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Adjusting for Confounding in Early Postlaunch Settings

Going Beyond Logistic Regression Models

Schmidt, Amand F.a,b,c,d; Klungel, Olaf H.a,b; Groenwold, Rolf H. H.a,b on behalf of the GetReal Consortium

Author Information
doi: 10.1097/EDE.0000000000000388


Nonrandomized studies on (pharmacologic) therapeutics are often conducted to complement results from randomized clinical trials (RCTs). For example, nonrandomized studies might be more appropriate to assess the occurrence of rare, but severe, adverse events.1–3 Furthermore, nonrandomized studies can be used to estimate the relative effectiveness in real-life clinical practice. Depending on the relationship between the intervention and the outcome, different degrees of confounding can be expected.1–3 For example, it might be expected that patients who responded poorly to older drugs will cross over to the new drug.4 Alternatively, as shown by Mack et al.,5 physicians might be hesitant to prescribe a novel drug to patients with comorbidities. Furthermore, depending (among other factors) on the speed of uptake, differences in patient populations pre- and post-launch or difference between early and late adopters may increase the potential for effect modification, further obstructing comparison of a new drug to older compounds.6,7

Frequently, the outcome of interest is dichotomous, such as mortality, in which case multivariable logistic regression8 is commonly used to adjust for confounding. One (of many) assumption(s) is that associations between confounders and the outcome are sufficiently estimated to adjust for confounding bias. In settings (e.g., nonrandomized early postlaunch studies) where both the number of events and the number of exposed subjects are small, controlling for confounding can be problematic. Further complicating the matter is that it is not uncommon to consider more than 100 potential confounders.9 Simulation studies showed that for prognostic logistic regression models, 10 or more events per coefficient were needed to get unbiased estimates.10,11 In prognostic studies, the interest lies in correctly estimating all associations between possible predictors and the outcome, whereas in nonrandomized therapeutic studies, the interest is usually in estimating a single association adjusted for potential confounders. Vittinghoff and McCulloch12 showed that in this case, logistic regression models with events per coefficient as small as six can adequately adjust for confounding.

In settings where logistic regression models are expected to perform poorly (i.e., events per coefficient smaller than six), propensity score,13,14 disease risk score,15–19 or inverse probability weighting,20–22 methods can be applied to summarize information of multiple confounders into a single variable. It remains unclear how many events/exposures per variable are needed to sufficiently control for confounding using propensity score, disease risk score, and inverse probability-weighting methods. Furthermore, in training (i.e., developing) disease risk score models, it is often implicitly assumed that there is no treatment effect or no treatment by confounder interaction. However, there might be considerable differences between post- and pre-launch patients, increasing the potential for previously unrecognized interaction. The sensitivity of disease risk score models to model misspecification due to omitting a main or interaction effect is unknown, particularly when the disease risk score model is trained in a prelaunch dataset and applied in a postlaunch dataset (two-sample disease risk score). To explore these issues, we conducted a simulation study comparing logistic regression, propensity score, and inverse probability weighting and four kinds of disease risk score models with varying amounts of events or exposed subjects per coefficient, under different levels of model misspecification.


Simulation Set-up

We focused on a scenario in which the effect of a new drug (or any other type of medical intervention) is evaluated postlaunch in an observational study. In each simulation, a training dataset was generated containing prelaunch information (n = 5,000) and a test dataset (n = 400) containing postlaunch information. In both datasets, half of the subjects experienced an event and, independent of outcome status, half were exposed to the comparator drug C. In the training data, the other half were exposed to drug B, and in the test data to drug A. The training and test datasets were generated using the same algorithm, containing a single continuous confounder


binary confounders (see eAppendix 1 for the algorithm applied;

