diff --git a/DESCRIPTION b/DESCRIPTION index 78f92207..94738140 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: CohortMethod Type: Package Title: New-User Cohort Method with Large Scale Propensity and Outcome Models Version: 4.2.0 -Date: 2021-06-16 +Date: 2021-06-17 Authors@R: c( person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut", "cre")), person("Marc", "Suchard", role = c("aut")), @@ -28,9 +28,9 @@ BugReports: https://github.com/OHDSI/CohortMethod/issues Depends: R (>= 3.5.0), DatabaseConnector (>= 4.0.0), - Cyclops (>= 3.1.1), + Cyclops (>= 3.1.2), FeatureExtraction (>= 3.0.0), - Andromeda (>= 0.3.0) + Andromeda (>= 0.4.0) Imports: methods, ggplot2, @@ -55,8 +55,7 @@ Suggests: EmpiricalCalibration, Eunomia Remotes: - ohdsi/FeatureExtraction, - ohdsi/Cyclops + ohdsi/FeatureExtraction LinkingTo: Rcpp NeedsCompilation: yes RoxygenNote: 7.1.1 diff --git a/NEWS.md b/NEWS.md index 40703bfd..bb26bd2c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -5,7 +5,7 @@ Changes: 1. Adding the `trimByIptw()` function. -2. Adding the `estimator` argument to the `fitOutcomeModel()` function to select 'ate' (average treatment effect) or 'att' (average treatement effect in the treated) when performing IPTW. +2. Adding the `estimator` argument to the `fitOutcomeModel()` function to select 'ate' (average treatment effect) or 'att' (average treatment effect in the treated) when performing IPTW. 3. Added the `maxWeight` argument to the `fitOutcomeModel()` function. Weights greater than this value will be set to this value. @@ -26,7 +26,7 @@ CohortMethod 4.1.0 Changes: -1. Dropped `insertDbPopulation()` function. This didn't seem to be used by anyone, and would have required carying the person ID throughout the pipeline. +1. Dropped `insertDbPopulation()` function. This didn't seem to be used by anyone, and would have required carrying the person ID throughout the pipeline. 2. Introducing new unique person identified called `personSeqId`, generated during data extraction. Person ID is now downloaded as string to avoid issues with 64-bit integers. Person ID is not used by CohortMethod, and is provided for reference only. diff --git a/R/Analyses.R b/R/Analyses.R index 764ec5ee..f7221248 100644 --- a/R/Analyses.R +++ b/R/Analyses.R @@ -207,7 +207,7 @@ loadCmAnalysisList <- function(file) { #' provided instead. In the analysis, the name of the number to be #' used can be specified using the #' \code{comparatorType} #' parameter in the [createCmAnalysis()] function. -#' @param outcomeIds A vector of concept IDs indentifying the outcome(s) in the +#' @param outcomeIds A vector of concept IDs identifying the outcome(s) in the #' outcome table. #' @param excludedCovariateConceptIds A list of concept IDs that cannot be used to construct #' covariates. This argument is to be used only for exclusion diff --git a/R/CreateArgFunctions.R b/R/CreateArgFunctions.R index 3e4d2cba..fe883db7 100644 --- a/R/CreateArgFunctions.R +++ b/R/CreateArgFunctions.R @@ -1,4 +1,4 @@ -# This file has been autogenerated. Do not change by hand. +# This file has been autogenerated. Do not change by hand. #' Create a parameter object for the function getDbCohortMethodData #' @@ -129,7 +129,7 @@ createCreateStudyPopulationArgs <- function(firstExposureOnly = FALSE, #' the treatment assignment. If any covariate has an unusually high #' correlation (either positive or negative), this will throw and #' error. -#' @param stopOnError If an error occurr, should the function stop? Else, the two cohorts +#' @param stopOnError If an error occur, should the function stop? Else, the two cohorts #' will be assumed to be perfectly separable. #' @param prior The prior used to fit the model. See Cyclops::createPrior() for #' details. diff --git a/R/PsFunctions.R b/R/PsFunctions.R index 99ca92f9..9ba9f646 100644 --- a/R/PsFunctions.R +++ b/R/PsFunctions.R @@ -42,7 +42,7 @@ #' the treatment assignment. If any covariate has an unusually high #' correlation (either positive or negative), this will throw and #' error. -#' @param stopOnError If an error occurr, should the function stop? Else, the two cohorts +#' @param stopOnError If an error occur, should the function stop? Else, the two cohorts #' will be assumed to be perfectly separable. #' @param prior The prior used to fit the model. See #' [Cyclops::createPrior()] for details. diff --git a/R/StudyPopulation.R b/R/StudyPopulation.R index d071b089..fd047c43 100644 --- a/R/StudyPopulation.R +++ b/R/StudyPopulation.R @@ -240,9 +240,11 @@ createStudyPopulation <- function(cohortMethodData, idx <- population$riskEnd > population$daysToObsEnd population$riskEnd[idx] <- population$daysToObsEnd[idx] - idx <- population$riskEnd > population$riskStart + maxDaysAtRisk - if (any(idx)) { - population$riskEnd[idx] <- population$riskStart[idx] + maxDaysAtRisk + if (!missing(maxDaysAtRisk) && !is.null(maxDaysAtRisk)) { + idx <- population$riskEnd > population$riskStart + maxDaysAtRisk + if (any(idx)) { + population$riskEnd[idx] <- population$riskStart[idx] + maxDaysAtRisk + } } if (censorAtNewRiskWindow) { ParallelLogger::logInfo("Censoring time at risk of recurrent subjects at start of new time at risk") @@ -338,10 +340,10 @@ getCounts <- function(population, description = "") { targetExposures <- length(population$personSeqId[population$treatment == 1]) comparatorExposures <- length(population$personSeqId[population$treatment == 0]) counts <- dplyr::tibble(description = description, - targetPersons = targetPersons, - comparatorPersons = comparatorPersons, - targetExposures = targetExposures, - comparatorExposures = comparatorExposures) + targetPersons = targetPersons, + comparatorPersons = comparatorPersons, + targetExposures = targetExposures, + comparatorExposures = comparatorExposures) return(counts) } @@ -468,17 +470,17 @@ plotTimeToEvent <- function(cohortMethodData, idxInPeriod <- outcomes$daysToEvent >= start & outcomes$daysToEvent < end idxPopInPeriod <- -population$daysFromObsStart <= start & population$daysToObsEnd >= end dplyr::tibble(number = number, - start = start, - end = end, - eventsExposed = 0, - eventsUnexposed = 0, - observed = 0, - eventsExposedTarget = sum(idxInPeriod & idxExposed & idxTarget), - eventsExposedComparator = sum(idxInPeriod & idxExposed & !idxTarget), - eventsUnexposedTarget = sum(idxInPeriod & !idxExposed & idxTarget), - eventsUnexposedComparator = sum(idxInPeriod & !idxExposed & !idxTarget), - observedTarget = sum(idxPopInPeriod & population$treatment), - observedComparator = sum(idxPopInPeriod & !population$treatment)) + start = start, + end = end, + eventsExposed = 0, + eventsUnexposed = 0, + observed = 0, + eventsExposedTarget = sum(idxInPeriod & idxExposed & idxTarget), + eventsExposedComparator = sum(idxInPeriod & idxExposed & !idxTarget), + eventsUnexposedTarget = sum(idxInPeriod & !idxExposed & idxTarget), + eventsUnexposedComparator = sum(idxInPeriod & !idxExposed & !idxTarget), + observedTarget = sum(idxPopInPeriod & population$treatment), + observedComparator = sum(idxPopInPeriod & !population$treatment)) } periods <- lapply(-floor(numberOfPeriods/2):ceiling(numberOfPeriods/2), createPeriod) periods <- do.call("rbind", periods) @@ -489,25 +491,25 @@ plotTimeToEvent <- function(cohortMethodData, periods$rateTarget <- (periods$eventsExposedTarget + periods$eventsUnexposedTarget) / periods$observedTarget periods$rateComparator <- (periods$eventsExposedComparator + periods$eventsUnexposedComparator) / periods$observedComparator vizData <- rbind(dplyr::tibble(start = periods$start, - end = periods$end, - rate = periods$rateExposedTarget, - status = "Exposed events", - type = targetLabel), + end = periods$end, + rate = periods$rateExposedTarget, + status = "Exposed events", + type = targetLabel), dplyr::tibble(start = periods$start, - end = periods$end, - rate = periods$rateUnexposedTarget, - status = "Unexposed events", - type = targetLabel), + end = periods$end, + rate = periods$rateUnexposedTarget, + status = "Unexposed events", + type = targetLabel), dplyr::tibble(start = periods$start, - end = periods$end, - rate = periods$rateExposedComparator, - status = "Exposed events", - type = comparatorLabel), + end = periods$end, + rate = periods$rateExposedComparator, + status = "Exposed events", + type = comparatorLabel), dplyr::tibble(start = periods$start, - end = periods$end, - rate = periods$rateUnexposedComparator, - status = "Unexposed events", - type = comparatorLabel)) + end = periods$end, + rate = periods$rateUnexposedComparator, + status = "Unexposed events", + type = comparatorLabel)) vizData$type <- factor(vizData$type, levels = c(targetLabel, comparatorLabel)) plot <- ggplot2::ggplot(vizData, ggplot2::aes(x = .data$start + periodLength / 2, diff --git a/_pkgdown.yml b/_pkgdown.yml index 41f07270..e5e37f81 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -28,6 +28,7 @@ reference: - matchOnPsAndCovariates - trimByPs - trimByPsToEquipoise + - trimByIptw - stratifyByPs - stratifyByPsAndCovariates - title: "Outcome models" diff --git a/docs/404.html b/docs/404.html index 50b46358..7ebc845b 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/articles/MultipleAnalyses.html b/docs/articles/MultipleAnalyses.html index c2b51801..3de1f241 100644 --- a/docs/articles/MultipleAnalyses.html +++ b/docs/articles/MultipleAnalyses.html @@ -31,7 +31,7 @@ CohortMethod - 4.1.0 + 4.2.0 @@ -91,7 +91,7 @@

