The target population r target$name
is defined as:
markdown <- CirceR::cohortPrintFriendly(target$expression) markdown <- gsub('###', '####',markdown) cat(markdown)
Additional inclusion criteria:
if(populationSettings$firstExposureOnly){ cat('\n - Patients are only in the cohort once. The earliest index date is used per patient. \n') } if(restrictPlpDataSettings$washoutPeriod > populationSettings$washoutPeriod){ washout <- restrictPlpDataSettings$washoutPeriod } else{ washout <- populationSettings$washoutPeriod } if(washout > target$expression$PrimaryCriteria$ObservationWindow[1]){ cat('\n - Patients with less than ', washout,' days observation prior to index', ' are excluded \n') } if(populationSettings$removeSubjectsWithPriorOutcome){ cat('\n - Patients with the outcome within ', populationSettings$priorOutcomeLookback,' days prior to index', ' are excluded \n') } if(populationSettings$requireTimeAtRisk){ cat('\n - Patients who are lost to follow up within ', populationSettings$minTimeAtRisk,' days post index', ' are excluded \n') if(populationSettings$includeAllOutcomes){ cat('\n - Except patients with the outcome who are lost to follow up within', populationSettings$minTimeAtRisk,' days post index', ' (they are still included) \n') } } if(restrictPlpDataSettings$studyStartDate != ""){ cat('\n - Restrict to patients with an index date on or after ',restrictPlpDataSettings$studyStartDate,' \n') } if(restrictPlpDataSettings$studyEndDate != ""){ cat('\n - Restrict to patients with an index date on or before ',restrictPlpDataSettings$studyEndDate,' \n') }
Sampling
if(!is.null(restrictPlpDataSettings$sampleSize)){ cat('\n Randomly sample ',restrictPlpDataSettings$sampleSize,' patients from the target population \n') } if(attr(sampleSettings[[1]],"fun") == 'sameData'){ cat('\n No over/under-sampling of the patients based on class was done \n') } if(attr(sampleSettings[[1]],"fun") != 'sameData'){ cat('\n An over/under-sampling of the patients based on class was done using ', attr(sampleSettings[[1]],"fun"),' with the settings: \n') sampleDat <- data.frame( names = names(sampleSettings[[1]]), values = unlist(lapply(sampleSettings[[1]], function(x) paste(x, sep='-', collapse = '-'))) ) print(knitr::kable(x = sampleDat, caption = paste('Sampling settings'))) }
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