Disease risk score models were derived in the training data. We then used to the test data to compare the estimated effect of the intervention (drug A vs. C) obtained through the disease risk score, logistic regression, inverse probability weighting, and propensity score methods (see eAppendix 1 for a description of the methods; Depending on the size of the training dataset, a (very) large number of confounders can be included. Ideally, the training dataset consists exclusively of untreated patients.19 Otherwise disease risk score models might be biased by possible treatment by confounder interaction. To explore how sensitive this method is to unobserved interaction, we compared four disease risk score models. The first disease risk score model, DRS 1, reflecting current practice in most prediction models,23 ignored treatment in the training data. In DRS 2, the treatment variable was included in the training model. In DRS 3, a treatment by confounder

interaction was included. Instead of assuming that all interactions are appropriately modeled, DRS 4 prevents interaction by restricting the training dataset to subjects treated with drug C (the reference). We implemented propensity score adjustment by including the estimated propensity score as a continuous covariate in a regression model.

Simulation Scenarios

In both the training and test datasets (unless stated otherwise), the association of confounder

with treatment and outcome was set to an odds ratio (OR) of 0.60. The associations of the remaining confounders with treatment and the outcome were set to an OR of 0.97, to minimize the difference in the amount of confounding bias between the different events per coefficient scenarios. The association of treatment with the outcome was set to an OR of 1.00. See Table 1 for an overview.

Simulation Scenarios, Assessing Performance of Different Confounding Adjustment Methods

In scenario I, different events per coefficient were generated by increasing the number of coefficients from 20 to 400. In scenarios II and III, events per coefficient was set to 10, the treatment and interaction OR in the training data were set to 0.30 and 0.30 (for scenario II) or 0.30 and 3.00 (for scenario III). To further determine the susceptibility of the disease risk score models for misspecification, the interaction effect in the training data was set to 0.30, 0.70, 1.00, 1.50, and 3.00 in scenario IV, while the events per coefficient was set to 2.5. In scenario V, the treatment OR in the training data was set to 0.30, 0.70, 1.00, 1.50, and 3.00 and the interaction effect to 3.00. In scenario VI, power (i.e., the probability to detect an association if it is present) was explored by setting the treatment OR in the test data to 0.30, 0.70, 1.00, 1.50, and 3.00. Note that we focus exclusively on power because the conditional OR will differ from the marginal OR due to noncollapsibility24; other performance metrics (see below) are presented in the eTables 1–6 ( Scenario VII explores performance in less extreme settings (Table 1). Finally, to gain insight into the influence of the size of the disease risk score training data, scenario 1 was repeated with training sample sizes of 5,000, 2,500, 1,000, and 400.

All simulations were repeated 10,000 times and were performed with the statistical package R version 3.1.125 for Linux. We chose the number of replications to ensure sufficient precision to detect small deviations from the typical confidence interval coverage rate of 0.95 (the 95% lower and upper bounds are 0.946 and 0.954),26,27 and a mean OR 1.00 (the 95% lower and upper bounds are 0.996 and 1.004).

Performance Metrics

The different methods were compared on the mean OR, mean relative bias (presented in eTables 1–6;, the coverage rate, the mean estimated standard error (SE; presented in eTables 1–6;,18 the empirical SE (presented in eTables 1–6;, the square root of the mean squared error,26 power, number of models that failed to converge and the number of models with implausible estimates.

Mean relative bias was defined as

, where

indicates the average estimated treatment OR, and true OR the simulated treatment OR. Coverage was defined as the number of times the true value was included in the Wald-based 95% confidence interval. The mean SE was defined as the mean of the estimated SEs.18,26 The empirical SE was estimated by taking the standard deviation of the

distribution. The root mean squared error was calculated by taking the square root of the sum of the squared bias and the squared empirical SE.26 Power equaled the proportion of simulations in which the null hypothesis of

was correctly rejected (scenario VI). Implausible estimates were defined as treatment

. Finally, we note that model convergence depends on the convergence criterion. For the current analysis, the R default criterion, <10−8, was used.

