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REPEATED EVENTS ANALYSES
12/17/2012
1
Outline for Talk
๏‚จ Recurrent Events
๏‚จ Analyses for Count Outcomes
๏‚จ Survival Analysis Approaches for Repeated Events
๏‚จ Parametric Analyses for Counts
๏‚ค Poisson Regression
๏‚ค Negative Binomial
๏‚จ Non-parametric Analyses for Counts
๏‚ค Mean of Ratios (Q)
๏‚ค Ratio of Means (R)
2
Recurrent Events
๏‚จ Usually in survival studies subjects are followed until
they experience a single index event
๏‚ค Death
๏‚ค Cancer
๏‚ค Return to employment
๏‚จ But there are many events of interest that are
repeatable
๏‚ค Seizures
๏‚ค Infections
๏‚ค Hospitalizations
3
Recurrent Events
๏‚จ Most of the methods employed in survival analysis
are set up for a single event
๏‚จ But, there have been methods developed for use
with repeated events
๏‚ค Some of these methods come out of the area of
statistical methods developed for count data โ€“ these
focus on the count of the number of recurrent event
๏‚ค Some methods come directly out of survival analysis
methods โ€“ these focus on the time duration between the
recurrent events
4
Recurrent Events
๏‚จ Methods coming out of either area need to address
the domain of the other methods
๏‚ค The count methods also need to address the time
component
๏‚ค The survival methods need to address the number of
events as well as the gap times between events
5
Diabetes Control and Complications
Trial (DCCT)
๏‚จ NIH-funded trial
๏‚จ Launched in 1981
๏‚จ To evaluate the effect of intensive blood glucose-
lowering on risk of albuminuria in diabetic subjects
๏‚จ Subjects were randomized to either intensive blood
glucose lowering or conventional treatment
๏‚จ Intensive glucose lowering used self-monitoring 4 or
5 times daily, multiple daily insulin injections or a
pump, diet and exercise
6
Diabetes Control and Complications
Trial (DCCT)
๏‚จ A concern was that the intensive glucose lowering
could lead to hypoglycemia
๏‚ค Dizzy spells
๏‚ค Possible comas
๏‚ค Seizures
๏‚จ Hypoglycemia events were tracked as a secondary
outcome (DCCT 1997)
7
Diabetes Control and Complications
Trial (DCCT)
Intensive
Treatment
Conventional
Treatment
Subjects 363 352
Hypoglycemia
Events
1723 543
Person-Years of
Follow-Up
2598.5 2480.8
Rate per 100
Person-Years
66.3 21.9
8
Count Outcome Approaches
๏‚จ The most basic analysis for count outcomes comes
from the Poisson distribution
๏‚จ ๐‘ƒ๐‘ƒ ๐‘ฆ๐‘ฆ|๐œ†๐œ† =
๐‘’๐‘’โˆ’๐œ†๐œ† ๐œ†๐œ† ๐‘ฆ๐‘ฆ
๐‘ฆ๐‘ฆ!
๏‚ค Here ๐œ†๐œ† is the mean count
๏‚ค y is the observed count (non-negative integer)
๏‚จ One feature of the Poisson distribution is that
๏‚ค Variance = Mean = ๐œ†๐œ†
9
Poisson Densities
10
Count Outcome Approaches
๏‚จ The maximum likelihood estimator of the mean is
provided by the sample average
๏‚ค ฬ‚๐œ†๐œ† =
๐‘ฆ๐‘ฆ1+๐‘ฆ๐‘ฆ2+โ‹ฏ+๐‘ฆ๐‘ฆ๐‘›๐‘›
๐‘›๐‘›
๏‚จ Often people are followed for somewhat different
lengths of time, giving some people more
opportunity to get larger event counts
๏‚ค In this case ๐œ†๐œ† is standardized to be per-unit of time
11
Count Outcome Approaches
๏‚จ With unequal follow-up times ๐‘ก๐‘ก1, ๐‘ก๐‘ก2, โ€ฆ , ๐‘ก๐‘ก๐‘›๐‘›
๏‚จ ๐‘ƒ๐‘ƒ ๐‘ฆ๐‘ฆ|๐‘ก๐‘ก, ๐œ†๐œ† =
๐‘’๐‘’โˆ’๐œ†๐œ†๐‘ก๐‘ก(๐œ†๐œ†๐‘ก๐‘ก)๐‘ฆ๐‘ฆ
๐‘ฆ๐‘ฆ!
๏‚จ Where ๐‘ก๐‘ก is the length of follow-up
๏‚จ With unequal follow-up, the MLE for ๐œ†๐œ† is provided
by
๏‚ค ฬ‚๐œ†๐œ† =
๐‘ฆ๐‘ฆ1+๐‘ฆ๐‘ฆ2+โ‹ฏ+๐‘ฆ๐‘ฆ๐‘›๐‘›
๐‘ก๐‘ก1+๐‘ก๐‘ก2+โ‹ฏ+๐‘ก๐‘ก๐‘›๐‘›
=
๏ฟฝ๐‘ฆ๐‘ฆ
ฬ…๐‘ก๐‘ก
=
๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘› ๐‘œ๐‘œ๐‘œ๐‘œ ๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’
๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘โˆ’๐‘ก๐‘ก๐‘ก๐‘ก ๐‘ก๐‘ก๐‘ก๐‘ก ๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“ ๐‘“๐‘“โˆ’๐‘ข๐‘ข๐‘ข๐‘ข
12
Count Outcome Approaches
๏‚จ With unequal follow-up times ๐‘ก๐‘ก1, ๐‘ก๐‘ก2, โ€ฆ , ๐‘ก๐‘ก๐‘›๐‘›
๏‚จ ๐‘ƒ๐‘ƒ ๐‘ฆ๐‘ฆ|๐‘ก๐‘ก, ๐œ†๐œ† =
๐‘’๐‘’โˆ’๐œ†๐œ†๐‘ก๐‘ก(๐œ†๐œ†๐‘ก๐‘ก)๐‘ฆ๐‘ฆ
๐‘ฆ๐‘ฆ!
