diff --git a/.gitignore b/.gitignore index f6a14aa3..559ca9b5 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,4 @@ /.idea/ rsconnect/rconnect.jnj.com/NHall6/phevaluator_v01.dcf errorReportSql.txt +tests/testthat/Rplots.pdf diff --git a/DESCRIPTION b/DESCRIPTION index 435a7e89..02eff0e2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: OhdsiShinyModules Type: Package Title: Repository of Shiny Modules for OHDSI Result Viewers -Version: 3.0.2 +Version: 3.1.0 Authors@R: c( person("Jenna", "Reps", email = "jreps@its.jnj.com", role = c("aut", "cre")), person("Nathan", "Hall", role = c("aut")), diff --git a/NEWS.md b/NEWS.md index 47bfb716..cb3823d9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +OhdsiShinyModules v3.1.0 +======================== +- Removed percentage calculation from records field in CohortDiagnostics +- Updated the About module to reflect new module names and structure +- Updated module description vignette files to reflect new module names and structure +- Added interactive scatterplots for binary covariates when doing database and cohort comparisons in Characterization + OhdsiShinyModules v3.0.2 ======================== - Fixed bug with orphan concepts not loading diff --git a/R/about-main.R b/R/about-main.R index f5225ad7..2c0c9a4d 100644 --- a/R/about-main.R +++ b/R/about-main.R @@ -65,10 +65,12 @@ aboutViewer <- function(id = 'homepage') { shinydashboard::valueBoxOutput(ns("cohortDiagnosticsBox"), width = 3) ), shiny::fluidRow( - shinydashboard::valueBoxOutput(ns("cohortMethodBox"), width = 3), + shinydashboard::valueBoxOutput(ns("estimationBox"), width = 3), shinydashboard::valueBoxOutput(ns("predictionBox"), width = 3), - shinydashboard::valueBoxOutput(ns("sccsBox"), width = 3), - shinydashboard::valueBoxOutput(ns("evidenceSynthesisBox"), width = 3) + shinydashboard::valueBoxOutput(ns("reportGeneratorBox"), width = 3) + # , + # shinydashboard::valueBoxOutput(ns("sccsBox"), width = 3), + # shinydashboard::valueBoxOutput(ns("evidenceSynthesisBox"), width = 3) ) ) } @@ -127,7 +129,7 @@ aboutServer <- function(id = 'homepage', value = "Data Sources", subtitle = "Data sources used in this analysis", icon = shiny::icon("database"), - color = "aqua", + color = "olive", href = "https://ohdsi.github.io/OhdsiShinyModules/articles/DataSources.html" ) } else { @@ -169,7 +171,7 @@ aboutServer <- function(id = 'homepage', value = "Characterization", subtitle = "Characterization results for this analysis", icon = shiny::icon("table"), - color = "teal", + color = "red", href = "https://ohdsi.github.io/OhdsiShinyModules/articles/Characterization.html" ) } else { @@ -205,23 +207,23 @@ aboutServer <- function(id = 'homepage', }) - output$cohortMethodBox <- + output$estimationBox <- shinydashboard::renderValueBox({ - if ("CohortMethod" %in% tab_names) { + if ("Estimation" %in% tab_names) { targetedValueBox( - value = "Cohort Method", - subtitle = "Cohort Method results for this analysis", + value = "Estimation", + subtitle = "Population-level effect estimation results for this analysis", icon = shiny::icon("chart-column"), color = "maroon", - href = "https://ohdsi.github.io/OhdsiShinyModules/articles/CohortMethod.html" + href = "https://ohdsi.github.io/OhdsiShinyModules/articles/Estimation.html" ) } else { targetedValueBox( - value = "Cohort Method", + value = "Estimation", subtitle = "This module was not included in this analysis", icon = shiny::icon("chart-column"), color = "black", - href = "https://ohdsi.github.io/OhdsiShinyModules/articles/CohortMethod.html" + href = "https://ohdsi.github.io/OhdsiShinyModules/articles/Estimation.html" ) } }) @@ -231,7 +233,7 @@ aboutServer <- function(id = 'homepage', if ("Prediction" %in% tab_names) { targetedValueBox( value = "Prediction", - subtitle = "Patient-level Prediction results for this analysis", + subtitle = "Patient-level prediction results for this analysis", icon = shiny::icon("chart-line"), color = "blue", href = "https://ohdsi.github.io/OhdsiShinyModules/articles/Prediction.html" @@ -290,5 +292,27 @@ aboutServer <- function(id = 'homepage', } }) + output$reportGeneratorBox <- + shinydashboard::renderValueBox({ + if ("Report" %in% tab_names) { + targetedValueBox( + value = "Report", + subtitle = "Report Generator for this analysis", + icon = shiny::icon("book"), + color = "teal", + href = "https://ohdsi.github.io/OhdsiShinyModules/articles/ReportGenerator.html" + ) + } else { + targetedValueBox( + value = "Report", + subtitle = + "This module was not included in this analysis", + icon = shiny::icon("book"), + color = "black", + href = "https://ohdsi.github.io/OhdsiShinyModules/articles/ReportGenerator.html" + ) + } + }) + }) } diff --git a/R/characterization-cohorts.R b/R/characterization-cohorts.R index 5ce7ccdc..69fb4f6a 100644 --- a/R/characterization-cohorts.R +++ b/R/characterization-cohorts.R @@ -49,7 +49,20 @@ characterizationCohortComparisonViewer <- function(id) { ), shiny::tabPanel( title = 'Binary', - resultTableViewer(id = ns('mainTable'), boxTitle = 'Binary') + shiny::tabsetPanel( + type = 'pills', + id = ns('binaryPanel'), + shiny::tabPanel( + title = "Table", + resultTableViewer(id = ns('mainTable'), boxTitle = 'Binary') + ), + shiny::tabPanel( + title = "Plot", + shinycssloaders::withSpinner( + plotly::plotlyOutput(ns('scatterPlot')) + ) + ) + ) ), shiny::tabPanel( title = 'Continuous', @@ -281,9 +294,80 @@ characterizationCohortComparisonServer <- function( elementId = session$ns('count-table-filter') ), elementId = session$ns('count-table-filter') - )} + ) + + } + + #scatterplots + + plotDf <- shiny::reactive({ + + # Get the filtered and processed plot data + plotData <- resultTable %>% + replace(is.na(.), 0) %>% + dplyr::mutate(domain = dplyr::case_when( + grepl("condition_", covariateName) | sub("\\s.*", "", covariateName) == "condition" ~ "Condition", + grepl("drug_", covariateName) | sub("\\s.*", "", covariateName) == "drug" ~ "Drug", + grepl("procedure_", covariateName) | sub("\\s.*", "", covariateName) == "procedure" ~ "Procedure", + grepl("measurement_", covariateName) | sub("\\s.*", "", covariateName) == "measurement" ~ "Measurement", + grepl("observation_", covariateName) | sub("\\s.*", "", covariateName) == "observation" ~ "Observation", + grepl("device_", covariateName) | sub("\\s.*", "", covariateName) == "device" ~ "Device", + grepl("cohort_", covariateName) | sub("\\s.*", "", covariateName) == "cohort" ~ "Cohort", + grepl("visit_", covariateName) | sub("\\s.*", "", covariateName) == "visit" ~ "Visit", + .default = "Demographic" + )) + + # Create hover text for plotly + plotData$hoverText <- paste( + "Covariate Name:", plotData$covariateName, + "
", "Target", ":", scales::percent(plotData$averageValue_1), + "
", "Comparator", ":", scales::percent(plotData$averageValue_2) + ) + + #removing negatives, which come from "< min threshold" + plotData$averageValue_1[plotData$averageValue_1 < 0] <- 0 + plotData$averageValue_2[plotData$averageValue_2 < 0] <- 0 + + return(plotData) + + }) + + shiny::observe({ + output$scatterPlot <- plotly::renderPlotly({ + + plotData <- plotDf() + + # Create the scatter plot with the diagonal line (x = y) + p <- ggplot2::ggplot(plotData, ggplot2::aes( x = .data$averageValue_1, + y = .data$averageValue_2, + color = .data$domain, + text = .data$hoverText)) + # Use hoverText for hover labels + ggplot2::geom_point(size = 2) + # Smaller point size + ggplot2::geom_abline(slope = 1, intercept = 0, linetype = "dashed", color = "black") + # Diagonal x=y line in black + ggplot2::labs( + x = paste0("Target", " %"), + y = paste0("Comparator", " %"), + color = "Domain", + title = paste0("Database: ", names(inputVals()$databaseIds)[input$databaseId == inputVals()$databaseIds]) + ) + + ggplot2::theme_minimal() + # Optional: use a clean theme + ggplot2::theme( + plot.title = ggplot2::element_text(margin = ggplot2::margin(b = 10), hjust = 0.5, size = 25, face="bold"), + legend.position = "right", # Position legend as needed + axis.title = ggplot2::element_text(size = 12), # Adjust axis title size + axis.text = ggplot2::element_text(size = 10) # Adjust axis text size + ) + + ggplot2::scale_x_continuous(labels = scales::percent_format()) + # Format x-axis as percentage + ggplot2::scale_y_continuous(labels = scales::percent_format()) # Format y-axis as percentage + + # Convert to a plotly object for interactivity + plotly::ggplotly(p, tooltip = "text") # Use the custom hover text + }) + }) }) + + return(invisible(NULL)) @@ -777,7 +861,7 @@ characterizatonGetCohortData <- function( } shiny::withProgress(message = 'characterizatonGetCohortData', value = 0, { - + shiny::incProgress(1/4, detail = paste("Setting types")) types <- data.frame( @@ -862,13 +946,15 @@ characterizatonGetCohortData <- function( result <- result %>% dplyr::select(-"firstVar",-"secondVar", -"N_1", -"N_2") } else{ + NULL shiny::showNotification('Unable to add SMD due to missing columns') } } shiny::incProgress(4/4, detail = paste("Done")) }) - return(result) + return(result) + } @@ -1014,3 +1100,61 @@ characterizationGetCohortsInputs <- function( ) ) } + +characterizationGetCohortComparisonDataRaw <- function( + connectionHandler, + resultDatabaseSettings, + targetIds, + databaseIds, + minThreshold = 0.01, + addSMD = F +){ + + if(is.null(targetIds) | is.null(databaseIds)){ + warning('Ids cannot be NULL') + return(NULL) + } + + sql <- "select d.cdm_source_abbreviation, + ref.covariate_name, + s.min_prior_observation, + cov.target_cohort_id as cohort_definition_id, + cg.cohort_name, + cov.* from + @schema.@c_table_prefixCOVARIATES cov + inner join + @schema.@c_table_prefixcovariate_ref ref + on cov.covariate_id = ref.covariate_id + and cov.setting_id = ref.setting_id + and cov.database_id = ref.database_id + inner join + @schema.@c_table_prefixsettings s + on s.database_id = cov.database_id + and s.setting_id = cov.setting_id + inner join + @schema.@database_table d + on cov.database_id = d.database_id + inner join + @schema.@cg_table_prefixcohort_definition cg + on cov.target_cohort_id = cg.cohort_definition_id + + where + cov.target_cohort_id in (@target_ids) + and cov.cohort_type = 'Target' + AND cov.database_id in (@database_ids) + AND cov.average_value >= @min_threshold;" + + # settings.min_characterization_mean needed? + res <- connectionHandler$queryDb( + sql = sql, + target_ids = paste0(targetIds, collapse = ','), + database_ids = paste0("'",databaseIds,"'", collapse = ','), + schema = resultDatabaseSettings$schema, + c_table_prefix = resultDatabaseSettings$cTablePrefix, + min_threshold = minThreshold, + database_table = resultDatabaseSettings$databaseTable, + cg_table_prefix = resultDatabaseSettings$cgTablePrefix + ) + + return(res) +} diff --git a/R/characterization-database.R b/R/characterization-database.R index e787ee8e..f0104a28 100644 --- a/R/characterization-database.R +++ b/R/characterization-database.R @@ -48,7 +48,21 @@ characterizationDatabaseComparisonViewer <- function(id) { ), shiny::tabPanel( title = 'Binary', - resultTableViewer(id = ns('mainTable'), boxTitle = 'Binary') + shiny::tabsetPanel( + type = 'pills', + id = ns('binaryPanel'), + shiny::tabPanel( + title = "Table", + resultTableViewer(id = ns('mainTable'), boxTitle = 'Binary') + ), + shiny::tabPanel( + title = "Plot", + shiny::uiOutput(ns('plotInputs')), + shinycssloaders::withSpinner( + plotly::plotlyOutput(ns('scatterPlot')) + ) + ) + ) ), shiny::tabPanel( title = 'Continuous', @@ -277,6 +291,208 @@ characterizationDatabaseComparisonServer <- function( ), elementId = session$ns('continuous-table-filter') ) + + + #scatterplots + + plotResult <- characterizatonGetDatabaseComparisonDataRaw( + connectionHandler = connectionHandler, + resultDatabaseSettings = resultDatabaseSettings, + targetIds = subTargetId(), + databaseIds = input$databaseIds, + minThreshold = input$minThreshold + ) + + names(plotResult$databaseId) <- plotResult$cdmSourceAbbreviation + + output$plotInputs <- shiny::renderUI({ + shiny::div( + shiny::fluidRow( + shiny::column(width = 5, + shinyWidgets::pickerInput( + inputId = session$ns('xAxis'), + label = 'X-Axis Database: ', + choices = unique(plotResult$cdmSourceAbbreviation), + selected = unique(plotResult$cdmSourceAbbreviation)[1], + multiple = F, + options = shinyWidgets::pickerOptions( + actionsBox = TRUE, + liveSearch = TRUE, + size = 10, + dropupAuto = TRUE, + liveSearchStyle = "contains", + liveSearchPlaceholder = "Type here to search", + virtualScroll = 50 + ) + ) + ), + shiny::column(width = 5, + shinyWidgets::pickerInput( + inputId = session$ns('yAxis'), + label = 'Y-Axis Database: ', + choices = unique(plotResult$cdmSourceAbbreviation), + selected = unique(plotResult$cdmSourceAbbreviation)[2], + multiple = F, + options = shinyWidgets::pickerOptions( + actionsBox = TRUE, + liveSearch = TRUE, + size = 10, + dropupAuto = TRUE, + liveSearchStyle = "contains", + liveSearchPlaceholder = "Type here to search", + virtualScroll = 50 + ) + ) + ) + ), + shiny::fluidRow( + shiny::column( + width = 4, + shiny::actionButton( + inputId = session$ns('generatePlot'), + label = 'Generate Plot' + ) + ) + ) + ) + }) + + #get results + selectedPlotDbs <- shiny::reactiveVal() + shiny::observeEvent(input$generatePlot,{ + + plotDf <- shiny::reactive({ + + # Filter the plot result based on selected xAxis and yAxis inputs + plotResult2 <- plotResult %>% + dplyr::filter(.data$cdmSourceAbbreviation %in% c(input$xAxis, input$yAxis)) + + # Group and split the data by cdmSourceAbbreviation + plotResultDbSplit <- plotResult2 %>% + dplyr::group_by(.data$cdmSourceAbbreviation) %>% + dplyr::group_split() + + # Initialize an empty list to store the processed dataframes + processedDfs <- list() + + # Loop over the split datasets and process each one + for (i in seq_along(plotResultDbSplit)) { + + currentDb <- plotResultDbSplit[[i]] + + currentDbDf <- currentDb %>% + dplyr::select(cdmSourceAbbreviation, + covariateName, + averageValue) + + # Ensure only rows with selected xAxis or yAxis inputs are kept + currentDbDf <- currentDbDf %>% + dplyr::filter(.data$cdmSourceAbbreviation %in% c(input$xAxis, input$yAxis)) + + # Get the name for this database (should be unique after filtering) + dbName <- unique(currentDbDf$cdmSourceAbbreviation) + + # Rename the averageValue column based on the database name + colnames(currentDbDf) <- c("cdmSourceAbbreviation", "covariateName", paste0(dbName, "_avg")) + + # Remove the cdmSourceAbbreviation column for joining later + currentDbDf <- currentDbDf %>% + dplyr::select(-cdmSourceAbbreviation) + + # Append the processed dataframe to the list + processedDfs[[i]] <- currentDbDf + } + + # Check if there's at least one dataframe to join + if (length(processedDfs) > 1) { + # Perform a left join across all processed dataframes + plotResultDbComb <- Reduce(function(x, y) dplyr::left_join(x, y, by = "covariateName"), processedDfs) + } else { + # If there's only one dataframe, no need for joining + plotResultDbComb <- processedDfs[[1]] + } + + # Replace NA values with 0 + plotResultDbComb <- plotResultDbComb %>% + replace(is.na(.), 0) %>% + dplyr::mutate(domain = dplyr::case_when( + grepl("condition_", covariateName) | sub("\\s.*", "", covariateName) == "condition" ~ "Condition", + grepl("drug_", covariateName) | sub("\\s.*", "", covariateName) == "drug" ~ "Drug", + grepl("procedure_", covariateName) | sub("\\s.*", "", covariateName) == "procedure" ~ "Procedure", + grepl("measurement_", covariateName) | sub("\\s.*", "", covariateName) == "measurement" ~ "Measurement", + grepl("observation_", covariateName) | sub("\\s.*", "", covariateName) == "observation" ~ "Observation", + grepl("device_", covariateName) | sub("\\s.*", "", covariateName) == "device" ~ "Device", + grepl("cohort_", covariateName) | sub("\\s.*", "", covariateName) == "cohort" ~ "Cohort", + grepl("visit_", covariateName) | sub("\\s.*", "", covariateName) == "visit" ~ "Visit", + .default = "Demographic" + )) + + return(plotResultDbComb) + + + + }) + + #plot + + shiny::observe({ + output$scatterPlot <- plotly::renderPlotly({ + + # Get the filtered and processed plot data + plotData <- plotDf() + + # Ensure that the reactive inputs are valid and accessible + xAxisInput <- input$xAxis + yAxisInput <- input$yAxis + + # Sanitize the xAxis and yAxis input values by replacing spaces with underscores + xAxisSafe <- gsub(" ", "_", xAxisInput) + yAxisSafe <- gsub(" ", "_", yAxisInput) + + # Sanitize column names in plotData to replace spaces with underscores + colnames(plotData) <- gsub(" ", "_", colnames(plotData)) + + # Ensure that the column names exist in plotData + if (!all(c(paste0(xAxisSafe, "_avg"), paste0(yAxisSafe, "_avg")) %in% colnames(plotData))) { + stop("Selected columns not found in data.") + } + + # Create hover text for plotly + plotData$hoverText <- paste( + "Covariate Name:", plotData$covariateName, + "
", xAxisInput, ":", scales::percent(plotData[[paste0(xAxisSafe, "_avg")]]), + "
", yAxisInput, ":", scales::percent(plotData[[paste0(yAxisSafe, "_avg")]]) + ) + + # Create the scatter plot with the diagonal line (x = y) + p <- ggplot2::ggplot(plotData, ggplot2::aes_string(x = paste0(xAxisSafe, "_avg"), + y = paste0(yAxisSafe, "_avg"), + color = "domain", + text = "hoverText")) + # Use hoverText for hover labels + ggplot2::geom_point(size = 2) + # Smaller point size + ggplot2::geom_abline(slope = 1, intercept = 0, linetype = "dashed", color = "black") + # Diagonal x=y line in black + ggplot2::labs( + x = paste0(xAxisInput, " %"), + y = paste0(yAxisInput, " %"), + color = "Domain" + ) + + ggplot2::theme_minimal() + # Optional: use a clean theme + ggplot2::theme( + legend.position = "right", # Position legend as needed + axis.title = ggplot2::element_text(size = 12), # Adjust axis title size + axis.text = ggplot2::element_text(size = 10) # Adjust axis text size + ) + + ggplot2::scale_x_continuous(labels = scales::percent_format()) + # Format x-axis as percentage + ggplot2::scale_y_continuous(labels = scales::percent_format()) # Format y-axis as percentage + + # Convert to a plotly object for interactivity + plotly::ggplotly(p, tooltip = "text") # Use the custom hover text + }) + }) + + + }) + }) @@ -327,3 +543,56 @@ characterizatonGetDatabaseComparisonData <- function( ) } + +characterizatonGetDatabaseComparisonDataRaw <- function( + connectionHandler, + resultDatabaseSettings, + targetIds, + databaseIds, + minThreshold = 0.01, + addSMD = F +){ + + if(is.null(targetIds) | is.null(databaseIds)){ + warning('Ids cannot be NULL') + return(NULL) + } + + sql <- "select d.cdm_source_abbreviation, + ref.covariate_name, + s.min_prior_observation, + cov.target_cohort_id as cohort_definition_id, + cov.* from + @schema.@c_table_prefixCOVARIATES cov + inner join + @schema.@c_table_prefixcovariate_ref ref + on cov.covariate_id = ref.covariate_id + and cov.setting_id = ref.setting_id + and cov.database_id = ref.database_id + inner join + @schema.@c_table_prefixsettings s + on s.database_id = cov.database_id + and s.setting_id = cov.setting_id + inner join + @schema.@database_table d + on cov.database_id = d.database_id + + where + cov.target_cohort_id in (@target_ids) + and cov.cohort_type = 'Target' + AND cov.database_id in (@database_ids) + AND cov.average_value >= @min_threshold;" + + # settings.min_characterization_mean needed? + res <- connectionHandler$queryDb( + sql = sql, + target_ids = paste0(targetIds, collapse = ','), + database_ids = paste0("'",databaseIds,"'", collapse = ','), + schema = resultDatabaseSettings$schema, + c_table_prefix = resultDatabaseSettings$cTablePrefix, + min_threshold = minThreshold, + database_table = resultDatabaseSettings$databaseTable + ) + + return(res) +} diff --git a/R/cohort-diagnostics-indexEventBreakdown.R b/R/cohort-diagnostics-indexEventBreakdown.R index 25a3ea2f..b47416c9 100644 --- a/R/cohort-diagnostics-indexEventBreakdown.R +++ b/R/cohort-diagnostics-indexEventBreakdown.R @@ -69,7 +69,7 @@ indexEventBreakdownView <- function(id) { shiny::tags$td( shiny::checkboxInput( inputId = ns("showAsPercent"), - label = "Show as percentage", + label = "Show persons as percentage", value = TRUE ) ) @@ -232,17 +232,20 @@ indexEventBreakdownModule <- function(id, if (showDataAsPercent) { data <- data %>% dplyr::rename( - "persons" = "subjectPercent", - "records" = "conceptPercent" + "persons" = "subjectPercent" ) } else { data <- data %>% dplyr::rename( - "persons" = "subjectCount", - "records" = "conceptCount" + "persons" = "subjectCount" ) } + data <- data %>% + dplyr::rename( + "records" = "conceptCount" + ) + data <- data %>% dplyr::arrange(dplyr::desc(abs(dplyr::across( c("records", "persons") @@ -278,6 +281,7 @@ indexEventBreakdownModule <- function(id, countLocation = countLocation, dataColumns = dataColumnFields, showDataAsPercent = showDataAsPercent, + excludedColumnFromPercentage = "records", sort = TRUE ) }) diff --git a/R/cohort-diagnostics-main.R b/R/cohort-diagnostics-main.R index c669aaf9..825c9128 100644 --- a/R/cohort-diagnostics-main.R +++ b/R/cohort-diagnostics-main.R @@ -621,6 +621,9 @@ cohortDiagnosticsServer <- function(id, if (!hasData(targetCohortId())) { return(NULL) } + if (sum(c('cohortId','conceptSetName') %in% colnames(dataSource$conceptSets)) !=2) { + return(NULL) + } dataSource$conceptSets %>% dplyr::filter(.data$cohortId == targetCohortId()) %>% dplyr::mutate(name = .data$conceptSetName) %>% diff --git a/docs/404.html b/docs/404.html index 34ed2cc6..8ad319b3 100644 --- a/docs/404.html +++ b/docs/404.html @@ -18,7 +18,7 @@ - +
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    Nathan Hall

