# T est: Compa ring

```Comparing two proportions
Example:
Chinook Salmon
Ho : Sex ratio is the same for the
two capture methods during
the early run
Test:
H0 : 1 = 2 vs. HA : 1 6= 2
Data:
A 2 2 contingency table
Dene
1 = Probability of catching a
female with hook and line
during the early run
1 = Probability of catching a
female with a net during
the early run
Females
Hook
and
Line
Net
Y1 = 172
Y2 = 165
Males n1 Y1 = 119 n2 Y2 = 202
Totals
n1 = 291
n2 = 367
124
Estimated proportions:
Estimated variance:
Y
172 = 0:5911
p1 = 1 =
n1 291
p2 =
Y2 165
=
= 0:4496
n2 367
Sp21 p2 =
p1(1 p1) p2(1 p2)
+
n1
n2
= (:5911)(:4089) + (:4496)(:5504)
291
367
= :0015
Is the dierence between
p1 = 0:5911 and p2 = 0:4496
greater than what can be
attributed to sampling variation?
V ar(p1 p2) = V ar(p1) + V ar(p2)
2Cov(p1; p2)
= 1(1 1) + 2(1 2)
n1
125
n2
126
Standard Error:
p
Sp1 p2 = :0015 = :0388
127
Test:
p1 p2
Sp1 p2
= :5911 :4496
:0388
= 3:65
95% condence interval for 1 2
Z =
(p1 p2) z=2Sp1 p2
%
.5911
)
&quot;
.4496
(separate variance estimates)
&quot;
z:025 = 1:96
.0388
0:1415 :0760
)
(:064; :218)
p-value = 2(:00013) = :00026
Conclusion:
Conclusion:
128
Test:
(pooled variance estimates)
First compute a pooled estimate of the
success probability
n p + n2p2
= Y1 + Y2
p= 1 1
n1 + n2
n1 + n + 2
= 172 + 165 = :51216
291 + 367
Estimate
V ar(p1 p2) = V ar(p1) + V ar(p2)
as
= p(1 p) + p(1 p) = :00154
S2
p1 p2
Then
n1
n2
129
and
p1 p2
Sp1 p2
= :5911 :4496
:0392
= 3:61
Z =
p-value = 2(:000156) = :00031
Note:
Z 2 is equal to the Pearson
chi-square statistic .
p
Sp1 p2 = :00154 = :03924
130
2-sample test for equality of proportions
without continuity correction
S-PLUS for windows:
data: V1 and V2 from data set salmon2
X-square = 13.0018, df = 1, p-value = 0.0003
alternative hypothesis: two.sided
95 percent confidence interval:
0.06544146 0.21750656
sample estimates:
prop'n in Group 1 prop'n in Group 2
0.5910653
0.4495913
V1 V2
1 172 291
2-sample test for equality of proportions
with continuity correction
2 165 367
Statistics ) Compare samples
) Counts and proportions
) proportion parameters
data: V1 and V2 from data set salmon2
X-square = 12.4417, df = 1, p-value = 0.0004
alternative hypothesis: two.sided
95 percent confidence interval:
0.06236085 0.22058717
sample estimates:
prop'n in Group 1 prop'n in Group 2
0.5910653
0.4495913
Fill in the boxes and check o
Yates continuity correction
131
S-PLUS code
#
#
#
#
This code compares proportions
for two independent binomial samples
It is stored in the file
binomial2.ssc
sep=c(1, 5, 7, 9, 10, 11, 12, 14, 15 ),
col.names=c(&quot;year&quot;,&quot;month&quot;,&quot;day&quot;,&quot;biweek&quot;,&quot;run&quot;,
&quot;gear&quot;,&quot;age&quot;, &quot;sex&quot;, &quot;length&quot; ))
