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The OmopViewer package generates shiny apps from
predefined configurations, you can check the existent panels using the
defaultPanels() function:
defaultPanels()
#> [1] "summarise_omop_snapshot"
#> [2] "summarise_observation_period"
#> [3] "summarise_clinical_records"
#> [4] "summarise_record_count"
#> [5] "summarise_missing_data"
#> [6] "summarise_in_observation"
#> [7] "orphan_code_use"
#> [8] "cohort_code_use"
#> [9] "code_use"
#> [10] "achilles_code_use"
#> [11] "unmapped_codes"
#> [12] "summarise_cohort_overlap"
#> [13] "summarise_cohort_count"
#> [14] "summarise_cohort_attrition"
#> [15] "summarise_cohort_timing"
#> [16] "summarise_characteristics"
#> [17] "summarise_large_scale_characteristics"
#> [18] "incidence"
#> [19] "incidence_attrition"
#> [20] "prevalence"
#> [21] "prevalence_attrition"
#> [22] "summarise_dose_coverage"
#> [23] "summarise_proportion_of_patients_covered"
#> [24] "summarise_drug_restart"
#> [25] "summarise_drug_utilisation"
#> [26] "summarise_indication"
#> [27] "summarise_treatment"
#> [28] "default"You can check the details of a panel using getPanel()
function:
getPanel("incidence")
#> Incidence (OmopViewer panel)
#> • icon: chart-line
#> • data: result_type: <incidence>
#> • filters: 1 filters + 6 automatic filters
#> • content: Tidy (DT); Table Incidence (gt); Plot Incidence (plot)The exported object omopViewerPanels contains all the defined panels in the package:
omopViewerPanels
#> $summarise_omop_snapshot
#> Snapshot (OmopViewer panel)
#> • icon: clipboard-list
#> • data: result_type: <summarise_omop_snapshot>
#> • filters: 1 filters + 1 automatic filters
#> • content: Tidy (DT); Table Snapshot (gt)
#>
#> $summarise_observation_period
#> Observation period (OmopViewer panel)
#> • icon: eye
#> • data: result_type: <summarise_observation_period>
#> • filters: 1 filters + 4 automatic filters
#> • content: Tidy (DT); Table Observation period (gt); Plot Observation period
#> (plot)
#>
#> $summarise_clinical_records
#> Clinical records (OmopViewer panel)
#> • icon: bars-staggered
#> • data: result_type: <summarise_clinical_records>
#> • filters: 1 filters + 6 automatic filters
#> • content: Tidy (DT); Table Clinical records (gt)
#>
#> $summarise_record_count
#> Record count (OmopViewer panel)
#> • icon: signal
#> • data: result_type: <summarise_record_count>
#> • filters: 1 filters + 6 automatic filters
#> • content: Tidy (DT); Plot record count (plot)
#>
#> $summarise_missing_data
#> Missing data (OmopViewer panel)
#> • icon: circle-exclamation
#> • data: result_type: <summarise_missing_data>
#> • filters: 1 filters + 6 automatic filters
#> • content: Tidy (DT); Table Missing data (gt)
#>
#> $summarise_in_observation
#> In Observation (OmopViewer panel)
#> • icon: explosion
#> • data: result_type: <summarise_in_observation>
#> • filters: 1 filters + 6 automatic filters
#> • content: Tidy (DT); Plot in observation (plot)
#>
#> $orphan_code_use
#> Orphan codes (OmopViewer panel)
#> • icon: magnifying-glass-arrow-right
#> • data: result_type: <orphan_code_use>
#> • filters: 1 filters + 4 automatic filters
#> • content: Tidy (DT); Table Orphan codes (gt)
#>
#> $cohort_code_use