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    - - + + diff --git a/docs/articles/DataSources.html b/docs/articles/DataSources.html index dbfd6cdb..39d24a82 100644 --- a/docs/articles/DataSources.html +++ b/docs/articles/DataSources.html @@ -12,14 +12,13 @@ - - +
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    Data Sources

    Nathan Hall

    -

    2024-09-27

    - +

    2024-10-07

    +
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    Example OMOP-mapped Datasets - -

    + @@ -236,16 +230,16 @@

    Example OMOP-mapped Datasets

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/Estimation.html b/docs/articles/Estimation.html new file mode 100644 index 00000000..bc5e8ebd --- /dev/null +++ b/docs/articles/Estimation.html @@ -0,0 +1,511 @@ + + + + + + + +Estimation • OhdsiShinyModules + + + + + + + + + + + +
    +
    + + + + +
    +
    +
    +

    Estimation

    +

    Nathan +Hall

    + +

    2024-10-07

    + + + + +
    + + + + +
    +

    Introduction +

    +

    Observational healthcare data, comprising administrative claims and +electronic health records, present a rich source for generating +real-world evidence pertinent to treatment effects that directly impact +patient well-being. Within this realm, population-level effect +estimation assumes a pivotal role, focusing on elucidating the average +causal effects of exposures—such as medical interventions like drug +exposures or procedures—on specific health outcomes of interest. +Population-level effect estimation delves into two primary realms: +direct effect estimation and comparative effect estimation. In direct +effect estimation, the focus lies on discerning the effect of an +exposure on the risk of an outcome compared to no exposure, while +comparative effect estimation aims to delineate the effect of a target +exposure against a comparator exposure. By contrasting factual outcomes +with counterfactual scenarios—what happened versus what would have +occurred under different circumstances—these estimation tasks offer +critical insights into treatment selection, safety surveillance, and +comparative effectiveness. Whether probing individual hypotheses or +exploring multiple hypotheses concurrently, the overarching goal remains +consistent: to derive high-quality estimates of causal effects from the +intricate fabric of observational healthcare data.

    +
    +
    +

    1. CohortMethod +

    +
    +

    Features and Functionalities +

    +

    The CohortMethod R package, a cornerstone of +population-level estimation within the OHDSI framework, offers a robust +methodology for conducting comparative effectiveness research and +pharmacoepidemiology studies. Some of the features offered by conducting +population-level effect estimation using the CohortMethod module +are:

    +
      +
    1. +Data Extraction: Extracts necessary data from +databases structured in the OMOP Common Data Model (CDM) format, +ensuring uniformity and compatibility across diverse healthcare +settings.
      2. +
    2. +Covariate Selection: Utilizing a comprehensive set +of covariates, including drugs, diagnoses, procedures, age, and +comorbidity indexes, CohortMethod constructs propensity and outcome +models tailored to specific research questions.
      3. +
    3. +Large-Scale Regularized Regression: Employing +large-scale regularized regression techniques, CohortMethod fits +propensity and outcome models with precision and efficiency, +accommodating the complexities of real-world healthcare data.
      4. +
    4. +Propensity Score Adjustment: Facilitates propensity +score adjustment through trimming, stratification, matching, and +weighting, enabling researchers to address confounding and balance +covariate distributions across treatment groups. Results are viewable +both graphically and in tabular form to assess the model.
      5. +
    5. +Diagnostic Functions: Diagnostic functions within +CohortMethod offer insights into propensity score distributions and +covariate balance before and after matching or trimming, enhancing +transparency and robustness in estimation procedures.
      6. +
    6. +Supported Outcome Models: Supported outcome models +include (conditional) logistic regression, (conditional) Poisson +regression, and (conditional) Cox regression, providing flexibility in +modeling various types of outcomes in observational health data +research.
      7. +
    7. +Power: Incorporates power analysis techniques to +estimate the statistical power of the study design, aiding in sample +size determination and study planning, and provides a minimum-detectable +relative risk (MDRR) statistic.
      8. +
    8. +Attrition: Assesses attrition rates within cohorts, +providing insights into potential biases introduced by data loss during +the study period, and provides a visualization of attrition across +various cohort criteria.
      9. +
    9. +Population Characteristics: Analyzes population +characteristics to understand the demographic and clinical makeup of the +study cohorts, informing interpretation of estimation results both +before and after propensity score matching.
      10. +
    10. +Covariate Balance: Visually monitors covariate +balance before and after matching or trimming, ensuring that confounding +variables are adequately controlled for in the analysis.
      11. +
    11. +Systematic Error: Assesses effect size estimates +for negative controls (true hazard ratio = 1) and positive controls +(true hazard ratio > 1) both before and after calibration. Estimates +below the diagonal dashed lines are statistically significant (alpha = +0.05) different from the true effect size. A well-calibrated estimator +should have the true effect size within the 95 percent confidence +interval 95 percent of times, providing researchers with confidence in +the reliability of the estimation process and the accuracy of the +obtained results.
      12. +
    +
    +
    +

    Utility and Application +

    +

    Comparative Effectiveness Research: CohortMethod +empowers researchers to conduct comparative effectiveness studies by +estimating treatment effects while accounting for potential confounding +factors and bias inherent in observational data.

    +

    Pharmacoepidemiology and Drug Safety Studies: In +pharmacoepidemiology research, CohortMethod facilitates the evaluation +of drug safety and effectiveness by quantifying the association between +drug exposures and clinical outcomes in real-world populations.

    +
    +
    +
    +

    2. Self-Controlled Case Series +

    +
    +

    Introduction +

    +

    The Self-Controlled Case Series (SCCS) method offers a nuanced +approach to investigating the relationship between exposures and +outcomes within individual patients over time. SCCS designs are +particularly adept at comparing the rate of outcomes during times of +exposure to rates during periods of non-exposure, including before, +between, and after exposure episodes. By leveraging a Poisson regression +that is conditioned on the individual, the SCCS design inherently +addresses the question: “Given that a patient has the outcome, is the +outcome more likely to occur during exposed time compared to non-exposed +time?” The design choices outlined in the method are pivotal for +defining an SCCS question, with each choice playing a critical role in +the study’s design and outcomes:

    +

    Target Cohort: This represents the treatment under +investigation. Outcome Cohort: This cohort signifies +the outcome of interest. Time-at-Risk: Identifies the +specific times when the risk of the outcome is considered, often +relative to the start and end dates of the target cohort. +Model: Defines the statistical model used to estimate +the effect, including adjustments for time-varying confounders if +necessary.

    +

    One of the SCCS design’s strengths is its robustness to confounding +by factors that differ between individuals, as each participant serves +as their own control. However, it remains sensitive to time-varying +confounding factors. To mitigate this, adjustments can be made for +factors such as age, seasonality, and calendar time, enhancing the +model’s accuracy.

    +

    An advanced variant of the SCCS also considers all other drug +exposures recorded in the database, significantly expanding the model’s +variables. This approach employs L1-regularization, with +cross-validation used to select the regularization hyperparameter for +all exposures except the one of interest.

    +

    An important assumption of the SCCS is that the observation period’s +end is independent of the outcome date. This may not hold true for +outcomes that can be fatal, such as stroke. To address this, extensions +to the SCCS model have been developed that correct for any dependency +between the observation period end and the outcome.

    +
    +
    +

    Features and Functionalities +

    +

    The SelfControlledCaseSeries R package allows the user to +perform SCCS analyses in an observational database in the OMOP Common +Data Model. Some of the features offered by the SCCS module include:

    +
      +
    1. **Data Extraction: Extracts necessary data from databases structured +in the OMOP Common Data Model (CDM) format, ensuring uniformity and +compatibility across diverse healthcare settings.
      2. +
    2. +Seasonality Adjustment: Offers the option to adjust +for seasonality effects using a spline function, enhancing the model’s +accuracy by accounting for seasonal variation in exposure and outcome +rates.
      3. +
    3. +Age Adjustment: Provides the option to incorporate +age adjustments using a spline function, allowing for more nuanced +analyses that consider the impact of age on the exposure-outcome +relationship.
      4. +
    4. +Calendar Time Adjustment: Enables the inclusion of +calendar time adjustments using a spline function, addressing potential +temporal trends in the data that could confound the exposure-outcome +relationship.
      5. +
    5. +Event-dependent Censoring Correction: Features the +ability to correct for event-dependent censoring of the observation +period, ensuring that the end of the observation period is appropriately +handled, especially in cases where it might be related to the +outcome.
      6. +
    6. +Comprehensive Covariate Inclusion: Allows for the +addition of a wide array of covariates in one analysis, such as all +recorded drug exposures, facilitating a thorough examination of +potential confounders and effect modifiers.
      7. +
    7. +Risk Window Customization: Supports the +construction of various types of covariates and risk windows, including +pre-exposure windows, to capture contra-indications and other relevant +temporal patterns related to exposure and outcome.
      8. +
    8. +Regularization of Covariates: Applies +regularization to all covariates except the outcome of interest, +employing techniques like L1-regularization with cross-validation for +selecting the regularization hyperparameter, thereby preventing +overfitting and enhancing model reliability.
      9. +
    9. +Self-Controlled Risk Interval Design: Incorporates +the self-controlled risk interval design as a specific application of +the SCCS method, offering additional methodological flexibility for +studying short-term effects of exposures.
      10. +
    10. +Power: Incorporates power analysis techniques to +estimate the statistical power of the study design, aiding in sample +size determination and study planning, and provides a minimum-detectable +relative risk (MDRR) statistic.
      11. +
    11. +Attrition: Assesses attrition rates within cohorts, +providing insights into potential biases introduced by data loss during +the study period, and provides a visualization of attrition across +various cohort criteria.
      12. +
    12. +Spanning: Analyzes the number of subjects observed +for 3 consecutive months, providing insights into the cohort’s +consistency and stability over time.
      13. +
    13. +Time Trend: Assesses the ratio of observed to +expected outcomes per month, with adjustments for calendar time, +seasonality, and/or age as specified in the model, to examine time +trends in the data.
      14. +
    14. +Time to Event: Evaluates the number of events and +subjects observed per week relative to the start of the first exposure, +offering critical insights into the temporal relationship between +exposure and outcome.
      15. +
    15. +Event-dependent Observation: Provides histograms +for the time between the first occurrence of the outcome and the end of +observation, stratified by censored and uncensored ends of observation, +to assess the impact of event-dependent observation periods.
      16. +
    16. +Systematic Error: Assesses effect size estimates +for negative controls (true hazard ratio = 1) and positive controls +(true hazard ratio > 1) both before and after calibration. Estimates +below the diagonal dashed lines are statistically significant (alpha = +0.05) different from the true effect size. A well-calibrated estimator +should have the true effect size within the 95 percent confidence +interval 95 percent of times, providing researchers with confidence in +the reliability of the estimation process and the accuracy of the +obtained results.
      17. +
    +
    +
    +

    Utility and Application +

    +

    The SCCS method is particularly applicable in several key areas of +epidemiological research and pharmacovigilance:

    +

    Drug Safety Surveillance: The SCCS method is widely +used in drug safety surveillance to identify adverse effects of +medications post-marketing. It is well-suited to detect short-term risks +associated with drug exposures, especially where the onset of the +adverse event is expected to be temporally close to the exposure.

    +

    Vaccine Safety Evaluation: The SCCS design is ideal +for assessing the safety of vaccines, especially in evaluating the risk +of adverse events following immunization. Its self-controlled nature +helps to address concerns about confounding by indication and other +biases that can affect observational studies in vaccine safety.

    +

    Comparative Effectiveness Research: While primarily +designed for evaluating the safety of medical interventions, the SCCS +method can also be adapted to compare the effectiveness of different +treatments or interventions within the same individual over time, +particularly for acute conditions.

    +

    Epidemiological Research: More broadly, the SCCS +method is used in epidemiological research to study the temporal +relationships between exposures and outcomes, offering insights into the +causality and mechanisms underlying health conditions and diseases.

    +
    +
    +
    +

    3. Evidence Synthesis (Meta, Meta Analysis) +

    +
    +

    Introduction +

    +

    Meta-analysis plays a pivotal role in healthcare research by enabling +the synthesis of findings from multiple studies to draw more +generalizable conclusions. In the context of distributed health data +networks, where data are spread across various sites with diverse +populations and practices, synthesizing evidence becomes both a +challenge and a necessity. The EvidenceSynthesis R package addresses +these challenges head-on. It offers a suite of tools designed for +combining causal effect estimates and study diagnostics from multiple +data sites, all while adhering to stringent patient privacy requirements +and navigating the complexities inherent to observational data. This +approach enhances the robustness of meta-analytical conclusions and +extends the utility of distributed health data for research +purposes.

    +
    +
    +

    Features and Functionalities +

    +

    The Meta module which utilizes the EvidenceSynthesis R package makes +use of the following features to summarize the results of a study:

    +
      +
    1. +Meta-Analysis Methods: Facilitates both traditional +fixed-effects and random-effects meta-analyses, accommodating studies +with different degrees of between-site or between-database +variability.
      2. +
    2. +Forest Plot Generation: Provides capabilities for +creating forest plots, visual summaries that illustrate the effects +estimated by individual studies, their confidence intervals, and the +synthesized overall effect.
      3. +
    3. +Non-Normal Likelihood Approximations: Utilizes +non-normal approximations for the per-data-site likelihood function to +reduce bias in scenarios with small or zero counts, a frequent issue in +distributed research environments.
      4. +
    +

    The syntheses are generated for both Cohort Method and +Self-Controlled Case Series estimation results from the study, providing +both information on the diagnostic results within each database and the +visualized and tabular results of the meta analysis.

    +
    +
    +

    Utility and Application +

    +

    The EvidenceSynthesis package is instrumental in synthesizing +evidence from observational studies across multiple healthcare +databases. Its significance is underscored in scenarios characterized +by:

    +

    Comparative Effectiveness Research: Synthesizing +evidence from disparate sources allows for stronger, more reliable +comparisons of treatment outcomes, enriching the foundation for clinical +decision-making.