Sensitivity Analysis

Instead of using disease risk score models when the number of events per coefficient is very small, Firth penalized logistic regression models have shown promise.28–30 Firth suggested to use a Jeffrey’s prior to penalize the size of the regression coefficient toward zero. To evaluate this penalization in low events per coefficient settings, scenario I was repeated implementing logistic regression, propensity score, inverse probability weighting, and disease risk score methods using Firth’s penalized logistic regression. For purposes of comparison, Wald-based P values and confidence intervals were calculated; however, better performance is expected using profile likelihood P values. All estimates were derived using the R package logistf version 1.21.31

In all the above-mentioned scenarios, the covariates included in the various models are true confounders (i.e., a common cause of both the exposure and the outcome). Obviously, in empirical settings, it is unknown whether variables are true confounders or not. Erroneous inclusion of instrumental variables (i.e., variables independent of true confounders and only related to the outcome via the exposure), in the presence of residual confounding, increases bias. However, this bias has been shown, typically, to be minimal compared with the amount of residual confounding.32 To evaluate the susceptibility of the different methods to erroneous inclusion of instruments, scenario 1 was repeated including two binary instruments; probability 0.10 and 0.35 and an OR with treatment of 5.0.

Finally, while it is tempting to distil a rule of thumb for the number of events per coefficient required, performance is probably highly dependent on the simulation scenario used; therefore, it is more useful to focus on relative (i.e., between methods) performance. To underline this, we repeated scenario 1 with the OR for

set to 15 for both the outcome and exposure, and the remainder of the confounder ORs set to 0.90.


Table 2 shows the results of the simulations evaluating the logistic regression, propensity score, inverse probability weighting, and disease risk score models under different events per coefficient (scenario I), in the absence of a treatment effect. Relative bias of the logistic regression, inverse probability weighting, and propensity score models were similar up to and including an events per coefficient value of 2.5. After this, the logistic regression model showed extreme bias. Relative bias of the propensity score and inverse probability weighting models increased to 8.74% and −8.49%, respectively, at an events per coefficient of 1.0. Mean and empirical SE (eTable 1; increased for these methods as events per coefficient increased and extreme estimates were seen after events per coefficient of 2.5 (for the logistic regression model) and 1.0 (for the propensity score model). At an events per coefficient of 0.5, the propensity score and logistic regression methods both showed extreme bias of −100%, with 24.55% the bias of the inverse probability weighting approximated that of the crude analysis 25.55%, indicating that the inverse probability weighting failed to adjust for confounding in this setting. The coverage rate of logistic regression models started to deviate from 0.95 at events per coefficient of 5.0 (0.941), with more serious deviation at an events per coefficient of 1.0 (0.656). For the propensity score models, the coverage rate started to deviate from 0.05 at an events per coefficient of 1.0 (0.945).

Simulation Results from Scenario I Assessing Performance of Different Confounding Adjustment Methods with Different Events Per Coefficient

In the same scenario I, the mean ORs of the different disease risk score methods deviated more than could be explained by random error at an events per coefficient of 10. However, the bias was small (1.36%), with a maximum of 18.83% at an events per coefficient of 0.5. The relative bias of disease risk score model 4 was consistently larger than that of the other disease risk score models. After an events per coefficient of 5.0, the coverage rates of the disease risk score models were less than 0.95.

In scenarios II and III, model misspecification of DRS 1 and 2 were introduced by adding a treatment by confounder interaction to the training data. In scenario II (interaction OR 0.30), the relative bias was small and the coverage rates were close to 0.95 for all methods (Table 3 and eTable 2; In scenario III (interaction OR 3.00), DRS 1 and 2 showed relative bias of 8.75% and 16.55%, respectively. Similarly, the coverage rates of these models were 0.931 and 0.879. Disease risk score models 3 and 4 showed coverage rates close to 0.95 and relative bias of 1.49% and 2.83%.