Running multiple analyses at once using the CohortMethod package

Martijn J. Schuemie, Marc A. Suchard and Patrick Ryan

-

2021-03-19

+

2021-06-17

Source: vignettes/MultipleAnalyses.Rmd @@ -442,7 +442,7 @@

Now that we have produced estimates for all outcomes including our negative controls, we can perform empirical calibration to estimate the bias of the various analyses included in our study. We will create the calibration effect plots for every analysis ID. In each plot, the blue dots represent our negative control outcomes, and the yellow diamond represents our health outcome of interest: GI bleed. An unbiased, well-calibrated analysis should have 95% of the negative controls between the dashed lines (ie. 95% should have p > .05).

 install.packages("EmpiricalCalibration")
-library(EmpiricalCalibration)
+library(EmpiricalCalibration)
 
 # Analysis 1: No matching, simple outcome model
 negCons <- analysisSum[analysisSum$analysisId == 1 & analysisSum$outcomeId != 192671, ]
@@ -504,14 +504,14 @@ 

 ## To cite package 'CohortMethod' in publications use:
 ## 
 ##   Martijn Schuemie, Marc Suchard and Patrick Ryan (2021). CohortMethod:
-##   New-user cohort method with large scale propensity and outcome
-##   models. https://ohdsi.github.io/CohortMethod,
+##   New-User Cohort Method with Large Scale Propensity and Outcome
+##   Models. https://ohdsi.github.io/CohortMethod,
 ##   https://github.com/OHDSI/CohortMethod.
 ## 
 ## A BibTeX entry for LaTeX users is
 ## 
 ##   @Manual{,
-##     title = {CohortMethod: New-user cohort method with large scale propensity and outcome models},
+##     title = {CohortMethod: New-User Cohort Method with Large Scale Propensity and Outcome Models},
 ##     author = {Martijn Schuemie and Marc Suchard and Patrick Ryan},
 ##     year = {2021},
 ##     note = {https://ohdsi.github.io/CohortMethod, https://github.com/OHDSI/CohortMethod},
diff --git a/docs/articles/SingleStudies.html b/docs/articles/SingleStudies.html
index 3fce69c6..a132f3fc 100644
--- a/docs/articles/SingleStudies.html
+++ b/docs/articles/SingleStudies.html
@@ -31,7 +31,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
@@ -91,7 +91,7 @@

