Difference between revisions of "SMHS MethodsHeterogeneity MetaAnalysis"
(→Predictive risk models) 
(→Simulation Example 1) 

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−  The <b>forest plo</b>t shows the  +  The <b>forest plo</b>t shows the ''I''<sup>2</sup> test indicates the evidence to reject the null hypothesis (no study heterogeneity and the fixed effects model should be used). 
==Series of “N of 1” trials==  ==Series of “N of 1” trials== 
Revision as of 13:45, 23 May 2016
Contents
 1 Methods for Studying Heterogeneity of Treatment Effects, CaseStudies of Comparative Effectiveness Research  MetaAnalyses
 2 Metaanalysis
 3 Series of “N of 1” trials
 4 Quantile Treatment Effect (QTE)
 5 Nonparametric Regression Methods
 6 Predictive risk models
 7 Next see: Comparative Effectiveness Research (CER)
Methods for Studying Heterogeneity of Treatment Effects, CaseStudies of Comparative Effectiveness Research  MetaAnalyses
Metaanalysis
Overview
Metaanalysis is an approach to combine treatment effects across trials or studies into an aggregated treatment effect with higher statistical power than observed in each individual trials. It may detect HTE by testing for differences in treatment effects across similar RCTs. It requires that the individual treatment effects are similar to ensure pooling is meaningful. In the presence of large clinical or methodological differences between the trials, it may be to avoid metaanalyses. The presence of HTE across studies in a metaanalysis may be due to differences in the design or execution of the individual trials (e.g., randomization methods, patient selection criteria). Cochran's Q is a methods for detection of heterogeneity, which is computed as the weighted sum of squared differences between each study's treatment effect and the pooled effects across the studies. It is a barometer of intertrial differences impacting the observed study result. A possible source of error in a metaanalysis is publication bias. Trial size may introduce publication bias since larger trials are more likely to be published. Language and accessibility represent other potential confounding factors. When the heterogeneity is not due to poor study design, it may be useful to optimize the treatment benefits for different cohorts of participants.
Cochran's Q statistics is the weighted sum of squares on a standardized scale^{8}. The corresponding P value indicates the strength of the evidence of presence of heterogeneity. This test may have low power to detect heterogeneity sometimes and it is suggested to use a value of 0.10 as a cutoff for significance (Higgins et al., 2003). The Q statistics also may have too much power as a test of heterogeneity when the number of studies is large.
Simulation Example 1
# Install and Load library install.packages("meta") library(meta) # Set number of studies n.studies = 15 # number of treatments: case1, case2, control n.trt = 3 # number of outcomes n.event = 2 # simulate the (balanced) number of cases (case1 and case2) and controls in each study ctl.group = rbinom(n = n.studies, size = 200, prob = 0.3) case1.group = rbinom(n = n.studies, size = 200, prob = 0.3) case2.group = rbinom(n = n.studies, size = 200, prob = 0.3)
# Simulate the number of outcome events (e.g., deaths) and no events in the control group event.ctl.group = rbinom(n = n.studies, size = ctl.group, prob = rep(0.1, length(ctl.group))) noevent.ctl.group = ctl.group  event.ctl.group # Simulate the number of events and no events in the case1 group event.case1.group = rbinom(n = n.studies, size = case1.group, prob = rep(0.5, length(case1.group))) noevent.case1.group = case1.group  event.case1.group
# Simulate the number of events and no events in the case2 group event.case2.group = rbinom(n = n.studies, size = case2.group, prob = rep(0.6, length(case2.group))) noevent.case2.group = case2.group  event.case2.group
# Run the univariate metaanalysis using metabin(), Metaanalysis of binary outcome data – # Calculation of fixed and random effects estimates (risk ratio, odds ratio, risk difference or arcsine # difference) for metaanalyses with binary outcome data. MantelHaenszel (MH), # inverse variance and Peto method are available for pooling.
