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Exercise 9: smoke
Day 4
Summarizing homework exercises.
Mogens Erlandsen
Deptartment of Biostatistics
Aarhus University
70 80 90
Inverse Normal
100
120
Weight (kg)
80
100
40
60
70
80 90 100 110
Inverse Normal
2 20
60
70
80
90
Inverse Normal
100
150
160 170
180
Inverse Normal
190
220
60
220
50
G3
60
Weight (kg)
80
100
40
40
0.9745
G2
60
60
correlation
Height (cm)
180
200
160
140
140
160
0.9266
160
Height (cm)
180
200
Height (cm)
180
200
0.9763
1 40
group |
weight
height
-------+-------------------1 |
25
25
|
76.024
171.32
| 12.93478
13.8916
-------+-------------------2 |
25
25
|
83.14
179.2
| 12.47624
14.5545
-------+-------------------3 |
25
25
|
78.5
170.16
| 9.852623 11.33093
-------+--------------------
G1
Weight (kg)
80
100
120
140
160
180
200
Inverse Normal
We ight (kg)
80
100
120
Weight (kg)
70 80 90 10 0
Group 1
50
60
60
Variable
140
160
180
Height (cm)
200
140
160
180
Height (cm)
200
220
sdtest
ttest
Weight
0.19
0.45
height
0.32
0.75
10 0
Group 3
Weight (kg)
70
80
90
60
150
160
170
180
Height (cm)
190
Confidence ellipse
85
Means centered
p-value
(t-test)
0.45
Height (cm)
0.75
70
Group 1 3
Weight (kg)
Difference
(95% - CI)
-2.48 (-9.01; 4.06)
Weight (kg)
75
80
165
170
175
180
Height (cm)
1
wmean
Model validation
Presenting the results
9
Exercise 5, 6 and 8:
Exercise 5, 6 and 8:
CRP
10
CRP
Variability increase
with time?
creac_p
10
15
15
Sham
20
CPB
10
3
time
time
Graphs by Group
mean CPB
m ean Sham
ln(CRP)
Sham
2.5
CPB
CRP
The distance between
curves increase with
time?
1.5
ln(CRP)
Constant distance, i.e.
parallel curves?
.5
lcreac_p
ln(CRP)
Variability more
homogeneous?
1
time
time
Graphs by Group
mean CPB
m ean Sham
11
12
Note:
ln(CRP)
.7
.8
CRP
.5
(sd) creac_p
.4
And if accepted, then test whether the sds and corrs in each
group are equal (homogeneity/heterogeneity)
6
8
(mean) creac_p
(sd) creac_p
10
12
.5
(sd) creac_p
1.5
2
(mean) lcreac_p
(sd) lcreac_p
2.5
(sd) lcreac_p
13
CRP
Group 2
Group 1
-2
-1
Inverse Normal
-.8
-4
-2
0
Inverse Normal
-1
d34
-5
-3
-2
-1
Inverse No rmal
-.4
-.2
Inverse Normal
0
Inverse Normal
.5
-.6
- .4
Inverse Normal
-.2
.2
-.8
lnd23
- 1 - .5 0 .5 1
-6
-10
d34
-5
- 10
-4
-.6
-.5
lnd34
- 2- 1.5- 1 - .5 0 .5
-1
0
Inverse No rmal
lnd12
-1 -.5 0
-8
-6
-4
Inverse Normal
-2
-1
-.6
-.4
-.2
Inverse Normal
lnd23
-1 -.5 0 .5 1
-3
-2
-3
.5
.5
lnd12
- 1 - .5 0
-4
-1
-.5
0
Inverse Normal
.5
-1.5
-1
-.5
Inverse Normal
.5
lnd34
-2-1.5-1 -.5 0 .5
d23
-8 -6 -4 -2 0 2
-1
0
Inverse No rmal
d23
-8 -6 -4 -2 0 2
-2
Group 2
ln(CRP)
d12
-4 -3 -2 -1 0 1
d12
- 4 -3 - 2 - 1 0 1
Group 1
14
-.8
15
16
Differences
in each group
Prob. Plots
Homogeneity of
sds and corrs
between groups
Parallel curves
CRP
ln(CRP)
OK
p=0.035
OK
p=0.31
On the log-scale homogeneity between the two groups with respect to the
standard deviations on and the correlations between the four time points was
accepted, p=0.31.
Furthermore, a test for parallel curves was accepted, p=0.72 (Hotellings t-test
on the successive differences between time points).
A test for equal curves (distance = 0) was rejected, p=0.003.
p=0.019
In each group a test for a constant curve was rejected (G1: p=0.006 and G2:
p=0.007).
p=0.72
The constant distance (CPB-Sham) between the two time curves (ln-scale) was
estimated to : -0.58 ( -0.93; -0.22).
Bback-transforming with exponential function the median level in the CPBgroup was 56% (39%; 80%) lower than in the sham group.
18
Test the assumption with equal sds and equal corrs in each
group (compound symmetry):
id|group
Levels:
22
id
group
(20 df)
Huynh-Feldt epsilon
Adjusted LR chi2(8) =
6.66
0.5734
Accept!