    +

    Safety Surveillance: Aggregated safety data across +databases enhance the detection and understanding of adverse drug +reactions, contributing to safer patient care.

    +

    Policy and Clinical Guidelines Development: +Meta-analytical findings informed by comprehensive, real-world data can +guide policy formulation and the updating of clinical guidelines, +ensuring they are grounded in broad-based evidence.

    +

    Addressing Challenges of Small Sample Sizes: The +EvidenceSynthesis package notably advances the field by tackling the +issue of small sample sizes and zero event counts, which traditional +meta-analytical methods often handle poorly. Its innovative use of +non-normal likelihood approximations enables more precise effect size +estimation under such conditions, ensuring that the insights derived +from meta-analyses are both accurate and meaningful. This attribute is +particularly beneficial in distributed health data networks, where +individual site/database data may be limited but collectively hold +significant informational value.

    +
    +
    +
    + + + +
    + + + +
    +

    +

    Developed by Jenna Reps, Nathan Hall, Jamie Gibert.

    +
    + +
    +

    +

    Site built with pkgdown 2.1.0.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/articles/EvidenceSynthesis.html b/docs/articles/EvidenceSynthesis.html index 7c3cd941..f44676b0 100644 --- a/docs/articles/EvidenceSynthesis.html +++ b/docs/articles/EvidenceSynthesis.html @@ -12,14 +12,13 @@ - - +
    - +
    @@ -118,9 +120,9 @@

    Evidence Synthesis (Meta, Meta Analysis)

    Nathan Hall

    -

    2024-09-27

    - +

    2024-10-04

    +
    @@ -208,9 +210,7 @@

    Utility and Application - -

    +
    @@ -223,16 +223,16 @@

    Utility and Application

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/Prediction.html b/docs/articles/Prediction.html index 9b4a0827..bf31d92e 100644 --- a/docs/articles/Prediction.html +++ b/docs/articles/Prediction.html @@ -12,14 +12,13 @@ - - +
    @@ -42,7 +41,7 @@
  • - +
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    • @@ -98,7 +94,7 @@
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    • @@ -109,7 +105,7 @@
    - +
    @@ -118,9 +114,9 @@

    Prediction

    Nathan Hall

    -

    2024-09-27

    - +

    2024-10-07

    +
    @@ -211,9 +207,7 @@

    Utility and Application - -

    + @@ -226,16 +220,16 @@

    Utility and Application

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/ReportGenerator.html b/docs/articles/ReportGenerator.html new file mode 100644 index 00000000..2a703391 --- /dev/null +++ b/docs/articles/ReportGenerator.html @@ -0,0 +1,184 @@ + + + + + + + +Report Generator • OhdsiShinyModules + + + + + + + + + + + +
    +
    + + + + +
    +
    +
    +

    Report Generator

    +

    Nathan +Hall

    + +

    2024-10-07

    + + + + +
    + + + + +
    +

    Introduction +

    +

    ReportGenerator is a tool used to create a summary presentation +document using results from a Strategus execution which should be stored +in a results database.

    +
    +
    +

    Description +

    +

    The Report Generator module allows the user to choose which target +(T), subgroup (indication & extra inclusions), comparator (C), and +outcome(s) (O) they would like a downloaded report on. In the last +section of the module, the user’s selections are reported back to them +for review before downloading. Here, the user can also choose to +restrict the study date and/or the age range of people included in the +report.

    +
    +

    Notes +

    +

    Please note that this package is currently under development, so +results may vary or may not be available at the time of report +generation.

    +
    +
    +
    + + + +
    + + + +
    +

    +

    Developed by Jenna Reps, Nathan Hall, Jamie Gibert.

    +
    + +
    +

    +

    Site built with pkgdown 2.1.0.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/articles/SelfControlledCaseSeries.html b/docs/articles/SelfControlledCaseSeries.html index 30c6697c..346f8d28 100644 --- a/docs/articles/SelfControlledCaseSeries.html +++ b/docs/articles/SelfControlledCaseSeries.html @@ -12,14 +12,13 @@ - - +
    - +
    @@ -118,9 +120,9 @@

    Self-Controlled Case Series

    Nathan Hall

    -

    2024-09-27

    - +

    2024-10-04

    +
    @@ -293,9 +295,7 @@

    Utility and Application - -

    +
    @@ -308,16 +308,16 @@

    Utility and Application

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/index.html b/docs/articles/index.html index 2a478dbe..48d06b34 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -3,7 +3,7 @@ - +
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    - +
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    All vignettes

    Cohort Diagnostics
    -
    Cohort Method (Estimation)
    -
    Cohorts
    Data Sources
    -
    Evidence Synthesis (Meta, Meta Analysis)
    +
    Estimation
    Prediction
    -
    Self-Controlled Case Series
    +
    Report Generator
    @@ -124,15 +119,15 @@

    All vignettes

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/authors.html b/docs/authors.html index 4702d974..bec37db2 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -93,37 +90,37 @@

    Authors and Citation

    - +
    • -

      Jenna Reps. Author, maintainer. +

      Jenna Reps. Author, maintainer.

    • -

      Nathan Hall. Author. +

      Nathan Hall. Author.

    • -

      Jamie Gibert. Author. +

      Jamie Gibert. Author.

    Citation

    - +

    Reps J, Hall N, Gibert J (2024). OhdsiShinyModules: Repository of Shiny Modules for OHDSI Result Viewers. -R package version 3.0.2. +R package version 3.1.0. 

    @Manual{,
   title = {OhdsiShinyModules: Repository of Shiny Modules for OHDSI Result Viewers},
   author = {Jenna Reps and Nathan Hall and Jamie Gibert},
   year = {2024},
-  note = {R package version 3.0.2},
+  note = {R package version 3.1.0},
 }
    @@ -137,15 +134,15 @@

    Citation

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/index.html b/docs/index.html index 779fc3a2..600565e8 100644 --- a/docs/index.html +++ b/docs/index.html @@ -19,7 +19,7 @@ - +
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    Developers

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/news/index.html b/docs/news/index.html index 9f4d13a6..15ccf1a7 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Changelog

    - +
    +
    +

    OhdsiShinyModules v3.1.0

    +
    • Removed percentage calculation from records field in CohortDiagnostics
      • +
    • Updated the About module to reflect new module names and structure
      • +
    • Updated module description vignette files to reflect new module names and structure
      • +
    • Added interactive scatterplots for binary covariates when doing database and cohort comparisons in Characterization
      • +

    OhdsiShinyModules v3.0.2

    • Fixed bug with orphan concepts not loading
      • @@ -208,15 +212,15 @@

      OhdsiS

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 49657cad..9449d457 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,15 +1,13 @@ pandoc: '3.2' -pkgdown: 2.0.9 +pkgdown: 2.1.0 pkgdown_sha: ~ articles: AddingShinyModules: AddingShinyModules.html Characterization: Characterization.html CohortDiagnostics: CohortDiagnostics.html - CohortMethod: CohortMethod.html Cohorts: Cohorts.html DataSources: DataSources.html - EvidenceSynthesis: EvidenceSynthesis.html + Estimation: Estimation.html Prediction: Prediction.html - SelfControlledCaseSeries: SelfControlledCaseSeries.html -last_built: 2024-09-27T15:53Z - + ReportGenerator: ReportGenerator.html +last_built: 2024-10-07T15:13Z diff --git a/docs/reference/LargeDataTable.html b/docs/reference/LargeDataTable.html index 2841ef56..13f6b753 100644 --- a/docs/reference/LargeDataTable.html +++ b/docs/reference/LargeDataTable.html @@ -10,7 +10,7 @@ - +
    @@ -32,7 +32,7 @@
    - +

    Large Data Table

    - +
    @@ -132,7 +129,7 @@

    Public fields

    Methods

    - +

    Public methods

    @@ -276,15 +273,15 @@

    Arguments -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/OhdsiShinyModules.html b/docs/reference/OhdsiShinyModules.html index 71e1b8be..a205f06b 100644 --- a/docs/reference/OhdsiShinyModules.html +++ b/docs/reference/OhdsiShinyModules.html @@ -3,7 +3,7 @@ - +
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    OhdsiShinyModules

    - +
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    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/aboutHelperFile.html b/docs/reference/aboutHelperFile.html index 9711c7ed..278c0bdc 100644 --- a/docs/reference/aboutHelperFile.html +++ b/docs/reference/aboutHelperFile.html @@ -3,7 +3,7 @@ - +
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    - +

    The location of the about module helper file

    - +
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    The location of the about module helper file

    Value

    - - -

    string location of the about helper file

    +

    string location of the about helper file

    Details

    @@ -114,7 +109,7 @@

    Details

    See also

    -

    Other About: +

    Other About: aboutServer(), aboutViewer()

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    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/aboutServer.html b/docs/reference/aboutServer.html index ca5897ff..e917e216 100644 --- a/docs/reference/aboutServer.html +++ b/docs/reference/aboutServer.html @@ -3,7 +3,7 @@ - +
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    The module server for the shiny app home

    - +
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    The module server for the shiny app home

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the characterization result schema, dbms, tablePrefix, databaseTable and cgTablePrefix

    -
    config
    +
    config

    the config from the app.R file that contains a list of which modules to include

    Value

    - - -

    The server for the shiny app home

    +

    The server for the shiny app home

    Details

    @@ -137,7 +134,7 @@

    Details

    See also

    -

    Other About: +

    Other About: aboutHelperFile(), aboutViewer()

    @@ -154,15 +151,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/aboutViewer.html b/docs/reference/aboutViewer.html index 99df8738..183dca7e 100644 --- a/docs/reference/aboutViewer.html +++ b/docs/reference/aboutViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for the shiny app home

    - +
    @@ -104,15 +101,15 @@

    The module viewer for the shiny app home

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the home page module

    +

    The user interface to the home page module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other About: +

    Other About: aboutHelperFile(), aboutServer()

    @@ -137,15 +134,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/characterizationHelperFile.html b/docs/reference/characterizationHelperFile.html index 226eaacd..ed7edb25 100644 --- a/docs/reference/characterizationHelperFile.html +++ b/docs/reference/characterizationHelperFile.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The location of the characterization module helper file

    - +
    @@ -104,9 +101,7 @@

    The location of the characterization module helper file

    Value

    - - -

    string location of the characterization helper file

    +

    string location of the characterization helper file

    Details

    @@ -114,7 +109,7 @@

    Details

    See also

    -

    Other Characterization: +

    Other Characterization: characterizationIncidenceServer(), characterizationIncidenceViewer(), characterizationServer(), @@ -133,15 +128,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/characterizationIncidenceServer.html b/docs/reference/characterizationIncidenceServer.html index d2b96876..60470985 100644 --- a/docs/reference/characterizationIncidenceServer.html +++ b/docs/reference/characterizationIncidenceServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring incidence results

    - +
    @@ -112,39 +109,39 @@

    The module server for exploring incidence results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the characterization result schema, dbms, tablePrefix, databaseTable and cgTablePrefix

    -
    parents
    +
    parents

    a list of parent cohorts

    -
    parentIndex
    +
    parentIndex

    an integer specifying the parent index of interest

    -
    outcomes
    +
    outcomes

    a reactive object specifying the outcomes of interest

    -
    targetIds
    +
    targetIds

    a reactive vector of integer specifying the targetIds of interest

    Value

    - - -

    The server to the prediction incidence module

    +

    The server to the prediction incidence module

    Details

    @@ -152,7 +149,7 @@

    Details

    See also

    -

    Other Characterization: +

    Other Characterization: characterizationHelperFile(), characterizationIncidenceViewer(), characterizationServer(), @@ -171,15 +168,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/characterizationIncidenceViewer.html b/docs/reference/characterizationIncidenceViewer.html index f2c55350..ad3bd6f1 100644 --- a/docs/reference/characterizationIncidenceViewer.html +++ b/docs/reference/characterizationIncidenceViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring incidence results

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring incidence results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the description incidence module

    +

    The user interface to the description incidence module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other Characterization: +

    Other Characterization: characterizationHelperFile(), characterizationIncidenceServer(), characterizationServer(), @@ -139,15 +136,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/characterizationServer.html b/docs/reference/characterizationServer.html index c6e908ac..64d74634 100644 --- a/docs/reference/characterizationServer.html +++ b/docs/reference/characterizationServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring characterization studies

    - +
    @@ -108,23 +105,23 @@

    The module server for exploring characterization studies

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the characterization result schema, dbms, tablePrefix, databaseTable and cgTablePrefix

    Value

    - - -

    The server for the characterization module

    +

    The server for the characterization module

    Details

    @@ -132,7 +129,7 @@

    Details

    See also

    -

    Other Characterization: +

    Other Characterization: characterizationHelperFile(), characterizationIncidenceServer(), characterizationIncidenceViewer(), @@ -151,15 +148,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/characterizationViewer.html b/docs/reference/characterizationViewer.html index f7b57dd0..37f2b12d 100644 --- a/docs/reference/characterizationViewer.html +++ b/docs/reference/characterizationViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring characterization studies

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring characterization studies

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the characterization viewer module

    +

    The user interface to the characterization viewer module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other Characterization: +

    Other Characterization: characterizationHelperFile(), characterizationIncidenceServer(), characterizationIncidenceViewer(), @@ -139,15 +136,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortCountsModule.html b/docs/reference/cohortCountsModule.html index 8cc8482c..220c27a4 100644 --- a/docs/reference/cohortCountsModule.html +++ b/docs/reference/cohortCountsModule.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Shiny module for cohort counts

    - +
    @@ -112,37 +109,39 @@

    Shiny module for cohort counts

    Arguments

    -
    id
    + + +
    id

    namespace id

    -
    dataSource
    +
    dataSource

    Backend Data source (DatabaseConnection)

    -
    cohortTable
    +
    cohortTable

    data.frame of all cohorts

    -
    databaseTable
    +
    databaseTable

    data.frame of all databases

    -
    selectedCohorts
    +
    selectedCohorts

    shiny::reactive - should return cohorts selected or NULL

    -
    selectedDatabaseIds
    +
    selectedDatabaseIds

    shiny::reactive - should return cohorts selected or NULL

    -
    cohortIds
    +
    cohortIds

    shiny::reactive - should return cohorts selected integers or NULL

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsView(), cohortDefinitionsModule(), cohortDefinitionsView(), @@ -177,15 +176,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortCountsView.html b/docs/reference/cohortCountsView.html index 80699c75..44efb217 100644 --- a/docs/reference/cohortCountsView.html +++ b/docs/reference/cohortCountsView.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Cohort Counts View

    - +
    @@ -104,13 +101,15 @@

    Cohort Counts View

    Arguments

    -
    id
    + + +
    id

    Namespace id

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortDefinitionsModule(), cohortDefinitionsView(), @@ -145,15 +144,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortDefinitionsModule.html b/docs/reference/cohortDefinitionsModule.html index d9b447b3..ab312d7b 100644 --- a/docs/reference/cohortDefinitionsModule.html +++ b/docs/reference/cohortDefinitionsModule.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Cohort Definition module

    - +
    @@ -111,33 +108,35 @@

    Cohort Definition module

    Arguments

    -
    id
    + + +
    id

    Namespace id

    -
    dataSource
    +
    dataSource

    DatabaseConnection

    -
    cohortDefinitions
    +
    cohortDefinitions

    reactive of cohort definitions to display

    -
    cohortTable
    +
    cohortTable

    data.frame of cohorts, cohortId, cohortName

    -
    cohortCountTable
    +
    cohortCountTable

    data.frame of cohortCounts, cohortId, subjects records

    -
    databaseTable
    +
    databaseTable

    data.frame of databasese, databaseId, name

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsView(), @@ -172,15 +171,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortDefinitionsView.html b/docs/reference/cohortDefinitionsView.html index 01bc64f7..e4da463d 100644 --- a/docs/reference/cohortDefinitionsView.html +++ b/docs/reference/cohortDefinitionsView.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Cohort Definitions View

    - +
    @@ -104,13 +101,15 @@

    Cohort Definitions View

    Arguments

    -
    id
    + + +
    id

    Namespace id for module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -145,15 +144,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortDiagCharacterizationView.html b/docs/reference/cohortDiagCharacterizationView.html index d03da87e..824baec8 100644 --- a/docs/reference/cohortDiagCharacterizationView.html +++ b/docs/reference/cohortDiagCharacterizationView.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    characterization

    - +
    @@ -104,13 +101,15 @@

    characterization

    Arguments

    -
    id
    + + +
    id

    Namespace Id - use namespaced id ns("characterization") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -145,15 +144,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortDiagnosticsHelperFile.html b/docs/reference/cohortDiagnosticsHelperFile.html index b6320ccf..0c576e76 100644 --- a/docs/reference/cohortDiagnosticsHelperFile.html +++ b/docs/reference/cohortDiagnosticsHelperFile.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The location of the description module helper file

    - +
    @@ -104,9 +101,7 @@

    The location of the description module helper file

    Value

    - - -

    string location of the description helper file

    +

    string location of the description helper file

    Details

    @@ -114,7 +109,7 @@

    Details

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -149,15 +144,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortDiagnosticsServer.html b/docs/reference/cohortDiagnosticsServer.html index 6aeb4d86..4e60cb44 100644 --- a/docs/reference/cohortDiagnosticsServer.html +++ b/docs/reference/cohortDiagnosticsServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Cohort Diagnostics Explorer main module

    - +
    @@ -109,25 +106,27 @@

    Cohort Diagnostics Explorer main module

    Arguments

    -
    id
    + + +
    id

    module Id

    -
    connectionHandler
    +
    connectionHandler

    ResultModelManager ConnectionHander instance

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    results database settings

    -
    dataSource
    +
    dataSource

    dataSource optionally created with createCdDatabaseDataSource

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -162,15 +161,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortDiagnosticsView.html b/docs/reference/cohortDiagnosticsView.html index 7ee9cd06..a9754916 100644 --- a/docs/reference/cohortDiagnosticsView.html +++ b/docs/reference/cohortDiagnosticsView.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    View for cohort diagnostics module

    - +
    @@ -104,15 +101,15 @@

    View for cohort diagnostics module

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the cohort diagnostics viewer module

    +

    The user interface to the cohort diagnostics viewer module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -155,15 +152,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortGeneratorHelperFile.html b/docs/reference/cohortGeneratorHelperFile.html index de343e98..1dfd9e06 100644 --- a/docs/reference/cohortGeneratorHelperFile.html +++ b/docs/reference/cohortGeneratorHelperFile.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The location of the cohort-generator module helper file

    - +
    @@ -104,9 +101,7 @@

    The location of the cohort-generator module helper file

    Value

    - - -

    string location of the cohort-generator helper file

    +

    string location of the cohort-generator helper file

    Details

    @@ -114,7 +109,7 @@

    Details

    See also

    -

    Other CohortGenerator: +

    Other CohortGenerator: cohortGeneratorServer(), cohortGeneratorViewer()