# method = A character string indicating which method is to be used for pooling of studies. # one of "MH" , "Inverse" , or "Cochran" # sm = A character string indicating which summary measure (“OR”, "RR" "RD"=risk difference) is to be # used for pooling of studies
# Control vs. Case1, n.e and n.c are numbers in experimental and control groups meta.ctr_case1 < metabin(event.e = event.case1.group, n.e = case1.group, event.c = event.ctl.group, n.c = ctl.group, method = "MH", sm = "OR") # in this case we use Odds Ratio, of the odds of death in the experimental and control studies forest(meta.ctr_case1)
# Control vs. Case2 meta.ctr_case2 < metabin(event.e = event.case2.group, n.e = case2.group, event.c = event.ctl.group, n.c = ctl.group, method = "MH", sm = "OR") forest(meta.ctr_case2)
# Case1 vs. Case2 meta.case1_case2 < metabin(event.e = event.case1.group, n.e = case1.group, event.c = event.case2.group, n.c = case2.group, method = "MH", sm = "OR") forest(meta.case1_case2) summary(meta.case1_case2)
Test of heterogeneity: Q d.f. pvalue 11.99 14 0.6071
The forest plot shows the I^{2} test indicates the evidence to reject the null hypothesis (no study heterogeneity and the fixed effects model should be used).
Series of “N of 1” trials
This technique combines (a “series of”) nof1 trial data to identify HTE. An nof1 trial is a repeated crossover trial for a single patient, which randomly assigns the patient to one treatment vs. another for a given time period, after which the patient is rerandomized to treatment for the next time period, usually repeated for 46 time periods. Such trials are most feasibly done in chronic conditions, where little or no washout period is needed between treatments and treatment effects are identifiable in the shortterm, such as pain or reliable surrogate markers. Combining data from identical nof1 trials across a set of patients enables the statistical analysis controlling for patient fixed or random effects, covariates, centers, or sequence effects, see Figure below. These combined trials are often analyzed within a Bayesian context using shrinkage estimators that combine individual and group mean treatment effects to create a “posterior” individual mean treatment effect estimate which is a form of inverse varianceweighted average of the individual and group effects. Such trials are typically more expensive than standard RCTs on a perpatient basis, however, they require much smaller sample sizes, often less than 100 patients (due to the efficient individualasowncontrol design), and create individual treatment effect estimates that are not possible in a noncrossover design . For the individual patient, the treatment effect can be reestimated after each time period, and the trial stopped at any point when the more effective treatment is identified with reasonable statistical certainty.
Example
A study involving 8 participants collected data across 30 days, in which 15 treatment days and 15 control days are randomly assigned within each participant. The treatment effect is represented as a binary variable (control day=0; treatment day=1). The outcome variable represents the response to the intervention within each of the 8 participants. Study employed a fixedeffects modeling. By creating N − 1 dummycoded variables representing the N=8 participants, where the last (i=8) participant serves as the reference (i.e., as the model intercept). So, each dummycoded variable represents the difference between each participant (i) and the 8th participant. Thus, all other patients' values will be relative to the values of the 8th (reference) subject. The overall differences across participants in fixed effects can be evaluated with multiple degreeoffreedom Ftests.
ID  Day  Tx  SelfEff  SelfEff25  WPSS  SocSuppt  PMss  PMss3  PhyAct 
1  1  1  33  8  0.97  5.00  4.03  1.03  53 
1  2  1  33  8  0.17  3.87  4.03  1.03  73 
1  3  0  33  8  0.81  4.84  4.03  1.03  23 
1  4  0  33  8  0.41  3.62  4.03  1.03  36 
...  ...  ...  ...  ...  ...  ...  ...  ...  ... 
Complete data is available in the Appendix.