๏‚จ Where ๐‘ก๐‘ก is the length of follow-up
๏‚จ With unequal follow-up, the MLE for ๐œ†๐œ† is provided
by
๏‚ค ฬ‚๐œ†๐œ† =
๐‘ฆ๐‘ฆ1+๐‘ฆ๐‘ฆ2+โ‹ฏ+๐‘ฆ๐‘ฆ๐‘›๐‘›
๐‘ก๐‘ก1+๐‘ก๐‘ก2+โ‹ฏ+๐‘ก๐‘ก๐‘›๐‘›
=
๏ฟฝ๐‘ฆ๐‘ฆ
ฬ…๐‘ก๐‘ก
=
๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘› ๐‘œ๐‘œ๐‘œ๐‘œ ๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’
๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘โˆ’๐‘ก๐‘ก๐‘ก๐‘ก ๐‘ก๐‘ก๐‘ก๐‘ก ๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“ ๐‘“๐‘“โˆ’๐‘ข๐‘ข๐‘ข๐‘ข
๏‚จ We will see this again
13
Link From Poisson to Exponential
๏‚จ If the count of events follows a Poisson distribution,
then the times between events follow an exponential
distribution
๏‚จ ๐‘“๐‘“ ๐‘ก๐‘ก ๐œ†๐œ† = ๐œ†๐œ†๐‘’๐‘’โˆ’๐œ†๐œ†๐œ†๐œ†
๏‚จ A feature of exponential survival times is that the
hazard event rate is ๐œ†๐œ† and is constant over time
๏‚จ The mean time to an event is
1
๐œ†๐œ†
๏‚จ Gives a way to estimate ๐œ†๐œ† in a survival analysis
setting (rather than a count data setting)
14
Exponential Densities
15
Poisson Regression
๏‚จ In Poisson regression we model the expected count
for an observation as a function of predictor
variables
๏‚จ Poisson regression is a log-linear model so that the
log of the mean is set equal to a linear combination
of the predictors
16
Poisson Regression
๏‚จ ๐‘™๐‘™๐‘™๐‘™ ๐‘™๐‘™ ๐œ†๐œ†๐œ†๐œ† = ๐›ฝ๐›ฝ0 + ๐›ฝ๐›ฝ1 ๐‘ฅ๐‘ฅ
๏‚ค This leads to
๏‚จ ๐‘™๐‘™๐‘™๐‘™ ๐‘™๐‘™ ๐œ†๐œ† + ๐‘™๐‘™๐‘™๐‘™ ๐‘™๐‘™ ๐‘ก๐‘ก = ๐›ฝ๐›ฝ0 + ๐›ฝ๐›ฝ1 ๐‘ฅ๐‘ฅ
๏‚ค So, we get
๏‚จ ๐‘™๐‘™๐‘™๐‘™ ๐‘™๐‘™ ๐œ†๐œ† = ๐›ฝ๐›ฝ0 + ๐›ฝ๐›ฝ1 ๐‘ฅ๐‘ฅ โˆ’ ๐‘™๐‘™๐‘™๐‘™ ๐‘™๐‘™ ๐‘ก๐‘ก
๏‚จ The โˆ’๐‘™๐‘™๐‘™๐‘™ ๐‘™๐‘™ ๐‘ก๐‘ก is called the offset and corrects for the
differences in follow-up time between subjects
๏‚จ The model can be expressed ๐œ†๐œ† = ๐‘’๐‘’ ๐›ฝ๐›ฝ0+๐›ฝ๐›ฝ1 ๐‘ฅ๐‘ฅโˆ’๐‘™๐‘™๐‘™๐‘™๐‘™๐‘™ ๐‘ก๐‘ก
17
Poisson Regression
๏‚จ This model is fit using maximum likelihood
๏‚จ SAS GENMOD
๏‚จ The ๐›ฝ๐›ฝ estimates for predictors are interpreted as
logs of incidence rate ratios
๏‚ค A one-unit increase in ๐‘ฅ๐‘ฅ gives a ratio of ๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’ ๐›ฝ๐›ฝ1 in the
expected count
๏‚ค If ๐‘ฅ๐‘ฅ codes for a group difference (0 = control, 1 =
treatment), then ๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’ ๐›ฝ๐›ฝ1 corresponds to the ratio of
counts in the treated group divided by counts in the
control group
18
Poisson Regression in DCCT
proc genmod;
model nevents = group
/ dist = poisson
link = log
offset = lnyears;
TITLE1 'Poisson regression models of risk
of hypoglycemia';
title2 'unadjusted treatment group effect';
19
Poisson Regression in DCCT
20
Analysis Of Parameter Estimates
Parameter DF Estimate
Standard
Error
Wald 95%
Confidence Limits Chi-Square Pr > ChiSq
Intercept 1 -1.5190 0.0429 -1.6031 -1.4349 1252.90 <.0001
group Exp 1 1.1081 0.0492 1.0117 1.2046 507.01 <.0001
group Std 0 0.0000 0.0000 0.0000 0.0000 . .
Scale 0 1.0000 0.0000 1.0000 1.0000
Poisson Regression in DCCT
21
Highly significant result!
But, is it based on a reasonable model
for the data?
Analysis Of Parameter Estimates
Parameter DF Estimate
Standard
Error
Wald 95%
Confidence Limits Chi-Square Pr > ChiSq
Intercept 1 -1.5190 0.0429 -1.6031 -1.4349 1252.90 <.0001
group Exp 1 1.1081 0.0492 1.0117 1.2046 507.01 <.0001
group Std 0 0.0000 0.0000 0.0000 0.0000 . .
Scale 0 1.0000 0.0000 1.0000 1.0000
Poisson Regression
๏‚จ The big limitation for Poisson regression is
overdispersion
๏‚ค The data are overdispersed when the variation in the
observed counts is greater that the mean value
๏ฎ Under Poisson model these should match
๏‚ค Variance in the counts much greater than the means
๏‚จ Goodness of fit testing for overdispersion is
typically done in Poisson regression
22
Overdispersion in DCCT
23
Criteria For Assessing Goodness Of Fit
Criterion DF Value Value/DF
Deviance 713 3928.7828 5.5102
Scaled Deviance 713 3928.7828 5.5102
Pearson Chi-Square 713 5131.3429 7.1968
Scaled Pearson X2 713 5131.3429 7.1968
Log Likelihood 775.1804
Overdispersion in DCCT
24
Criteria For Assessing Goodness Of Fit
Criterion DF Value Value/DF
Deviance 713 3928.7828 5.5102
Scaled Deviance 713 3928.7828 5.5102
Pearson Chi-Square 713 5131.3429 7.1968
Scaled Pearson X2 713 5131.3429 7.1968
Log Likelihood 775.1804
If model fits well then Value/DF should be close to 1.0
โ€ข Large ratios indicate overdispersion or model
misspecification
Poisson Regression
๏‚จ For a clinical trial, our primary goal is a good test
of treatment effect, so wouldnโ€™t normally need to
include covariates
๏‚จ But, could try to remove excess variation by
controlling for covariates
25
Poisson Regression in DCCT
proc genmod; class group;
model nevents = group
insulin duration female
adult bcval5 hbael hxcoma
/ dist = poisson
link = log
offset = lnyears
covb;
title2 'covariate adjusted treatment group
effect';
26
Poisson Regression in DCCT
27
Analysis Of Parameter Estimates
Parameter DF Estimate
Standard
Error
Wald 95%
Confidence Limits Chi-Square Pr > ChiSq
Intercept 1 -0.9568 0.2174 -1.3829 -0.5308 19.38 <.0001
group Exp 1 1.0845 0.0493 0.9879 1.1812 483.91 <.0001
group Std 0 0.0000 0.0000 0.0000 0.0000 . .
insulin 1 0.0051 0.0995 -0.1898 0.2000 0.00 0.9593
duration 1 0.0015 0.0006 0.0004 0.0026 6.79 0.0092
female 1 0.1794 0.0424 0.0963 0.2624 17.93 <.0001
adult 1 -0.5980 0.0656 -0.7265 -0.4694 83.13 <.0001
bcval5 1 -0.5283 0.3630 -1.2398 0.1833 2.12 0.1456
hbael 1 -0.0335 0.0151 -0.0631 -0.0038 4.89 0.0271
hxcoma 1 0.6010 0.0685 0.4669 0.7352 77.09 <.0001
Scale 0 1.0000 0.0000 1.0000 1.0000
Poisson Regression in DCCT
28
Analysis Of Parameter Estimates
Parameter DF Estimate
Standard
Error
Wald 95%
Confidence Limits Chi-Square Pr > ChiSq
Intercept 1 -0.9568 0.2174 -1.3829 -0.5308 19.38 <.0001
group Exp 1 1.0845 0.0493 0.9879 1.1812 483.91 <.0001
group Std 0 0.0000 0.0000 0.0000 0.0000 . .
insulin 1 0.0051 0.0995 -0.1898 0.2000 0.00 0.9593
duration 1 0.0015 0.0006 0.0004 0.0026 6.79 0.0092
female 1 0.1794 0.0424 0.0963 0.2624 17.93 <.0001
adult 1 -0.5980 0.0656 -0.7265 -0.4694 83.13 <.0001
bcval5 1 -0.5283 0.3630 -1.2398 0.1833 2.12 0.1456
hbael 1 -0.0335 0.0151 -0.0631 -0.0038 4.89 0.0271
hxcoma 1 0.6010 0.0685 0.4669 0.7352 77.09 <.0001
Scale 0 1.0000 0.0000 1.0000 1.0000
Still very significant, but does the model fit better?
Poisson Regression in DCCT
29
Criteria For Assessing Goodness Of Fit
Criterion DF Value Value/DF
Deviance 706 3707.7027 5.2517
Scaled Deviance 706 3707.7027 5.2517
Pearson Chi-Square 706 4792.7876 6.7887
Scaled Pearson X2 706 4792.7876 6.7887
Log Likelihood 885.7204
The fit is better with the covariates included, but still very
overdispersed.
Poisson Regression
๏‚จ Another approach that can be used to remove
overdispersion is to use a variance correction
๏‚ค Pearson correction
๏ฎ Standard approach โ€“ has the actual variance equal the
modeled variance multiplied by an estimated overdispersion
parameter
๏ฎ Corrects the standard errors and test results to account for
the overdispersion
๏‚ค GEE correction based on robust sandwich variance
estimator
๏ฎ Based on a robust sandwich-variance estimator
30
GEE Poisson Regression in DCCT
proc genmod;
class group subnum;
model nevents = group
/ dist = poisson
link = log
offset = lnyears
type3;
repeated subject=subnum / type=unstr;
title2 โ€˜GEE unadjusted treatment group
effect';
31
GEE Poisson Regression in DCCT
32
Analysis Of GEE Parameter Estimates
Empirical Standard Error Estimates
Parameter Estimate
Standard
Error
95% Confidence
Limits Z Pr > |Z|
Intercept -1.5190 0.1003 -1.7155 -1.3225 -15.15 <.0001
group Exp 1.1081 0.1256 0.8620 1.3543 8.82 <.0001
group Std 0.0000 0.0000 0.0000 0.0000 . .