# Construct a 2x2 contingency table
# for the sex by gear categories
# for the two runs
132
# Construct vector of total counts
# (all fish caught for the two gear
# types in the early run)
ny &lt;- apply(ytab[,,1],2,sum)
#
#
#
#
#
#
Apply the prop.test function to
test the null hypothesis of equal
proportions. The alt=&quot;two.sided&quot;
option specifies a two-sided
alternative. The correct=&quot;F&quot; option
turns off the continuity correction
prop.test(y,ny,alt=&quot;two.sided&quot;,correct=&quot;F&quot;)
ytab&lt;-table(cdat\$sex,cdat\$gear,cdat\$run)
# Repeat the test with continuity correction
prop.test(y,ny,alt=&quot;two.sided&quot;,correct=&quot;T&quot;)
# Construct vector of success counts
# (female counts for the two gear types
# in the early run)
# Make a 99% confidence interval
prop.test(y,ny,conf.level=.99)\$conf.int
y &lt;- ytab[1,,1]
133
134
SAS code
/* Program to analyze the 1999 Chinook
salmon data. This program is stored
in the file chinook2.sas
*/
data set1;
infile 'c:\courses\st557\sas\hdata.dat';
input (year month day biweek run gear
age sexa length)
(4. 2. 2. 1. 1. 1. 2. \$1. 4.);
rage=int(age/10);
oage=age-(10*rage);
if(sexa = 'F') then sex=1; else sex=2;
run;
/* Attach labels to categories */
proc format;
value run 1 = 'Early'
2 = 'Late';
value sex 1 = 'Female'
2 = 'Male';
value gear 1 = 'Hook'
2 = 'Net';
run;
/* Examine partial association between
sex and method of capture within
each run. */
proc sort data=set1; by run;
run;
proc freq data=set1; by run;
table gear*sex / chisq Fisher
nopercent nocol expected;
format sex sex. gear gear. run run.;
run;
136
135
Frequency
Expected
Row Pct Female Male
Sample Size Determination
Hook
172
119
149.04 141.96
59.11 40.89
291
Net
165
202
187.96 179.04
44.96 55.04
367
Total
337
(n responses in each group)
Total
321
95% condence interval for 1 2
p1 p 2
658
]
%
(p1
j
Statistic
DF
Value
Prob
Chi-Square
1 13.0018 0.0003
Likelihood Ratio Chi-Square 1 13.0545 0.0003
1 12.4417 0.0004
p2) + z=2Sp1 p2
]
&quot;
L = half length
Sample size needed for each group
z=2 #2
n=
[1(1 1) + 2(1 2)]
L
&quot;
Fisher's Exact Test
Table Probability (P)
Two-sided Pr &lt;= P
j
%
[
9.352E-05
4.022E-04
137
138
Sample Size Determination
Two sided alternative:
(n responses in each group)
Ha : 1 6= 2
Test of the null hypothesis
Compute
Ho : 1 2
p =
Signicance level ( = :05)
R =
Power (power = 1 = :80)
1 2
v
u
u
t
2
2p(1 p)
1(1 1) + 2(1 2)
Sample size needed for each group
2
z + Rz=2 [1(1 1) + 2(1 2)]
n=
(1 2)2
Size of alternative
j1 2j = 0:08
140
139
One sided alternative:
Ha : 1 &gt; 2 or Ha : 1 &lt; 2
Correction given by Fleiss, J. L.
(1981), Statisitcal Methods for Rates
and Proportions, Wiley, New York.