Single studies using the CohortMethod package

Martijn J. Schuemie, Marc A. Suchard and Patrick Ryan

-

2021-03-19

+

2021-06-17

Source: vignettes/SingleStudies.Rmd @@ -268,7 +268,7 @@

## ## Inherits from Andromeda: ## # Andromeda object -## # Physical location: C:\Users\mschuemi\AppData\Local\Temp\RtmpuouZ4L\file7b10195d5853.sqlite +## # Physical location: C:\Users\mschuemi\AppData\Local\Temp\RtmpGsJdnq\file2e880126615c.sqlite ## ## Tables: ## $analysisRef (analysisId, analysisName, domainId, startDay, endDay, isBinary, missingMeansZero) @@ -749,13 +749,13 @@ 

## 
 ## To cite package 'CohortMethod' in publications use:
 ## 
-##   Martijn Schuemie, Marc Suchard and Patrick Ryan (2021). CohortMethod: New-user cohort method with large scale propensity and outcome models.
+##   Martijn Schuemie, Marc Suchard and Patrick Ryan (2021). CohortMethod: New-User Cohort Method with Large Scale Propensity and Outcome Models.
 ##   https://ohdsi.github.io/CohortMethod, https://github.com/OHDSI/CohortMethod.
 ## 
 ## A BibTeX entry for LaTeX users is
 ## 
 ##   @Manual{,
-##     title = {CohortMethod: New-user cohort method with large scale propensity and outcome models},
+##     title = {CohortMethod: New-User Cohort Method with Large Scale Propensity and Outcome Models},
 ##     author = {Martijn Schuemie and Marc Suchard and Patrick Ryan},
 ##     year = {2021},
 ##     note = {https://ohdsi.github.io/CohortMethod, https://github.com/OHDSI/CohortMethod},
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 98110a39..5f1708e2 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -71,7 +71,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
diff --git a/docs/authors.html b/docs/authors.html
index 95dcb74e..cd6e7390 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -71,7 +71,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
diff --git a/docs/index.html b/docs/index.html
index 5e1b8ac0..bbfa0cc2 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -5,16 +5,16 @@
 
 
 
-New-user cohort method with large scale propensity and outcome models • CohortMethod
+New-User Cohort Method with Large Scale Propensity and Outcome Models • CohortMethod
 
 
 
 
 
-
-
+
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
@@ -152,7 +152,7 @@ 

 

 

 System Requirements

-
Requires R (version 3.6.0 or higher). Installation on Windows requires RTools. Libraries used in CohortMethod require Java.

+
Requires R (version 3.6.0 or higher). Installation on Windows requires RTools. Libraries used in CohortMethod require Java.

 

 

 

diff --git a/docs/news/index.html b/docs/news/index.html
index 7069c81d..5b48ca6c 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -71,7 +71,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     

 
@@ -132,12 +132,29 @@ 
Changelog 

       Source: NEWS.md
     
 
+    

+

+CohortMethod 4.2.0

+
Changes:

+
    
+
  1. Adding the trimByIptw() function.
    2. 
+
  2. Adding the estimator argument to the fitOutcomeModel() function to select ‘ate’ (average treatment effect) or ‘att’ (average treatment effect in the treated) when performing IPTW.
    3. 
+
  3. Added the maxWeight argument to the fitOutcomeModel() function. Weights greater than this value will be set to this value.
    4. 
+
  4. Adding option to use adaptive likelihood profiling, and making this the default.
    5. 
+
  5. Adding maxDaysAtRisk argument to the createStudyPopulation() and createCreateStudyPopulationArgs() functions.
    6. 
+

+
Bug fixes:

+
    
+
  1. Fixing IPTW.
    2. 
+
  2. Fixing error when stratifying and base population is empty (but overall population is not).
    3. 
+

+

     

 

 CohortMethod 4.1.0

 
Changes:

 
    
-
  1. Dropped insertDbPopulation() function. This didn’t seem to be used by anyone, and would have required carying the person ID throughout the pipeline.
    2. 
+
  2. Dropped insertDbPopulation() function. This didn’t seem to be used by anyone, and would have required carrying the person ID throughout the pipeline.
    3. 
 
  3. Introducing new unique person identified called personSeqId, generated during data extraction. Person ID is now downloaded as string to avoid issues with 64-bit integers. Person ID is not used by CohortMethod, and is provided for reference only.
    4. 
 
  4. Adding log likelihood ratio to outcome model object.
    5. 
 
  5. Deprecating oracleTempSchema argument in favor of tempEmulationSchema in line with new SqlRender interface.
    6. 
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index ccca64af..8e57dede 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   MultipleAnalyses: MultipleAnalyses.html
   SingleStudies: SingleStudies.html
-last_built: 2021-03-19T14:16Z
+last_built: 2021-06-17T09:54Z
 
diff --git a/docs/pull_request_template.html b/docs/pull_request_template.html
index 95e4f780..b1ee3bb0 100644
--- a/docs/pull_request_template.html
+++ b/docs/pull_request_template.html
@@ -71,7 +71,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     

 
diff --git a/docs/reference/CohortMethod-package.html b/docs/reference/CohortMethod-package.html
index ae64da5a..cca3ce16 100644
--- a/docs/reference/CohortMethod-package.html
+++ b/docs/reference/CohortMethod-package.html
@@ -6,7 +6,7 @@
 
 
 
-CohortMethod: New-user cohort method with large scale propensity and outcome models — CohortMethod-package • CohortMethod
+CohortMethod: New-User Cohort Method with Large Scale Propensity and Outcome Models — CohortMethod-package • CohortMethod
 
 
 
@@ -39,10 +39,10 @@
 
 
 
-
-
+
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
@@ -140,15 +140,15 @@
 

   

     

-    
CohortMethod: New-user cohort method with large scale propensity and outcome models

+    
CohortMethod: New-User Cohort Method with Large Scale Propensity and Outcome Models

     Source: R/CohortMethod.R
     
     

 
     