GEE Poisson Regression in DCCT
33
Analysis Of GEE Parameter Estimates
Empirical Standard Error Estimates
Parameter Estimate
Standard
Error
95% Confidence
Limits Z Pr > |Z|
Intercept -1.5190 0.1003 -1.7155 -1.3225 -15.15 <.0001
group Exp 1.1081 0.1256 0.8620 1.3543 8.82 <.0001
group Std 0.0000 0.0000 0.0000 0.0000 . .
Still very significant treatment effect, but note that standard error
is much larger in this model.
Standard error was 0.0492 in Poisson model with only treatment.
Negative Binomial Regression
๏‚จ The negative binomial distribution is another count
data distribution with more variance than the
Poisson
๏‚ค Can be used to give the probability that n trials are
required in order to get m successes (mโ‰คn)
๏‚จ Model takes the form ๐œ†๐œ† = ๐‘’๐‘’ ๐›ฝ๐›ฝ0+๐›ฝ๐›ฝ1 ๐‘ฅ๐‘ฅโˆ’๐‘™๐‘™๐‘™๐‘™๐‘™๐‘™ ๐‘ก๐‘ก +๐œ€๐œ€
๏‚ค Where ๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’ ๐œ€๐œ€ has a gamma distribution
๏‚ค Can be considered to be a Poisson model with gamma-
distributed random effects
๏‚จ Parametric approach to overdispersion
34
Negative Binomial Regression in
DCCT
proc genmod;
class group;
model nevents = group
/ dist = negbin
link = log
offset = lnyears;
title2 โ€˜Neg Binomial unadjusted
treatment group effect';
35
Negative Binomial Regression in
DCCT36
Analysis Of Parameter Estimates
Parameter DF Estimate
Standard
Error
Wald 95%
Confidence
Limits Chi-Square Pr > ChiSq
Intercept 1 -1.5510 0.0902 -1.728 -1.374 295.60 <.0001
group Exp 1 1.1173 0.1215 0.8791 1.3555 84.52 <.0001
group Std 0 0.0000 0.0000 0.0000 0.0000 . .
Dispersion 1 2.1863 0.1649 1.8631 2.5095
Negative Binomial Regression in
DCCT37
Analysis Of Parameter Estimates
Parameter DF Estimate
Standard
Error
Wald 95%
Confidence
Limits Chi-Square Pr > ChiSq
Intercept 1 -1.5510 0.0902 -1.728 -1.374 295.60 <.0001
group Exp 1 1.1173 0.1215 0.8791 1.3555 84.52 <.0001
group Std 0 0.0000 0.0000 0.0000 0.0000 . .
Dispersion 1 2.1863 0.1649 1.8631 2.5095
The results here are quite similar to those of the GEE Poisson
model, with almost the same standard errors.
DCCT Treatment Results
38
Survival Analyses
๏‚จ Repeated events
๏‚ค Cox model on time to first event
๏‚ค Use Andersen-Gill approach and partition follow-up
time according to which event it applies
๏ฎ Restart the follow-up time clock after an event
๏ฎ Multiple observations per subject
๏ฎ Need to be concerned about correlation
๏ฎ Unobserved heterogeneity (due to the correlation) can bias
estimates downward while significance is overstated
39
Survival Analysis in DCCT
proc phreg data=three;
model stopday*event(0) =
intgroup/ risklimits;
title1 'Cox Model for First
Event';
run;
40
Survival Analysis in DCCT
41
Analysis of Maximum Likelihood Estimates
Variable DF
Parameter
Estimate
Standard
Error Chi-Square Pr > ChiSq
Hazard
Ratio
95% Hazard
Ratio
Confidence
Limits
INTGROUP 1 0.77252 0.10354 55.6711 <.0001 2.165 1.768 2.652
Survival Analysis in DCCT
proc phreg data=four;
model gaptime*event(0) =
intgroup priorgap /
risklimits;
title1 'Cox Model for
Second Event - Correlation';
run;
42
Survival Analysis in DCCT
43
Analysis of Maximum Likelihood Estimates
Variable DF
Parameter
Estimate
Standard
Error Chi-Square Pr > ChiSq
Hazard
Ratio
95% Hazard
Ratio
Confidence
Limits
INTGROUP 1 0.27790 0.12451 4.9814 0.0256 1.320 1.034 1.685
priorgap 1 -0.000523 0.000114 20.9317 <.0001 0.999 0.999 1.000
So, having a longer time to the first event reduces risk of the
second event. So correlation in these times to events is quite
substantial.
Survival Analysis in DCCT
proc phreg data=six
covsandwich(aggregate);
model gaptime*event(0) =
intgroup / risklimits;
id patient;
title1 'GEE Cox Model for
all Events';
run;
44
Survival Analysis in DCCT
45
Testing Global Null Hypothesis: BETA=0
Test Chi-Square DF Pr > ChiSq
Likelihood Ratio 74.8679 1 <.0001
Score (Model-Based) 72.4448 1 <.0001
Score (Sandwich) 51.8412 1 <.0001
Wald (Model-Based) 71.4253 1 <.0001
Wald (Sandwich) 40.2564 1 <.0001
Survival Analysis in DCCT
46
Analysis of Maximum Likelihood Estimates
Variable DF
Parameter
Estimate
Standard
Error
StdErr
Ratio Chi-Square Pr > ChiSq
Hazard
Ratio
95% Hazard
Ratio
Confidence
Limits
INTGROUP 1 0.67526 0.08988 1.808 56.4435 <.0001 1.965 1.647 2.343
So, accounting for the correlation increases the standard error by
about 80%. However, the resulting hazard ratio is much less than
the other estimates so far.
Nonparametric Analyses
๏‚จ Work done with Jing Xu
๏‚จ Motivated by his experiences with analysis of
repeated events at
๏‚ค The SDAC for the AIDS Clinical Trials Group
๏‚ค Later experience in the pharmaceutical industry
47
Nonparametric Analyses
๏‚จ In follow-up studies of recurrent events, there were
studies taking a non-parametric approach to
analysis of two-arm trials by
๏‚จ ๐‘ž๐‘ž๐‘–๐‘–๐‘–๐‘– =
๐‘ฆ๐‘ฆ๐‘–๐‘–๐‘–๐‘–
๐‘ก๐‘ก๐‘–๐‘–๐‘–๐‘–
๏‚ค ๐‘ฆ๐‘ฆ๐‘–๐‘–๐‘–๐‘– is the number of events for subject i in arm j
(j is 0 or 1)
๏‚ค ๐‘ก๐‘ก๐‘–๐‘–๐‘–๐‘– is the total length of follow-up for subject i in group j
๏‚จ ๐‘ž๐‘ž๐‘–๐‘–๐‘–๐‘– represents a subject-specific event rate
48
Nonparametric Analyses
๏‚จ ๐‘ž๐‘ž๐‘–๐‘–๐‘–๐‘– were analyzed without assuming any particular
distribution by standard two-sample tests
๏‚ค Student t-test
๏‚ค Wilcoxon test
๏‚ค Van der Waerden test
49
Nonparametric Analyses
๏‚จ For estimation, the means of the subject-specific
event rates were calculated for each group
๏‚จ ๏ฟฝ๐‘„๐‘„๐‘—๐‘— =
1
๐‘›๐‘›๐‘—๐‘—
โˆ‘๐‘–๐‘–=1
๐‘›๐‘›๐‘—๐‘—
๐‘ž๐‘ž๐‘–๐‘–๐‘–๐‘– =
1
๐‘›๐‘›๐‘—๐‘—
โˆ‘๐‘–๐‘–=1
๐‘›๐‘›๐‘—๐‘— ๐‘ฆ๐‘ฆ๐‘–๐‘–๐‘–๐‘–
๐‘ก๐‘ก๐‘–๐‘–๐‘–๐‘–
๏‚จ These ๏ฟฝ๐‘„๐‘„๐‘—๐‘— could then be used to estimate ratios of
the rates and differences in the rates by group
๏‚ค ๏ฟฝ๐‘…๐‘… ๐‘…๐‘…๐‘„๐‘„ =
๏ฟฝ๐‘„๐‘„1
๏ฟฝ๐‘„๐‘„0
๏‚ค ๏ฟฝ๐‘…๐‘… ๐‘…๐‘…๐‘„๐‘„ = ๏ฟฝ๐‘„๐‘„1 โˆ’ ๏ฟฝ๐‘„๐‘„0
50
Nonparametric Analyses
๏‚จ Our concern about this ๐‘ž๐‘ž๐‘–๐‘–๐‘–๐‘– approach was that
๏‚ค There could be outliers โ€“ subjects having a large
number of events in a short amount of time who then
drop out of the study early
๏‚ค The asymptotic consistency of the ๏ฟฝ๐‘„๐‘„๐‘—๐‘— estimators
depends on both the numbers of events and the amount
of follow-up increasing within all subjects
51
Nonparametric Analyses
๏‚จ A different approach had been suggested by L.J.