(pages 42-43 and Table A3)
Compute
p =
R =
1 2
v
u
u
t
2
2p(1 p)
1(1 1) + 2(1 2)
Sample size needed for each group
z + Rz 2 [1(1 1) + 2(1 2)]
n=
(1 2)2
141
ncorrected =
2
n4
4
v
u
u
t
1+ 1+
4
njp1 p2j
32
5
142
/* This program computes sample sizes
needed to obtain tests with a
specified power values for detecting
specified differences between two
proportions. This program is stored
in the file
size2p.sas
*/
* Enter a set of power values;
power = {.8 .9 .95 .99};
* Enter the type I error level;
alpha = .05;
options nodate nonumber linesize=68;
* Compute sample sizes;
proc iml;
start samples;
za = probit(1-alpha/2);
za1 = probit(1-alpha);
nb = ncol(power);
np = ncol(power);
size = j(1,np);
size1 = j(1,np);
/* Enter the probability of success
for the first population */
p1 = .58;
/* Enter the probability of success
for the second population */
p = (p1+p2)/2;
rp = sqrt(2*p*(1-p)/
(p1*(1-p1)+p2*(1-p2)));
p2 = .50;
144
143
* Cycle across power levels;
do i2 = 1 to np;
zb = probit(power[1,i2]);
size[1,i2] = ((za*rp+zb)**2)*
(p1*(1-p1)+p2*(1-p2))/((p1-p2)**2);
size1[1,i2] = ((za1*rp+zb)**2)*
(p1*(1-p1)+p2*(1-p2))/((p1-p2)**2);
end;
/* Compute corrected sample sizes using
the Fleiss (1981) correction */
sizec=(size/4)#(j(1,np)+sqrt(j(1,np)
+4/(size*abs(p1-p2))))##2;
print,,,,, 'Sample sizes for testing equality',
' of two proportions';
print, 'The number of observations needed',
' for each treatment group';
print,,, p1 p2 alpha power;
sizer = int(size) + j(1,np);
print 'Sample sizes (2-sided test):' sizer;
sizerc = int(sizec) + j(1,np);
print 'Corrected sizes (2-sided test):' sizerc;
size1c=(size1/4)#(j(1,np)+sqrt(j(1,np)
+4/(size1*abs(p1-p2))))##2;
size1rc = int(size1c) + j(1,np);
print 'Corrected sizes (1-sided test):' size1rc;
size1r = int(size1) + j(1,np);
print 'Sample sizes (1-sided test):' size1r;
145
146
/* Determine sample sizes for
constructing confidence intervals */
/* Enter confidence level */
level=0.95;
percent = level*100;
print,,,,'Sample sizes for' percent 'percent',
'
confidence intervals';
print,,'The number of observations for each',
' treatment group';
print,,,'
Half length
Sample size';
print me '
' n;
/* Enter values for margin of error */
me = {0.04, 0.03, 0.02, 0.01};
alpha = 1-level;
za = probit(1-alpha/2);
np = ncol(me);
size = j(1,np);
finish;
run samples;
/* Compute sample sizes */
n = ((za/me)##2)#(p1*(1-p1)+p2*(1-p2));
n = int(n) + j(np,1);
percent = level*100;
148
147
Sample sizes for testing equality
of two proportions
S-PLUS code:
The number of observations needed
for each treatment group
P1
P2
ALPHA
0.58
0.5
0.05
Sample sizes(2-sided test):
Sample sizes(1-sided test):
Corrected sizes (2-sided ):
Corrected sizes (1-sided ):
POWER
0.8
609
479
633
504
0.9 0.95 0.99
814 1006 1422
663 838 1220
839 1031 1447
688 863 1245
Sample sizes for 95 percent
confidence intervals
The number of observations for each
treatment group
Half length
ME
0.04
0.03
0.02
0.01
Sample size
N
1186
2107
4741
18962
149
#
#
#
#
#
#
#
#
This program computes sample sizes needed
to obtain a test of a hypothesis about a
difference between two proportion with a
specified power value. It also computes
the number of observations needed to obtain
a confidence interval with a specified
accuracy. This program is stored in the file
size2p.ssc
# Specify the probability of success
# for the first population
p1 &lt;- c(.58)
# Specify the probability of success
# for the second population
p2 &lt;- c(.50)
# Enter power values
power &lt;- c(.8, .9, .95, .99)
150
# Increase sample size to next largest integer
# and print results
# Enter the type I error level
alpha &lt;- .05
size &lt;- ceiling(size)
cat(&quot;\n \n \n p1=&quot;,p1,&quot;p2=&quot;, p2, &quot;alpha=&quot;,
alpha,&quot;power=&quot;, power)
cat(&quot;\n Sample sizes (2-sided test): &quot; , size)
za &lt;- qnorm(1-alpha/2)
za1 &lt;- qnorm(1-alpha)
nb &lt;- length(power)
p &lt;- (p1+p2)/2
va &lt;- p1*(1-p1)+p2*(1-p2)
rp &lt;- sqrt(2*p*(1-p)/va)
cat(&quot;Sample sizes for testing equality
of two proportions&quot;)
# Obtain a sample size for each of
# the requested power values
zb &lt;- qnorm(power)
size &lt;- ((za*rp+zb)^2)*va/((p1-p2)^2)
size1 &lt;- ((za1*rp+zb)^2)*va/((p1-p2)^2)
size1 &lt;- ceiling(size1)
cat(&quot;\n \n p1=&quot;,p1,&quot;p2=&quot;, p2, &quot;alpha=&quot;,
alpha,&quot;power=&quot;, power)
cat(&quot;\n Sample sizes (1-sided test): &quot; , size1)