-    
CohortMethod is an R package for performing new-user cohort studies
-	in an observational database in the OMOP Common Data Model. It extracts the
-	necessary data from a database and uses a large set of covariates for both the 
+    
Functions for performing new-user cohort studies
+	in an observational database in the OMOP Common Data Model. Can extract the
+	necessary data from a database and use a large set of covariates for both the 
 	propensity and outcome model, including for example all drugs, diagnoses, procedures, 
 	as well as age, comorbidity indexes, etc. Large scale regularized regression is used to 
 	fit the propensity and outcome models. Functions are included for trimming, stratifying, 
diff --git a/docs/reference/CohortMethodData-class.html b/docs/reference/CohortMethodData-class.html
index d3bfb426..74e04b5e 100644
--- a/docs/reference/CohortMethodData-class.html
+++ b/docs/reference/CohortMethodData-class.html
@@ -76,7 +76,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     

 
diff --git a/docs/reference/checkCmInstallation.html b/docs/reference/checkCmInstallation.html
index 372e01cc..91abb84b 100644
--- a/docs/reference/checkCmInstallation.html
+++ b/docs/reference/checkCmInstallation.html
@@ -72,7 +72,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     

 
diff --git a/docs/reference/cohortMethodDataSimulationProfile.html b/docs/reference/cohortMethodDataSimulationProfile.html
index 8ca6bf0d..5d05fc43 100644
--- a/docs/reference/cohortMethodDataSimulationProfile.html
+++ b/docs/reference/cohortMethodDataSimulationProfile.html
@@ -72,7 +72,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     

 
diff --git a/docs/reference/computeCovariateBalance.html b/docs/reference/computeCovariateBalance.html
index 4a72d593..530c5d05 100644
--- a/docs/reference/computeCovariateBalance.html
+++ b/docs/reference/computeCovariateBalance.html
@@ -74,7 +74,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
diff --git a/docs/reference/computeMdrr.html b/docs/reference/computeMdrr.html
index c671882f..18f6df96 100644
--- a/docs/reference/computeMdrr.html
+++ b/docs/reference/computeMdrr.html
@@ -72,7 +72,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
diff --git a/docs/reference/computePsAuc.html b/docs/reference/computePsAuc.html
index ddfc62eb..5c35c050 100644
--- a/docs/reference/computePsAuc.html
+++ b/docs/reference/computePsAuc.html
@@ -72,7 +72,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
diff --git a/docs/reference/createCmAnalysis.html b/docs/reference/createCmAnalysis.html
index 93574843..c253259b 100644
--- a/docs/reference/createCmAnalysis.html
+++ b/docs/reference/createCmAnalysis.html
@@ -72,7 +72,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
@@ -151,6 +151,8 @@ 
Create a CohortMethod analysis specification

   trimByPsArgs = NULL,
   trimByPsToEquipoise = FALSE,
   trimByPsToEquipoiseArgs = NULL,
+  trimByIptw = FALSE,
+  trimByIptwArgs = NULL,
   matchOnPs = FALSE,
   matchOnPsArgs = NULL,
   matchOnPsAndCovariates = FALSE,
@@ -190,98 +192,108 @@ 
Arg
     
       getDbCohortMethodDataArgs
       
An object representing the arguments to be used when calling
-the getDbCohortMethodData function.

+the getDbCohortMethodData() function.

     
     
       createStudyPopArgs
       
An object representing the arguments to be used when calling
-the createStudyPopulation function.

+the createStudyPopulation() function.

     
     
       createPs
-      
Should the createPs function be used in this
+      
Should the createPs() function be used in this
 analysis?

     
     
       createPsArgs
       
An object representing the arguments to be used when calling
-the createPs function.

+the createPs() function.

     
     
       trimByPs
-      
Should the trimByPs function be used in this
+      
Should the trimByPs() function be used in this
 analysis?

     
     
       trimByPsArgs
       
An object representing the arguments to be used when calling
-the trimByPs function.

+the trimByPs() function.

     
     
       trimByPsToEquipoise
-      
Should the trimByPsToEquipoise function be used
+      
Should the trimByPsToEquipoise() function be used
 in this analysis?

     
     
       trimByPsToEquipoiseArgs
       
An object representing the arguments to be used when calling
-the trimByPsToEquipoise function.

+the trimByPsToEquipoise() function.

+    
+    
+      trimByIptw
+      
Should the trimByPsToEquipoise() function be used
+in this analysis?

+    
+    
+      trimByIptwArgs
+      
An object representing the arguments to be used when calling
+the trimByIptw() function.

     
     
       matchOnPs
-      
Should the matchOnPs function be used in this
+      
Should the matchOnPs() function be used in this
 analysis?

     
     
       matchOnPsArgs
       
An object representing the arguments to be used when calling
-the matchOnPs function.

+the matchOnPs() function.

     
     
       matchOnPsAndCovariates
-      
Should the matchOnPsAndCovariates function be
+      
Should the matchOnPsAndCovariates() function be
 used in this analysis?

     
     
       matchOnPsAndCovariatesArgs
       
An object representing the arguments to be used when calling
-the matchOnPsAndCovariates function.

+the matchOnPsAndCovariates() function.

     
     
       stratifyByPs
-      
Should the stratifyByPs function be used in
+      
Should the stratifyByPs() function be used in
 this analysis?

     
     
       stratifyByPsArgs
       
An object representing the arguments to be used when calling
-the stratifyByPs function.

+the stratifyByPs() function.

     
     
       stratifyByPsAndCovariates
-      
Should the stratifyByPsAndCovariates function
+      
Should the stratifyByPsAndCovariates() function
 be used in this analysis?

     
     
       stratifyByPsAndCovariatesArgs
       
An object representing the arguments to be used when calling
-the stratifyByPsAndCovariates function.

+the stratifyByPsAndCovariates() function.

     
     
       fitOutcomeModel
-      
Should the fitOutcomeModel function be used in
+      
Should the fitOutcomeModel() function be used in
 this analysis?

     
     
       fitOutcomeModelArgs
       
An object representing the arguments to be used when calling
-the fitOutcomeModel function.

+the fitOutcomeModel() function.