Wei
๏‚จ ๏ฟฝ๐‘…๐‘…๐‘—๐‘— =
๐‘ฅ๐‘ฅ๐‘—๐‘—
๐‘ก๐‘ก๐‘—๐‘—
= ๏ฟฝ
โˆ‘๐‘–๐‘–=1
๐‘›๐‘›๐‘—๐‘—
๐‘ฅ๐‘ฅ๐‘–๐‘–๐‘–๐‘–
โˆ‘๐‘–๐‘–=1
๐‘›๐‘›๐‘—๐‘—
๐‘ก๐‘ก๐‘–๐‘–๐‘–๐‘–
=
๐‘ฅ๐‘ฅ๐‘—๐‘—
๏ฟฝ๐‘ก๐‘ก๐‘—๐‘—
๏‚จ Ratio of the means, not the mean of the ratios
52
Nonparametric Analyses
๏‚จ A different approach had been suggested by L.J.
Wei
๏‚จ ๏ฟฝ๐‘…๐‘…๐‘—๐‘— =
๐‘ฅ๐‘ฅ๐‘—๐‘—
๐‘ก๐‘ก๐‘—๐‘—
= ๏ฟฝ
โˆ‘๐‘–๐‘–=1
๐‘›๐‘›๐‘—๐‘—
๐‘ฅ๐‘ฅ๐‘–๐‘–๐‘–๐‘–
โˆ‘๐‘–๐‘–=1
๐‘›๐‘›๐‘—๐‘—
๐‘ก๐‘ก๐‘–๐‘–๐‘–๐‘–
=
๐‘ฅ๐‘ฅ๐‘—๐‘—
๏ฟฝ๐‘ก๐‘ก๐‘—๐‘—
๏‚จ Ratio of the means, not the mean of the ratios
๏‚จ This is just the standard Poisson events per person-
time without assuming the distribution
53
Nonparametric Analyses
๏‚จ Can use the ๏ฟฝ๐‘…๐‘…๐‘—๐‘— to estimate rate ratio and difference
in rates between groups
๏‚ค ๏ฟฝ๐‘…๐‘…๐‘…๐‘…๐‘…๐‘… =
๏ฟฝ๐‘…๐‘…1
๏ฟฝ๐‘…๐‘…0
๏‚ค ๏ฟฝ๐‘…๐‘… ๐‘…๐‘…๐‘…๐‘… = ๏ฟฝ๐‘…๐‘…1 โˆ’ ๏ฟฝ๐‘…๐‘…0
54
Nonparametric Analyses
๏‚จ ๏ฟฝ๐‘…๐‘…๐‘—๐‘— advantages
๏‚ค Average out any outliers
๏‚ค Makes consistency more reasonable as it uses the group
totals for number of events and total follow-up time
๏‚จ ๏ฟฝ๐‘…๐‘…๐‘—๐‘— disadvantages
๏‚ค Measure is group-specific and not subject-specific
๏‚ค Canโ€™t use standard 2-sample tests
55
Nonparametric Analyses
๏‚จ Asymptotic forms of the variance for the ๏ฟฝ๐‘…๐‘…
measures are in the Xu and LaValley paper in the
references
๏‚ค Confidence intervals based on Fiellerโ€™s method and
resampling
๏‚จ In this talk, Iโ€™ll use resampling methods to evaluate
the ๏ฟฝ๐‘…๐‘…๐‘—๐‘— measures
๏‚ค Permutation tests
๏‚ค Bootstrap confidence intervals
56
57
Nonparametric Analyses
๏‚จ In simulations, we found that the ๏ฟฝ๐‘„๐‘„๐‘—๐‘— with a non-
parametric test and the ๏ฟฝ๐‘…๐‘…๐‘—๐‘— methods maintained the
type-1 error and had comparable power over a
range of sample sizes
๏‚จ The ๏ฟฝ๐‘…๐‘…๐‘—๐‘— methods provided reasonable confidence
interval coverage if the sample sizes were at least
100 per group
58
Nonparametric Analyses
๏‚จ In the paper we use the nonparametric methods on
a dataset for recurrence of bladder cancer in a
two-arm clinical trial of the drug thiotepa
59
Nonparametric Analyses
๏‚จ Thiotepa trial results
๏‚จ Results are uniformly non-significant, with rate ratios
from 0.71 to 0.84
60
Nonparametric Analyses
๏‚จ Thiotepa trial results
๏‚จ These are the results that I trust the most out of
these
61
Nonparametric Analyses in DCCT
62
Intensive
Treatment
Conventional
Treatment
๐‘›๐‘› Subjects 363 352
๏ฟฝ๐‘ฆ๐‘ฆ Hypoglycemia
Events/Subject
4.75 1.54
ฬ…๐‘ก๐‘ก Person-Years of
Follow-Up/Subject
7.16 7.05
๏ฟฝ
๏ฟฝ๐‘ฆ๐‘ฆ
ฬ…๐‘ก๐‘ก
๏ฟฝ๐‘…๐‘…๐‘—๐‘— 0.66 0.22
๏ฟฝ๐‘„๐‘„๐‘—๐‘— 0.65 0.21
Nonparametric Analyses in DCCT
63
Distribution
of qij by
group
Nonparametric Analyses in DCCT
64
Test Test Statistic P-value
t-test of qij 8.28 P < 0.0001
Van der Waerden
test of qij
8.77 P < 0.0001
Wilcoxon test of qij 8.57 P < 0.0001
Nonparametric Analyses in DCCT
65
Estimator Estimate Permutation Test
P-value*
Rate Difference (Q) 0.43681 P < 0.0005
Rate Difference (R) 0.44415 P < 0.0005
Rate Ratio (Q) 3.08059 P < 0.0005
Rate Ratio (R) 3.02872 P < 0.0005
*Based on 2000
permutations
Nonparametric Analyses in DCCT
66
Q versus R
measures of rate
difference across
2000 permuted
datasets
Nonparametric Analyses in DCCT
67
Estimator Estimate Bootstrap
Confidence Interval
Rate Difference (Q) 0.43681 (0.329, 0.549)
Rate Difference (R) 0.44415 (0.329, 0.561)
Rate Ratio (Q) 3.08059 (2.399, 3.979)
Rate Ratio (R) 3.02872 (2.333, 3.951)
Nonparametric Analyses in DCCT
68
Q versus R
measures of rate
difference across
2000 bootstrap
samples
Nonparametric Analyses
๏‚จ Both Q and R measures work well for reasonable
sized datasets
๏‚จ In these DCCT data, both are fine
๏‚จ In the bladder cancer data, the R (ratio of means)
seems to have a slight edge
69
Conclusions
๏‚จ There are a lot of good options for the analysis of
repeated events
๏‚ค GEE Survival models
๏‚ค Gee Poisson Regression
๏‚ค Negative binomial regression
๏‚ค Q and R measures โ€“ especially in clinical trial setting
๏‚จ Worthwhile to work with several as secondary
analyses to verify consistency
70
Main References
๏‚จ Allison PD. Survival Analysis Using SAS: a Practical
Guide, second edition. SAS Publishing, 2010.
๏‚จ Lachin JM. Biostatistical Methods: the Assessment of
Relative Risks. Wiley, 2000.
๏‚จ Xu J, LaValley M. One-sample and two-sample
analysis of heterogeneous person-time data in
clinical trials. Pharmaceutical Statistics 2012; 11:
194 โ€“ 203.