Intercept  Constant 
Physical Activity  PhyAct 
Intervention  Tx 
WP Social Support  WPSS 
PM Social Support (13)  PMss3 
Self Efficacy  SelfEff25 
rm(list=ls()) Nof1 <read.table("https://umich.instructure.com/files/330385/download?download_frd=1&verifier=DwJUGSd6t24dvK7uYmzA2aDyzlmsohyaK6P7jK0Q", sep=",", header = TRUE) # 02_Nof1_Data.csv attach(Nof1) head(Nof1)
ID  Day  Tx  SelfEff  SelfEff25  WPSS  SocSuppt  PMss  PMss3  PhyAct  
1  1  1  1  33  8  0.97  5.00  4.03  1.03  53 
2  1  2  1  33  8  0.17  3.87  4.03  1.03  73 
3  1  3  0  33  8  0.81  4.84  4.03  1.03  23 
4  1  4  0  33  8  0.41  3.62  4.03  1.03  36 
5  1  5  1  33  8  0.59  4.62  4.03  1.03  21 
6  1  6  1  33  8  1.16  2.87  4.03  1.03  0 
df.1 = data.frame(PhyAct, Tx, WPSS, PMss3, SelfEff25)
# library("lme4")
lm.1 = model.lmer < lmer(PhyAct ~ Tx + SelfEff + Tx*SelfEff + (1Day) + (1ID) , data= df.1) summary(lm.1)
Linear mixed model fit by REML ['lmerMod'] Formula: PhyAct ~ Tx + SelfEff + Tx * SelfEff + (1  Day) + (1  ID) Data: df.1
REML criterion at convergence: 8820
Min  1Q  Median  3Q  Max 
Groups  Name  Variance  Std.Dev. 
Day  (Intercept)  0.0  0.00 
ID  (Intercept)  601.5  24.53 
Residual  969.0  31.13 
Number of obs: 900, groups: Day, 30; ID, 30
Estimate  Std.  Error  t value 
(Intercept)  38.3772  14.4738  2.651 
Tx  4.0283  6.3745  0.632 
SelfEff  0.5818  0.5942  0.979 
Tx:SelfEff  0.9702  0.2617  3.708 
(Intr)  Tx  SlfEff  
Tx  0.220  
SelfEff  0.946  0.208  
Tx:SelfEff  0.208  0.946  0.220 
# Model: PhyAct = Tx + WPSS + PMss3 + Tx*WPSS + Tx*PMss3 + SelfEff25 + Tx*SelfEff25 + ε lm.2 = lm(PhyAct ~ Tx + WPSS + PMss3 + Tx*WPSS + Tx*PMss3 + SelfEff25 + Tx*SelfEff25, df.1) summary(lm.2)
Call: lm(formula = PhyAct ~ Tx + WPSS + PMss3 + Tx * WPSS + Tx * PMss3 + SelfEff25 + Tx * SelfEff25, data = df.1)
Min  1Q  Median  3Q  Max 
102.39  28.24  1.47  25.16  122.41 
Estimate  Std. Error  t value  t)$  
(Intercept)  52.0067  1.8080  28.764  < 2e16 *** 
Tx  27.7366  2.5569  10.848  < 2e16 *** 
WPSS  1.9631  2.4272  0.809  0.418853 
PMss3  13.5110  2.7853  4.851  1.45e06 *** 
SelfEff25  0.6289  0.2205  2.852  0.004439 ** 
Tx:WPSS  9.9114  3.4320  2.888  0.003971 ** 
Tx:PMss3  8.8422  3.9390  2.245  0.025025 * 
Tx:SelfEff25  1.0460  0.3118  3.354  0.000829 ***

[Using SAS (StudyI_Analyses.sas, StudyIIab_Analyses.sas)]
Effect  Num DF  Den DF  F Value  $Pr>F$ 
Tx  1  224  67.46  <.0001 
ID  7  224  25.95  <.0001 
Tx*ID  7  224  2.92  0.0060 
Quantile Treatment Effect (QTE)
QTE employs quantile regression estimation (QRE) to examine the central tendency and statistical dispersion of the treatment effect in a population. These may not be revealed by the conventional mean estimation in RCTs. For instance, patients with different comorbidity scores may respond differently to a treatment. Quantile regression has the ability to reveal HTE according to the ranking of patients’ comorbidity scores or some other relevant covariate by which patients may be ranked. Therefore, in an attempt to inform patientcentered care, quantile regression provides more information on the distribution of the treatment effect than typical conditional mean treatment effect estimation. QTE characterizes the heterogeneous treatment effect on individuals and groups across various positions in the distributions of different outcomes of interest. This unique feature has given quantile regression analysis substantial attention and has been employed across a wide range of applications, particularly when evaluating the economic effects of welfare reform.