Source |
0.1403
1.0708
Greenhouse-Geisser epsilon =
0.8759
0.3333
Adjusted LR chi2(8) =
df
Regular
H-F
G-G
Box
-----------+---------------------------------------------------time |
26.02
0.0000
0.0000
0.0000
0.0001
time*group |
0.56
0.6406
0.6406
0.6184
0.4612
Residual |
60
20
Output continued
Output continued
Prob > F
time |
-----------+----------------------------------------------------
Source |
Model |
Partial SS
28.7046272
df
MS
24
1.19602613
10.50
0.0000
Residual |
8.91097139
2.9703238
7.17326304
63
.113861318
26.09
0.0000
-----------+----------------------------------------------------
group |
7.24130137
7.24130137
id|group |
12.5523544
20
.627617722
11.54
0.0029
Total |
35.8778902
87
.412389543
df
Regular
H-F
G-G
Box
-----------+---------------------------------------------------time |
Residual |
63
26.09
0.0000
0.0000
0.0000
0.0000
.6
.4
1
Residuals
-.5
0
.5
-.2
Residuals
0
.2
residual probability-plot
ln(CRP)
-1
-.4
22
.5
1.5
2
Linear prediction
2.5
-.5
0
Inverse Normal
.5
sW
sB
sT
Correlation
0.3079
0.2973
0.4280
0.4823
0.3775
0.4196
0.5644
0.5527
0.3410
0.3575
0.4941
0.5237
combined
-1
-1
-.5
Residuals
-.5
0
.5
Residuals
0
.5
residual probability-plot
group
.5
1.5
2
Linear prediction
2.5
-.5
0
Inverse Normal
.5
CV = exp( 2 ) 1
23
24
---------------------------------------------------------------------------
-------------------------------------------------------------------------
lcreac_p |
Coef.
Std. Err.
P>|z|
lcreac_p |
Coef.
Std. Err.
P>|z|
-----------+------------------------------------------------------------
-------------+------------------------------------------------------------_Igroup_2 | .4552144
.1915084
2.38
0.017
.0798649
.8305639
_Igroup_2 | .5522262
.1706731
3.24
0.001
.217713
.8867394
time1 | .2336667
.0483935
4.83
0.000
.1388172
.3285161
time1 | .2702991
.0358923
7.53
0.000
.1999515
.3406468
_cons | .763155
.1229118
6.21
0.000
.5222524
1.004058
_IgroXtime~2 | .0805914
.0717791
1.12
0.262
-.0600931
.2212759
_cons | .8072513
.1291149
6.25
0.000
.5541907
1.060312
-------------------------------------------------------------------------
---------------------------------------------------------------------------
.6
1
Residuals
0
.5
Exercise 9: Smoke
Complicated design: cross-over experiment with 3 treatments.
5 factors to consider:
G1
OK
-1
-.4
-.5
-.2
Resid uals
0
.2 .4
0
Inverse Normal
.5
-1
-1
-.5
-.5
-.5
Re siduals
0
.5
1.6
1
1.2
1.4
Linear predicti on, fixed portion
Resid ua ls
0
.5
.8
1.4
1.6
1.8
2
Linear predicti on, fixed portion
2.2
-1
-.5
0
Inverse Normal
.5
27
28
Exercise 9: Smoke
Exercise 9: Smoke
200 0 ug/m3
0 ug/m3
Sub
Sub x Day
Residual
Similar developements.
More comments:
Order is nested within Sub
Conc is nested within Sub x Day
400 ug/m3
6
Time
Graphs by Smoke concentration
29
Exercise 9: Smoke
4.5
30
(mean) fev1
3
3.5
bse(sub#day) repeated(time)
2.5
2
Time
0 My-g/m 3
400 My-g/m3
1. Order/Sub
2. Day Conc/Sub#Day
3. Time Conc#Time
200 My-g/m3
31
32
180
R-squared
Root MSE
Source |
Exercise 9: Smoke
0.7883
= .545361
Partial SS
df
Adj R-squared =
MS
0.7130
Prob > F
-----------+---------------------------------------------------Model |
146.22137
47
3.11109298
10.46
0.0000
0.44
0.8054
|
order |
11.2357365
2.24714731
sub |
30.4588088
5.07646813
-----------+---------------------------------------------------day |
2.10456305
1.05228152
2.15
0.1428
conc |
6.31116623
3.15558312
6.44
0.0069
sub#day |
9.79468626
20
.489734313
-----------+---------------------------------------------------time |
38.7599307
9.68998269
32.58
0.0000
conc#time |
26.3799861
3.29749827
11.09
0.0000
39.2593241
132
.297419122
|
Residual |
-----------+---------------------------------------------------Total |
185.480694
179
1.036205
33
Exercise 9: Smoke
Is FEV1 back to normal after 6 hours?
Residuals
0
-.5
3.5
4
4.5
Linear prediction
2
3
4
Linear prediction
1.5
1.5
1
----------------------------------------------------------------fev1 |
Coef.
Std. Err.
t
P>|t|
[95% Conf. Interval]
------+---------------------------------------------------------(1) | -.01583
.22264
-0.07
0.943
-.45624
.42457
-----------------------------------------------------------------
Residuals
0
.5
Residuals
0
.5
(2) | -.08250
.22264
-0.37
0.712
-.52291
.35791
-----------------------------------------------------------------
-1
-.5
-.5
-1
-.5
0
.5
Inverse Normal
2
4
Linear prediction
residual probability-plot
residual probability-plot
1.5
Residuals
0
.5
-.5
-1
-1
bse(sub#day) repeated(time)
0
residual probability-plot
-1
-1
-1
- .5
.5
1.5
Residuals
0
.5
-.5
Conc 400
Conc 200
Residu als
0
.5
Conc 0
-1
-.5
0
.5
Inverse Normal
34
-1
-.5
0
.5
Inverse Normal
(3) |
.98917
.22264
4.44
0.000
.54876
1.4296
-----------------------------------------------------------------
35
36