71

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Repeated events analyses

  • 2. Outline for Talk ๏‚จ Recurrent Events ๏‚จ Analyses for Count Outcomes ๏‚จ Survival Analysis Approaches for Repeated Events ๏‚จ Parametric Analyses for Counts ๏‚ค Poisson Regression ๏‚ค Negative Binomial ๏‚จ Non-parametric Analyses for Counts ๏‚ค Mean of Ratios (Q) ๏‚ค Ratio of Means (R) 2
  • 3. Recurrent Events ๏‚จ Usually in survival studies subjects are followed until they experience a single index event ๏‚ค Death ๏‚ค Cancer ๏‚ค Return to employment ๏‚จ But there are many events of interest that are repeatable ๏‚ค Seizures ๏‚ค Infections ๏‚ค Hospitalizations 3
  • 4. Recurrent Events ๏‚จ Most of the methods employed in survival analysis are set up for a single event ๏‚จ But, there have been methods developed for use with repeated events ๏‚ค Some of these methods come out of the area of statistical methods developed for count data โ€“ these focus on the count of the number of recurrent event ๏‚ค Some methods come directly out of survival analysis methods โ€“ these focus on the time duration between the recurrent events 4
  • 5. Recurrent Events ๏‚จ Methods coming out of either area need to address the domain of the other methods ๏‚ค The count methods also need to address the time component ๏‚ค The survival methods need to address the number of events as well as the gap times between events 5
  • 6. Diabetes Control and Complications Trial (DCCT) ๏‚จ NIH-funded trial ๏‚จ Launched in 1981 ๏‚จ To evaluate the effect of intensive blood glucose- lowering on risk of albuminuria in diabetic subjects ๏‚จ Subjects were randomized to either intensive blood glucose lowering or conventional treatment ๏‚จ Intensive glucose lowering used self-monitoring 4 or 5 times daily, multiple daily insulin injections or a pump, diet and exercise 6
  • 7. Diabetes Control and Complications Trial (DCCT) ๏‚จ A concern was that the intensive glucose lowering could lead to hypoglycemia ๏‚ค Dizzy spells ๏‚ค Possible comas ๏‚ค Seizures ๏‚จ Hypoglycemia events were tracked as a secondary outcome (DCCT 1997) 7
  • 8. Diabetes Control and Complications Trial (DCCT) Intensive Treatment Conventional Treatment Subjects 363 352 Hypoglycemia Events 1723 543 Person-Years of Follow-Up 2598.5 2480.8 Rate per 100 Person-Years 66.3 21.9 8
  • 9. Count Outcome Approaches ๏‚จ The most basic analysis for count outcomes comes from the Poisson distribution ๏‚จ ๐‘ƒ๐‘ƒ ๐‘ฆ๐‘ฆ|๐œ†๐œ† = ๐‘’๐‘’โˆ’๐œ†๐œ† ๐œ†๐œ† ๐‘ฆ๐‘ฆ ๐‘ฆ๐‘ฆ! ๏‚ค Here ๐œ†๐œ† is the mean count ๏‚ค y is the observed count (non-negative integer) ๏‚จ One feature of the Poisson distribution is that ๏‚ค Variance = Mean = ๐œ†๐œ† 9
  • 11. Count Outcome Approaches ๏‚จ The maximum likelihood estimator of the mean is provided by the sample average ๏‚ค ฬ‚๐œ†๐œ† = ๐‘ฆ๐‘ฆ1+๐‘ฆ๐‘ฆ2+โ‹ฏ+๐‘ฆ๐‘ฆ๐‘›๐‘› ๐‘›๐‘› ๏‚จ Often people are followed for somewhat different lengths of time, giving some people more opportunity to get larger event counts ๏‚ค In this case ๐œ†๐œ† is standardized to be per-unit of time 11
  • 12. Count Outcome Approaches ๏‚จ With unequal follow-up times ๐‘ก๐‘ก1, ๐‘ก๐‘ก2, โ€ฆ , ๐‘ก๐‘ก๐‘›๐‘› ๏‚จ ๐‘ƒ๐‘ƒ ๐‘ฆ๐‘ฆ|๐‘ก๐‘ก, ๐œ†๐œ† = ๐‘’๐‘’โˆ’๐œ†๐œ†๐‘ก๐‘ก(๐œ†๐œ†๐‘ก๐‘ก)๐‘ฆ๐‘ฆ ๐‘ฆ๐‘ฆ! ๏‚จ Where ๐‘ก๐‘ก is the length of follow-up ๏‚จ With unequal follow-up, the MLE for ๐œ†๐œ† is provided by ๏‚ค ฬ‚๐œ†๐œ† = ๐‘ฆ๐‘ฆ1+๐‘ฆ๐‘ฆ2+โ‹ฏ+๐‘ฆ๐‘ฆ๐‘›๐‘› ๐‘ก๐‘ก1+๐‘ก๐‘ก2+โ‹ฏ+๐‘ก๐‘ก๐‘›๐‘› = ๏ฟฝ๐‘ฆ๐‘ฆ ฬ…๐‘ก๐‘ก = ๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘› ๐‘œ๐‘œ๐‘œ๐‘œ ๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’ ๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘โˆ’๐‘ก๐‘ก๐‘ก๐‘ก ๐‘ก๐‘ก๐‘ก๐‘ก ๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“ ๐‘“๐‘“โˆ’๐‘ข๐‘ข๐‘ข๐‘ข 12
  • 13. Count Outcome Approaches ๏‚จ With unequal follow-up times ๐‘ก๐‘ก1, ๐‘ก๐‘ก2, โ€ฆ , ๐‘ก๐‘ก๐‘›๐‘› ๏‚จ ๐‘ƒ๐‘ƒ ๐‘ฆ๐‘ฆ|๐‘ก๐‘ก, ๐œ†๐œ† = ๐‘’๐‘’โˆ’๐œ†๐œ†๐‘ก๐‘ก(๐œ†๐œ†๐‘ก๐‘ก)๐‘ฆ๐‘ฆ ๐‘ฆ๐‘ฆ! ๏‚จ Where ๐‘ก๐‘ก is the length of follow-up ๏‚จ With unequal follow-up, the MLE for ๐œ†๐œ† is provided by ๏‚ค ฬ‚๐œ†๐œ† = ๐‘ฆ๐‘ฆ1+๐‘ฆ๐‘ฆ2+โ‹ฏ+๐‘ฆ๐‘ฆ๐‘›๐‘› ๐‘ก๐‘ก1+๐‘ก๐‘ก2+โ‹ฏ+๐‘ก๐‘ก๐‘›๐‘› = ๏ฟฝ๐‘ฆ๐‘ฆ ฬ…๐‘ก๐‘ก = ๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘›๐‘› ๐‘œ๐‘œ๐‘œ๐‘œ ๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’ ๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘๐‘โˆ’๐‘ก๐‘ก๐‘ก๐‘ก ๐‘ก๐‘ก๐‘ก๐‘ก ๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“๐‘“ ๐‘“๐‘“โˆ’๐‘ข๐‘ข๐‘ข๐‘ข ๏‚จ We will see this again 13
  • 14. Link From Poisson to Exponential ๏‚จ If the count of events follows a Poisson distribution, then the times between events follow an exponential distribution ๏‚จ ๐‘“๐‘“ ๐‘ก๐‘ก ๐œ†๐œ† = ๐œ†๐œ†๐‘’๐‘’โˆ’๐œ†๐œ†๐œ†๐œ† ๏‚จ A feature of exponential survival times is that the hazard event rate is ๐œ†๐œ† and is constant over time ๏‚จ The mean time to an event is 1 ๐œ†๐œ† ๏‚จ Gives a way to estimate ๐œ†๐œ† in a survival analysis setting (rather than a count data setting) 14
  • 16. Poisson Regression ๏‚จ In Poisson regression we model the expected count for an observation as a function of predictor variables ๏‚จ Poisson regression is a log-linear model so that the log of the mean is set equal to a linear combination of the predictors 16
  • 17. Poisson Regression ๏‚จ ๐‘™๐‘™๐‘™๐‘™ ๐‘™๐‘™ ๐œ†๐œ†๐œ†๐œ† = ๐›ฝ๐›ฝ0 + ๐›ฝ๐›ฝ1 ๐‘ฅ๐‘ฅ ๏‚ค This leads to ๏‚จ ๐‘™๐‘™๐‘™๐‘™ ๐‘™๐‘™ ๐œ†๐œ† + ๐‘™๐‘™๐‘™๐‘™ ๐‘™๐‘™ ๐‘ก๐‘ก = ๐›ฝ๐›ฝ0 + ๐›ฝ๐›ฝ1 ๐‘ฅ๐‘ฅ ๏‚ค So, we get ๏‚จ ๐‘™๐‘™๐‘™๐‘™ ๐‘™๐‘™ ๐œ†๐œ† = ๐›ฝ๐›ฝ0 + ๐›ฝ๐›ฝ1 ๐‘ฅ๐‘ฅ โˆ’ ๐‘™๐‘™๐‘™๐‘™ ๐‘™๐‘™ ๐‘ก๐‘ก ๏‚จ The โˆ’๐‘™๐‘™๐‘™๐‘™ ๐‘™๐‘™ ๐‘ก๐‘ก is called the offset and corrects for the differences in follow-up time between subjects ๏‚จ The model can be expressed ๐œ†๐œ† = ๐‘’๐‘’ ๐›ฝ๐›ฝ0+๐›ฝ๐›ฝ1 ๐‘ฅ๐‘ฅโˆ’๐‘™๐‘™๐‘™๐‘™๐‘™๐‘™ ๐‘ก๐‘ก 17