    @@ -131,15 +126,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortGeneratorServer.html b/docs/reference/cohortGeneratorServer.html index a651ac75..7ac888fb 100644 --- a/docs/reference/cohortGeneratorServer.html +++ b/docs/reference/cohortGeneratorServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for the main cohort generator module

    - +
    @@ -104,27 +101,27 @@

    The module server for the main cohort generator module

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a named list containing the cohort generator results database details (schema, table prefix)

    Value

    - - -

    the cohort generator results viewer main module server

    +

    the cohort generator results viewer main module server

    See also

    -

    Other CohortGenerator: +

    Other CohortGenerator: cohortGeneratorHelperFile(), cohortGeneratorViewer()

    @@ -141,15 +138,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortGeneratorViewer.html b/docs/reference/cohortGeneratorViewer.html index 2e62987b..92153549 100644 --- a/docs/reference/cohortGeneratorViewer.html +++ b/docs/reference/cohortGeneratorViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The viewer of the main cohort generator module

    - +
    @@ -104,19 +101,19 @@

    The viewer of the main cohort generator module

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the cohort generator results viewer

    +

    The user interface to the cohort generator results viewer

    See also

    -

    Other CohortGenerator: +

    Other CohortGenerator: cohortGeneratorHelperFile(), cohortGeneratorServer()

    @@ -133,15 +130,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodAttritionServer.html b/docs/reference/cohortMethodAttritionServer.html index 2990e32e..8a4b9fb7 100644 --- a/docs/reference/cohortMethodAttritionServer.html +++ b/docs/reference/cohortMethodAttritionServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for rendering the PLE attrition results

    - +
    @@ -109,31 +106,31 @@

    The module server for rendering the PLE attrition results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection to the PLE results database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    the PLE attrition results content server

    +

    the PLE attrition results content server

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), cohortMethodCovariateBalanceViewer(), @@ -166,15 +163,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodAttritionViewer.html b/docs/reference/cohortMethodAttritionViewer.html index d569dc7e..0af3f67e 100644 --- a/docs/reference/cohortMethodAttritionViewer.html +++ b/docs/reference/cohortMethodAttritionViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the PLE attrition results

    - +
    @@ -104,19 +101,19 @@

    The module viewer for rendering the PLE attrition results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the cohort method attrition

    +

    The user interface to the cohort method attrition

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodCovariateBalanceServer(), cohortMethodCovariateBalanceViewer(), @@ -149,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodCovariateBalanceServer.html b/docs/reference/cohortMethodCovariateBalanceServer.html index 363194f0..1a124066 100644 --- a/docs/reference/cohortMethodCovariateBalanceServer.html +++ b/docs/reference/cohortMethodCovariateBalanceServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for rendering the covariate balance plot

    - +
    @@ -110,35 +107,35 @@

    The module server for rendering the covariate balance plot

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection to the PLE results database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    -
    metaAnalysisDbIds
    +
    metaAnalysisDbIds

    metaAnalysisDbIds

    Value

    - - -

    the PLE covariate balance content server

    +

    the PLE covariate balance content server

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceViewer(), @@ -171,15 +168,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodCovariateBalanceViewer.html b/docs/reference/cohortMethodCovariateBalanceViewer.html index a0903dce..bb49b87c 100644 --- a/docs/reference/cohortMethodCovariateBalanceViewer.html +++ b/docs/reference/cohortMethodCovariateBalanceViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the PLE covariate balance analysis

    - +
    @@ -104,19 +101,19 @@

    The module viewer for rendering the PLE covariate balance analysis

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the cohort method covariate balance results

    +

    The user interface to the cohort method covariate balance results

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -149,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodKaplanMeierServer.html b/docs/reference/cohortMethodKaplanMeierServer.html index cbe646e4..cc1e00e8 100644 --- a/docs/reference/cohortMethodKaplanMeierServer.html +++ b/docs/reference/cohortMethodKaplanMeierServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for rendering the Kaplan Meier curve

    - +
    @@ -109,31 +106,31 @@

    The module server for rendering the Kaplan Meier curve

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection to the PLE results database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    the PLE Kaplain Meier content server

    +

    the PLE Kaplain Meier content server

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -166,15 +163,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodKaplanMeierViewer.html b/docs/reference/cohortMethodKaplanMeierViewer.html index fdc47ec0..8cfeda0e 100644 --- a/docs/reference/cohortMethodKaplanMeierViewer.html +++ b/docs/reference/cohortMethodKaplanMeierViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the PLE Kaplan Meier curve

    - +
    @@ -104,19 +101,19 @@

    The module viewer for rendering the PLE Kaplan Meier curve

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The module viewer for Kaplan Meier objects

    +

    The module viewer for Kaplan Meier objects

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -149,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodPopulationCharacteristicsServer.html b/docs/reference/cohortMethodPopulationCharacteristicsServer.html index 33fc26a4..33fdb88e 100644 --- a/docs/reference/cohortMethodPopulationCharacteristicsServer.html +++ b/docs/reference/cohortMethodPopulationCharacteristicsServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for rendering the population characteristics

    - +
    @@ -109,31 +106,31 @@

    The module server for rendering the population characteristics

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection to the PLE results database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    the PLE population characteristics content server

    +

    the PLE population characteristics content server

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -166,15 +163,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodPopulationCharacteristicsViewer.html b/docs/reference/cohortMethodPopulationCharacteristicsViewer.html index 007f58ab..e0bb426a 100644 --- a/docs/reference/cohortMethodPopulationCharacteristicsViewer.html +++ b/docs/reference/cohortMethodPopulationCharacteristicsViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the PLE population characteristics

    - +
    @@ -104,19 +101,19 @@

    The module viewer for rendering the PLE population characteristics

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the cohort method population characteristics objects

    +

    The user interface to the cohort method population characteristics objects

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -149,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodPowerServer.html b/docs/reference/cohortMethodPowerServer.html index 481f7a2e..2fa75281 100644 --- a/docs/reference/cohortMethodPowerServer.html +++ b/docs/reference/cohortMethodPowerServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for rendering the PLE power analysis results

    - +
    @@ -109,31 +106,31 @@

    The module server for rendering the PLE power analysis results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection to the PLE results database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    the PLE systematic error power server

    +

    the PLE systematic error power server

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -166,15 +163,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodPowerViewer.html b/docs/reference/cohortMethodPowerViewer.html index 8e0e388e..b98cb899 100644 --- a/docs/reference/cohortMethodPowerViewer.html +++ b/docs/reference/cohortMethodPowerViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the PLE power analysis

    - +
    @@ -104,19 +101,19 @@

    The module viewer for rendering the PLE power analysis

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the cohort method power calculation results

    +

    The user interface to the cohort method power calculation results

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -149,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodPropensityModelServer.html b/docs/reference/cohortMethodPropensityModelServer.html index 290b58a6..fae12a7a 100644 --- a/docs/reference/cohortMethodPropensityModelServer.html +++ b/docs/reference/cohortMethodPropensityModelServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for rendering the propensity score model

    - +
    @@ -109,31 +106,31 @@

    The module server for rendering the propensity score model

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection to the PLE results database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    the PLE propensity score model

    +

    the PLE propensity score model

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -166,15 +163,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodPropensityModelViewer.html b/docs/reference/cohortMethodPropensityModelViewer.html index 42b9618f..a0d9890c 100644 --- a/docs/reference/cohortMethodPropensityModelViewer.html +++ b/docs/reference/cohortMethodPropensityModelViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the PLE propensity score model covariates/coefficients

    - +
    @@ -104,19 +101,19 @@

    The module viewer for rendering the PLE propensity score model covariates/co

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the cohort method propensity score model covariates/coefficients

    +

    The user interface to the cohort method propensity score model covariates/coefficients

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -149,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodPropensityScoreDistServer.html b/docs/reference/cohortMethodPropensityScoreDistServer.html index e0fbf118..96a6da07 100644 --- a/docs/reference/cohortMethodPropensityScoreDistServer.html +++ b/docs/reference/cohortMethodPropensityScoreDistServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@

    - +

    The module server for rendering a PLE propensity score distribution

    - +
    @@ -110,35 +107,35 @@

    The module server for rendering a PLE propensity score distribution

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection to the PLE results database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    -
    metaAnalysisDbIds
    +
    metaAnalysisDbIds

    metaAnalysisDbIds

    Value

    - - -

    the PLE propensity score distribution content server

    +

    the PLE propensity score distribution content server

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -171,15 +168,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodPropensityScoreDistViewer.html b/docs/reference/cohortMethodPropensityScoreDistViewer.html index c4a7e2fd..670c354f 100644 --- a/docs/reference/cohortMethodPropensityScoreDistViewer.html +++ b/docs/reference/cohortMethodPropensityScoreDistViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the propensity score distribution

    - +
    @@ -104,19 +101,19 @@

    The module viewer for rendering the propensity score distribution

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the cohort method propensity score distribution

    +

    The user interface to the cohort method propensity score distribution

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -149,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodSystematicErrorServer.html b/docs/reference/cohortMethodSystematicErrorServer.html index 0f252d3d..cc528fda 100644 --- a/docs/reference/cohortMethodSystematicErrorServer.html +++ b/docs/reference/cohortMethodSystematicErrorServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for rendering the systematic error objects

    - +
    @@ -109,31 +106,31 @@

    The module server for rendering the systematic error objects

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection handler to the result databases

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    the PLE systematic error content server

    +

    the PLE systematic error content server

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -166,15 +163,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortMethodSystematicErrorViewer.html b/docs/reference/cohortMethodSystematicErrorViewer.html index 802e49bb..cc4eca0e 100644 --- a/docs/reference/cohortMethodSystematicErrorViewer.html +++ b/docs/reference/cohortMethodSystematicErrorViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the PLE systematic error objects

    - +
    @@ -104,19 +101,19 @@

    The module viewer for rendering the PLE systematic error objects

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the cohort method systematic error module

    +

    The user interface to the cohort method systematic error module

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -149,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cohortOverlapView.html b/docs/reference/cohortOverlapView.html index 9ba81967..4fa1d93d 100644 --- a/docs/reference/cohortOverlapView.html +++ b/docs/reference/cohortOverlapView.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Cohort Overlap View

    - +
    @@ -104,13 +101,15 @@

    Cohort Overlap View

    Arguments

    -
    id
    + + +
    id

    Namespace Id - use namespaced id ns("cohortOverlap") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -145,15 +144,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/compareCohortCharacterizationView.html b/docs/reference/compareCohortCharacterizationView.html index 2b58695e..4ff5d070 100644 --- a/docs/reference/compareCohortCharacterizationView.html +++ b/docs/reference/compareCohortCharacterizationView.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    compare characterization view

    - +
    @@ -107,17 +104,19 @@

    compare characterization view

    Arguments

    -
    id
    + + +
    id

    Namespace Id - use namespaced id ns("compareCohortCharacterization") inside diagnosticsExplorer module

    -
    title
    +
    title

    Optional string title field

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -152,15 +151,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/conceptsInDataSourceView.html b/docs/reference/conceptsInDataSourceView.html index 26065376..55678bdb 100644 --- a/docs/reference/conceptsInDataSourceView.html +++ b/docs/reference/conceptsInDataSourceView.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    concepts In DataSource View

    - +
    @@ -104,13 +101,15 @@

    concepts In DataSource View

    Arguments

    -
    id
    + + +
    id

    Namespace Id - use namespaced id ns("conceptsInDataSource") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -145,15 +144,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createCdDatabaseDataSource.html b/docs/reference/createCdDatabaseDataSource.html index 2edf10c7..a3c912c2 100644 --- a/docs/reference/createCdDatabaseDataSource.html +++ b/docs/reference/createCdDatabaseDataSource.html @@ -5,7 +5,7 @@ - +
    @@ -27,7 +27,7 @@
    - +

    Create a CD data source from a database

    - +
    @@ -116,35 +113,35 @@

    Create a CD data source from a database

    Arguments

    -
    connectionHandler
    + + +
    connectionHandler

    An instance of a ResultModelManager::connectionHander - manages a connection to a database.

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    -
    dataModelSpecificationsPath
    +
    dataModelSpecificationsPath

    The path to a file containing specifications for the data model used by the database.

    -
    dataMigrationsRef
    +
    dataMigrationsRef

    The path to a file listing all migrations for the data model that should have been applied

    -
    displayProgress
    +
    displayProgress

    display a progress messaage (can only be used inside a shiny reactive context)

    Value

    - - -

    An object of class `CdDataSource`.

    +

    An object of class `CdDataSource`.

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -179,15 +176,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createCustomColDefList.html b/docs/reference/createCustomColDefList.html index 4e388552..57f3a577 100644 --- a/docs/reference/createCustomColDefList.html +++ b/docs/reference/createCustomColDefList.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Creating a list of custom column definitions for use in reactables

    - +
    @@ -110,47 +107,47 @@

    Creating a list of custom column definitions for use in reactables

    Arguments

    -
    rawColNames
    + + +
    rawColNames

    The raw column names taken directly from the source data table that are to be overwritten in the reactable

    -
    niceColNames
    -

    The formatted column names that will appear as-specified in +

    niceColNames
    +

    The formatted column names that will appear as-specified in the reactable

    -
    tooltipText
    -

    The text to be displayed in a toolTip when hovering over the +

    tooltipText
    +

    The text to be displayed in a toolTip when hovering over the column in the reactable

    -
    case
    +
    case

    Optional argument to convert raw column names to snake or camel case. Defaults to NULL and preserves whatever raw column names are passed in

    -
    customColDefOptions
    +
    customColDefOptions

    A list of lists, where the inner lists are any custom options from reactable::colDef for each column

    Value

    - - -

    A named list of reactable::colDef objects

    +

    A named list of reactable::colDef objects

    See also

    -

    Other Utils: +

    Other Utils: datasourcesHelperFile(), datasourcesServer(), datasourcesViewer(), makeButtonLabel(), resultTableServer(), resultTableViewer()

    -

    Other Utils: +

    Other Utils: datasourcesHelperFile(), datasourcesServer(), datasourcesViewer(), @@ -171,15 +168,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createLargeSqlQueryDt.html b/docs/reference/createLargeSqlQueryDt.html index 4491c923..3d0de091 100644 --- a/docs/reference/createLargeSqlQueryDt.html +++ b/docs/reference/createLargeSqlQueryDt.html @@ -5,7 +5,7 @@ - +
    @@ -27,7 +27,7 @@
    - +

    Create Large Sql Query Data Table

    - +
    @@ -113,26 +110,28 @@

    Create Large Sql Query Data Table

    Arguments

    -
    connectionHandler
    + + +
    connectionHandler

    ResultModelManager connectionHandler instance

    -
    connectionDetails
    +
    connectionDetails

    DatabaseConnector connectionDetails instance

    -
    baseQuery
    +
    baseQuery

    base sql query

    -
    countQuery
    +
    countQuery

    count query string (should match query). Can be auto generated with sub query (default) but this will likely result in slow results

    See also

    -

    Other LargeTables: +

    Other LargeTables: largeTableServer(), largeTableView()

    @@ -149,15 +148,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/dataDiagnosticDrillServer.html b/docs/reference/dataDiagnosticDrillServer.html index a75e3083..6dbb5af7 100644 --- a/docs/reference/dataDiagnosticDrillServer.html +++ b/docs/reference/dataDiagnosticDrillServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction summary results

    - +
    @@ -104,23 +101,23 @@

    The module server for exploring prediction summary results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    The server to the summary module

    +

    The server to the summary module

    Details

    @@ -128,7 +125,7 @@

    Details

    See also

    -

    Other DataDiagnostics: +

    Other DataDiagnostics: dataDiagnosticDrillViewer(), dataDiagnosticHelperFile(), dataDiagnosticServer(), @@ -149,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/dataDiagnosticDrillViewer.html b/docs/reference/dataDiagnosticDrillViewer.html index dcd08cd2..1dfb5136 100644 --- a/docs/reference/dataDiagnosticDrillViewer.html +++ b/docs/reference/dataDiagnosticDrillViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring data-diagnostic results in more detail

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring data-diagnostic results in more detail

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the summary module

    +

    The user interface to the summary module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other DataDiagnostics: +

    Other DataDiagnostics: dataDiagnosticDrillServer(), dataDiagnosticHelperFile(), dataDiagnosticServer(), @@ -141,15 +138,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/dataDiagnosticHelperFile.html b/docs/reference/dataDiagnosticHelperFile.html index 458085b7..7147d9d2 100644 --- a/docs/reference/dataDiagnosticHelperFile.html +++ b/docs/reference/dataDiagnosticHelperFile.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The location of the data-diagnostic module helper file

    - +
    @@ -104,9 +101,7 @@

    The location of the data-diagnostic module helper file

    Value

    - - -

    string location of the data-diagnostic helper file

    +

    string location of the data-diagnostic helper file

    Details

    @@ -114,7 +109,7 @@

    Details

    See also

    -

    Other DataDiagnostics: +

    Other DataDiagnostics: dataDiagnosticDrillServer(), dataDiagnosticDrillViewer(), dataDiagnosticServer(), @@ -135,15 +130,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/dataDiagnosticServer.html b/docs/reference/dataDiagnosticServer.html index 9335f5de..f5c3ddf5 100644 --- a/docs/reference/dataDiagnosticServer.html +++ b/docs/reference/dataDiagnosticServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring data-diagnostic

    - +
    @@ -108,23 +105,23 @@

    The module server for exploring data-diagnostic

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the data-diagnostic result schema

    Value

    - - -

    The server for the data-diagnostic module

    +

    The server for the data-diagnostic module

    Details

    @@ -132,7 +129,7 @@

    Details

    See also

    -

    Other DataDiagnostics: +

    Other DataDiagnostics: dataDiagnosticDrillServer(), dataDiagnosticDrillViewer(), dataDiagnosticHelperFile(), @@ -153,15 +150,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/dataDiagnosticSummaryServer.html b/docs/reference/dataDiagnosticSummaryServer.html index 3e540d66..5d7344cd 100644 --- a/docs/reference/dataDiagnosticSummaryServer.html +++ b/docs/reference/dataDiagnosticSummaryServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction summary results

    - +
    @@ -104,23 +101,23 @@

    The module server for exploring prediction summary results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    The server to the summary module

    +

    The server to the summary module

    Details

    @@ -128,7 +125,7 @@

    Details

    See also

    -

    Other DataDiagnostics: +

    Other DataDiagnostics: dataDiagnosticDrillServer(), dataDiagnosticDrillViewer(), dataDiagnosticHelperFile(), @@ -149,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/dataDiagnosticSummaryViewer.html b/docs/reference/dataDiagnosticSummaryViewer.html index a0256093..1038a1b0 100644 --- a/docs/reference/dataDiagnosticSummaryViewer.html +++ b/docs/reference/dataDiagnosticSummaryViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring data-diagnostic summary results