#> Cohort code use (OmopViewer panel)
#> • icon: chart-column
#> • data: result_type: <cohort_code_use>
#> • filters: 1 filters + 4 automatic filters
#> • content: Tidy (DT); Table Cohort code use (gt)
#>
#> $code_use
#> Code use (OmopViewer panel)
#> • icon: chart-column
#> • data: result_type: <code_use>
#> • filters: 1 filters + 6 automatic filters
#> • content: Tidy (DT); Table Code use (gt)
#>
#> $achilles_code_use
#> Achilles code use (OmopViewer panel)
#> • icon: chart-column
#> • data: result_type: <achilles_code_use>
#> • filters: 1 filters + 6 automatic filters
#> • content: Tidy (DT); Table Achilles code use (gt)
#>
#> $unmapped_codes
#> Unmapped codes (OmopViewer panel)
#> • icon: chart-column
#> • data: result_type: <unmapped_codes>
#> • filters: 1 filters + 6 automatic filters
#> • content: Tidy (DT); Table Unmapped codes (gt)
#>
#> $summarise_cohort_overlap
#> Cohort Overlap (OmopViewer panel)
#> • icon: circle-half-stroke
#> • data: result_type: <summarise_cohort_overlap>
#> • filters: 1 filters + 5 automatic filters
#> • content: Tidy (DT); Table Overlap (gt); Plot Overlap (plot)
#>
#> $summarise_cohort_count
#> Cohort Count (OmopViewer panel)
#> • icon: users
#> • data: result_type: <summarise_cohort_count>
#> • filters: 1 filters + 4 automatic filters
#> • content: Tidy (DT); Table Counts (gt); Plot Counts (plot)
#>
#> $summarise_cohort_attrition
#> Cohort Attrition (OmopViewer panel)
#> • icon: layer-group
#> • data: result_type: <summarise_cohort_attrition>
#> • filters: 1 filters + 2 automatic filters
#> • content: Tidy (DT); Table Attrition (gt); Diagram (grViz)
#>
#> $summarise_cohort_timing
#> Cohort Timing (OmopViewer panel)
#> • icon: chart-simple
#> • data: result_type: <summarise_cohort_timing>
#> • filters: 1 filters + 2 automatic filters
#> • content: Tidy (DT); Table Timing (gt); Plot Timing (plot)
#>
#> $summarise_characteristics
#> Cohort Characteristics (OmopViewer panel)
#> • icon: users-gear
#> • data: result_type: <summarise_characteristics>
#> • filters: 1 filters + 4 automatic filters
#> • content: Tidy (DT); Table Characteristics (gt); Plot Characteristics (plot)
#>
#> $summarise_large_scale_characteristics
#> Large Scale Characteristics (OmopViewer panel)
#> • icon: arrow-up-right-dots
#> • data: result_type: <summarise_large_scale_characteristics>
#> • filters: 1 filters + 4 automatic filters
#> • content: Table (reactable); Most common codes (gt); Plot Compared (plotly)
#>
#> $incidence
#> Incidence (OmopViewer panel)
#> • icon: chart-line
#> • data: result_type: <incidence>
#> • filters: 1 filters + 6 automatic filters
#> • content: Tidy (DT); Table Incidence (gt); Plot Incidence (plot)
#>
#> $incidence_attrition
#> Incidence Attrition (OmopViewer panel)
#> • icon: layer-group
#> • data: result_type: <incidence_attrition>
#> • filters: 1 filters + 2 automatic filters
#> • content: Tidy (DT); Table Incidence Attrition (gt)
#>
#> $prevalence
#> Prevalence (OmopViewer panel)
#> • icon: chart-column
#> • data: result_type: <prevalence>
#> • filters: 1 filters + 6 automatic filters
#> • content: Tidy (DT); Table Prevalence (gt); Plot Prevalence (plot)
#>
#> $prevalence_attrition
#> Prevalence Attrition (OmopViewer panel)
#> • icon: layer-group