  • 18. Poisson Regression ๏‚จ This model is fit using maximum likelihood ๏‚จ SAS GENMOD ๏‚จ The ๐›ฝ๐›ฝ estimates for predictors are interpreted as logs of incidence rate ratios ๏‚ค A one-unit increase in ๐‘ฅ๐‘ฅ gives a ratio of ๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’ ๐›ฝ๐›ฝ1 in the expected count ๏‚ค If ๐‘ฅ๐‘ฅ codes for a group difference (0 = control, 1 = treatment), then ๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’ ๐›ฝ๐›ฝ1 corresponds to the ratio of counts in the treated group divided by counts in the control group 18
  • 19. Poisson Regression in DCCT proc genmod; model nevents = group / dist = poisson link = log offset = lnyears; TITLE1 'Poisson regression models of risk of hypoglycemia'; title2 'unadjusted treatment group effect'; 19
  • 20. Poisson Regression in DCCT 20 Analysis Of Parameter Estimates Parameter DF Estimate Standard Error Wald 95% Confidence Limits Chi-Square Pr > ChiSq Intercept 1 -1.5190 0.0429 -1.6031 -1.4349 1252.90 <.0001 group Exp 1 1.1081 0.0492 1.0117 1.2046 507.01 <.0001 group Std 0 0.0000 0.0000 0.0000 0.0000 . . Scale 0 1.0000 0.0000 1.0000 1.0000
  • 21. Poisson Regression in DCCT 21 Highly significant result! But, is it based on a reasonable model for the data? Analysis Of Parameter Estimates Parameter DF Estimate Standard Error Wald 95% Confidence Limits Chi-Square Pr > ChiSq Intercept 1 -1.5190 0.0429 -1.6031 -1.4349 1252.90 <.0001 group Exp 1 1.1081 0.0492 1.0117 1.2046 507.01 <.0001 group Std 0 0.0000 0.0000 0.0000 0.0000 . . Scale 0 1.0000 0.0000 1.0000 1.0000
  • 22. Poisson Regression ๏‚จ The big limitation for Poisson regression is overdispersion ๏‚ค The data are overdispersed when the variation in the observed counts is greater that the mean value ๏ฎ Under Poisson model these should match ๏‚ค Variance in the counts much greater than the means ๏‚จ Goodness of fit testing for overdispersion is typically done in Poisson regression 22
  • 23. Overdispersion in DCCT 23 Criteria For Assessing Goodness Of Fit Criterion DF Value Value/DF Deviance 713 3928.7828 5.5102 Scaled Deviance 713 3928.7828 5.5102 Pearson Chi-Square 713 5131.3429 7.1968 Scaled Pearson X2 713 5131.3429 7.1968 Log Likelihood 775.1804
  • 24. Overdispersion in DCCT 24 Criteria For Assessing Goodness Of Fit Criterion DF Value Value/DF Deviance 713 3928.7828 5.5102 Scaled Deviance 713 3928.7828 5.5102 Pearson Chi-Square 713 5131.3429 7.1968 Scaled Pearson X2 713 5131.3429 7.1968 Log Likelihood 775.1804 If model fits well then Value/DF should be close to 1.0 โ€ข Large ratios indicate overdispersion or model misspecification
  • 25. Poisson Regression ๏‚จ For a clinical trial, our primary goal is a good test of treatment effect, so wouldnโ€™t normally need to include covariates ๏‚จ But, could try to remove excess variation by controlling for covariates 25
  • 26. Poisson Regression in DCCT proc genmod; class group; model nevents = group insulin duration female adult bcval5 hbael hxcoma / dist = poisson link = log offset = lnyears covb; title2 'covariate adjusted treatment group effect'; 26
  • 27. Poisson Regression in DCCT 27 Analysis Of Parameter Estimates Parameter DF Estimate Standard Error Wald 95% Confidence Limits Chi-Square Pr > ChiSq Intercept 1 -0.9568 0.2174 -1.3829 -0.5308 19.38 <.0001 group Exp 1 1.0845 0.0493 0.9879 1.1812 483.91 <.0001 group Std 0 0.0000 0.0000 0.0000 0.0000 . . insulin 1 0.0051 0.0995 -0.1898 0.2000 0.00 0.9593 duration 1 0.0015 0.0006 0.0004 0.0026 6.79 0.0092 female 1 0.1794 0.0424 0.0963 0.2624 17.93 <.0001 adult 1 -0.5980 0.0656 -0.7265 -0.4694 83.13 <.0001 bcval5 1 -0.5283 0.3630 -1.2398 0.1833 2.12 0.1456 hbael 1 -0.0335 0.0151 -0.0631 -0.0038 4.89 0.0271 hxcoma 1 0.6010 0.0685 0.4669 0.7352 77.09 <.0001 Scale 0 1.0000 0.0000 1.0000 1.0000
  • 28. Poisson Regression in DCCT 28 Analysis Of Parameter Estimates Parameter DF Estimate Standard Error Wald 95% Confidence Limits Chi-Square Pr > ChiSq Intercept 1 -0.9568 0.2174 -1.3829 -0.5308 19.38 <.0001 group Exp 1 1.0845 0.0493 0.9879 1.1812 483.91 <.0001 group Std 0 0.0000 0.0000 0.0000 0.0000 . . insulin 1 0.0051 0.0995 -0.1898 0.2000 0.00 0.9593 duration 1 0.0015 0.0006 0.0004 0.0026 6.79 0.0092 female 1 0.1794 0.0424 0.0963 0.2624 17.93 <.0001 adult 1 -0.5980 0.0656 -0.7265 -0.4694 83.13 <.0001 bcval5 1 -0.5283 0.3630 -1.2398 0.1833 2.12 0.1456 hbael 1 -0.0335 0.0151 -0.0631 -0.0038 4.89 0.0271 hxcoma 1 0.6010 0.0685 0.4669 0.7352 77.09 <.0001 Scale 0 1.0000 0.0000 1.0000 1.0000 Still very significant, but does the model fit better?
  • 29. Poisson Regression in DCCT 29 Criteria For Assessing Goodness Of Fit Criterion DF Value Value/DF Deviance 706 3707.7027 5.2517 Scaled Deviance 706 3707.7027 5.2517 Pearson Chi-Square 706 4792.7876 6.7887 Scaled Pearson X2 706 4792.7876 6.7887 Log Likelihood 885.7204 The fit is better with the covariates included, but still very overdispersed.
  • 30. Poisson Regression ๏‚จ Another approach that can be used to remove overdispersion is to use a variance correction ๏‚ค Pearson correction ๏ฎ Standard approach โ€“ has the actual variance equal the modeled variance multiplied by an estimated overdispersion parameter ๏ฎ Corrects the standard errors and test results to account for the overdispersion ๏‚ค GEE correction based on robust sandwich variance estimator ๏ฎ Based on a robust sandwich-variance estimator 30
  • 31. GEE Poisson Regression in DCCT proc genmod; class group subnum; model nevents = group / dist = poisson link = log offset = lnyears type3; repeated subject=subnum / type=unstr; title2 โ€˜GEE unadjusted treatment group effect'; 31
  • 32. GEE Poisson Regression in DCCT 32 Analysis Of GEE Parameter Estimates Empirical Standard Error Estimates Parameter Estimate Standard Error 95% Confidence Limits Z Pr > |Z| Intercept -1.5190 0.1003 -1.7155 -1.3225 -15.15 <.0001 group Exp 1.1081 0.1256 0.8620 1.3543 8.82 <.0001 group Std 0.0000 0.0000 0.0000 0.0000 . .