Simulation Results from Scenarios II and III Comparing Different DRS Models in the Presence of an Interaction Effect in the Training Data

In Figure 1 the relative bias, coverage rates and root mean squared error of the simulation results of scenarios IV and V are presented. In scenario IV, the treatment by confounder interaction effect was iterated from 0.30 to 3.0 at an EPC of 2.5. As expected, the relative bias of the logistic regression, inverse probability weighting, and propensity score models were small, and the coverage rate of the logistic regression model was consistently 0.92, while the inverse probability weighting and propensity score estimates had coverages of 0.95 (Figure 1, left-hand side). The relative bias of disease risk score model 1 was more or less symmetric and peaked at 14.48% for an interaction effect of 3.0. At an interaction effect of 0.30, disease risk score model 2 had the least amount of bias (2.53%). This increased to a bias of 19.15% with an interaction effect of 3.00. The relative bias of disease risk score models 3 and 4 was constantly between 7% and 5% or 10% and 8%, respectively.

Simulation results from scenarios IV and V comparing different disease risk score models to inverse probability weights, propensity score, and logistic regression models on relative bias, coverage rate, and RMSE; the square root of the mean squared error. Solid line with a square logistic regression; solid line with a circle propensity score; solid line with triangle DRS 1 model; solid line with a plus DRS 2; solid line with a filled out square DRS 3; solid line with a filled out circle DRS 4; solid line with a filled out triangle inverse probability weights. DRS indicates disease risk score.

In scenario V (Figure 1, right-hand side), the treatment effect in the training data ranged from 0.30 to 3.00, while the interaction effect was kept constant at OR 3.00. All models performed similarly regardless of the treatment effect, except, disease risk score model 1 where the relative bias decreased from 14.50% to 8.28% as treatment increased to 3.00.

We explored empirical power in scenario VI (Figure 2 and eTable 3;, with events per coefficient 2.5. Power was below 0.40 for treatment effects between 0.70 and 1.50; at treatment ORs of 0.30 and 3.00 power was almost 1.00. Disease risk score and logistic regression models were consistently more powerful than propensity score and inverse probability weighting models.

Simulation results from scenario VI comparing different disease risk score models to inverse probability weights, propensity score, and logistic regression models on power. Solid line with a square symbol logistic regression; solid line with a circle propensity score; solid with triangle DRS 1 model; solid line with a plus DRS 2; solid line with a filled out square DRS 3; solid line with a filled out circle DRS 4; solid line with a filled out triangle inverse probability weights. DRS indicates disease risk score.

In scenario VII, disease risk score models were evaluated with an events per coefficient of 10 with smaller confounder and interaction effects. In these settings, the relative bias of the disease risk score models ranged from 1.37% (DRS 3) to 2.50% (DRS 4), compared with 0.01% for the logistic regression, 0.06 for the inverse probability weighting, and −0.02% for the propensity score models, with coverage rates close to 0.95 for all methods.

To assess the impact of the disease risk score training sample size, scenario 1 was repeated with different sample sizes (Figure 3). Given the similar performance of the disease risk score methods in this scenario, we focused on DRS 2. Obviously, relative bias and root mean squared error increased as sample size decreased. However, even with a training dataset of 400 subjects (equal to the test sample size), the disease risk score method outperformed the logistic regression method at events per coefficient of 1.0 and 0.5. The root mean square error of disease risk score trained with 5,000 and 2,500 subjects was relatively similar up to an events per coefficient of 2.5 indicating sufficiency of both sample sizes.

Simulation results from scenario I with different sized training datasets, comparing disease risk score model 2 to a logistic regression model. Line with a square logistic regression; line with a plus disease risk score model 2. Vertical values above the x axis represent the y values of the logistic regression model. RMSE, square root of the mean squared error; EPC, events per coefficient.

In all scenarios, all disease risk score, propensity score, and logistic regression models converged and no estimates were excluded. However, in scenario I, 2,763 inverse probability weighting models failed to converge at events per coefficient of 1.0, while at events per coefficient of 0.5 all models converged again. Arbitrarily defining extreme estimates, as an absolute estimate above five on the natural logarithmic scale, resulted in 7,219 and 9,415 extreme estimates for the logistic regression method (events per coefficient of 1.0 and 0.5). For the propensity score model, 4,706 extreme estimates occurred at events per coefficient of 0.53 and 672 extreme inverse probability weighted estimates were observed at an events per coefficient of 1.0 and zero at an events per coefficient of 0.5.