     
     
 
     
Details

 
-    
Create a set of analysis choices, to be used with the runCmAnalyses function.

+    
Create a set of analysis choices, to be used with the runCmAnalyses() function.

 
   
   
 
diff --git a/docs/reference/createCohortMethodDataSimulationProfile.html b/docs/reference/createCohortMethodDataSimulationProfile.html
index cab84f09..6e74a9ba 100644
--- a/docs/reference/createCohortMethodDataSimulationProfile.html
+++ b/docs/reference/createCohortMethodDataSimulationProfile.html
@@ -74,7 +74,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
diff --git a/docs/reference/createCreatePsArgs.html b/docs/reference/createCreatePsArgs.html
index 6fec4c93..11b31df8 100644
--- a/docs/reference/createCreatePsArgs.html
+++ b/docs/reference/createCreatePsArgs.html
@@ -72,7 +72,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
@@ -177,7 +177,7 @@ 
Arg
     
     
       stopOnError
-      
If an error occurr, should the function stop? Else, the two cohorts
+      
If an error occur, should the function stop? Else, the two cohorts
 will be assumed to be perfectly separable.

     
     
diff --git a/docs/reference/createCreateStudyPopulationArgs.html b/docs/reference/createCreateStudyPopulationArgs.html
index c427004c..4da97fbb 100644
--- a/docs/reference/createCreateStudyPopulationArgs.html
+++ b/docs/reference/createCreateStudyPopulationArgs.html
@@ -72,7 +72,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
@@ -146,6 +146,7 @@ 
Create a parameter object for the function createStudyPopulation

   removeSubjectsWithPriorOutcome = TRUE,
   priorOutcomeLookback = 99999,
   minDaysAtRisk = 1,
+  maxDaysAtRisk = 99999,
   riskWindowStart = 0,
   addExposureDaysToStart = NULL,
   startAnchor = "cohort start",
@@ -189,7 +190,14 @@ 
Arg
     
     
       minDaysAtRisk
-      
The minimum required number of days at risk.

+      
The minimum required number of days at risk. Risk windows
+with fewer days than this number are removed from the
+analysis.

+    
+    
+      maxDaysAtRisk
+      
The maximum allowed number of days at risk. Risk windows
+that are longer will be truncated to this number of days.

     
     
       riskWindowStart
diff --git a/docs/reference/createFitOutcomeModelArgs.html b/docs/reference/createFitOutcomeModelArgs.html
index 42e06d4d..357f67f8 100644
--- a/docs/reference/createFitOutcomeModelArgs.html
+++ b/docs/reference/createFitOutcomeModelArgs.html
@@ -72,7 +72,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
@@ -143,10 +143,13 @@ 
Create a parameter object for the function fitOutcomeModel

   stratified = FALSE,
   useCovariates = FALSE,
   inversePtWeighting = FALSE,
+  estimator = "ate",
+  maxWeight = 0,
   interactionCovariateIds = c(),
   excludeCovariateIds = c(),
   includeCovariateIds = c(),
-  profileGrid = seq(log(0.1), log(10), length.out = 1000),
+  profileGrid = NULL,
+  profileBounds = c(log(0.1), log(10)),
   prior = createPrior("laplace", useCrossValidation = TRUE),
   control = createControl(cvType = "auto", seed = 1, startingVariance = 0.01, tolerance
     = 2e-07, cvRepetitions = 10, noiseLevel = "quiet")
@@ -175,6 +178,17 @@ 
Arg
       inversePtWeighting
       
Use inverse probability of treatment weighting (IPTW)? See details.

     
+    
+      estimator
+      
for IPTW: the type of estimator. Options are estimator = "ate" for
+the average treatment effect, and estimator = "att"for the average
+treatment effect in the treated.

+    
+    
+      maxWeight
+      
for IPTW: the maximum weight. Larger values will be truncated to
+this value. maxWeight = 0 means no truncation takes place.

+    
     
       interactionCovariateIds
       
An optional vector of covariate IDs to use to estimate interactions
@@ -191,8 +205,13 @@ 
Arg
     
       profileGrid
       
A one-dimensional grid of points on the log(relative risk) scale
-where the likelihood for the treatment variable coefficient is
-sampled. Set to NULL to skip profiling.

+where the likelihood for coefficient of variables is sampled. See
+details.

+    
+    
+      profileBounds
+      
The bounds (on the log relative risk scale) for the adaptive
+sampling of the likelihood function. See details.

     
     
       prior
diff --git a/docs/reference/createGetDbCohortMethodDataArgs.html b/docs/reference/createGetDbCohortMethodDataArgs.html
index 968a99fe..be2815fe 100644
--- a/docs/reference/createGetDbCohortMethodDataArgs.html
+++ b/docs/reference/createGetDbCohortMethodDataArgs.html
@@ -72,7 +72,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
diff --git a/docs/reference/createMatchOnPsAndCovariatesArgs.html b/docs/reference/createMatchOnPsAndCovariatesArgs.html
index 74e2abd3..e7904af4 100644
--- a/docs/reference/createMatchOnPsAndCovariatesArgs.html
+++ b/docs/reference/createMatchOnPsAndCovariatesArgs.html
@@ -72,7 +72,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
diff --git a/docs/reference/createMatchOnPsArgs.html b/docs/reference/createMatchOnPsArgs.html
index c41ffed1..d8bf8517 100644
--- a/docs/reference/createMatchOnPsArgs.html
+++ b/docs/reference/createMatchOnPsArgs.html
@@ -72,7 +72,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
diff --git a/docs/reference/createPs.html b/docs/reference/createPs.html
index 1f10acca..09a545b2 100644
--- a/docs/reference/createPs.html
+++ b/docs/reference/createPs.html
@@ -72,7 +72,7 @@
       
       
         CohortMethod
-        4.1.0
+        4.2.0
       
     
 
@@ -192,7 +192,7 @@ 
Arg
     
     
       stopOnError
-      
If an error occurr, should the function stop? Else, the two cohorts
+      
If an error occur, should the function stop? Else, the two cohorts
 will be assumed to be perfectly separable.