  • 33. GEE Poisson Regression in DCCT 33 Analysis Of GEE Parameter Estimates Empirical Standard Error Estimates Parameter Estimate Standard Error 95% Confidence Limits Z Pr > |Z| Intercept -1.5190 0.1003 -1.7155 -1.3225 -15.15 <.0001 group Exp 1.1081 0.1256 0.8620 1.3543 8.82 <.0001 group Std 0.0000 0.0000 0.0000 0.0000 . . Still very significant treatment effect, but note that standard error is much larger in this model. Standard error was 0.0492 in Poisson model with only treatment.
  • 34. Negative Binomial Regression ๏‚จ The negative binomial distribution is another count data distribution with more variance than the Poisson ๏‚ค Can be used to give the probability that n trials are required in order to get m successes (mโ‰คn) ๏‚จ Model takes the form ๐œ†๐œ† = ๐‘’๐‘’ ๐›ฝ๐›ฝ0+๐›ฝ๐›ฝ1 ๐‘ฅ๐‘ฅโˆ’๐‘™๐‘™๐‘™๐‘™๐‘™๐‘™ ๐‘ก๐‘ก +๐œ€๐œ€ ๏‚ค Where ๐‘’๐‘’๐‘’๐‘’๐‘’๐‘’ ๐œ€๐œ€ has a gamma distribution ๏‚ค Can be considered to be a Poisson model with gamma- distributed random effects ๏‚จ Parametric approach to overdispersion 34
  • 35. Negative Binomial Regression in DCCT proc genmod; class group; model nevents = group / dist = negbin link = log offset = lnyears; title2 โ€˜Neg Binomial unadjusted treatment group effect'; 35
  • 36. Negative Binomial Regression in DCCT36 Analysis Of Parameter Estimates Parameter DF Estimate Standard Error Wald 95% Confidence Limits Chi-Square Pr > ChiSq Intercept 1 -1.5510 0.0902 -1.728 -1.374 295.60 <.0001 group Exp 1 1.1173 0.1215 0.8791 1.3555 84.52 <.0001 group Std 0 0.0000 0.0000 0.0000 0.0000 . . Dispersion 1 2.1863 0.1649 1.8631 2.5095
  • 37. Negative Binomial Regression in DCCT37 Analysis Of Parameter Estimates Parameter DF Estimate Standard Error Wald 95% Confidence Limits Chi-Square Pr > ChiSq Intercept 1 -1.5510 0.0902 -1.728 -1.374 295.60 <.0001 group Exp 1 1.1173 0.1215 0.8791 1.3555 84.52 <.0001 group Std 0 0.0000 0.0000 0.0000 0.0000 . . Dispersion 1 2.1863 0.1649 1.8631 2.5095 The results here are quite similar to those of the GEE Poisson model, with almost the same standard errors.
  • 39. Survival Analyses ๏‚จ Repeated events ๏‚ค Cox model on time to first event ๏‚ค Use Andersen-Gill approach and partition follow-up time according to which event it applies ๏ฎ Restart the follow-up time clock after an event ๏ฎ Multiple observations per subject ๏ฎ Need to be concerned about correlation ๏ฎ Unobserved heterogeneity (due to the correlation) can bias estimates downward while significance is overstated 39
  • 40. Survival Analysis in DCCT proc phreg data=three; model stopday*event(0) = intgroup/ risklimits; title1 'Cox Model for First Event'; run; 40
  • 41. Survival Analysis in DCCT 41 Analysis of Maximum Likelihood Estimates Variable DF Parameter Estimate Standard Error Chi-Square Pr > ChiSq Hazard Ratio 95% Hazard Ratio Confidence Limits INTGROUP 1 0.77252 0.10354 55.6711 <.0001 2.165 1.768 2.652
  • 42. Survival Analysis in DCCT proc phreg data=four; model gaptime*event(0) = intgroup priorgap / risklimits; title1 'Cox Model for Second Event - Correlation'; run; 42
  • 43. Survival Analysis in DCCT 43 Analysis of Maximum Likelihood Estimates Variable DF Parameter Estimate Standard Error Chi-Square Pr > ChiSq Hazard Ratio 95% Hazard Ratio Confidence Limits INTGROUP 1 0.27790 0.12451 4.9814 0.0256 1.320 1.034 1.685 priorgap 1 -0.000523 0.000114 20.9317 <.0001 0.999 0.999 1.000 So, having a longer time to the first event reduces risk of the second event. So correlation in these times to events is quite substantial.
  • 44. Survival Analysis in DCCT proc phreg data=six covsandwich(aggregate); model gaptime*event(0) = intgroup / risklimits; id patient; title1 'GEE Cox Model for all Events'; run; 44
  • 45. Survival Analysis in DCCT 45 Testing Global Null Hypothesis: BETA=0 Test Chi-Square DF Pr > ChiSq Likelihood Ratio 74.8679 1 <.0001 Score (Model-Based) 72.4448 1 <.0001 Score (Sandwich) 51.8412 1 <.0001 Wald (Model-Based) 71.4253 1 <.0001 Wald (Sandwich) 40.2564 1 <.0001
  • 46. Survival Analysis in DCCT 46 Analysis of Maximum Likelihood Estimates Variable DF Parameter Estimate Standard Error StdErr Ratio Chi-Square Pr > ChiSq Hazard Ratio 95% Hazard Ratio Confidence Limits INTGROUP 1 0.67526 0.08988 1.808 56.4435 <.0001 1.965 1.647 2.343 So, accounting for the correlation increases the standard error by about 80%. However, the resulting hazard ratio is much less than the other estimates so far.
  • 47. Nonparametric Analyses ๏‚จ Work done with Jing Xu ๏‚จ Motivated by his experiences with analysis of repeated events at ๏‚ค The SDAC for the AIDS Clinical Trials Group ๏‚ค Later experience in the pharmaceutical industry 47
  • 48. Nonparametric Analyses ๏‚จ In follow-up studies of recurrent events, there were studies taking a non-parametric approach to analysis of two-arm trials by ๏‚จ ๐‘ž๐‘ž๐‘–๐‘–๐‘–๐‘– = ๐‘ฆ๐‘ฆ๐‘–๐‘–๐‘–๐‘– ๐‘ก๐‘ก๐‘–๐‘–๐‘–๐‘– ๏‚ค ๐‘ฆ๐‘ฆ๐‘–๐‘–๐‘–๐‘– is the number of events for subject i in arm j (j is 0 or 1) ๏‚ค ๐‘ก๐‘ก๐‘–๐‘–๐‘–๐‘– is the total length of follow-up for subject i in group j ๏‚จ ๐‘ž๐‘ž๐‘–๐‘–๐‘–๐‘– represents a subject-specific event rate 48
  • 49. Nonparametric Analyses ๏‚จ ๐‘ž๐‘ž๐‘–๐‘–๐‘–๐‘– were analyzed without assuming any particular distribution by standard two-sample tests ๏‚ค Student t-test ๏‚ค Wilcoxon test ๏‚ค Van der Waerden test 49