One caveat of applying QRE in clinical trials for examining HTE is that the QTE doesn’t demonstrate the treatment effect for a given patient. Instead, it focuses on the treatment effect among subjects within the qth quantile, such as those who are exactly at the top 10th percent in terms of blood pressure or a depression score for some covariate of interest, for example, comorbidity score. It is not uncommon for the qth quantiles to be two different sets of patients before and after the treatment. For this reason, we have to assume that these two groups of patients are homogeneous if they were in the same quantiles.
IncomeFood Expenditure Example: Let’s examine the Engel data (N=235) on the relationship between food expenditure (foodexp) and household income (income). We can plot the data and then explore the superposition of the six fitted quantile regression lines.
install.packages("quantreg") library(quantreg) data(engel) attach(engel)
Income  Foodexp  
1  420.1577  255.8394 
2  541.4117  310.9587 
3  901.1575  485.6800 
4  639.0802  402.9974 
5  750.8756  495.5608 
6  945.7989  633.7978 
Income  Foodexp  
Min  377.1  242.3 
1st Qu.  638.9  429.7 
Median  884.0  582.5 
Mean  982.5  624.2 
3rd Qu.  1164.0  743.9 
Max  4957.8  2032.7 
Note: If Y be a real valued random variable with cumulative distribution function F_{Y}(y)=P(Y≤ y), then the τquantile of Y is given by
where 0≤τ≤1.
# (1) Graphics plot(income, foodexp, cex=.25, type="n", xlab="Household Income", ylab="Food Expenditure") points(income, foodexp, cex=.5, col="blue")
# tau  the quantile(s) to be estimated, in the range from 0 to 1. An object "rq.process" and an object "rqs" # are returned containing the matrix of coefficient estimates at the specified quantiles. abline( rq(foodexp ~ income, tau=.5), col="blue") # Quantile Regression Model
abline( lm(foodexp ~ income), lty=2, lwd=3, col="red") # linear model taus < c(0.05, 0.1, 0.25, 0.75, 0.90, 0.95) colors < rainbow(length(taus))
models < vector(mode = "list", length = length(taus)) # define a vector of models to store QR for diff taus model.names < vector(mode = "list", length = length(taus)) # define a vector model names
for( i in 1:length(taus)){ modelsi < rq(foodexp ~ income, tau=taus[i]) var < taus[i] model.namesi < paste("Model [", i , "]: tau=", var) abline( modelsi, lwd=2, col= colorsi) } legend(3000, 1100, model.names, col= colors, pch= taus, bty='n', cex=.75)
# (2) Inference about quantile regression coefficients. As an alternative to the rankinversion confidence intervals, we can obtain a table of coefficients, standard errors, tstatistics, and pvalues using the summary function:
summary(models3, se = "nid")
Call: rq(formula = foodexp ~ income, tau = taus[i])
tau: [1] 0.25
Value  Std. Error  t Value  t)$  
(Intercept)  95.48354  21.39237  4.46344  0.00001 
Income  0.47410  0.02906  16.31729  0.00000 
# Alternatively, we can use summary.rq to compute bootstrapped standard errors. summary.rq(models3, se = "nid")
Call: rq(formula = foodexp ~ income, tau = taus[i]) tau: [1] 0.25
Value  Std. Error  t Value  t)$  
(Intercept)  95.48354  21.39237  4.46344  0.00001 
Income  0.47410  0.02906  16.31729  0.00000 
Nonparametric Regression Methods
Nonparametric regression enables dealing with HTE in RCTs. Different nonparametric methods, such as kernel smoothing methods and series methods, can be used to generate test statistics for examining the presence of HTE. A kernel method is a weighting scheme based on a kernel function (e.g. uniform, Gaussian). When evaluating the treatment effect of a patient in RCTs, the kernel method assigns larger weights to those observations with similar covariates. This is done because it is assumed that patients with similar covariates provide more relevant data on predicted treatment response. Examining participants that have different backgrounds (e.g., demographic, clinical), kernel smoothing methods utilize information from highly divergent participants when estimating a particular subject’s treatment effect. Lower weights are assigned to very different subjects and the kernel methods require choosing a set of smoothing parameters to group patients according to their relative degree of similarities. A drawback is that the corresponding proposed test statistics may be sensitive to the chosen bandwidths, which inhibits the interpretation of the results. Series methods use approximating functions (splines or power series of the explanatory variables) to construct test statistics. Compared to kernel smoothing methods, series methods normally have the advantage of computational convenience; however, the precision of test statistics depends on the number of terms selected in the series.