# Compute corrected sample sizes according to
# Fleiss, J. L. (1981) Statistical Methods for
# Rates and Proportions, Wiley, New York.
sizec&lt;-(size/4)*(1+sqrt(1+4/(size*abs(p1-p2))))^2
sizecr &lt;- ceiling(sizec)
cat(&quot;\n \n \n p1=&quot;,p1,&quot;p2=&quot;, p2, &quot;alpha=&quot;,
alpha,&quot;power=&quot;, power)
cat(&quot;\n Corrected sizes(2-sided test): &quot;,sizecr)
151
s1c&lt;-(size1/4)*(1+sqrt(1+4/(size1*abs(p1-p2))))^2
s1cr &lt;- ceiling(s1c)
cat(&quot;\n \n \n p1=&quot;,p1,&quot;p2=&quot;, p2, &quot;alpha=&quot;,
alpha,&quot;power=&quot;, power)
cat(&quot;\n Corrected sizes(1-sided test): &quot;,s1cr)
#
#
#
#
Compute sample size needed to obtain a
confidence interval for the difference
between the two proportions with a
specified margin of error
# Enter the confidence level
level &lt;- c(0.95)
152
# Compute needed sample sizes
alpha2 &lt;- (1.0-level)/2
np &lt;- length(me)
one &lt;- rep(1,np)
n &lt;-((qnorm(one-alpha2)/me)^2)*va
n &lt;- ceiling(n)
percent &lt;- level*100;
cat(&quot;\n \n \n Sample sizes for &quot;, percent,
&quot; percent confidence intervals: \n&quot;)
cat(&quot;margin of error: &quot;, me, &quot;\n&quot;)
cat(&quot;sample size:
&quot;, n, &quot;\n&quot;)
# Enter desired margin of error
me &lt;- c(0.04, .02, .01)
153
154
Sample sizes for testing equality
of two proportions
p1= 0.58 p2= 0.5 alpha= 0.05
power= 0.8 0.9 0.95 0.99
Sample sizes (2-sided test): 609 814 1006 1422
p1= 0.58 p2= 0.5 alpha= 0.05
power= 0.8 0.9 0.95 0.99
Sample sizes (1-sided test): 479 663 838 1220
p1= 0.58 p2= 0.5 alpha= 0.05
power= 0.8 0.9 0.95 0.99
Corrected sizes(2-sided test): 634 839 1031 1447
Sample sizes for 95 percent
confidence intervals:
margin of error: 0.04 0.02 0.01
sample size:
1186 4741 18962
p1= 0.58 p2= 0.5 alpha= 0.05
power= 0.8 0.9 0.95 0.99
Corrected sizes(1-sided test): 504 688 863 1245
156
155
S-PLUS for windows
Statistics
) Power and Sample size
) Binomial Proportion
) change Sample Type to
and specify
values of two proportions
Two Sample
*** Power Table ***
p1 p2 delta alpha
1 0.5 0.58 0.08 0.05
2 0.5 0.58 0.08 0.05
3 0.5 0.58 0.08 0.05
4 0.5 0.58 0.08 0.05
5 0.5 0.58 0.08 0.05
6 0.5 0.58 0.08 0.05
power
0.800
0.850
0.900
0.950
0.975
0.990
n1
634
721
839
1031
1214
1447
n2
634
721
839
1031
1214
1447
Comparing Several Proportions:
Several independent binomial
experiments (or samples)
Y1 = number of successful outcomes in
n1 trials for experiment 1
Bin(n1; 1)
Y2 = number of successful outcomes in
n2 trials for experiment 2
Bin(n2; 2)
..
..