Results of the sensitivity analysis replacing logistic regression by Firth’s penalized logistic regression showed improved performance of logistic regression and propensity score models (eTable 4; The other models performed similar as in scenario 1 using logistic regression, while disease risk score model 3 (modeling an interaction term) performed worse. Inclusion of two instrument variables did not impact results (eTable 5;, except for the inverse probability weighting approximating the crude estimate at an EPC of 1.0 instead of 0.5 (in the original simulation). Finally, repeating scenario 1 with extreme levels of confounding (eTable 6; showed the same relative performance with the logistic regression method being the first to show suboptimal coverage and bias, followed by the disease risk score and the propensity score models. However, due to the extreme bias, this occurred at higher events per coefficient than previous. Similarly, due to extreme estimates, the inverse probability weighting method already approximated the crude analysis at events per coefficient of 1.0.


This simulation study showed that in observational settings with a relatively small number of events/exposed per coefficient, disease risk score, and propensity score methods provided less biased estimates than did logistic regression and inverse probability weighted regression. In larger events per coefficient settings (e.g., 10), disease risk score methods remained biased while the other methods were not. Penalization of the likelihood markedly improved performance of the logistic regression, and propensity score, but not the performance of inverse probability weighted and disease risk score methods. In addition, depending on the magnitude and direction of treatment by covariate interaction in the disease risk score training data, disease risk score models ignoring this interaction (i.e., misspecified disease risk score models) were more biased.

Previous simulation studies on disease risk score models trained the disease risk score in the same test data.16,18 In contrast, we evaluated two-sample disease risk score models using an independent training dataset, which we showed increased performance of these models as long as the training dataset was sufficiently large and the model was correctly specified. Simulations with differently sized training data revealed that the disease risk score methods outperformed logistic regression even when the test and training dataset had the same sample size, and that the increased bias of DRS 4 was due to a reduction in sample size from 5,000 to 2,500. We note, however, that for most events per coefficient (except 0.5), the propensity score method was the least biased method. Increasing the size of the training data will likely increase disease risk score performance further, however, due to the two-sample nature, some residual bias will remain even in infinitely large training data. This residual confounding is due to the training data estimates being suboptimally tailored to the specific confounding structure of test dataset. Because the random difference between training and test data remained, penalized disease risk score models preformed similar as the regular disease risk score models. The worse performance of the penalized DRS 3 (including an interaction term) is likely due to the fact that the Jeffrey’s prior does not perform well in multidimensional settings. Performance of other penalization methods obviously deserves further attention (e.g., Lasso or Ridge penalizations or the use of informative Bayesian priors33).

Previously, Cepeda et al.34 also explored events per coefficient of propensity score models, focusing on the number of outcome events. Instead, the present simulations focused on the number of exposed subjects per coefficient, which is more influential in propensity score estimation. For comparisons sake, the expected number of exposed and events was kept equal. In most empirical studies, the proportion of exposed subjects will be closer to 0.50 than the proportion of events, thus the benefit of using propensity score models over logistic regression and disease risk score models is expected to be greater than shown here. We also note that in all simulations, the propensity score and inverse probability weighting models consistently included one coefficient less than the logistic regression and disease risk score models, resulting in a slightly larger events per coefficient: 10.53, 5.13, 2.53, 1.01, 0.50. This small difference seems unlikely to explain the improved performance of the propensity score model. At events per coefficient of 1.0, extreme inverse probability weights resulted in a great number of model failures. At an events per coefficient of 0.5, all models converged; however, the estimated propensity of treatment was approximately 0.5, resulting in inverse probability weighted estimates equal to the crude (unadjusted for confounding) logistic regression estimates. In low events per coefficient settings, essentially all methods failed and perhaps inclusion of additional subjects would be a more reasonable solution. Alternatively, the penalized regression model greatly improved performance and should more often be considered. One should take into account, however, that unless large effects (OR > 1.5) can be expected, power is likely limited in such settings. This underperformance of all methods at low events per coefficient settings is due to a combination of separation (i.e., no variation in outcome at certain levels of the predictors)28,29 and nonpositivity35 (i.e., absence of variation in exposure at certain levels of the covariates). In our simulation, nonpositivity was random by design, so interpolation of the (confounder) estimates is appropriate. In empirical data, one should asses, case by case, whether nonpositivity might be deterministic, which may invalidate any interpolation or extrapolation. Similarly, while separation can be dealt with analytically, for example, using penalized Firth regression, analytic strategies should only be applied after careful consideration of potential biological reasons for the lack of observed outcomes, which can be a valid result by itself.