  • 50. Nonparametric Analyses ๏‚จ For estimation, the means of the subject-specific event rates were calculated for each group ๏‚จ ๏ฟฝ๐‘„๐‘„๐‘—๐‘— = 1 ๐‘›๐‘›๐‘—๐‘— โˆ‘๐‘–๐‘–=1 ๐‘›๐‘›๐‘—๐‘— ๐‘ž๐‘ž๐‘–๐‘–๐‘–๐‘– = 1 ๐‘›๐‘›๐‘—๐‘— โˆ‘๐‘–๐‘–=1 ๐‘›๐‘›๐‘—๐‘— ๐‘ฆ๐‘ฆ๐‘–๐‘–๐‘–๐‘– ๐‘ก๐‘ก๐‘–๐‘–๐‘–๐‘– ๏‚จ These ๏ฟฝ๐‘„๐‘„๐‘—๐‘— could then be used to estimate ratios of the rates and differences in the rates by group ๏‚ค ๏ฟฝ๐‘…๐‘… ๐‘…๐‘…๐‘„๐‘„ = ๏ฟฝ๐‘„๐‘„1 ๏ฟฝ๐‘„๐‘„0 ๏‚ค ๏ฟฝ๐‘…๐‘… ๐‘…๐‘…๐‘„๐‘„ = ๏ฟฝ๐‘„๐‘„1 โˆ’ ๏ฟฝ๐‘„๐‘„0 50
  • 51. Nonparametric Analyses ๏‚จ Our concern about this ๐‘ž๐‘ž๐‘–๐‘–๐‘–๐‘– approach was that ๏‚ค There could be outliers โ€“ subjects having a large number of events in a short amount of time who then drop out of the study early ๏‚ค The asymptotic consistency of the ๏ฟฝ๐‘„๐‘„๐‘—๐‘— estimators depends on both the numbers of events and the amount of follow-up increasing within all subjects 51
  • 52. Nonparametric Analyses ๏‚จ A different approach had been suggested by L.J. Wei ๏‚จ ๏ฟฝ๐‘…๐‘…๐‘—๐‘— = ๐‘ฅ๐‘ฅ๐‘—๐‘— ๐‘ก๐‘ก๐‘—๐‘— = ๏ฟฝ โˆ‘๐‘–๐‘–=1 ๐‘›๐‘›๐‘—๐‘— ๐‘ฅ๐‘ฅ๐‘–๐‘–๐‘–๐‘– โˆ‘๐‘–๐‘–=1 ๐‘›๐‘›๐‘—๐‘— ๐‘ก๐‘ก๐‘–๐‘–๐‘–๐‘– = ๐‘ฅ๐‘ฅ๐‘—๐‘— ๏ฟฝ๐‘ก๐‘ก๐‘—๐‘— ๏‚จ Ratio of the means, not the mean of the ratios 52
  • 53. Nonparametric Analyses ๏‚จ A different approach had been suggested by L.J. Wei ๏‚จ ๏ฟฝ๐‘…๐‘…๐‘—๐‘— = ๐‘ฅ๐‘ฅ๐‘—๐‘— ๐‘ก๐‘ก๐‘—๐‘— = ๏ฟฝ โˆ‘๐‘–๐‘–=1 ๐‘›๐‘›๐‘—๐‘— ๐‘ฅ๐‘ฅ๐‘–๐‘–๐‘–๐‘– โˆ‘๐‘–๐‘–=1 ๐‘›๐‘›๐‘—๐‘— ๐‘ก๐‘ก๐‘–๐‘–๐‘–๐‘– = ๐‘ฅ๐‘ฅ๐‘—๐‘— ๏ฟฝ๐‘ก๐‘ก๐‘—๐‘— ๏‚จ Ratio of the means, not the mean of the ratios ๏‚จ This is just the standard Poisson events per person- time without assuming the distribution 53
  • 54. Nonparametric Analyses ๏‚จ Can use the ๏ฟฝ๐‘…๐‘…๐‘—๐‘— to estimate rate ratio and difference in rates between groups ๏‚ค ๏ฟฝ๐‘…๐‘…๐‘…๐‘…๐‘…๐‘… = ๏ฟฝ๐‘…๐‘…1 ๏ฟฝ๐‘…๐‘…0 ๏‚ค ๏ฟฝ๐‘…๐‘… ๐‘…๐‘…๐‘…๐‘… = ๏ฟฝ๐‘…๐‘…1 โˆ’ ๏ฟฝ๐‘…๐‘…0 54
  • 55. Nonparametric Analyses ๏‚จ ๏ฟฝ๐‘…๐‘…๐‘—๐‘— advantages ๏‚ค Average out any outliers ๏‚ค Makes consistency more reasonable as it uses the group totals for number of events and total follow-up time ๏‚จ ๏ฟฝ๐‘…๐‘…๐‘—๐‘— disadvantages ๏‚ค Measure is group-specific and not subject-specific ๏‚ค Canโ€™t use standard 2-sample tests 55
  • 56. Nonparametric Analyses ๏‚จ Asymptotic forms of the variance for the ๏ฟฝ๐‘…๐‘… measures are in the Xu and LaValley paper in the references ๏‚ค Confidence intervals based on Fiellerโ€™s method and resampling ๏‚จ In this talk, Iโ€™ll use resampling methods to evaluate the ๏ฟฝ๐‘…๐‘…๐‘—๐‘— measures ๏‚ค Permutation tests ๏‚ค Bootstrap confidence intervals 56
  • 57. 57
  • 58. Nonparametric Analyses ๏‚จ In simulations, we found that the ๏ฟฝ๐‘„๐‘„๐‘—๐‘— with a non- parametric test and the ๏ฟฝ๐‘…๐‘…๐‘—๐‘— methods maintained the type-1 error and had comparable power over a range of sample sizes ๏‚จ The ๏ฟฝ๐‘…๐‘…๐‘—๐‘— methods provided reasonable confidence interval coverage if the sample sizes were at least 100 per group 58
  • 59. Nonparametric Analyses ๏‚จ In the paper we use the nonparametric methods on a dataset for recurrence of bladder cancer in a two-arm clinical trial of the drug thiotepa 59
  • 60. Nonparametric Analyses ๏‚จ Thiotepa trial results ๏‚จ Results are uniformly non-significant, with rate ratios from 0.71 to 0.84 60
  • 61. Nonparametric Analyses ๏‚จ Thiotepa trial results ๏‚จ These are the results that I trust the most out of these 61
  • 62. Nonparametric Analyses in DCCT 62 Intensive Treatment Conventional Treatment ๐‘›๐‘› Subjects 363 352 ๏ฟฝ๐‘ฆ๐‘ฆ Hypoglycemia Events/Subject 4.75 1.54 ฬ…๐‘ก๐‘ก Person-Years of Follow-Up/Subject 7.16 7.05 ๏ฟฝ ๏ฟฝ๐‘ฆ๐‘ฆ ฬ…๐‘ก๐‘ก ๏ฟฝ๐‘…๐‘…๐‘—๐‘— 0.66 0.22 ๏ฟฝ๐‘„๐‘„๐‘—๐‘— 0.65 0.21
  • 63. Nonparametric Analyses in DCCT 63 Distribution of qij by group
  • 64. Nonparametric Analyses in DCCT 64 Test Test Statistic P-value t-test of qij 8.28 P < 0.0001 Van der Waerden test of qij 8.77 P < 0.0001 Wilcoxon test of qij 8.57 P < 0.0001
  • 65. Nonparametric Analyses in DCCT 65 Estimator Estimate Permutation Test P-value* Rate Difference (Q) 0.43681 P < 0.0005 Rate Difference (R) 0.44415 P < 0.0005 Rate Ratio (Q) 3.08059 P < 0.0005 Rate Ratio (R) 3.02872 P < 0.0005 *Based on 2000 permutations
  • 66. Nonparametric Analyses in DCCT 66 Q versus R measures of rate difference across 2000 permuted datasets
  • 67. Nonparametric Analyses in DCCT 67 Estimator Estimate Bootstrap Confidence Interval Rate Difference (Q) 0.43681 (0.329, 0.549) Rate Difference (R) 0.44415 (0.329, 0.561) Rate Ratio (Q) 3.08059 (2.399, 3.979) Rate Ratio (R) 3.02872 (2.333, 3.951)
  • 68. Nonparametric Analyses in DCCT 68 Q versus R measures of rate difference across 2000 bootstrap samples
  • 69. Nonparametric Analyses ๏‚จ Both Q and R measures work well for reasonable sized datasets ๏‚จ In these DCCT data, both are fine ๏‚จ In the bladder cancer data, the R (ratio of means) seems to have a slight edge 69
  • 70. Conclusions ๏‚จ There are a lot of good options for the analysis of repeated events ๏‚ค GEE Survival models ๏‚ค Gee Poisson Regression ๏‚ค Negative binomial regression ๏‚ค Q and R measures โ€“ especially in clinical trial setting ๏‚จ Worthwhile to work with several as secondary analyses to verify consistency 70
  • 71. Main References ๏‚จ Allison PD. Survival Analysis Using SAS: a Practical Guide, second edition. SAS Publishing, 2010. ๏‚จ Lachin JM. Biostatistical Methods: the Assessment of Relative Risks. Wiley, 2000. ๏‚จ Xu J, LaValley M. One-sample and two-sample analysis of heterogeneous person-time data in clinical trials. Pharmaceutical Statistics 2012; 11: 194 โ€“ 203. 71