Yk = number of successful outcomes in
nk trials for experiment k
Bin(nk; k)
157
158
Example:
Test:
Sunower seeds were stored in three
types of storage facilities. 100 seeds
were taken from each of the three facilities and the germination of each seed
was monitored. Dene
H0 : 1 = 2 = = k vs.
HA : i 6= j for some i 6= j
Note:
H0 : 1 = 2 = = k
is referred to as the hypothesis of
homogeneity
or
independence
i = proportion of seeds from the
i-th storage facility that will
germinate
%
the &quot;success rate&quot; i does not
depend on the experiment (or
population)
Are there dierences in germination
rates?
159
160
A 3 2 contingency table
Storage Number of Germination
Facility Seeds Tested
Rates
Type 1
100
69%
Type 2
100
58%
Type 3
100
41%
Total
300
56%
Storage Number that
Facility Germinated
Number that
failed to
Germinate
Totals
Type 1
Y11 = 69
Y12 = 31
n1 = 100
Type 2
Y21 = 58
Y22 = 42
n2 = 100
Type 3
Y31 = 41
Y32 = 59
n3 = 100
Totals
Y+1 = 168
Y+2 = 132
161
Y+j
\Expected counts&quot; m
^ ij = YiY+++
Pearson statistic:
m
^ 11 = 56 m
^ 12 = 44
m
^ 21 = 56 m
^ 22 = 44
m
^ 31 = 56 m
^ 32 = 44
Here
0
1
of seeds A
m
^ i1 = @ number
of type i
0
(Yij m
^ ij )2
m
^ ij
i=1 j =1
I
X
X2 =
1
A
overall germination
rate
@
J
X
2
2
= (69 56) + (31 44)
56
44
2
2
+ (58 56) + (42 44)
56
44
2
2
+ (41 56) + (59 44)
56
44
= 16:15
163
162
Deviance
Reject H0 : 1 = 2 = 3
if
G2 = 2
J
X
i=1 j =1
Yij log(Yij =m
^ ij )
= 2 69 log(69=56) + 31 log(31=44)
+58 log(58=56) + 42 log(42=44)
Note that
d:f:
I
X
2
6
4
X 2 &gt; 22;
22;:05
22;:005
(log-likelihood ratio test)
3
7
5
+41 log(41=56) + 59 log(59=44)
= 5:99
= 10:60
= 20:12
= (number of rows 1)
(of columns 1)
164
Reject H0 : 1 = 2 = 3 if
G2 &gt; 22;
X 2 and G2 have the same limiting cen-
tral chi-squared distribution when the
null hypthesis is true.
165
The joint probability function (or
likelihood function) is
Maximum likelihood estimation:
Y11
Bin(n1; 1)
Y21
Bin(n2; 2)
Y31
Bin(n3; 3)
Pr (Y11 = y11; Y21 = y21; Y31 = y31)
0
1
= @ yn1 A 1y11 (1 1)n1 y11
11
are independent binomial random
variables.
3
Y
0
@
0
@
1
n2 A y21(1 )n2 y21
2
y21 2
1
n3 A y31
n3 y31
y31 3 (1 3)
20
1
3
= [email protected] yni A iyi1(1 i)ni yi15
i1
i=1
= L(1; 2; 3; y11; y21; y31)
166
167
Since the natural logarithm is a monotone increasing function, the value
that maximizes L(; data) is obtained
by maximizing
Consider the hypothesized model
where
1 = 2 = 3 = ;
01
`(; data) = log[L(; data)]
=
Then the likelihood function becomes
L(; data) =
3
Y
i=1
2
4
3
ni!
yi1(1 )ni yi15
yi1!(ni yi1)!
168
3
X
[log(ni!) log(yi1!)
i=1
log((ni yi1)!)]
+ log()
3
X
i=1
+ log(1 )
yi1
3
X
i=1
(ni yi1)
169
Solve the likelihood equation
0 = @`( ; data)
@
3
X
=
i=1
yi1
Maximum likelihood estimators of
mean (or expected) counts:
3
X
ni yi1
i=1
1 The solution is the maximum likelihood
estimate for for the \independence&quot;
or \homogeneity&quot; model.