     
     
@@ -220,7 +220,7 @@ 
Examp
 
#> Removing 1 redundant covariates
 #> Removing 0 infrequent covariates
 #> Normalizing covariates
-#> Tidying covariates took 0.782 secs
#> Warning: All coefficients (except maybe the intercept) are zero. Either the covariates are completely uninformative or completely predictive of the treatment. Did you remember to exclude the treatment variables from the covariates?
#> Creating propensity scores took 3.79 secs

+#> Tidying covariates took 0.81 secs
#> Warning: All coefficients (except maybe the intercept) are zero. Either the covariates are completely uninformative or completely predictive of the treatment. Did you remember to exclude the treatment variables from the covariates?
#> Creating propensity scores took 3.82 secs
diff --git a/docs/reference/createStratifyByPsArgs.html b/docs/reference/createStratifyByPsArgs.html index 783eec32..39f449aa 100644 --- a/docs/reference/createStratifyByPsArgs.html +++ b/docs/reference/createStratifyByPsArgs.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/createStudyPopulation.html b/docs/reference/createStudyPopulation.html index 7d114b62..228a5122 100644 --- a/docs/reference/createStudyPopulation.html +++ b/docs/reference/createStudyPopulation.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 @@ -149,6 +149,7 @@

Create a study population

removeSubjectsWithPriorOutcome = TRUE, priorOutcomeLookback = 99999, minDaysAtRisk = 1, + maxDaysAtRisk = 99999, riskWindowStart = 0, addExposureDaysToStart = NULL, startAnchor = "cohort start", @@ -206,7 +207,13 @@

Arg minDaysAtRisk -

The minimum required number of days at risk.

+

The minimum required number of days at risk. Risk windows with fewer +days than this number are removed from the analysis.

+ + + maxDaysAtRisk +

The maximum allowed number of days at risk. Risk windows that are +longer will be truncated to this number of days.

riskWindowStart diff --git a/docs/reference/createTargetComparatorOutcomes.html b/docs/reference/createTargetComparatorOutcomes.html index 6d425b62..ef6138ca 100644 --- a/docs/reference/createTargetComparatorOutcomes.html +++ b/docs/reference/createTargetComparatorOutcomes.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 @@ -156,7 +156,7 @@

Arg tested in the analysis, a named list of numbers can be provided instead. In the analysis, the name of the number to be used can be specified using the #' targetType parameter in the -createCmAnalysis function.

+createCmAnalysis() function.

comparatorId @@ -165,11 +165,11 @@

Arg be tested in the analysis, a named list of numbers can be provided instead. In the analysis, the name of the number to be used can be specified using the #' comparatorType -parameter in the createCmAnalysis function.

+parameter in the createCmAnalysis() function.

outcomeIds -

A vector of concept IDs indentifying the outcome(s) in the +

A vector of concept IDs identifying the outcome(s) in the outcome table.

@@ -188,7 +188,7 @@

Arg

Details

-

Create a set of hypotheses of interest, to be used with the runCmAnalyses function.

+

Create a set of hypotheses of interest, to be used with the runCmAnalyses() function.

diff --git a/docs/reference/createTrimByPsToEquipoiseArgs.html b/docs/reference/createTrimByPsToEquipoiseArgs.html index 5c3fe53a..3800b48f 100644 --- a/docs/reference/createTrimByPsToEquipoiseArgs.html +++ b/docs/reference/createTrimByPsToEquipoiseArgs.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/drawAttritionDiagram.html b/docs/reference/drawAttritionDiagram.html index c30e9d2c..90bba84d 100644 --- a/docs/reference/drawAttritionDiagram.html +++ b/docs/reference/drawAttritionDiagram.html @@ -73,7 +73,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/fitOutcomeModel.html b/docs/reference/fitOutcomeModel.html index 417157ae..3fa54ae0 100644 --- a/docs/reference/fitOutcomeModel.html +++ b/docs/reference/fitOutcomeModel.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 @@ -145,10 +145,13 @@

Create an outcome model, and compute the relative risk

stratified = FALSE, useCovariates = FALSE, inversePtWeighting = FALSE, + estimator = "ate", + maxWeight = 0, interactionCovariateIds = c(), excludeCovariateIds = c(), includeCovariateIds = c(), - profileGrid = seq(log(0.1), log(10), length.out = 1000), + profileGrid = NULL, + profileBounds = c(log(0.1), log(10)), prior = createPrior("laplace", useCrossValidation = TRUE), control = createControl(cvType = "auto", seed = 1, startingVariance = 0.01, tolerance = 2e-07, cvRepetitions = 10, noiseLevel = "quiet") @@ -188,6 +191,17 @@

Arg inversePtWeighting

Use inverse probability of treatment weighting (IPTW)? See details.

+ + estimator +

for IPTW: the type of estimator. Options are estimator = "ate" for the +average treatment effect, and estimator = "att"for the average treatment +effect in the treated.

+ + + maxWeight +

for IPTW: the maximum weight. Larger values will be truncated to this +value. maxWeight = 0 means no truncation takes place.

+ interactionCovariateIds

An optional vector of covariate IDs to use to estimate interactions @@ -204,8 +218,12 @@

Arg profileGrid

A one-dimensional grid of points on the log(relative risk) scale where -the likelihood for the treatment variable coefficient is sampled. Set to -NULL to skip profiling.

+the likelihood for coefficient of variables is sampled. See details.

+ + + profileBounds +

The bounds (on the log relative risk scale) for the adaptive sampling +of the likelihood function. See details.

prior @@ -226,7 +244,11 @@

Value

confint are available.

Details

-

IPTW estimates the average treatment effect using stabilized inverse propensity scores (Xu et al. 2010).

+

IPTW estimates either the average treatment effect (ate) or average treatment effect in the treated +(att) using stabilized inverse propensity scores (Xu et al. 2010).

+

For likelihood profiling, either specify the profileGrid for a completely user- defined grid, or +profileBounds for an adaptive grid. Both should be defined on the log effect size scale. When both +profileGrid and profileGrid are NULL likelihood profiling is disabled.