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring data-diagnostic summary results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the summary module

    +

    The user interface to the summary module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other DataDiagnostics: +

    Other DataDiagnostics: dataDiagnosticDrillServer(), dataDiagnosticDrillViewer(), dataDiagnosticHelperFile(), @@ -141,15 +138,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/dataDiagnosticViewer.html b/docs/reference/dataDiagnosticViewer.html index f961a438..acc3a8da 100644 --- a/docs/reference/dataDiagnosticViewer.html +++ b/docs/reference/dataDiagnosticViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring data-diagnostic

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring data-diagnostic

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the data-diagnostic viewer module

    +

    The user interface to the data-diagnostic viewer module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other DataDiagnostics: +

    Other DataDiagnostics: dataDiagnosticDrillServer(), dataDiagnosticDrillViewer(), dataDiagnosticHelperFile(), @@ -141,15 +138,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/databaseInformationView.html b/docs/reference/databaseInformationView.html index 80f092e6..74fd2105 100644 --- a/docs/reference/databaseInformationView.html +++ b/docs/reference/databaseInformationView.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    database Information View

    - +
    @@ -104,13 +101,15 @@

    database Information View

    Arguments

    -
    id
    + + +
    id

    Namespace Id - use namespaced id ns("databaseInformation") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -145,15 +144,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/datasourcesHelperFile.html b/docs/reference/datasourcesHelperFile.html index e4c54363..d607c6c5 100644 --- a/docs/reference/datasourcesHelperFile.html +++ b/docs/reference/datasourcesHelperFile.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Define the helper file for the module

    - +
    @@ -104,20 +101,18 @@

    Define the helper file for the module

    Value

    - - -

    The helper html file for the datasources module

    +

    The helper html file for the datasources module

    See also

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesServer(), datasourcesViewer(), makeButtonLabel(), resultTableServer(), resultTableViewer()

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesServer(), datasourcesViewer(), @@ -138,15 +133,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/datasourcesServer.html b/docs/reference/datasourcesServer.html index 82cb6f10..53b6802a 100644 --- a/docs/reference/datasourcesServer.html +++ b/docs/reference/datasourcesServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The server function for the datasources module

    - +
    @@ -104,34 +101,34 @@

    The server function for the datasources module

    Arguments

    -
    id
    + + +
    id

    The unique id for the datasources server namespace

    -
    connectionHandler
    +
    connectionHandler

    A connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    A named list containing the cohort generator results database details (schema, table prefix)

    Value

    - - -

    The server for the datasources module

    +

    The server for the datasources module

    See also

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesViewer(), makeButtonLabel(), resultTableServer(), resultTableViewer()

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesViewer(), @@ -152,15 +149,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/datasourcesViewer.html b/docs/reference/datasourcesViewer.html index 728f4b32..efa84cb6 100644 --- a/docs/reference/datasourcesViewer.html +++ b/docs/reference/datasourcesViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The viewer function for hte datasources module

    - +
    @@ -104,26 +101,26 @@

    The viewer function for hte datasources module

    Arguments

    -
    id
    + + +
    id

    The unique id for the datasources viewer namespace

    Value

    - - -

    The UI for the datasources module

    +

    The UI for the datasources module

    See also

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), makeButtonLabel(), resultTableServer(), resultTableViewer()

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), @@ -144,15 +141,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/estimationHelperFile.html b/docs/reference/estimationHelperFile.html index 75ab4e3a..353c29dd 100644 --- a/docs/reference/estimationHelperFile.html +++ b/docs/reference/estimationHelperFile.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The location of the estimation module helper file

    - +
    @@ -104,9 +101,7 @@

    The location of the estimation module helper file

    Value

    - - -

    string location of the characterization helper file

    +

    string location of the characterization helper file

    Details

    @@ -114,7 +109,7 @@

    Details

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -147,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/estimationServer.html b/docs/reference/estimationServer.html index 6d53766d..8f1c79cc 100644 --- a/docs/reference/estimationServer.html +++ b/docs/reference/estimationServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring estimation studies

    - +
    @@ -108,23 +105,23 @@

    The module server for exploring estimation studies

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the characterization result schema, dbms, tablePrefix, databaseTable and cgTablePrefix

    Value

    - - -

    The server for the estimation module

    +

    The server for the estimation module

    Details

    @@ -132,7 +129,7 @@

    Details

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -165,15 +162,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/estimationViewer.html b/docs/reference/estimationViewer.html index 1e4b5261..b893545d 100644 --- a/docs/reference/estimationViewer.html +++ b/docs/reference/estimationViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring characterization studies

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring characterization studies

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the characterization viewer module

    +

    The user interface to the characterization viewer module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -153,15 +150,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/getCirceRenderedExpression.html b/docs/reference/getCirceRenderedExpression.html index dbf3b9cd..b9c3a34a 100644 --- a/docs/reference/getCirceRenderedExpression.html +++ b/docs/reference/getCirceRenderedExpression.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Returns list with circe generated documentation

    - +
    @@ -108,29 +105,29 @@

    Returns list with circe generated documentation

    Arguments

    -
    cohortDefinition
    + + +
    cohortDefinition

    An R object (list) with a list representation of the cohort definition expression, that may be converted to a cohort expression JSON using RJSONIO::toJSON(x = cohortDefinition, digits = 23, pretty = TRUE)

    -
    cohortName
    +
    cohortName

    Name for the cohort definition

    -
    includeConceptSets
    +
    includeConceptSets

    Do you want to inclued concept set in the documentation

    Value

    - - -

    list object

    +

    list object

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -165,15 +162,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/getEnabledCdReports.html b/docs/reference/getEnabledCdReports.html index afbaffe0..bfe2c539 100644 --- a/docs/reference/getEnabledCdReports.html +++ b/docs/reference/getEnabledCdReports.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Get enable cd reports from available data

    - +
    @@ -104,13 +101,15 @@

    Get enable cd reports from available data

    Arguments

    -
    dataSource
    + + +
    dataSource

    Cohort diagnostics data source

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -145,15 +144,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/getExampleConnectionDetails.html b/docs/reference/getExampleConnectionDetails.html index 5d1acf1e..b3527854 100644 --- a/docs/reference/getExampleConnectionDetails.html +++ b/docs/reference/getExampleConnectionDetails.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    A connection details to an example result database

    - +
    @@ -104,13 +101,11 @@

    A connection details to an example result database

    Value

    - - -

    The connection details to an example result database

    +

    The connection details to an example result database

    Details

    -

    Finds the location within the package of an sqlite database with example results for 1) CohortGenerator, +

    Finds the location within the package of an sqlite database with example results for 1) CohortGenerator, 2) Characterization, 3) PatientLevelPrediction, 4) CohortMethod, 5) SelfControlledCaseSeries and 6) CohortIncidence

    @@ -126,15 +121,15 @@

    Details

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/getLogoImage.html b/docs/reference/getLogoImage.html index 7a15d928..79059378 100644 --- a/docs/reference/getLogoImage.html +++ b/docs/reference/getLogoImage.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The location of the OHDSI logo

    - +
    @@ -104,9 +101,7 @@

    The location of the OHDSI logo

    Value

    - - -

    string location of the OHDSI logo

    +

    string location of the OHDSI logo

    Details

    @@ -125,15 +120,15 @@

    Details

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/homeHelperFile.html b/docs/reference/homeHelperFile.html index f625900b..2ead48f1 100644 --- a/docs/reference/homeHelperFile.html +++ b/docs/reference/homeHelperFile.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The location of the home module helper file

    - +
    @@ -104,9 +101,7 @@

    The location of the home module helper file

    Value

    - - -

    string location of the home helper file

    +

    string location of the home helper file

    Details

    @@ -114,7 +109,7 @@

    Details

    See also

    -

    Other Home: +

    Other Home: homeServer(), homeViewer()

    @@ -131,15 +126,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/homeServer.html b/docs/reference/homeServer.html index af67ea4e..15125146 100644 --- a/docs/reference/homeServer.html +++ b/docs/reference/homeServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring home

    - +
    @@ -104,23 +101,23 @@

    The module server for exploring home

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the prediction result schema and connection details

    Value

    - - -

    The server for the home module

    +

    The server for the home module

    Details

    @@ -128,7 +125,7 @@

    Details

    See also

    -

    Other Home: +

    Other Home: homeHelperFile(), homeViewer()

    @@ -145,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/homeViewer.html b/docs/reference/homeViewer.html index e8a509d2..36cd980d 100644 --- a/docs/reference/homeViewer.html +++ b/docs/reference/homeViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring home

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring home

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the home viewer module

    +

    The user interface to the home viewer module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other Home: +

    Other Home: homeHelperFile(), homeServer()

    @@ -137,15 +134,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/incidenceRatesView.html b/docs/reference/incidenceRatesView.html index 8051dbcc..61a73b14 100644 --- a/docs/reference/incidenceRatesView.html +++ b/docs/reference/incidenceRatesView.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    incidence Rates View

    - +
    @@ -104,13 +101,15 @@

    incidence Rates View

    Arguments

    -
    id
    + + +
    id

    Namespace Id - use namespaced id ns("incidenceRates") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -145,15 +144,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/inclusionRulesView.html b/docs/reference/inclusionRulesView.html index 162511c5..b58fe654 100644 --- a/docs/reference/inclusionRulesView.html +++ b/docs/reference/inclusionRulesView.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    inclusion Rules View

    - +
    @@ -104,13 +101,15 @@

    inclusion Rules View

    Arguments

    -
    id
    + + +
    id

    Namespace Id - use namespaced id ns("inclusionRules") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -145,15 +144,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index b4e80c30..8dbcd0b3 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,9 +1,9 @@ -Function reference • OhdsiShinyModulesPackage index • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +
    @@ -581,13 +578,13 @@

    Large Table

    Utilities for tables that contain large amounts of rows

    -

    LargeDataTable

    - -

    Large Data Table

    -

    createLargeSqlQueryDt()

    Create Large Sql Query Data Table

    + +

    LargeDataTable

    + +

    Large Data Table

    largeTableServer()

    @@ -665,15 +662,15 @@

    Home

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/indexEventBreakdownView.html b/docs/reference/indexEventBreakdownView.html index 967c4f1c..e91dfb88 100644 --- a/docs/reference/indexEventBreakdownView.html +++ b/docs/reference/indexEventBreakdownView.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Index event breakdown view

    - +
    @@ -104,13 +101,15 @@

    Index event breakdown view

    Arguments

    -
    id
    + + +
    id

    Namespace Id - use namespaced id ns("indexEvents") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -145,15 +144,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/largeTableServer.html b/docs/reference/largeTableServer.html index 9072de7a..8c2fc2bc 100644 --- a/docs/reference/largeTableServer.html +++ b/docs/reference/largeTableServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Large Table Component Server

    - +
    @@ -111,34 +108,36 @@

    Large Table Component Server

    Arguments

    -
    id
    + + +
    id

    Shiny module id. Must match Large Table Viewer

    -
    ldt
    +
    ldt

    LargeDataTable instance

    -
    inputParams
    +
    inputParams

    reactive that returns list of parameters to be passed to ldt

    -
    modifyData
    +
    modifyData

    optional callback function that takes the data page, page number, page size as parameters must return data.frame compatable instance

    -
    columns
    +
    columns

    List or reactable returning list of reactable::columnDef objects

    -
    ...
    +
    ...

    Additional reactable options (searchable, sortable

    See also

    -

    Other LargeTables: +

    Other LargeTables: createLargeSqlQueryDt(), largeTableView()

    @@ -155,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/largeTableView.html b/docs/reference/largeTableView.html index 29b69dea..8397a6c2 100644 --- a/docs/reference/largeTableView.html +++ b/docs/reference/largeTableView.html @@ -5,7 +5,7 @@ - +
    @@ -27,7 +27,7 @@
    - +

    Large Table Component Viewer

    - +
    @@ -113,25 +110,27 @@

    Large Table Component Viewer

    Arguments

    -
    id
    + + +
    id

    Shiny module id. Must match largeTableServer

    -
    pageSizeChoices
    +
    pageSizeChoices

    numeric selection options for pages

    -
    selectedPageSize
    +
    selectedPageSize

    numeric selection options for pages

    -
    fullDownloads
    +
    fullDownloads

    allow download button of full dataset from query

    See also

    -

    Other LargeTables: +

    Other LargeTables: createLargeSqlQueryDt(), largeTableServer()

    @@ -148,15 +147,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/makeButtonLabel.html b/docs/reference/makeButtonLabel.html index 187fce70..eff24662 100644 --- a/docs/reference/makeButtonLabel.html +++ b/docs/reference/makeButtonLabel.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Make a label for an html button

    - +
    @@ -104,26 +101,26 @@

    Make a label for an html button

    Arguments

    -
    label
    + + +
    label

    The desired label for hte button

    Value

    - - -

    html code to make a button label

    +

    html code to make a button label

    See also

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), datasourcesViewer(), resultTableServer(), resultTableViewer()

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), @@ -144,15 +141,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/orpahanConceptsView.html b/docs/reference/orpahanConceptsView.html index 9c52f45f..433eed90 100644 --- a/docs/reference/orpahanConceptsView.html +++ b/docs/reference/orpahanConceptsView.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Orphan Concepts View

    - +
    @@ -104,13 +101,15 @@

    Orphan Concepts View

    Arguments

    -
    id
    + + +
    id

    Namespace Id - use namespaced id ns("orphanConcepts") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -131,7 +130,7 @@

    See also

    indexEventBreakdownView(), timeDistributionsView(), visitContextView()

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -166,15 +165,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionCalibrationServer.html b/docs/reference/patientLevelPredictionCalibrationServer.html index 2864b7f4..a065bd10 100644 --- a/docs/reference/patientLevelPredictionCalibrationServer.html +++ b/docs/reference/patientLevelPredictionCalibrationServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction validation results

    - +
    @@ -110,31 +107,31 @@

    The module server for exploring prediction validation results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    performanceId
    +
    performanceId

    the performance id in the database

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    inputSingleView
    +
    inputSingleView

    the current tab

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    The server to the prediction calibration module

    +

    The server to the prediction calibration module

    Details

    @@ -142,7 +139,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), patientLevelPredictionCovariateSummaryViewer(), @@ -179,15 +176,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionCalibrationViewer.html b/docs/reference/patientLevelPredictionCalibrationViewer.html index 4d58ab9e..88285cd3 100644 --- a/docs/reference/patientLevelPredictionCalibrationViewer.html +++ b/docs/reference/patientLevelPredictionCalibrationViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction model calibration results

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring prediction model calibration results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the prediction model calibration module

    +

    The user interface to the prediction model calibration module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCovariateSummaryServer(), patientLevelPredictionCovariateSummaryViewer(), @@ -157,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionCovariateSummaryServer.html b/docs/reference/patientLevelPredictionCovariateSummaryServer.html index 300ee090..acba2c1f 100644 --- a/docs/reference/patientLevelPredictionCovariateSummaryServer.html +++ b/docs/reference/patientLevelPredictionCovariateSummaryServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction covariate summary results

    - +
    @@ -112,39 +109,39 @@

    The module server for exploring prediction covariate summary results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    modelDesignId
    +
    modelDesignId

    unique id for the model design

    -
    developmentDatabaseId
    +
    developmentDatabaseId

    unique id for the development database

    -
    performanceId
    +
    performanceId

    unique id for the performance results

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    inputSingleView
    +
    inputSingleView

    the current tab

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    The server to the covariate summary module

    +

    The server to the covariate summary module

    Details

    @@ -152,7 +149,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryViewer(), @@ -189,15 +186,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionCovariateSummaryViewer.html b/docs/reference/patientLevelPredictionCovariateSummaryViewer.html index ab3b3670..7547d5fa 100644 --- a/docs/reference/patientLevelPredictionCovariateSummaryViewer.html +++ b/docs/reference/patientLevelPredictionCovariateSummaryViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction covariate summary results

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring prediction covariate summary results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the covariate summary module

    +

    The user interface to the covariate summary module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -157,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionCutoffServer.html b/docs/reference/patientLevelPredictionCutoffServer.html index 3594b29c..6da203d4 100644 --- a/docs/reference/patientLevelPredictionCutoffServer.html +++ b/docs/reference/patientLevelPredictionCutoffServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction cut-off results

    - +
    @@ -110,31 +107,31 @@

    The module server for exploring prediction cut-off results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    performanceId
    +
    performanceId

    the performance id in the database

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    inputSingleView
    +
    inputSingleView

    the current tab

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    The server to the prediction cut-off module

    +

    The server to the prediction cut-off module

    Details

    @@ -142,7 +139,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -179,15 +176,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionCutoffViewer.html b/docs/reference/patientLevelPredictionCutoffViewer.html index 261243b4..1c2c5b58 100644 --- a/docs/reference/patientLevelPredictionCutoffViewer.html +++ b/docs/reference/patientLevelPredictionCutoffViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction cut-off results

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring prediction cut-off results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the prediction cut-off module

    +

    The user interface to the prediction cut-off module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -157,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionDesignSummaryServer.html b/docs/reference/patientLevelPredictionDesignSummaryServer.html index b8672abf..9b3b41d8 100644 --- a/docs/reference/patientLevelPredictionDesignSummaryServer.html +++ b/docs/reference/patientLevelPredictionDesignSummaryServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction designs in the results

    - +
    @@ -108,23 +105,23 @@

    The module server for exploring prediction designs in the results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    The server to the prediction design module

    +

    The server to the prediction design module

    Details

    @@ -132,7 +129,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -169,15 +166,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionDesignSummaryViewer.html b/docs/reference/patientLevelPredictionDesignSummaryViewer.html index fc18ade8..0ad4b4e7 100644 --- a/docs/reference/patientLevelPredictionDesignSummaryViewer.html +++ b/docs/reference/patientLevelPredictionDesignSummaryViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction designs that have been run

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring prediction designs that have been run

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the prediction design module

    +

    The user interface to the prediction design module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -157,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionDiagnosticsServer.html b/docs/reference/patientLevelPredictionDiagnosticsServer.html index c5c61e2d..4314ffc9 100644 --- a/docs/reference/patientLevelPredictionDiagnosticsServer.html +++ b/docs/reference/patientLevelPredictionDiagnosticsServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction diagnostic results

    - +
    @@ -109,27 +106,27 @@

    The module server for exploring prediction diagnostic results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    modelDesignId
    +
    modelDesignId

    the unique id for the model design

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    The server to the prediction diagnostic module

    +

    The server to the prediction diagnostic module

    Details

    @@ -137,7 +134,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -174,15 +171,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionDiagnosticsViewer.html b/docs/reference/patientLevelPredictionDiagnosticsViewer.html index 16a5f280..eb343b94 100644 --- a/docs/reference/patientLevelPredictionDiagnosticsViewer.html +++ b/docs/reference/patientLevelPredictionDiagnosticsViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction diagnostic results