3
X
^ =
i=1
yi1
3
X
i=1
ni
= y+1
y++
For this model: Yi1 Bin(ni; )
and mi1 = E (Yi1) = ni
Then E (Yi2) = E (ni Yi1) = ni(1 )
m
^ i1 = ni^ = Yi+Y+1
Y++
m
^ i2 = ni(1 ^) = Yi+Y+2
Y++
Formula for \expected counts
0
10
1
total
for
total
for
@
[email protected]
A
i th row
j th column
0
1
m
^ ij =
total
for
the
@
A
entire table
The formula for the \expected&quot; counts
corresponds to the maximum likelihood
estimators for the means of the counts
for the specied model.
171
170
Maximum likelihood estimates
for the alternative model
(model A):
Yi1 Bin(ni; i)
0 i 1
i = 1; 2; 3
0 = @`
@i
= yi1 ni yi1 ; i = 1; 2; 3
i 1 i
log-likelihood function
`(1; 2; 3; data) =
3
X
i=1
flog(ni!) log(y1i!) log((ni y1i)!)g
+
+
3
X
i=1
3
X
i=1
Likelihood equations:
yi1 log(i)
Solutions:
y
^i = i1 = pi ; i = 1; 2; 3
ni
(ni yi1) log(1 i)
172
173
Maximum likelihood estimates
of expected counts for the
alternative model
m
^ i1 = ni^i =
1
0
yi 1 A
@
ni
ni
m
^ i2 = ni(1 ^i) =
1
yi1 A
ni
nested models;
Model A: Yi1 Bin(ni; i) i = 1; 2; 3
are independent random counts.
= yi1
0
n
ni @ i
Likelihood ratio tests for comparing
= yi2
Maximum likelihood estimators are
Y11
n1
Y
^2 = p2 = 21
n2
Y
^3 = p3 = 31
n3
^1 = p1 =
are the observed counts.
This is called a \saturated&quot;
model because it contains as
many parameters (1; 2; 3)
as independent counts
(Y11; Y21; Y31).
175
174
Ratio of Likelihoods:
^ =
Model B: Model A with the added restrictions that 1 = 2 = 3 = 3
X
^ =
i=1
Yi1
3
X
i=1
ni
Lmodel B(^; data)
Lmodel A(^1; ^2; ^3; data)
ni!
^yi1(1 ^)ni yi1
y
!(
n
y
)!
i
1
i
i
1
i
=1
= Y3
ni !
^iyi1(1 ^i)ni yi1
i=1 yi1!(ni yi1)!
3
Y
=
3
Y
i=1
2 3y
2
i1 4
4 5
^
^i
3
1 ^ 5ni yi2
1 ^i
Note that 0 ^ 1 and small
values of ^ suggest that model
A is substantially better than
model B.
176
177
2
3
of parameter 5
d.f. = 4 dimension
space for model A
2
3
dimension
of
parameter
4
5
space for model B
When the null hypothesis
(model B) is correct and
each ni is \large&quot;, then
= 3 1= 2
and in this case
2 log(^ ) 2d:f :
2 log(^ ) = 2
8
3
&lt;X
:
^i !
yi1 log
^
i=1
9
1
^i !=
+ yi2 log
1 ^ ;
i=1
3
X
=2
3
X
2
X
i=1 j =1
yij
1
0
m
A;ij
A
log @
^
m
^ B;ij
179
178
\Expected&quot; counts:
Model A: m
^ A;i1 = ni^i = yi1
m
^ B;i2 = ni(1 ^i)
= (ni yi1) = yi2
Model B: m
^ B;i1 = ni^ = m
^ i1
m
^ B;i1 = ni(1 ^) = m
^ i2
Then
0
1
y
yij log @ ij A
m
^ ij
i j
= G2:
2 log(^ ) = 2
X X
180
The general form for the Pearson
chi-squared statistic is
X X (m
^ A;ij m
^ B;ij )2
X2 =
:
m
^ B;ij
i j
When model A (the alternative
hypothesis) places no restrictions on
the parameters it is called the
general alternative and
m
^ A;ij = Yij :
Simplifying the notation, m
^ ij = m
^ B;ij;
the Pearson statistic becomes
X X (Yij
m
^ ij )2
X2 =
m
^ ij
i j
181
```