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--- development:best_practices_estimation [2016/04/01 08:38] – schuemie
+++ development:best_practices_estimation [2020/03/09 05:18] (current) – schuemie
@@ Line 7: / Line 7: @@
   * **Transparency**: others should be able to reproduce your study in every detail using the information you provide.
   * **Prespecify** what you're going to estimate and how: this will avoid hidden multiple testing (fishing expeditions, p-value hacking). Run your analysis only once.
   * **Validation of your analysis**: you should have evidence that your analysis does what you say it does (showing that statistics that are produced have nominal operating characteristics (e.g. p-value calibration), showing that specific important assumptions are met (e.g. covariate balance), using unit tests to validate pieces of code, etc.)
 ===== Best practices (generic) =====
+  * **Write a full protocol**, and make it public prior to running the study. This should include
+    * Research question + hypotheses to be tested
+    * Which method(s), data, cohort definitions.
+    * What is the primary analyses and what are sensitivity analyses?
+    * Quality control
+    * Amendments and Updates
+  * **Validate** all code used to produce estimates. The purpose of validation is to ensure the code is doing what we require it to do. Possible options are:
+    * Unit testing
+    * Simulation
+    * Double coding
+    * Code review
-  * Make all analysis code available as open source
+  * Include **negative controls** (exposure-outcome pairs where we believe there is no effect)
-  * Include negative controls (exposure-outcome pairs where we believe there is no effect)
-  * Produce calibrated p-values
+  * Produce **calibrated p-values**
+  * Make all analysis code available as **open source** so others can easily replicate your study
 ===== Best practices (new-user cohort design) =====
+  * Use **propensity scores** (PS)
+  * Build PS model using **regularized regression** and a **large set of candidate covariates** (as implemented in the CohortMethod package)
+  * Use either **variable-ratio matching** or **stratification** on the PS
+  * **Compute covariate balance** after matching for all covariates, and terminate study if a covariate has standardized difference > 0.1
 ===== Best practices (self-controlled case series) =====
+  * Include a **risk window just prior to start of exposure** to detect time-varying confounding (e.g. contra-indications, protopathic bias)
+===== Best practices ((nested) case-control) =====
-  * Include a risk window just prior to start of exposure to detect time-varying confounding (e.g. contra-indications, protopathic bias)
+  * **Don't** do a case-control study