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring prediction diagnostic results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the prediction diagnostic module

    +

    The user interface to the prediction diagnostic module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -157,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionDiscriminationServer.html b/docs/reference/patientLevelPredictionDiscriminationServer.html index 201fea37..773d977d 100644 --- a/docs/reference/patientLevelPredictionDiscriminationServer.html +++ b/docs/reference/patientLevelPredictionDiscriminationServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction model discrimination results

    - +
    @@ -110,31 +107,31 @@

    The module server for exploring prediction model discrimination results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    performanceId
    +
    performanceId

    the performance id in the database

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    inputSingleView
    +
    inputSingleView

    the current tab

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    The server to the model discrimination module

    +

    The server to the model discrimination module

    Details

    @@ -142,7 +139,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -179,15 +176,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionDiscriminationViewer.html b/docs/reference/patientLevelPredictionDiscriminationViewer.html index 73819ec8..fa6a8e5e 100644 --- a/docs/reference/patientLevelPredictionDiscriminationViewer.html +++ b/docs/reference/patientLevelPredictionDiscriminationViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction model discrimination results

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring prediction model discrimination results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the model discrimination results module

    +

    The user interface to the model discrimination results module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -157,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionHelperFile.html b/docs/reference/patientLevelPredictionHelperFile.html index 8acbbb03..0843ce69 100644 --- a/docs/reference/patientLevelPredictionHelperFile.html +++ b/docs/reference/patientLevelPredictionHelperFile.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The location of the prediction module helper file

    - +
    @@ -104,9 +101,7 @@

    The location of the prediction module helper file

    Value

    - - -

    string location of the prediction helper file

    +

    string location of the prediction helper file

    Details

    @@ -114,7 +109,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -151,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionModelSummaryServer.html b/docs/reference/patientLevelPredictionModelSummaryServer.html index e3b6ab8a..4170d5ce 100644 --- a/docs/reference/patientLevelPredictionModelSummaryServer.html +++ b/docs/reference/patientLevelPredictionModelSummaryServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction summary results

    - +
    @@ -109,27 +106,27 @@

    The module server for exploring prediction summary results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    -
    modelDesignId
    +
    modelDesignId

    a reactable id specifying the prediction model design identifier

    Value

    - - -

    The server to the summary module

    +

    The server to the summary module

    Details

    @@ -137,7 +134,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -174,15 +171,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionModelSummaryViewer.html b/docs/reference/patientLevelPredictionModelSummaryViewer.html index edf6c8d6..a3468208 100644 --- a/docs/reference/patientLevelPredictionModelSummaryViewer.html +++ b/docs/reference/patientLevelPredictionModelSummaryViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction summary results

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring prediction summary results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the summary module

    +

    The user interface to the summary module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -157,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionNbServer.html b/docs/reference/patientLevelPredictionNbServer.html index 5f03799b..82e74f16 100644 --- a/docs/reference/patientLevelPredictionNbServer.html +++ b/docs/reference/patientLevelPredictionNbServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction net-benefit results

    - +
    @@ -110,31 +107,31 @@

    The module server for exploring prediction net-benefit results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    performanceId
    +
    performanceId

    the performance id in the database

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    inputSingleView
    +
    inputSingleView

    the current tab

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    The server to the net-benefit module

    +

    The server to the net-benefit module

    Details

    @@ -142,7 +139,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -179,15 +176,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionNbViewer.html b/docs/reference/patientLevelPredictionNbViewer.html index 4c234760..812439e5 100644 --- a/docs/reference/patientLevelPredictionNbViewer.html +++ b/docs/reference/patientLevelPredictionNbViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction net-benefit results

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring prediction net-benefit results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the net-benefit module

    +

    The user interface to the net-benefit module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -157,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionServer.html b/docs/reference/patientLevelPredictionServer.html index 395816b4..e22f6862 100644 --- a/docs/reference/patientLevelPredictionServer.html +++ b/docs/reference/patientLevelPredictionServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring PatientLevelPrediction

    - +
    @@ -108,23 +105,23 @@

    The module server for exploring PatientLevelPrediction

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the prediction result schema and connection details

    Value

    - - -

    The server for the PatientLevelPrediction module

    +

    The server for the PatientLevelPrediction module

    Details

    @@ -132,7 +129,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -169,15 +166,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionSettingsServer.html b/docs/reference/patientLevelPredictionSettingsServer.html index 2417f42b..1a67b538 100644 --- a/docs/reference/patientLevelPredictionSettingsServer.html +++ b/docs/reference/patientLevelPredictionSettingsServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction settings

    - +
    @@ -112,39 +109,39 @@

    The module server for exploring prediction settings

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    modelDesignId
    +
    modelDesignId

    unique id for the model design

    -
    developmentDatabaseId
    +
    developmentDatabaseId

    unique id for the development database

    -
    performanceId
    +
    performanceId

    unique id for the performance results

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    inputSingleView
    +
    inputSingleView

    the current tab

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    The server to the settings module

    +

    The server to the settings module

    Details

    @@ -152,7 +149,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -189,15 +186,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionSettingsViewer.html b/docs/reference/patientLevelPredictionSettingsViewer.html index 80eaf807..1e4de580 100644 --- a/docs/reference/patientLevelPredictionSettingsViewer.html +++ b/docs/reference/patientLevelPredictionSettingsViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction settings

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring prediction settings

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the settings module

    +

    The user interface to the settings module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -157,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionValidationServer.html b/docs/reference/patientLevelPredictionValidationServer.html index 6685163e..9860d1f9 100644 --- a/docs/reference/patientLevelPredictionValidationServer.html +++ b/docs/reference/patientLevelPredictionValidationServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction validation results

    - +
    @@ -112,39 +109,39 @@

    The module server for exploring prediction validation results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    modelDesignId
    +
    modelDesignId

    identifier for the model design

    -
    developmentDatabaseId
    +
    developmentDatabaseId

    identifier for the development database

    -
    performanceId
    +
    performanceId

    identifier for the performance

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    inputSingleView
    +
    inputSingleView

    the current tab

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    - - -

    The server to the validation module

    +

    The server to the validation module

    Details

    @@ -152,7 +149,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -189,15 +186,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionValidationViewer.html b/docs/reference/patientLevelPredictionValidationViewer.html index e79e22ad..b4010978 100644 --- a/docs/reference/patientLevelPredictionValidationViewer.html +++ b/docs/reference/patientLevelPredictionValidationViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction validation results

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring prediction validation results

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the validation module

    +

    The user interface to the validation module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -157,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/patientLevelPredictionViewer.html b/docs/reference/patientLevelPredictionViewer.html index 332d3f10..e46404af 100644 --- a/docs/reference/patientLevelPredictionViewer.html +++ b/docs/reference/patientLevelPredictionViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring PatientLevelPrediction

    - +
    @@ -104,15 +101,15 @@

    The module viewer for exploring PatientLevelPrediction

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the PatientLevelPrediction viewer module

    +

    The user interface to the PatientLevelPrediction viewer module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -157,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/phevaluatorHelperFile.html b/docs/reference/phevaluatorHelperFile.html index f98d15c6..509aad3c 100644 --- a/docs/reference/phevaluatorHelperFile.html +++ b/docs/reference/phevaluatorHelperFile.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The location of the phevaluator module helper file

    - +
    @@ -104,9 +101,7 @@

    The location of the phevaluator module helper file

    Value

    - - -

    String location of the phevaluator helper file

    +

    String location of the phevaluator helper file

    Details

    @@ -114,10 +109,10 @@

    Details

    See also

    -

    Other PheValuator: +

    Other PheValuator: phevaluatorServer(), phevaluatorViewer()

    -

    Other PheValuator: +

    Other PheValuator: phevaluatorServer(), phevaluatorViewer()

    @@ -134,15 +129,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/phevaluatorServer.html b/docs/reference/phevaluatorServer.html index b162161d..ef567cb8 100644 --- a/docs/reference/phevaluatorServer.html +++ b/docs/reference/phevaluatorServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for the main phevaluator module

    - +
    @@ -104,30 +101,30 @@

    The module server for the main phevaluator module

    Arguments

    -
    id
    + + +
    id

    The unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    A connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    A named list containing the cohort generator results database details (schema, table prefix)

    Value

    - - -

    The phevaluator main module server

    +

    The phevaluator main module server

    See also

    -

    Other PheValuator: +

    Other PheValuator: phevaluatorHelperFile(), phevaluatorViewer()

    -

    Other PheValuator: +

    Other PheValuator: phevaluatorHelperFile(), phevaluatorViewer()

    @@ -144,15 +141,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/phevaluatorViewer.html b/docs/reference/phevaluatorViewer.html index af8507e9..a661b9e0 100644 --- a/docs/reference/phevaluatorViewer.html +++ b/docs/reference/phevaluatorViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The viewer of the phevaluator module

    - +
    @@ -104,22 +101,22 @@

    The viewer of the phevaluator module

    Arguments

    -
    id
    + + +
    id

    The unique reference id for the module

    Value

    - - -

    The user interface to the phevaluator results viewer

    +

    The user interface to the phevaluator results viewer

    See also

    -

    Other PheValuator: +

    Other PheValuator: phevaluatorHelperFile(), phevaluatorServer()

    -

    Other PheValuator: +

    Other PheValuator: phevaluatorHelperFile(), phevaluatorServer()

    @@ -136,15 +133,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/reportHelperFile.html b/docs/reference/reportHelperFile.html index 719b2588..e14196a1 100644 --- a/docs/reference/reportHelperFile.html +++ b/docs/reference/reportHelperFile.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The location of the report module helper file

    - +
    @@ -104,9 +101,7 @@

    The location of the report module helper file

    Value

    - - -

    string location of the report helper file

    +

    string location of the report helper file

    Details

    @@ -114,7 +109,7 @@

    Details

    See also

    -

    Other Report: +

    Other Report: reportServer(), reportViewer()

    @@ -131,15 +126,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/reportServer.html b/docs/reference/reportServer.html index 0037752a..502ee584 100644 --- a/docs/reference/reportServer.html +++ b/docs/reference/reportServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module server for the shiny app report module

    - +
    @@ -112,39 +109,39 @@

    The module server for the shiny app report module

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the characterization result schema, dbms, tablePrefix, databaseTable and cgTablePrefix

    -
    server
    +
    server

    server for the connection to the results for quarto

    -
    username
    +
    username

    username for the connection to the results for quarto

    -
    password
    +
    password

    password for the connection to the results for quarto

    -
    dbms
    +
    dbms

    dbms for the connection to the results for quarto

    Value

    - - -

    The server for the shiny app home

    +

    The server for the shiny app home

    Details

    @@ -152,7 +149,7 @@

    Details

    See also

    -

    Other Report: +

    Other Report: reportHelperFile(), reportViewer()

    @@ -169,15 +166,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/reportViewer.html b/docs/reference/reportViewer.html index 0e88f6ff..233ee0c7 100644 --- a/docs/reference/reportViewer.html +++ b/docs/reference/reportViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for the shiny app report module

    - +
    @@ -104,15 +101,15 @@

    The module viewer for the shiny app report module

    Arguments

    -
    id
    + + +
    id

    the unique reference id for the module

    Value

    - - -

    The user interface to the home page module

    +

    The user interface to the home page module

    Details

    @@ -120,7 +117,7 @@

    Details

    See also

    -

    Other Report: +

    Other Report: reportHelperFile(), reportServer()

    @@ -137,15 +134,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/resultTableServer.html b/docs/reference/resultTableServer.html index 0f1bd74a..d3a33a80 100644 --- a/docs/reference/resultTableServer.html +++ b/docs/reference/resultTableServer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Result Table Server

    - +
    @@ -115,63 +112,63 @@

    Result Table Server

    Arguments

    -
    id
    + + +
    id

    string, table id must match resultsTableViewer function

    -
    df
    +
    df

    reactive that returns a data frame

    -
    colDefsInput
    +
    colDefsInput

    named list of reactable::colDefs

    -
    details
    +
    details

    The details of the results such as cohort names and database names

    -
    selectedCols
    +
    selectedCols

    string vector of columns the reactable should display to start by default. Defaults to ALL if not specified.

    -
    sortedCols
    +
    sortedCols

    string vector of columns the reactable should sort by by default. Defaults to no sort if not specified.

    -
    elementId
    +
    elementId

    optional string vector of element Id name for custom dropdown filtering if present in the customColDef list. Defaults to NULL.

    -
    addActions
    +
    addActions

    add a button row selector column to the table to a column called 'actions'. actions must be a column in df

    -
    downloadedFileName
    +
    downloadedFileName

    string, desired name of downloaded data file. can use the name from the module that is being used

    -
    groupBy
    +
    groupBy

    The columns to group by

    Value

    - - -

    shiny module server

    +

    shiny module server

    See also

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), datasourcesViewer(), makeButtonLabel(), resultTableViewer()

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), @@ -192,15 +189,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/resultTableViewer.html b/docs/reference/resultTableViewer.html index 3121d1c1..d36b0371 100644 --- a/docs/reference/resultTableViewer.html +++ b/docs/reference/resultTableViewer.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Result Table Viewer

    - +
    @@ -108,34 +105,34 @@

    Result Table Viewer

    Arguments

    -
    id
    + + +
    id

    string

    -
    downloadedFileName
    +
    downloadedFileName

    string, desired name of downloaded data file. can use the name from the module that is being used

    -
    boxTitle
    +
    boxTitle

    the title added to the box

    Value

    - - -

    shiny module UI

    +

    shiny module UI

    See also

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), datasourcesViewer(), makeButtonLabel(), resultTableServer()

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), @@ -156,15 +153,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/timeDistributionsView.html b/docs/reference/timeDistributionsView.html index c504ffe5..cd23118e 100644 --- a/docs/reference/timeDistributionsView.html +++ b/docs/reference/timeDistributionsView.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    timeDistributions view

    - +
    @@ -104,13 +101,15 @@

    timeDistributions view

    Arguments

    -
    id
    + + +
    id

    Namespace Id - use namespaced id ns("imeDistributions") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -145,15 +144,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/visitContextView.html b/docs/reference/visitContextView.html index 10cc2f30..78bfcf43 100644 --- a/docs/reference/visitContextView.html +++ b/docs/reference/visitContextView.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Visit context module view

