprocal sqrts.

Stat 110 bheavlin@stat.stanford.edu

linear vs log: plots of transformed data

Ra226 (linear) log2 Ra226

0 1 2 3 4 5 6 7 8 9 -3 -2 -1 0 1 2 3

g2

g2

A A

B B

C C

D D

E E

F F

G G

H H

linear logarithms

Stat 110 bheavlin@stat.stanford.edu

Mis-calibration:

thickness

Target thickness

β (mean) is β to

target

thickness deviation is (β – b)to is

b

actual proportional to

time mean.

to

So multiplicative relationships tend to promote

constant coefficients of variation, and log

transforms.

Stat 110 bheavlin@stat.stanford.edu

sums of small positive errors

actual thickness

Examples:

= ( Σ bi Δt i ) Poisson mean = λ

with variance with variance = λ

= ( Σ Δti2 Var(bi) ) sums of independent

Poissons are Poisson

= (Δt Var(b)) ΣiΔti

= σbΔ2 to so variance is Chi-square (gamma):

proportional to square root

mean =ν

of mean.

variance = 2 ν

sums of independent chi-

squares still chi-squares

Stat 110 bheavlin@stat.stanford.edu

Why Box-Cox works:

Background theory: Setup:

g(X) ≈ g(μ) + g'(μ)(X – μ ) or log( σ(μ) ) = k + r log(μ) or

g(X) – g(μ) ≈ g'(μ)(X – μ ) so log(σ2(μ)) = 2k + 2rlog(μ) or

E(g(X) – g(μ))2 σ2(μ)) = c μ2r

≈ g'(μ)2 E(X – μ)2 so

Var(g(X)) ≈ g'(μ)2 Var(X) Suppose g(x) = x1– r then

g'(x) = (1–r) x– r or

g'(x)2 = (1–r)2 x–2r so

Var(g(X)) ≈ g'(μ)2 Var(X)

= (1–r)2 μ–2r c μ2r

≈ constant with respect to μ

Stat 110 bheavlin@stat.stanford.edu

The other two-sample t-test

populations,

E( X1 – X2 ) = μ1 – μ2 ,

2 2 “classical”

Var( X1 – X2 ) = σ1/n1 + σ2/n2

So a natural two-sample t-statistic is

x1 – x2 x1 – x2

not

2 2

[ s1/n1 + s2/n2 ]1/2 sp [1/n1+1/n2 ]1/2

2 2

where s =[ (n1–1)s + (n2–1)s ]

p

2

1 2

Stat 110

(n1–1) + (n2–1)

bheavlin@stat.stanford.edu

issues

In larger samples can the differences among s1, s2,

sp be worrisome, but M&S distinguish between

them by whether n1 ≠ n2 or n1 = n2.

For the “unequal variances” procedure, there is no

clear theory for its sampling distribution…in

particular we need to figure out the associated

degrees of freedom.

Degrees of freedom for unequal variances t

Lemma: Let s be a standard deviation from

independent normals with same mean and

variance σ2, and ν degrees of freedom.

Var( s2 ) = 2 σ 4 / ν .

So Var( s12/n1 + s22/n2 )

= 2[σ12/n1]2 /ν1 + 2[σ22/n2]2/ν2, (set equal to)

= 2 σ 4 / ν, where σ =[σ12/n1 + σ22/n2 ]1/2 . Of course,

we don’t know σ1 or σ2 , so we “plug in” s1,s2:

So, [s12/n1+s22/n2]2/ν = (s12/n1)2/ν1+(s22/n2)2/ν2, from

which we solve for ν.

Stat 110 bheavlin@stat.stanford.edu

Clearout 5 split + 21 unsplit

split unsplit sum

ng 5 21

mean = xg –7.2 3.49

standard deviation = sg 11.52 7.04

df = νg = ng –1 4 20

[sg2 / ng]2 / νg 176.1205 0.278498 176.399

…continued

–7.2 – 3.49

= -1.988 = t with df=4.735

[ 28.902 ]1/2

or

p-value (two tail) = 0.118

0.059 0.059

Conventional pooled t

with df=24, p-values

= 0.0292, 0.0583 -5 -4 -3 -2 -1 0 1 2 3 4 5

comments

Different variances in different groups,

• This can often be of intrinsic interest, with groups

with smaller variation usually more desirable.

• When variation tracks with the mean level (usually

higher going with higher), Box-Cox power

transformations are suggested.

• When differences in means are still of interest (in

spite of differences among groups in variation), the

alternative t-test conservatively adjusts the degrees

of freedom.

• Note df≈5 vs 24, p-value=0.053 vs 0.029

• This low power is why M&S recommend Wilcoxon.

Stat 110 bheavlin@stat.stanford.edu

Metrology study

date mean stdev

Monitor of the same 17-Sep 1051 2.2

linewidth (same spot)

22-Sep 1062 4.3

on 10 days,

28-Sep 1063 3.1

5 readings each day.

28-Sep 1058 4.7

29-Sep 1057 3.6

30-Sep 1060 3.3

1-Oct 1062 4.1

2-Oct 1066 4.7

5-Oct 1061 4.1

6-Oct 1060 3.4

components of variance

day-to-day: σday

d

meas-to-meas: σmeas

(repeatability) +m

total variation:

2 2

σtotal = [σday +σmeas]1/2

d+m

(reproducibility)

Stat 110 bheavlin@stat.stanford.edu

Estimating these two variances

= RMS( 2.2, 4.3, …, 3.4 )

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