References

Xu S, Ross C, Raebel MA, Shetterly S, Blanchette C, Smith D. Use of stabilized inverse propensity scores diff --git a/docs/reference/getAttritionTable.html b/docs/reference/getAttritionTable.html index cac2eeb0..03944e44 100644 --- a/docs/reference/getAttritionTable.html +++ b/docs/reference/getAttritionTable.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/getDbCohortMethodData.html b/docs/reference/getDbCohortMethodData.html index 48487201..24ffa183 100644 --- a/docs/reference/getDbCohortMethodData.html +++ b/docs/reference/getDbCohortMethodData.html @@ -73,7 +73,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/getDefaultCmTable1Specifications.html b/docs/reference/getDefaultCmTable1Specifications.html index a7458cf8..e7d0e06e 100644 --- a/docs/reference/getDefaultCmTable1Specifications.html +++ b/docs/reference/getDefaultCmTable1Specifications.html @@ -74,7 +74,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/getFollowUpDistribution.html b/docs/reference/getFollowUpDistribution.html index 68f983a6..5bf1057d 100644 --- a/docs/reference/getFollowUpDistribution.html +++ b/docs/reference/getFollowUpDistribution.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/getOutcomeModel.html b/docs/reference/getOutcomeModel.html index 7454f87f..cc3bc1fc 100644 --- a/docs/reference/getOutcomeModel.html +++ b/docs/reference/getOutcomeModel.html @@ -73,7 +73,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/getPsModel.html b/docs/reference/getPsModel.html index 740ff616..a4e52e74 100644 --- a/docs/reference/getPsModel.html +++ b/docs/reference/getPsModel.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index 58296057..9cd7b9f4 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -71,7 +71,7 @@ CohortMethod - 4.1.0 + 4.2.0 @@ -238,6 +238,12 @@

trimByIptw()

+ +

Remove subjects with a high IPTW

+ +

stratifyByPs()

@@ -433,6 +439,12 @@

createTrimByIptwArgs()

+ +

Create a parameter object for the function trimByIptw

+ +

createTrimByPsArgs()

diff --git a/docs/reference/isCohortMethodData.html b/docs/reference/isCohortMethodData.html index 74e599eb..7502f901 100644 --- a/docs/reference/isCohortMethodData.html +++ b/docs/reference/isCohortMethodData.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/loadCmAnalysisList.html b/docs/reference/loadCmAnalysisList.html index 7cc69578..7df5d879 100644 --- a/docs/reference/loadCmAnalysisList.html +++ b/docs/reference/loadCmAnalysisList.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/loadCohortMethodData.html b/docs/reference/loadCohortMethodData.html index fa93cc01..b447e628 100644 --- a/docs/reference/loadCohortMethodData.html +++ b/docs/reference/loadCohortMethodData.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/loadTargetComparatorOutcomesList.html b/docs/reference/loadTargetComparatorOutcomesList.html index 778cbe54..54babdcb 100644 --- a/docs/reference/loadTargetComparatorOutcomesList.html +++ b/docs/reference/loadTargetComparatorOutcomesList.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/matchOnPs.html b/docs/reference/matchOnPs.html index 5997c56e..39446bde 100644 --- a/docs/reference/matchOnPs.html +++ b/docs/reference/matchOnPs.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/matchOnPsAndCovariates.html b/docs/reference/matchOnPsAndCovariates.html index 2e36a2ee..d569dfcb 100644 --- a/docs/reference/matchOnPsAndCovariates.html +++ b/docs/reference/matchOnPsAndCovariates.html @@ -73,7 +73,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/plotCovariateBalanceOfTopVariables.html b/docs/reference/plotCovariateBalanceOfTopVariables.html index 46df3402..e2373d15 100644 --- a/docs/reference/plotCovariateBalanceOfTopVariables.html +++ b/docs/reference/plotCovariateBalanceOfTopVariables.html @@ -74,7 +74,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/plotCovariateBalanceScatterPlot.html b/docs/reference/plotCovariateBalanceScatterPlot.html index 042c8ebe..3ccea461 100644 --- a/docs/reference/plotCovariateBalanceScatterPlot.html +++ b/docs/reference/plotCovariateBalanceScatterPlot.html @@ -73,7 +73,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/plotFollowUpDistribution.html b/docs/reference/plotFollowUpDistribution.html index c67d038b..1cdf87e9 100644 --- a/docs/reference/plotFollowUpDistribution.html +++ b/docs/reference/plotFollowUpDistribution.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/plotKaplanMeier.html b/docs/reference/plotKaplanMeier.html index e4ff4fa8..f9763485 100644 --- a/docs/reference/plotKaplanMeier.html +++ b/docs/reference/plotKaplanMeier.html @@ -76,7 +76,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/plotPs.html b/docs/reference/plotPs.html index 3c340be2..758db143 100644 --- a/docs/reference/plotPs.html +++ b/docs/reference/plotPs.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/plotTimeToEvent.html b/docs/reference/plotTimeToEvent.html index d6b30b57..87e16b2c 100644 --- a/docs/reference/plotTimeToEvent.html +++ b/docs/reference/plotTimeToEvent.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/runCmAnalyses.html b/docs/reference/runCmAnalyses.html index e48dbc97..53a28164 100644 --- a/docs/reference/runCmAnalyses.html +++ b/docs/reference/runCmAnalyses.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 @@ -171,8 +171,7 @@

Arg connectionDetails

An R object of type connectionDetails created using the -function createConnectionDetails in the -DatabaseConnector package.