    - +
    @@ -104,13 +101,15 @@

    Visit context module view

    Arguments

    -
    id
    + + +
    id

    Namespace Id - use namespaced id ns("vistConext") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -145,15 +144,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index b2bdf26e..4ac5ca64 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,618 +1,210 @@ - - - - /404.html - - - /articles/AddingShinyModules.html - - - /articles/Characterization.html - - - /articles/CohortDiagnostics.html - - - /articles/CohortMethod.html - - - /articles/Cohorts.html - - - /articles/DataSources.html - - - /articles/EvidenceSynthesis.html - - - /articles/Prediction.html - - - /articles/SelfControlledCaseSeries.html - - - /articles/index.html - - - /authors.html - - - /index.html - - - /news/index.html - - - /reference/LargeDataTable.html - - - /reference/OhdsiShinyModules.html - - - /reference/aboutHelperFile.html - - - /reference/aboutServer.html - - - /reference/aboutViewer.html - - - /reference/characterizationAggregateFeaturesServer.html - - - /reference/characterizationAggregateFeaturesViewer.html - - - /reference/characterizationDechallengeRechallengeServer.html - - - /reference/characterizationDechallengeRechallengeViewer.html - - - /reference/characterizationHelperFile.html - - - /reference/characterizationIncidenceServer.html - - - /reference/characterizationIncidenceViewer.html - - - /reference/characterizationServer.html - - - /reference/characterizationTableServer.html - - - /reference/characterizationTableViewer.html - - - /reference/characterizationTimeToEventServer.html - - - /reference/characterizationTimeToEventViewer.html - - - /reference/characterizationView.html - - - /reference/characterizationViewer.html - - - /reference/cohortCountsModule.html - - - /reference/cohortCountsView.html - - - /reference/cohortDefinitionsModule.html - - - /reference/cohortDefinitionsView.html - - - /reference/cohortDiagCharacterizationView.html - - - /reference/cohortDiagnosticsHelperFile.html - - - /reference/cohortDiagnosticsServer.html - - - /reference/cohortDiagnosticsSever.html - - - /reference/cohortDiagnosticsView.html - - - /reference/cohortGeneratorHelperFile.html - - - /reference/cohortGeneratorServer.html - - - /reference/cohortGeneratorViewer.html - - - /reference/cohortMethodAttritionServer.html - - - /reference/cohortMethodAttritionViewer.html - - - /reference/cohortMethodCovariateBalanceServer.html - - - /reference/cohortMethodCovariateBalanceViewer.html - - - /reference/cohortMethodDiagnosticsSummaryServer.html - - - /reference/cohortMethodDiagnosticsSummaryViewer.html - - - /reference/cohortMethodHelperFile.html - - - /reference/cohortMethodKaplanMeierServer.html - - - /reference/cohortMethodKaplanMeierViewer.html - - - /reference/cohortMethodPopulationCharacteristicsServer.html - - - /reference/cohortMethodPopulationCharacteristicsViewer.html - - - /reference/cohortMethodPowerServer.html - - - /reference/cohortMethodPowerViewer.html - - - /reference/cohortMethodPropensityModelServer.html - - - /reference/cohortMethodPropensityModelViewer.html - - - /reference/cohortMethodPropensityScoreDistServer.html - - - /reference/cohortMethodPropensityScoreDistViewer.html - - - /reference/cohortMethodResultSummaryServer.html - - - /reference/cohortMethodResultSummaryViewer.html - - - /reference/cohortMethodServer.html - - - /reference/cohortMethodSystematicErrorServer.html - - - /reference/cohortMethodSystematicErrorViewer.html - - - /reference/cohortMethodViewer.html - - - /reference/cohortOverlapView.html - - - /reference/compareCohortCharacterizationView.html - - - /reference/conceptsInDataSourceView.html - - - /reference/createCdDatabaseDataSource.html - - - /reference/createCustomColDefList.html - - - /reference/createLargeSqlQueryDt.html - - - /reference/dataDiagnosticDrillServer.html - - - /reference/dataDiagnosticDrillViewer.html - - - /reference/dataDiagnosticHelperFile.html - - - /reference/dataDiagnosticServer.html - - - /reference/dataDiagnosticSummaryServer.html - - - /reference/dataDiagnosticSummaryViewer.html - - - /reference/dataDiagnosticViewer.html - - - /reference/databaseInformationView.html - - - /reference/datasourcesHelperFile.html - - - /reference/datasourcesServer.html - - - /reference/datasourcesViewer.html - - - /reference/descriptionAggregateFeaturesServer.html - - - /reference/descriptionAggregateFeaturesViewer.html - - - /reference/descriptionDechallengeRechallengeServer.html - - - /reference/descriptionDechallengeRechallengeViewer.html - - - /reference/descriptionHelperFile.html - - - /reference/descriptionIncidenceServer.html - - - /reference/descriptionIncidenceViewer.html - - - /reference/descriptionServer.html - - - /reference/descriptionTableServer.html - - - /reference/descriptionTableViewer.html - - - /reference/descriptionTimeToEventServer.html - - - /reference/descriptionTimeToEventViewer.html - - - /reference/descriptionViewer.html - - - /reference/estimationAttritionServer.html - - - /reference/estimationAttritionViewer.html - - - /reference/estimationCovariateBalanceServer.html - - - /reference/estimationCovariateBalanceViewer.html - - - /reference/estimationDiagnosticsSummaryServer.html - - - /reference/estimationDiagnosticsSummaryViewer.html - - - /reference/estimationForestPlotServer.html - - - /reference/estimationForestPlotViewer.html - - - /reference/estimationHelperFile.html - - - /reference/estimationKaplanMeierServer.html - - - /reference/estimationKaplanMeierViewer.html - - - /reference/estimationPopulationCharacteristicsServer.html - - - /reference/estimationPopulationCharacteristicsViewer.html - - - /reference/estimationPowerServer.html - - - /reference/estimationPowerViewer.html - - - /reference/estimationPropensityModelServer.html - - - /reference/estimationPropensityModelViewer.html - - - /reference/estimationPropensityScoreDistServer.html - - - /reference/estimationPropensityScoreDistViewer.html - - - /reference/estimationResultsTableServer.html - - - /reference/estimationResultsTableViewer.html - - - /reference/estimationServer.html - - - /reference/estimationSubgroupsServer.html - - - /reference/estimationSubgroupsViewer.html - - - /reference/estimationSystematicErrorServer.html - - - /reference/estimationSystematicErrorViewer.html - - - /reference/estimationTitlePanelServer.html - - - /reference/estimationTitlePanelViewer.html - - - /reference/estimationViewer.html - - - /reference/evidenceSynthesisHelperFile.html - - - /reference/evidenceSynthesisServer.html - - - /reference/evidenceSynthesisViewer.html - - - /reference/getCirceRenderedExpression.html - - - /reference/getEnabledCdReports.html - - - /reference/getExampleConnectionDetails.html - - - /reference/getLogoImage.html - - - /reference/homeHelperFile.html - - - /reference/homeServer.html - - - /reference/homeViewer.html - - - /reference/incidenceRatesView.html - - - /reference/inclusionRulesView.html - - - /reference/index.html - - - /reference/indexEventBreakdownView.html - - - /reference/largeTableServer.html - - - /reference/largeTableView.html - - - /reference/makeButtonLabel.html - - - /reference/orpahanConceptsView.html - - - /reference/patientLevelPredictionCalibrationServer.html - - - /reference/patientLevelPredictionCalibrationViewer.html - - - /reference/patientLevelPredictionCovariateSummaryServer.html - - - /reference/patientLevelPredictionCovariateSummaryViewer.html - - - /reference/patientLevelPredictionCutoffServer.html - - - /reference/patientLevelPredictionCutoffViewer.html - - - /reference/patientLevelPredictionDesignSummaryServer.html - - - /reference/patientLevelPredictionDesignSummaryViewer.html - - - /reference/patientLevelPredictionDiagnosticsServer.html - - - /reference/patientLevelPredictionDiagnosticsViewer.html - - - /reference/patientLevelPredictionDiscriminationServer.html - - - /reference/patientLevelPredictionDiscriminationViewer.html - - - /reference/patientLevelPredictionHelperFile.html - - - /reference/patientLevelPredictionModelSummaryServer.html - - - /reference/patientLevelPredictionModelSummaryViewer.html - - - /reference/patientLevelPredictionNbServer.html - - - /reference/patientLevelPredictionNbViewer.html - - - /reference/patientLevelPredictionServer.html - - - /reference/patientLevelPredictionSettingsServer.html - - - /reference/patientLevelPredictionSettingsViewer.html - - - /reference/patientLevelPredictionValidationServer.html - - - /reference/patientLevelPredictionValidationViewer.html - - - /reference/patientLevelPredictionViewer.html - - - /reference/phevaluatorHelperFile.html - - - /reference/phevaluatorServer.html - - - /reference/phevaluatorViewer.html - - - /reference/predictionCalibrationServer.html - - - /reference/predictionCalibrationViewer.html - - - /reference/predictionCovariateSummaryServer.html - - - /reference/predictionCovariateSummaryViewer.html - - - /reference/predictionCutoffServer.html - - - /reference/predictionCutoffViewer.html - - - /reference/predictionDesignSummaryServer.html - - - /reference/predictionDesignSummaryViewer.html - - - /reference/predictionDiagnosticsServer.html - - - /reference/predictionDiagnosticsViewer.html - - - /reference/predictionDiscriminationServer.html - - - /reference/predictionDiscriminationViewer.html - - - /reference/predictionHelperFile.html - - - /reference/predictionModelSummaryServer.html - - - /reference/predictionModelSummaryViewer.html - - - /reference/predictionNbServer.html - - - /reference/predictionNbViewer.html - - - /reference/predictionServer.html - - - /reference/predictionSetingsServer.html - - - /reference/predictionSettingsServer.html - - - /reference/predictionSettingsViewer.html - - - /reference/predictionValidationServer.html - - - /reference/predictionValidationViewer.html - - - /reference/predictionViewer.html - - - /reference/reportHelperFile.html - - - /reference/reportServer.html - - - /reference/reportViewer.html - - - /reference/resultTableServer.html - - - /reference/resultTableViewer.html - - - /reference/sccsHelperFile.html - - - /reference/sccsServer.html - - - /reference/sccsView.html - - - /reference/timeDistributionsView.html - - - /reference/visitContextView.html - + +/404.html +/articles/AddingShinyModules.html +/articles/Characterization.html +/articles/CohortDiagnostics.html +/articles/CohortMethod.html +/articles/Cohorts.html +/articles/DataSources.html +/articles/Estimation.html +/articles/EvidenceSynthesis.html +/articles/index.html +/articles/Prediction.html +/articles/ReportGenerator.html +/articles/SelfControlledCaseSeries.html +/authors.html +/index.html +/news/index.html +/reference/aboutHelperFile.html +/reference/aboutServer.html +/reference/aboutViewer.html +/reference/characterizationAggregateFeaturesServer.html +/reference/characterizationAggregateFeaturesViewer.html +/reference/characterizationDechallengeRechallengeServer.html +/reference/characterizationDechallengeRechallengeViewer.html +/reference/characterizationHelperFile.html 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+/reference/resultTableViewer.html +/reference/sccsHelperFile.html +/reference/sccsServer.html +/reference/sccsView.html +/reference/timeDistributionsView.html +/reference/visitContextView.html + diff --git a/vignettes/CohortMethod.Rmd b/vignettes/CohortMethod.Rmd deleted file mode 100644 index e83f05d6..00000000 --- a/vignettes/CohortMethod.Rmd +++ /dev/null @@ -1,60 +0,0 @@ ---- -title: "Cohort Method (Estimation)" -author: "Nathan Hall" -date: '`r Sys.Date()`' -header-includes: - - \usepackage{fancyhdr} - - \pagestyle{fancy} - - \fancyhead{} - - \fancyfoot[LE,RO]{\thepage} - - \renewcommand{\headrulewidth}{0.4pt} - - \renewcommand{\footrulewidth}{0.4pt} - - \fancyfoot[CO,CE]{OhdsiShinyModules Package Version `r utils::packageVersion("OhdsiShinyModules")`} -output: - html_document: - number_sections: yes - toc: yes - word_document: - toc: yes - pdf_document: - includes: - in_header: preamble.tex - number_sections: yes - toc: yes ---- - -```{=html} - -``` -```{r include=FALSE} -knitr::opts_chunk$set(echo = TRUE) -``` - -# Introduction - -Observational healthcare data, comprising administrative claims and electronic health records, present a rich source for generating real-world evidence pertinent to treatment effects that directly impact patient well-being. Within this realm, population-level effect estimation assumes a pivotal role, focusing on elucidating the average causal effects of exposures—such as medical interventions like drug exposures or procedures—on specific health outcomes of interest. Population-level effect estimation delves into two primary realms: direct effect estimation and comparative effect estimation. In direct effect estimation, the focus lies on discerning the effect of an exposure on the risk of an outcome compared to no exposure, while comparative effect estimation aims to delineate the effect of a target exposure against a comparator exposure. By contrasting factual outcomes with counterfactual scenarios—what happened versus what would have occurred under different circumstances—these estimation tasks offer critical insights into treatment selection, safety surveillance, and comparative effectiveness. Whether probing individual hypotheses or exploring multiple hypotheses concurrently, the overarching goal remains consistent: to derive high-quality estimates of causal effects from the intricate fabric of observational healthcare data. - -# Features and Functionalities - -The [CohortMethod](https://ohdsi.github.io/CohortMethod/ "CohortMethod") R package, a cornerstone of population-level estimation within the OHDSI framework, offers a robust methodology for conducting comparative effectiveness research and pharmacoepidemiology studies. Some of the features offered by conducting population-level effect estimation using the CohortMethod module are: - -1. **Data Extraction**: Extracts necessary data from databases structured in the OMOP Common Data Model (CDM) format, ensuring uniformity and compatibility across diverse healthcare settings. -2. **Covariate Selection**: Utilizing a comprehensive set of covariates, including drugs, diagnoses, procedures, age, and comorbidity indexes, CohortMethod constructs propensity and outcome models tailored to specific research questions. -3. **Large-Scale Regularized Regression**: Employing large-scale regularized regression techniques, CohortMethod fits propensity and outcome models with precision and efficiency, accommodating the complexities of real-world healthcare data. -4. **Propensity Score Adjustment**: Facilitates propensity score adjustment through trimming, stratification, matching, and weighting, enabling researchers to address confounding and balance covariate distributions across treatment groups. Results are viewable both graphically and in tabular form to assess the model. -5. **Diagnostic Functions**: Diagnostic functions within CohortMethod offer insights into propensity score distributions and covariate balance before and after matching or trimming, enhancing transparency and robustness in estimation procedures. -6. **Supported Outcome Models**: Supported outcome models include (conditional) logistic regression, (conditional) Poisson regression, and (conditional) Cox regression, providing flexibility in modeling various types of outcomes in observational health data research. -7. **Power**: Incorporates power analysis techniques to estimate the statistical power of the study design, aiding in sample size determination and study planning, and provides a minimum-detectable relative risk (MDRR) statistic. -8. **Attrition**: Assesses attrition rates within cohorts, providing insights into potential biases introduced by data loss during the study period, and provides a visualization of attrition across various cohort criteria. -9. **Population Characteristics**: Analyzes population characteristics to understand the demographic and clinical makeup of the study cohorts, informing interpretation of estimation results both before and after propensity score matching. -10. **Covariate Balance**: Visually monitors covariate balance before and after matching or trimming, ensuring that confounding variables are adequately controlled for in the analysis. -11. **Systematic Error**: Assesses effect size estimates for negative controls (true hazard ratio = 1) and positive controls (true hazard ratio > 1) both before and after calibration. Estimates below the diagonal dashed lines are statistically significant (alpha = 0.05) different from the true effect size. A well-calibrated estimator should have the true effect size within the 95 percent confidence interval 95 percent of times, providing researchers with confidence in the reliability of the estimation process and the accuracy of the obtained results. - -# Utility and Application - -**Comparative Effectiveness Research**: CohortMethod empowers researchers to conduct comparative effectiveness studies by estimating treatment effects while accounting for potential confounding factors and bias inherent in observational data. - -**Pharmacoepidemiology and Drug Safety Studies**: In pharmacoepidemiology research, CohortMethod facilitates the evaluation of drug safety and effectiveness by quantifying the association between drug exposures and clinical outcomes in real-world populations. diff --git a/vignettes/Estimation.Rmd b/vignettes/Estimation.Rmd new file mode 100644 index 00000000..72a32e33 --- /dev/null +++ b/vignettes/Estimation.Rmd @@ -0,0 +1,136 @@ +--- +title: "Estimation" +author: "Nathan Hall" +date: '`r Sys.Date()`' +header-includes: + - \usepackage{fancyhdr} + - \pagestyle{fancy} + - \fancyhead{} + - \fancyfoot[LE,RO]{\thepage} + - \renewcommand{\headrulewidth}{0.4pt} + - \renewcommand{\footrulewidth}{0.4pt} + - \fancyfoot[CO,CE]{OhdsiShinyModules Package Version `r utils::packageVersion("OhdsiShinyModules")`} +output: + html_document: + number_sections: yes + toc: yes + word_document: + toc: yes + pdf_document: + includes: + in_header: preamble.tex + number_sections: yes + toc: yes +--- + + + +```{r include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` + +## Introduction + +Observational healthcare data, comprising administrative claims and electronic health records, present a rich source for generating real-world evidence pertinent to treatment effects that directly impact patient well-being. Within this realm, population-level effect estimation assumes a pivotal role, focusing on elucidating the average causal effects of exposures—such as medical interventions like drug exposures or procedures—on specific health outcomes of interest. Population-level effect estimation delves into two primary realms: direct effect estimation and comparative effect estimation. In direct effect estimation, the focus lies on discerning the effect of an exposure on the risk of an outcome compared to no exposure, while comparative effect estimation aims to delineate the effect of a target exposure against a comparator exposure. By contrasting factual outcomes with counterfactual scenarios—what happened versus what would have occurred under different circumstances—these estimation tasks offer critical insights into treatment selection, safety surveillance, and comparative effectiveness. Whether probing individual hypotheses or exploring multiple hypotheses concurrently, the overarching goal remains consistent: to derive high-quality estimates of causal effects from the intricate fabric of observational healthcare data. + +# 1. CohortMethod + +## Features and Functionalities + +The [CohortMethod](https://ohdsi.github.io/CohortMethod/ "CohortMethod") R package, a cornerstone of population-level estimation within the OHDSI framework, offers a robust methodology for conducting comparative effectiveness research and pharmacoepidemiology studies. Some of the features offered by conducting population-level effect estimation using the CohortMethod module are: + +1. **Data Extraction**: Extracts necessary data from databases structured in the OMOP Common Data Model (CDM) format, ensuring uniformity and compatibility across diverse healthcare settings. +2. **Covariate Selection**: Utilizing a comprehensive set of covariates, including drugs, diagnoses, procedures, age, and comorbidity indexes, CohortMethod constructs propensity and outcome models tailored to specific research questions. +3. **Large-Scale Regularized Regression**: Employing large-scale regularized regression techniques, CohortMethod fits propensity and outcome models with precision and efficiency, accommodating the complexities of real-world healthcare data. +4. **Propensity Score Adjustment**: Facilitates propensity score adjustment through trimming, stratification, matching, and weighting, enabling researchers to address confounding and balance covariate distributions across treatment groups. Results are viewable both graphically and in tabular form to assess the model. +5. **Diagnostic Functions**: Diagnostic functions within CohortMethod offer insights into propensity score distributions and covariate balance before and after matching or trimming, enhancing transparency and robustness in estimation procedures. +6. **Supported Outcome Models**: Supported outcome models include (conditional) logistic regression, (conditional) Poisson regression, and (conditional) Cox regression, providing flexibility in modeling various types of outcomes in observational health data research. +7. **Power**: Incorporates power analysis techniques to estimate the statistical power of the study design, aiding in sample size determination and study planning, and provides a minimum-detectable relative risk (MDRR) statistic. +8. **Attrition**: Assesses attrition rates within cohorts, providing insights into potential biases introduced by data loss during the study period, and provides a visualization of attrition across various cohort criteria. +9. **Population Characteristics**: Analyzes population characteristics to understand the demographic and clinical makeup of the study cohorts, informing interpretation of estimation results both before and after propensity score matching. +10. **Covariate Balance**: Visually monitors covariate balance before and after matching or trimming, ensuring that confounding variables are adequately controlled for in the analysis. +11. **Systematic Error**: Assesses effect size estimates for negative controls (true hazard ratio = 1) and positive controls (true hazard ratio \> 1) both before and after calibration. Estimates below the diagonal dashed lines are statistically significant (alpha = 0.05) different from the true effect size. A well-calibrated estimator should have the true effect size within the 95 percent confidence interval 95 percent of times, providing researchers with confidence in the reliability of the estimation process and the accuracy of the obtained results. + +## Utility and Application + +**Comparative Effectiveness Research**: CohortMethod empowers researchers to conduct comparative effectiveness studies by estimating treatment effects while accounting for potential confounding factors and bias inherent in observational data. + +**Pharmacoepidemiology and Drug Safety Studies**: In pharmacoepidemiology research, CohortMethod facilitates the evaluation of drug safety and effectiveness by quantifying the association between drug exposures and clinical outcomes in real-world populations. + +# 2. Self-Controlled Case Series + +## Introduction + +The Self-Controlled Case Series (SCCS) method offers a nuanced approach to investigating the relationship between exposures and outcomes within individual patients over time. SCCS designs are particularly adept at comparing the rate of outcomes during times of exposure to rates during periods of non-exposure, including before, between, and after exposure episodes. By leveraging a Poisson regression that is conditioned on the individual, the SCCS design inherently addresses the question: “Given that a patient has the outcome, is the outcome more likely to occur during exposed time compared to non-exposed time?” The design choices outlined in the method are pivotal for defining an SCCS question, with each choice playing a critical role in the study's design and outcomes: + +**Target Cohort**: This represents the treatment under investigation. **Outcome Cohort**: This cohort signifies the outcome of interest. **Time-at-Risk**: Identifies the specific times when the risk of the outcome is considered, often relative to the start and end dates of the target cohort. **Model**: Defines the statistical model used to estimate the effect, including adjustments for time-varying confounders if necessary. + +One of the SCCS design's strengths is