Canadian Wage Data Example: Nonparametric regression extends the classical parametric regression (e.g., lm, lmer) involving one continuous dependent variable, y, and (1 or more) continuous explanatory variable(s), x. Let’s start with a popular parametric model of a wage equation that we can extend to a fully nonparametric regression model. First, we will compare and contrast the parametric and nonparametric approach towards univariate regression and then proceed to multivariate regression.
Let’s use the Canadian crosssection wage data (cps71) consisting of a random sample taken from the 1971 Canadian Census for male individuals having common education (HighSchool). N=205 observations, 2 variables, the logarithm of the individual’s wage (logwage) and their age (age). The classical wage equation model includes a quadratic term of age.
# install.packages("np") library("np") data("cps71")
# (1) Linear Model > R^{2} = 0.2308 model.lin < lm( logwage ~ age + I(age^2), data = cps71) summary(model.lin)
Call: lm(formula = logwage ~ age + I(age^2), data = cps71)
Residuals: Min 1Q Median 3Q Max 2.4041 0.1711 0.0884 0.3182 1.3940
Estimate  Std. Error  t Value  t)$  
(Intercept)  10.0419773  0.4559986  22.022  < 2e16 *** 
Age  0.1731310  0.0238317  7.265  7.96e12 *** 
I(age^2)  0.0019771  0.0002898  6.822  1.02e10 *** 
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.5608 on 202 degrees of freedom Multiple Rsquared: 0.2308, Adjusted Rsquared: 0.2232 Fstatistic: 30.3 on 2 and 202 DF, pvalue: 3.103e12
# (2) Next, we consider the local linear nonparametric method employing crossvalidated # bandwidth selection and estimation in one step. Start with computing the leastsquares # crossvalidated bandwidths for the local constant estimator (default). # Note that R^{2} = 0.3108675 bandwidth < npregbw(formula= logwage ~ age, data = cps71) model.np < npreg(bandwidth, regtype = "ll", bwmethod = "cv.aic", gradients = TRUE, data = cps71) summary(model.np)
Regression Data: 205 training points, in 1 variable(s) age Bandwidth(s): 1.892157 Kernel Regression Estimator: LocalConstant Bandwidth Type: Fixed Residual standard error: 0.5307943 Rsquared: 0.3108675 Continuous Kernel Type: SecondOrder Gaussian No. Continuous Explanatory Vars.: 1
# NP model significance may be tested by npsigtest(model.np)
Kernel Regression Significance Test Type I Test with IID Bootstrap (399 replications, Pivot=TRUE, joint=FALSE) Explanatory variables tested for significance: age (1)
age Bandwidth(s): 1.892157
Individual Significance Tests P Value: age < 2.22e16 ***
# So, as was the case for the linear parametric model, Age is significant in the local linear NPmodel
# (3) Graphical comparison of parametric and nonparametric models. plot(cps71$\$$age, cps71$\$$logwage, xlab = "age", ylab = "log(wage)", cex=.1) lines(cps71$\$$age, fitted(model.lin), lty = 2, col = " red") lines(cps71$\$$age, fitted(model.np), lty = 1, col = "blue") legend("topright", c("Data", "Linear", "Nonlinear"), col=c("Black", "Red", "Blue"), pch = c(1, 1, 1), bty='n', cex=.75)
# some additional plots resenting the parametric (quadratic, dashed line) and the nonparametric estimates # (solid line) of the regression function for the cps71 data. plot(model.np, plot.errors.method = "asymptotic") plot(model.np, gradients = TRUE) lines(cps71$\$$age, coef(model.lin)[2]+2*cps71$\$$age*coef(model.lin)[3], lty = 2, col = "red") plot(model.np, gradients = TRUE, plot.errors.method = "asymptotic")
# (4) using the Lin and NL models to generate predictions based on the obtained appropriate # bandwidths and estimated a nonparametric model. We need to create a set of explanatory # variables for which to generate predictions. These can be part of the original dataset or be # outside its scope. Typically, we don’t have the outcome for the evaluation data and need only # provide the explanatory variables for which predicted values are generated by the models. # Occasionally, splitting the dataset into two independent samples (training/testing), allows estimation # of a model on one sample, and evaluation of its performance on another.