+DatabaseConnector::createConnectionDetails() function.

cdmDatabaseSchema diff --git a/docs/reference/saveCmAnalysisList.html b/docs/reference/saveCmAnalysisList.html index ba548f37..ec06faaf 100644 --- a/docs/reference/saveCmAnalysisList.html +++ b/docs/reference/saveCmAnalysisList.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/saveCohortMethodData.html b/docs/reference/saveCohortMethodData.html index 8bba31b3..037f9e20 100644 --- a/docs/reference/saveCohortMethodData.html +++ b/docs/reference/saveCohortMethodData.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/saveTargetComparatorOutcomesList.html b/docs/reference/saveTargetComparatorOutcomesList.html index 16bfd190..661ebf6e 100644 --- a/docs/reference/saveTargetComparatorOutcomesList.html +++ b/docs/reference/saveTargetComparatorOutcomesList.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/simulateCohortMethodData.html b/docs/reference/simulateCohortMethodData.html index 6e0b77d0..183462df 100644 --- a/docs/reference/simulateCohortMethodData.html +++ b/docs/reference/simulateCohortMethodData.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/stratifyByPs.html b/docs/reference/stratifyByPs.html index edbffc70..d72eac93 100644 --- a/docs/reference/stratifyByPs.html +++ b/docs/reference/stratifyByPs.html @@ -73,7 +73,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/stratifyByPsAndCovariates.html b/docs/reference/stratifyByPsAndCovariates.html index 62e930e8..9274edaf 100644 --- a/docs/reference/stratifyByPsAndCovariates.html +++ b/docs/reference/stratifyByPsAndCovariates.html @@ -73,7 +73,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/summarizeAnalyses.html b/docs/reference/summarizeAnalyses.html index a5a09665..9140ef4c 100644 --- a/docs/reference/summarizeAnalyses.html +++ b/docs/reference/summarizeAnalyses.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/trimByIptw.html b/docs/reference/trimByIptw.html new file mode 100644 index 00000000..c7142acc --- /dev/null +++ b/docs/reference/trimByIptw.html @@ -0,0 +1,211 @@ + + + + + + + + +Remove subjects with a high IPTW — trimByIptw • CohortMethod + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+ +
+
+
+

Remove subjects with a high IPTW

+ Source: R/PsFunctions.R + +
+ +
+

Compute the inverse probability of treatment weights (IPTW) using the propensity scores, and remove +subjects having a weight higher than the user-specified threshold.

+
+ + 
trimByIptw(population, maxWeight = 10, estimator = "ate")
+ +

Arguments

+ + + + + + + + + + + + + + +
population

A data frame with at least the three columns described below.

maxWeight

The maximum allowed IPTW.

estimator

The type of estimator. Options are estimator = "ate" for the average treatment +effect, and estimator = "att"for the average treatment effect in the treated.

+ +

Value

+ +

Returns a tibble with the same columns as the input, as well as a weights column containing the +IPTW.

+

Details

+ +

The data frame should have the following three columns:

    +

  • rowId (numeric): A unique identifier for each row (e.g. the person ID).

    • +

  • treatment (integer): Column indicating whether the person is in the target (1) or comparator (0) group.

    • +

  • propensityScore (numeric): Propensity score.

    • +
+ + +

Examples

+ 
rowId <- 1:2000
+treatment <- rep(0:1, each = 1000)
+propensityScore <- c(runif(1000, min = 0, max = 1), runif(1000, min = 0, max = 1))
+data <- data.frame(rowId = rowId, treatment = treatment, propensityScore = propensityScore)
+result <- trimByIptw(data)
+
+
+
+ +
+ + +
+
+

Developed by Martijn Schuemie, Marc Suchard, Patrick Ryan.

+
+ +
+

Site built with pkgdown 1.6.1.

+
+ +
+
+ + + + + + + + diff --git a/docs/reference/trimByPs.html b/docs/reference/trimByPs.html index c821b82f..ff214829 100644 --- a/docs/reference/trimByPs.html +++ b/docs/reference/trimByPs.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/docs/reference/trimByPsToEquipoise.html b/docs/reference/trimByPsToEquipoise.html index b410e121..6aa06204 100644 --- a/docs/reference/trimByPsToEquipoise.html +++ b/docs/reference/trimByPsToEquipoise.html @@ -72,7 +72,7 @@ CohortMethod - 4.1.0 + 4.2.0 diff --git a/extras/CohortMethod.pdf b/extras/CohortMethod.pdf index 0d8ab036..4bd9348d 100644 Binary files a/extras/CohortMethod.pdf and b/extras/CohortMethod.pdf differ diff --git a/inst/doc/MultipleAnalyses.pdf b/inst/doc/MultipleAnalyses.pdf index cb69b795..a594155f 100644 Binary files a/inst/doc/MultipleAnalyses.pdf and b/inst/doc/MultipleAnalyses.pdf differ diff --git a/inst/doc/SingleStudies.pdf b/inst/doc/SingleStudies.pdf index 6b2a5113..ac09857e 100644 Binary files a/inst/doc/SingleStudies.pdf and b/inst/doc/SingleStudies.pdf differ diff --git a/man/createCreatePsArgs.Rd b/man/createCreatePsArgs.Rd index 105e853e..0d2e9df7 100644 --- a/man/createCreatePsArgs.Rd +++ b/man/createCreatePsArgs.Rd @@ -31,7 +31,7 @@ the treatment assignment. If any covariate has an unusually high correlation (either positive or negative), this will throw and error.} -\item{stopOnError}{If an error occurr, should the function stop? Else, the two cohorts +\item{stopOnError}{If an error occur, should the function stop? Else, the two cohorts will be assumed to be perfectly separable.} \item{prior}{The prior used to fit the model. See Cyclops::createPrior() for diff --git a/man/createPs.Rd b/man/createPs.Rd index 6793e9a0..1ec92cb5 100644 --- a/man/createPs.Rd +++ b/man/createPs.Rd @@ -42,7 +42,7 @@ the treatment assignment. If any covariate has an unusually high correlation (either positive or negative), this will throw and error.} -\item{stopOnError}{If an error occurr, should the function stop? Else, the two cohorts +\item{stopOnError}{If an error occur, should the function stop? Else, the two cohorts will be assumed to be perfectly separable.} \item{prior}{The prior used to fit the model. See diff --git a/man/createTargetComparatorOutcomes.Rd b/man/createTargetComparatorOutcomes.Rd index bcf5d09b..c8d24e6a 100644 --- a/man/createTargetComparatorOutcomes.Rd +++ b/man/createTargetComparatorOutcomes.Rd @@ -27,7 +27,7 @@ provided instead. In the analysis, the name of the number to be used can be specified using the #' \code{comparatorType} parameter in the \code{\link[=createCmAnalysis]{createCmAnalysis()}} function.} -\item{outcomeIds}{A vector of concept IDs indentifying the outcome(s) in the +\item{outcomeIds}{A vector of concept IDs identifying the outcome(s) in the outcome table.} \item{excludedCovariateConceptIds}{A list of concept IDs that cannot be used to construct