#> • data: result_type: <prevalence_attrition>
#> • filters: 1 filters + 2 automatic filters
#> • content: Tidy (DT); Table Prevalence Attrition (gt)
#>
#> $summarise_dose_coverage
#> Dose coverage (OmopViewer panel)
#> • icon: pills
#> • data: result_type: <summarise_dose_coverage>
#> • filters: 1 filters + 6 automatic filters
#> • content: Tidy (DT); Table Dose coverage (gt)
#>
#> $summarise_proportion_of_patients_covered
#> Proportion of patients covered (OmopViewer panel)
#> • icon: chart-gantt
#> • data: result_type: <summarise_proportion_of_patients_covered>
#> • filters: 1 filters + 3 automatic filters
#> • content: Tidy (DT); Table PPC (gt); Plot PPC (plot)
#>
#> $summarise_drug_restart
#> Drug Restart (OmopViewer panel)
#> • icon: chart-gantt
#> • data: result_type: <summarise_drug_restart>
#> • filters: 1 filters + 3 automatic filters
#> • content: Tidy (DT); Table Drug Restart (gt); Plot Drug Restart (plot)
#>
#> $summarise_drug_utilisation
#> Drug Utilisation (OmopViewer panel)
#> • icon: capsules
#> • data: result_type: <summarise_drug_utilisation>
#> • filters: 1 filters + 6 automatic filters
#> • content: Tidy (DT); Table Drug Utilisation (gt); Plot Drug Utilisation (plot)
#>
#> $summarise_indication
#> Indication (OmopViewer panel)
#> • icon: disease
#> • data: result_type: <summarise_indication>
#> • filters: 1 filters + 7 automatic filters
#> • content: Tidy (DT); Table Indication (gt); Plot Indication (plot)
#>
#> $summarise_treatment
#> Treatments (OmopViewer panel)
#> • icon: disease
#> • data: result_type: <summarise_treatment>
#> • filters: 1 filters + 7 automatic filters
#> • content: Tidy (DT); Table Treatments (gt); Plot Treatment (plot)
#>
#> $default
#> <result_type> (OmopViewer panel)
#> • icon: folder
#> • data: -no data-
#> • filters: 1 filters + 6 automatic filters
#> • content: Tidy (DT); Table (gt)Panel details print shows:
shinyWidgets::pickerInput) will
be created to filter the result.More details on the internal structure and how to define new panels
is explained in adding_new_panels. To see the internal
structure you can use unclass:
unclass(getPanel("incidence"))
#> $title
#> [1] "Incidence"
#>
#> $icon
#> [1] "chart-line"
#>
#> $data
#> $data$result_type
#> [1] "incidence"
#>
#>
#> $automatic_filters
#> [1] "group" "strata" "additional" "settings"
#> [5] "variable_name" "estimate_name"
#>
#> $exclude_filters
#> [1] "denominator_cohort_name" "incidence_end_date"
#>
#> $filters
#> $filters$cdm_name
#> $filters$cdm_name$button_type
#> [1] "pickerInput"
#>
#> $filters$cdm_name$label
#> [1] "CDM name"
#>
#> $filters$cdm_name$column
#> [1] "cdm_name"
#>
#> $filters$cdm_name$column_type
#> [1] "main"
#>
#> $filters$cdm_name$choices
#> [1] "choices$"
#>
#> $filters$cdm_name$selected
#> [1] "selected$"
#>
#> $filters$cdm_name$multiple
#> [1] TRUE
#>
#>
#>
#> $content
#> $content$tidy
#> $content$tidy$title
#> [1] "Tidy"
#>
#> $content$tidy$output_type
#> [1] "DT"
#>
#> $content$tidy$render
#> [1] "tidyDT(<filtered_data>, input$columns, input$pivot_estimates)"
#>
#> $content$tidy$filters
#> $content$tidy$filters$columns
#> $content$tidy$filters$columns$button_type
#> [1] "pickerInput"
#>
#> $content$tidy$filters$columns$label
#> [1] "Columns"
#>