cps.eval.data < data.frame(age = seq(10,70, by=10)) # simulate some explanatory X values (ages) pred.lin < predict(model.lin, newdata = cps.eval.data) # Linear Prediction of log(Wage) pred.np < predict(model.np, newdata = cps.eval.data) # nonLinear Prediction of log(Wage) plot(pred.lin, pred.np) abline(lm(pred.np ~ pred.lin))
. . .
Predictive risk models
Predictive risk models represent a class of methods for identifying potential for HTE when the individual patient risk for diseaserelated events at baseline depends on observed factors. For instance, common measures are disease staging criteria, such as those used in COPD or heart failure, Framingham risk scores for cardiovascular event risk, or genetic variations, e.g., HER2 for breast cancer. Initial predictive risk modeling, aka risk function estimation, is often performed without accounting for treatment effects. Least squares or Cox proportional hazards regression methods are appropriate in many cases and provide relatively more interpretable risk functions, but rely on linearity assumptions and may not provide optimal predictive metrics. Partial least squares is an extension of least squares methods that can reduce the dimensionality of the predictor space by interposing latent variables, predicted by linear combinations of observable characteristics, as the intermediate predictors of one or more outcomes. Recursive partitioning, such as random forests, support vector machines, and neural networks represent latter methods with better predictive power than linear methods. Risk function estimation can range from highly exploratory analyses to near metaanalytic model validation, and may be useful at any stage of product development.
HIV Example: The “hmohiv” dataset represents a study of HIV positive patients examining whether there was a difference in survival times of HIV positive patients between a cohort using intravenous drugs (drug=1) and a cohort not using the IV drug (drug=0). The hmohiv data includes the following variables:
ID  Time  Age  Drug  Censor  Entdate  Enddate 
1  5  46  0  1  5/15/1990  10/14/1990 
2  6  35  1  0  9/19/1989  3/20/1990 
3  8  30  1  1  4/21/1991  12/20/1991 
4  3  30  1  1  1/3/1991  4/4/1991 
5  22  36  0  1  9/18/1989  7/19/1991 
6  1  32  1  0  3/18/1991  4/17/1991 
...  ...  ...  ...  ...  ...  ...

#cleaning up environment rm(list=ls())
# load survival library library(survival)
# load hmohiv data hmohiv<read.table("http://www.ats.ucla.edu/stat/r/examples/asa/hmohiv.csv", sep=",", header = TRUE) attach(hmohiv)
# Fit Cox proportional hazards regression model cox.model < coxph( Surv(time, censor) ~ drug, method="breslow") fit.1 < survfit(cox.model, newdata=drug.new)
# construct a frame of the 2 cohorts IV_drug and noIVdrug drug.new<data.frame(drug=c(0,1))
# plot results plot(fit.1, xlab="Survival Time (Months)", ylab="Survival Probability") points(fit.1$\$$time, fit.1$\$$surv[,1], pch=1) points(fit.1$\$$time, fit.1$\$$surv[,2], pch=2) legend(40, .8, c("Drug Absent", "Drug Present"), pch=c(1,2))
# to inslect the resulting Cox Proportional Hazard Model cox.model Call: coxph(formula = Surv(time, censor) ~ drug, method = "breslow")
coef exp(coef) se(coef) z p drug 0.779 2.18 0.242 3.22 0.0013
Likelihood ratio test=10.2 on 1 df, p=0.00141 n= 100, number of events= 80
Footnotes
^{8} http://onlinelibrary.wiley.com/enhanced/doi/10.1002/jrsm.54
Next see: Comparative Effectiveness Research (CER)
 SOCR Home page: http://www.socr.umich.edu
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