In empirical analyses, besides deciding on the confounding adjustment method, it is important to take account of the inherent time-dependent nature of most confounding biases, especially in pharmacoepidemiology.7 An important initial assessment might be to explore how patient characteristics change over time and monitor the proportion of new initiators.4,36 When there is a large fluctuation between time points, options are to model time explicitly,5 focus on a subset of patients that show similar characteristics,6 or refrain from performing a comparison until a more stable pattern emerges.4 Finally, data over multiple years of follow-up might be used to emulate an RCT as described by Hernán et al.37 While erroneous inclusion of instrumental variables did not impact our results (eTable 5;, likely due to the already large bias caused by nonpositivity and separation, if instruments are available researchers could consider performing an instrumental variable analysis.38,39 Similar to an RCT, results from an instrumental variable analysis are unaffected by observed and unobserved confounders. Conditional on the speed of uptake and the observed difference between early and late initiating patients (or prescribers), the impact of treatment effect modification should also be considered.6 We showed that the disease risk score method is fairly robust for unobserved interaction (or exclusion of the main effect of treatment) in the training data, unless of course this interaction effect is very large, which is unlikely to go unrecognized for drugs that have been marketed for a longer period. Depending on the likelihood of (unobserved) interaction in the test data, one might apply logistic regression, disease risk score, inverse probability weighting, or propensity score (included as a covariate) to estimate a population average effect,40,41 or a matched propensity score adjustment to estimate the treatment effect in the exposed.42

The simulations presented here are naturally limited and the following points merit discussion. First, as we showed in a sensitivity analysis, changing the simulation parameters will result in worse or better performance at a particular events per coefficient value. Therefore, instead of distilling a rule of thumb for the events per coefficient required, one should focus on the relative (i.e., between methods) difference in performance, which we showed to be more robust. Second, previous studies that explored events per coefficient fixed both the number of events and the number of covariates. In this article, the number of covariates was fixed, and the number of events was an average. We feel that this approach more closely follows research practice, where at the design phase it is possible to specify which and how many confounders would be considered, but only an expected number of events can be specified.43 Third, while we focused on the situation where confounders are prespecified,44 results are also relevant for researchers wishing to reduce model complexity using, for example, backward selection methods. In the first stage of such an approach, a full model is constructed which is equal to the prespecified model applied here, hence similar concerns about model misspecification and events per coefficient apply. Note, however, that applying model selection in logistic regression models will increase the type 1 error rate of the treatment associations beyond the level shown.45,46

In conclusion, when the number of events and the number of exposed subjects are equally sparse relative to the number of coefficients (e.g., events per coefficient of 0.5), disease risk models result in the least biased point estimates, albeit at the cost of a smaller coverage rate. While propensity score estimates were more biased at low events per coefficient, coverage remained closest to 0.95. At higher events per coefficient, propensity score models typically performed better than disease risk and logistic regression models. Depending on the settings and aim of the research, estimation or testing, a different method might be preferred. However, at very low events per coefficient (0.5), all methods had unacceptable levels of bias and coverage and a better approach might be to include more subjects or to use penalized likelihood methods.


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