#> $content$tidy$filters$columns$choices
#> [1] "cdm_name" "<group>" "<strata>" "<additional>"
#> [5] "<settings>" "variable_name" "variable_level"
#>
#> $content$tidy$filters$columns$selected
#> [1] "cdm_name" "<group>" "<strata>" "<additional>"
#> [5] "variable_name" "variable_level"
#>
#> $content$tidy$filters$columns$multiple
#> [1] TRUE
#>
#>
#> $content$tidy$filters$pivot_estimates
#> $content$tidy$filters$pivot_estimates$button_type
#> [1] "checkbox"
#>
#> $content$tidy$filters$pivot_estimates$label
#> [1] "Pivot estimates"
#>
#> $content$tidy$filters$pivot_estimates$value
#> [1] TRUE
#>
#>
#>
#> $content$tidy$download
#> $content$tidy$download$label
#> [1] "Download csv"
#>
#> $content$tidy$download$render
#> [1] "<filtered_data> |>\n omopgenerics::tidy() |>\n readr::write_csv(file = file)"
#>
#> $content$tidy$download$filename
#> [1] "tidy_results.csv"
#>
#>
#>
#> $content$table
#> $content$table$title
#> [1] "Table Incidence"
#>
#> $content$table$output_type
#> [1] "gt"
#>
#> $content$table$render
#> [1] "res <- <filtered_data>\n res |>\n IncidencePrevalence::tableIncidence(\n header = input$header,\n groupColumn = input$group_column,\n hide = input$hide,\n settingsColumn = omopgenerics::settingsColumns(res)\n )"
#>
#> $content$table$filters
#> $content$table$filters$none
#> $content$table$filters$none$button_type
#> [1] "rank_list"
#>
#> $content$table$filters$none$text
#> [1] "None"
#>
#> $content$table$filters$none$labels
#> [1] "<strata>" "incidence_start_date" "incidence_end_date"
#> [4] "denominator_age_group" "denominator_sex"
#>
#>
#> $content$table$filters$header
#> $content$table$filters$header$button_type
#> [1] "rank_list"
#>
#> $content$table$filters$header$text
#> [1] "Header"
#>
#> $content$table$filters$header$labels
#> [1] "estimate_name"
#>
#>
#> $content$table$filters$group_column
#> $content$table$filters$group_column$button_type
#> [1] "rank_list"
#>
#> $content$table$filters$group_column$text
#> [1] "Group columns"
#>
#> $content$table$filters$group_column$labels
#> [1] "cdm_name" "outcome_cohort_name"
#>
#>
#> $content$table$filters$hide
#> $content$table$filters$hide$button_type
#> [1] "rank_list"
#>
#> $content$table$filters$hide$text
#> [1] "Hide"
#>
#> $content$table$filters$hide$labels
#> [1] "denominator_cohort_name"
#> [2] "analysis_interval"
#> [3] "analysis_censor_cohort_name"
#> [4] "analysis_complete_database_intervals"
#> [5] "analysis_outcome_washout"
#> [6] "analysis_repeated_events"
#> [7] "denominator_days_prior_observation"
#> [8] "denominator_end_date"
#> [9] "denominator_requirements_at_entry"
#> [10] "denominator_start_date"
#> [11] "denominator_target_cohort_name"
#> [12] "denominator_time_at_risk"
#>
#>
#>
#> $content$table$download
#> $content$table$download$label
#> [1] "Download table"
#>
#> $content$table$download$filters
#> $content$table$download$filters$format
#> $content$table$download$filters$format$button_type
#> [1] "pickerInput"
#>
#> $content$table$download$filters$format$label
#> [1] "Format"
#>
#> $content$table$download$filters$format$choices
#> [1] "docx" "png" "pdf" "html"
#>
#> $content$table$download$filters$format$selected
#> [1] "docx"
#>
#> $content$table$download$filters$format$multiple
#> [1] FALSE
#>
#>