its robustness to confounding by factors that differ between individuals, as each participant serves as their own control. However, it remains sensitive to time-varying confounding factors. To mitigate this, adjustments can be made for factors such as age, seasonality, and calendar time, enhancing the model's accuracy. + +An advanced variant of the SCCS also considers all other drug exposures recorded in the database, significantly expanding the model's variables. This approach employs L1-regularization, with cross-validation used to select the regularization hyperparameter for all exposures except the one of interest. + +An important assumption of the SCCS is that the observation period's end is independent of the outcome date. This may not hold true for outcomes that can be fatal, such as stroke. To address this, extensions to the SCCS model have been developed that correct for any dependency between the observation period end and the outcome. + +## Features and Functionalities + +The [SelfControlledCaseSeries](https://ohdsi.github.io/SelfControlledCaseSeries/ "SCCS") R package allows the user to perform SCCS analyses in an observational database in the OMOP Common Data Model. Some of the features offered by the SCCS module include: + +1. \*\*Data Extraction: Extracts necessary data from databases structured in the OMOP Common Data Model (CDM) format, ensuring uniformity and compatibility across diverse healthcare settings. +2. **Seasonality Adjustment**: Offers the option to adjust for seasonality effects using a spline function, enhancing the model's accuracy by accounting for seasonal variation in exposure and outcome rates. +3. **Age Adjustment**: Provides the option to incorporate age adjustments using a spline function, allowing for more nuanced analyses that consider the impact of age on the exposure-outcome relationship. +4. **Calendar Time Adjustment**: Enables the inclusion of calendar time adjustments using a spline function, addressing potential temporal trends in the data that could confound the exposure-outcome relationship. +5. **Event-dependent Censoring Correction**: Features the ability to correct for event-dependent censoring of the observation period, ensuring that the end of the observation period is appropriately handled, especially in cases where it might be related to the outcome. +6. **Comprehensive Covariate Inclusion**: Allows for the addition of a wide array of covariates in one analysis, such as all recorded drug exposures, facilitating a thorough examination of potential confounders and effect modifiers. +7. **Risk Window Customization**: Supports the construction of various types of covariates and risk windows, including pre-exposure windows, to capture contra-indications and other relevant temporal patterns related to exposure and outcome. +8. **Regularization of Covariates**: Applies regularization to all covariates except the outcome of interest, employing techniques like L1-regularization with cross-validation for selecting the regularization hyperparameter, thereby preventing overfitting and enhancing model reliability. +9. **Self-Controlled Risk Interval Design**: Incorporates the self-controlled risk interval design as a specific application of the SCCS method, offering additional methodological flexibility for studying short-term effects of exposures. +10. **Power**: Incorporates power analysis techniques to estimate the statistical power of the study design, aiding in sample size determination and study planning, and provides a minimum-detectable relative risk (MDRR) statistic. +11. **Attrition**: Assesses attrition rates within cohorts, providing insights into potential biases introduced by data loss during the study period, and provides a visualization of attrition across various cohort criteria. +12. **Spanning**: Analyzes the number of subjects observed for 3 consecutive months, providing insights into the cohort's consistency and stability over time. +13. **Time Trend**: Assesses the ratio of observed to expected outcomes per month, with adjustments for calendar time, seasonality, and/or age as specified in the model, to examine time trends in the data. +14. **Time to Event**: Evaluates the number of events and subjects observed per week relative to the start of the first exposure, offering critical insights into the temporal relationship between exposure and outcome. +15. **Event-dependent Observation**: Provides histograms for the time between the first occurrence of the outcome and the end of observation, stratified by censored and uncensored ends of observation, to assess the impact of event-dependent observation periods. +16. **Systematic Error**: Assesses effect size estimates for negative controls (true hazard ratio = 1) and positive controls (true hazard ratio \> 1) both before and after calibration. Estimates below the diagonal dashed lines are statistically significant (alpha = 0.05) different from the true effect size. A well-calibrated estimator should have the true effect size within the 95 percent confidence interval 95 percent of times, providing researchers with confidence in the reliability of the estimation process and the accuracy of the obtained results. + +## Utility and Application + +The SCCS method is particularly applicable in several key areas of epidemiological research and pharmacovigilance: + +**Drug Safety Surveillance**: The SCCS method is widely used in drug safety surveillance to identify adverse effects of medications post-marketing. It is well-suited to detect short-term risks associated with drug exposures, especially where the onset of the adverse event is expected to be temporally close to the exposure. + +**Vaccine Safety Evaluation**: The SCCS design is ideal for assessing the safety of vaccines, especially in evaluating the risk of adverse events following immunization. Its self-controlled nature helps to address concerns about confounding by indication and other biases that can affect observational studies in vaccine safety. + +**Comparative Effectiveness Research**: While primarily designed for evaluating the safety of medical interventions, the SCCS method can also be adapted to compare the effectiveness of different treatments or interventions within the same individual over time, particularly for acute conditions. + +**Epidemiological Research**: More broadly, the SCCS method is used in epidemiological research to study the temporal relationships between exposures and outcomes, offering insights into the causality and mechanisms underlying health conditions and diseases. + +# 3. Evidence Synthesis (Meta, Meta Analysis) + +## Introduction + +Meta-analysis plays a pivotal role in healthcare research by enabling the synthesis of findings from multiple studies to draw more generalizable conclusions. In the context of distributed health data networks, where data are spread across various sites with diverse populations and practices, synthesizing evidence becomes both a challenge and a necessity. The [EvidenceSynthesis](https://github.com/OHDSI/EvidenceSynthesis "EvidenceSynthesis") R package addresses these challenges head-on. It offers a suite of tools designed for combining causal effect estimates and study diagnostics from multiple data sites, all while adhering to stringent patient privacy requirements and navigating the complexities inherent to observational data. This approach enhances the robustness of meta-analytical conclusions and extends the utility of distributed health data for research purposes. + +## Features and Functionalities + +The Meta module which utilizes the EvidenceSynthesis R package makes use of the following features to summarize the results of a study: + +1. **Meta-Analysis Methods**: Facilitates both traditional fixed-effects and random-effects meta-analyses, accommodating studies with different degrees of between-site or between-database variability. +2. **Forest Plot Generation**: Provides capabilities for creating forest plots, visual summaries that illustrate the effects estimated by individual studies, their confidence intervals, and the synthesized overall effect. +3. **Non-Normal Likelihood Approximations**: Utilizes non-normal approximations for the per-data-site likelihood function to reduce bias in scenarios with small or zero counts, a frequent issue in distributed research environments. + +The syntheses are generated for both Cohort Method and Self-Controlled Case Series estimation results from the study, providing both information on the diagnostic results within each database and the visualized and tabular results of the meta analysis. + +## Utility and Application + +The EvidenceSynthesis package is instrumental in synthesizing evidence from observational studies across multiple healthcare databases. Its significance is underscored in scenarios characterized by: + +**Comparative Effectiveness Research**: Synthesizing evidence from disparate sources allows for stronger, more reliable comparisons of treatment outcomes, enriching the foundation for clinical decision-making. + +**Safety Surveillance**: Aggregated safety data across databases enhance the detection and understanding of adverse drug reactions, contributing to safer patient care. + +**Policy and Clinical Guidelines Development**: Meta-analytical findings informed by comprehensive, real-world data can guide policy formulation and the updating of clinical guidelines, ensuring they are grounded in broad-based evidence. + +**Addressing Challenges of Small Sample Sizes**: The EvidenceSynthesis package notably advances the field by tackling the issue of small sample sizes and zero event counts, which traditional meta-analytical methods often handle poorly. Its innovative use of non-normal likelihood approximations enables more precise effect size estimation under such conditions, ensuring that the insights derived from meta-analyses are both accurate and meaningful. This attribute is particularly beneficial in distributed health data networks, where individual site/database data may be limited but collectively hold significant informational value. diff --git a/vignettes/EvidenceSynthesis.Rmd b/vignettes/EvidenceSynthesis.Rmd deleted file mode 100644 index 39e2edcc..00000000 --- a/vignettes/EvidenceSynthesis.Rmd +++ /dev/null @@ -1,60 +0,0 @@ ---- -title: "Evidence Synthesis (Meta, Meta Analysis)" -author: "Nathan Hall" -date: '`r Sys.Date()`' -header-includes: - - \usepackage{fancyhdr} - - \pagestyle{fancy} - - \fancyhead{} - - \fancyfoot[LE,RO]{\thepage} - - \renewcommand{\headrulewidth}{0.4pt} - - \renewcommand{\footrulewidth}{0.4pt} - - \fancyfoot[CO,CE]{OhdsiShinyModules Package Version `r utils::packageVersion("OhdsiShinyModules")`} -output: - html_document: - number_sections: yes - toc: yes - word_document: - toc: yes - pdf_document: - includes: - in_header: preamble.tex - number_sections: yes - toc: yes ---- - -```{=html} - -``` -```{r include=FALSE} -knitr::opts_chunk$set(echo = TRUE) -``` - -# Introduction - -Meta-analysis plays a pivotal role in healthcare research by enabling the synthesis of findings from multiple studies to draw more generalizable conclusions. In the context of distributed health data networks, where data are spread across various sites with diverse populations and practices, synthesizing evidence becomes both a challenge and a necessity. The [EvidenceSynthesis](https://github.com/OHDSI/EvidenceSynthesis "EvidenceSynthesis") R package addresses these challenges head-on. It offers a suite of tools designed for combining causal effect estimates and study diagnostics from multiple data sites, all while adhering to stringent patient privacy requirements and navigating the complexities inherent to observational data. This approach enhances the robustness of meta-analytical conclusions and extends the utility of distributed health data for research purposes. - -# Features and Functionalities - -The Meta module which utilizes the EvidenceSynthesis R package makes use of the following features to summarize the results of a study: - -1. **Meta-Analysis Methods**: Facilitates both traditional fixed-effects and random-effects meta-analyses, accommodating studies with different degrees of between-site or between-database variability. -2. **Forest Plot Generation**: Provides capabilities for creating forest plots, visual summaries that illustrate the effects estimated by individual studies, their confidence intervals, and the synthesized overall effect. -3. **Non-Normal Likelihood Approximations**: Utilizes non-normal approximations for the per-data-site likelihood function to reduce bias in scenarios with small or zero counts, a frequent issue in distributed research environments. - -The syntheses are generated for both Cohort Method and Self-Controlled Case Series estimation results from the study, providing both information on the diagnostic results within each database and the visualized and tabular results of the meta analysis. - -# Utility and Application - -The EvidenceSynthesis package is instrumental in synthesizing evidence from observational studies across multiple healthcare databases. Its significance is underscored in scenarios characterized by: - -**Comparative Effectiveness Research**: Synthesizing evidence from disparate sources allows for stronger, more reliable comparisons of treatment outcomes, enriching the foundation for clinical decision-making. - -**Safety Surveillance**: Aggregated safety data across databases enhance the detection and understanding of adverse drug reactions, contributing to safer patient care. - -**Policy and Clinical Guidelines Development**: Meta-analytical findings informed by comprehensive, real-world data can guide policy formulation and the updating of clinical guidelines, ensuring they are grounded in broad-based evidence. - -**Addressing Challenges of Small Sample Sizes**: The EvidenceSynthesis package notably advances the field by tackling the issue of small sample sizes and zero event counts, which traditional meta-analytical methods often handle poorly. Its innovative use of non-normal likelihood approximations enables more precise effect size estimation under such conditions, ensuring that the insights derived from meta-analyses are both accurate and meaningful. This attribute is particularly beneficial in distributed health data networks, where individual site/database data may be limited but collectively hold significant informational value. diff --git a/vignettes/ReportGenerator.Rmd b/vignettes/ReportGenerator.Rmd new file mode 100644 index 00000000..14df6222 --- /dev/null +++ b/vignettes/ReportGenerator.Rmd @@ -0,0 +1,47 @@ +--- +title: "Report Generator" +author: "Nathan Hall" +date: '`r Sys.Date()`' +header-includes: + - \usepackage{fancyhdr} + - \pagestyle{fancy} + - \fancyhead{} + - \fancyfoot[CO,CE]{OhdsiShinyModules Package Version `r utils::packageVersion("OhdsiShinyModules")`} + - \fancyfoot[LE,RO]{\thepage} + - \renewcommand{\headrulewidth}{0.4pt} + - \renewcommand{\footrulewidth}{0.4pt} +output: + pdf_document: + includes: + in_header: preamble.tex + number_sections: yes + toc: yes + word_document: + toc: yes + html_document: + number_sections: yes + toc: yes +--- + + +```{r include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` + +# Introduction + +ReportGenerator is a tool used to create a summary presentation document using results from a Strategus execution which should be stored in a results database. + +# Description + +The Report Generator module allows the user to choose which target (T), subgroup (indication & extra inclusions), comparator (C), and outcome(s) (O) they would like a downloaded report on. In the last section of the module, the user's selections are reported back to them for review before downloading. Here, the user can also choose to restrict the study date and/or the age range of people included in the report. + +## Notes + +Please note that this package is currently under development, so results may vary or may not be available at the time of report generation. + + + diff --git a/vignettes/SelfControlledCaseSeries.Rmd b/vignettes/SelfControlledCaseSeries.Rmd deleted file mode 100644 index 9f72d894..00000000 --- a/vignettes/SelfControlledCaseSeries.Rmd +++ /dev/null @@ -1,82 +0,0 @@ ---- -title: "Self-Controlled Case Series" -author: "Nathan Hall" -date: '`r Sys.Date()`' -header-includes: - - \usepackage{fancyhdr} - - \pagestyle{fancy} - - \fancyhead{} - - \fancyfoot[LE,RO]{\thepage} - - \renewcommand{\headrulewidth}{0.4pt} - - \renewcommand{\footrulewidth}{0.4pt} - - \fancyfoot[CO,CE]{OhdsiShinyModules Package Version `r utils::packageVersion("OhdsiShinyModules")`} -output: - html_document: - number_sections: yes - toc: yes - word_document: - toc: yes - pdf_document: - includes: - in_header: preamble.tex - number_sections: yes - toc: yes ---- - -```{=html} - -``` -```{r include=FALSE} -knitr::opts_chunk$set(echo = TRUE) -``` - -# Introduction - -The Self-Controlled Case Series (SCCS) method offers a nuanced approach to investigating the relationship between exposures and outcomes within individual patients over time. SCCS designs are particularly adept at comparing the rate of outcomes during times of exposure to rates during periods of non-exposure, including before, between, and after exposure episodes. By leveraging a Poisson regression that is conditioned on the individual, the SCCS design inherently addresses the question: “Given that a patient has the outcome, is the outcome more likely to occur during exposed time compared to non-exposed time?” The design choices outlined in the method are pivotal for defining an SCCS question, with each choice playing a critical role in the study's design and outcomes: - -**Target Cohort**: This represents the treatment under investigation. -**Outcome Cohort**: This cohort signifies the outcome of interest. -**Time-at-Risk**: Identifies the specific times when the risk of the outcome is considered, often relative to the start and end dates of the target cohort. -**Model**: Defines the statistical model used to estimate the effect, including adjustments for time-varying confounders if necessary. - -One of the SCCS design's strengths is its robustness to confounding by factors that differ between individuals, as each participant serves as their own control. However, it remains sensitive to time-varying confounding factors. To mitigate this, adjustments can be made for factors such as age, seasonality, and calendar time, enhancing the model's accuracy. - -An advanced variant of the SCCS also considers all other drug exposures recorded in the database, significantly expanding the model's variables. This approach employs L1-regularization, with cross-validation used to select the regularization hyperparameter for all exposures except the one of interest. - -An important assumption of the SCCS is that the observation period's end is independent of the outcome date. This may not hold true for outcomes that can be fatal, such as stroke. To address this, extensions to the SCCS model have been developed that correct for any dependency between the observation period end and the outcome. - -# Features and Functionalities - -The [SelfControlledCaseSeries](https://ohdsi.github.io/SelfControlledCaseSeries/ "SCCS") R package allows the user to perform SCCS analyses in an observational database in the OMOP Common Data Model. Some of the features offered by the SCCS module include: - -1. **Data Extraction: Extracts necessary data from databases structured in the OMOP Common Data Model (CDM) format, ensuring uniformity and compatibility across diverse healthcare settings. -2. **Seasonality Adjustment**: Offers the option to adjust for seasonality effects using a spline function, enhancing the model's accuracy by accounting for seasonal variation in exposure and outcome rates. -3. **Age Adjustment**: Provides the option to incorporate age adjustments using a spline function, allowing for more nuanced analyses that consider the impact of age on the exposure-outcome relationship. -4. **Calendar Time Adjustment**: Enables the inclusion of calendar time adjustments using a spline function, addressing potential temporal trends in the data that could confound the exposure-outcome relationship. -5. **Event-dependent Censoring Correction**: Features the ability to correct for event-dependent censoring of the observation period, ensuring that the end of the observation period is appropriately handled, especially in cases where it might be related to the outcome. -6. **Comprehensive Covariate Inclusion**: Allows for the addition of a wide array of covariates in one analysis, such as all recorded drug exposures, facilitating a thorough examination of potential confounders and effect modifiers. -7. **Risk Window Customization**: Supports the construction of various types of covariates and risk windows, including pre-exposure windows, to capture contra-indications and other relevant temporal patterns related to exposure and outcome. -8. **Regularization of Covariates**: Applies regularization to all covariates except the outcome of interest, employing techniques like L1-regularization with cross-validation for selecting the regularization hyperparameter, thereby preventing overfitting and enhancing model reliability. -9. **Self-Controlled Risk Interval Design**: Incorporates the self-controlled risk interval design as a specific application of the SCCS method, offering additional methodological flexibility for studying short-term effects of exposures. -10. **Power**: Incorporates power analysis techniques to estimate the statistical power of the study design, aiding in sample size determination and study planning, and provides a minimum-detectable relative risk (MDRR) statistic. -11. **Attrition**: Assesses attrition rates within cohorts, providing insights into potential biases introduced by data loss during the study period, and provides a visualization of attrition across various cohort criteria. -12. **Spanning**: Analyzes the number of subjects observed for 3 consecutive months, providing insights into the cohort's consistency and stability over time. -13. **Time Trend**: Assesses the ratio of observed to expected outcomes per month, with adjustments for calendar time, seasonality, and/or age as specified in the model, to examine time trends in the data. -14. **Time to Event**: Evaluates the number of events and subjects observed per week relative to the start of the first exposure, offering critical insights into the temporal relationship between exposure and outcome. -15. **Event-dependent Observation**: Provides histograms for the time between the first occurrence of the outcome and the end of observation, stratified by censored and uncensored ends of observation, to assess the impact of event-dependent observation periods. -16. **Systematic Error**: Assesses effect size estimates for negative controls (true hazard ratio = 1) and positive controls (true hazard ratio > 1) both before and after calibration. Estimates below the diagonal dashed lines are statistically significant (alpha = 0.05) different from the true effect size. A well-calibrated estimator should have the true effect size within the 95 percent confidence interval 95 percent of times, providing researchers with confidence in the reliability of the estimation process and the accuracy of the obtained results. - -# Utility and Application - -The SCCS method is particularly applicable in several key areas of epidemiological research and pharmacovigilance: - -**Drug Safety Surveillance**: The SCCS method is widely used in drug safety surveillance to identify adverse effects of medications post-marketing. It is well-suited to detect short-term risks associated with drug exposures, especially where the onset of the adverse event is expected to be temporally close to the exposure. - -**Vaccine Safety Evaluation**: The SCCS design is ideal for assessing the safety of vaccines, especially in evaluating the risk of adverse events following immunization. Its self-controlled nature helps to address concerns about confounding by indication and other biases that can affect observational studies in vaccine safety. - -**Comparative Effectiveness Research**: While primarily designed for evaluating the safety of medical interventions, the SCCS method can also be adapted to compare the effectiveness of different treatments or interventions within the same individual over time, particularly for acute conditions. - -**Epidemiological Research**: More broadly, the SCCS method is used in epidemiological research to study the temporal relationships between exposures and outcomes, offering insights into the causality and mechanisms underlying health conditions and diseases.