#>
#> $content$table$download$render
#> [1] "gt::gtsave(<rendered_data>, file)"
#>
#> $content$table$download$filename
#> [1] "paste0(\"table_incidence.\", input$format)"
#>
#>
#>
#> $content$plot
#> $content$plot$title
#> [1] "Plot Incidence"
#>
#> $content$plot$output_type
#> [1] "plot"
#>
#> $content$plot$render
#> [1] "<filtered_data> |>\n IncidencePrevalence::plotIncidence(\n x = input$x,\n facet = input$facet,\n colour = input$colour\n )"
#>
#> $content$plot$filters
#> $content$plot$filters$x
#> $content$plot$filters$x$button_type
#> [1] "pickerInput"
#>
#> $content$plot$filters$x$label
#> [1] "x axis"
#>
#> $content$plot$filters$x$choices
#> [1] "cdm_name" "<group>" "<strata>" "<additional>" "<settings>"
#>
#> $content$plot$filters$x$selected
#> [1] "incidence_start_date"
#>
#> $content$plot$filters$x$multiple
#> [1] FALSE
#>
#>
#> $content$plot$filters$facet
#> $content$plot$filters$facet$button_type
#> [1] "pickerInput"
#>
#> $content$plot$filters$facet$label
#> [1] "Facet"
#>
#> $content$plot$filters$facet$choices
#> [1] "cdm_name" "<group>" "<strata>" "<additional>" "<settings>"
#>
#> $content$plot$filters$facet$selected
#> [1] "cdm_name"
#>
#> $content$plot$filters$facet$multiple
#> [1] TRUE
#>
#>
#> $content$plot$filters$colour
#> $content$plot$filters$colour$button_type
#> [1] "pickerInput"
#>
#> $content$plot$filters$colour$label
#> [1] "Colour"
#>
#> $content$plot$filters$colour$choices
#> [1] "cdm_name" "<group>" "<strata>" "<additional>" "<settings>"
#>
#> $content$plot$filters$colour$selected
#> [1] "outcome_cohort_name"
#>
#> $content$plot$filters$colour$multiple
#> [1] TRUE
#>
#>
#>
#> $content$plot$download
#> $content$plot$download$label
#> [1] "Download plot"
#>
#> $content$plot$download$filters
#> $content$plot$download$filters$width
#> $content$plot$download$filters$width$button_type
#> [1] "numericInput"
#>
#> $content$plot$download$filters$width$label
#> [1] "Width"
#>
#> $content$plot$download$filters$width$value
#> [1] 15
#>
#>
#> $content$plot$download$filters$height
#> $content$plot$download$filters$height$button_type
#> [1] "numericInput"
#>
#> $content$plot$download$filters$height$label
#> [1] "Height"
#>
#> $content$plot$download$filters$height$value
#> [1] 15
#>
#>
#> $content$plot$download$filters$units
#> $content$plot$download$filters$units$button_type
#> [1] "pickerInput"
#>
#> $content$plot$download$filters$units$label
#> [1] "Units"
#>
#> $content$plot$download$filters$units$selected
#> [1] "cm"
#>
#> $content$plot$download$filters$units$choices
#> [1] "px" "cm" "inch"
#>
#> $content$plot$download$filters$units$multiple
#> [1] FALSE
#>
#>
#> $content$plot$download$filters$dpi
#> $content$plot$download$filters$dpi$button_type
#> [1] "numericInput"
#>
#> $content$plot$download$filters$dpi$label
#> [1] "DPI"
#>
#> $content$plot$download$filters$dpi$value
#> [1] 300
#>
#>
#>
#> $content$plot$download$render
#> [1] "plt <- <rendered_data>\n ggplot2::ggsave(\n filename = file,\n plot = plt,\n width = as.numeric(input$width),\n height = as.numeric(input$height),\n units = input$units,\n dpi = as.numeric(input$dpi)\n )"
#>
#> $content$plot$download$filename
#> [1] "plot_incidence.png"These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.