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inst/shiny/ui.R
In PhenotypeR: Assess Study Cohorts Using a Common Data Model
# Generated by OmopViewer 0.1.0
# Be careful editing this file
ui <- bslib::page_navbar(
theme = bs_theme(bootswatch = "pulse"),
# zephyr
title = "PhenotypeR",
bslib::nav_panel(
title = "Background",
icon = shiny::icon("disease"),
shiny::includeMarkdown(path = "background.md")
),
# Database diagnostics -----
bslib::nav_menu(
title = "Database diagnostics",
icon = shiny::icon("list"),
## snapshot -----
bslib::nav_panel(
title = "Snapshot",
icon = shiny::icon("clipboard-list"),
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_omop_snapshot_gt_download", label = ""),
class = "text-end"
),
gt::gt_output("summarise_omop_snapshot_gt") |> withSpinner()
)
),
## observation periods -----
bslib::nav_panel(
title = "Observation periods",
icon = shiny::icon("eye"),
bslib::nav_panel(
title = "Table observation period",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_observation_period_gt_download", label = ""),
class = "text-end"
),
gt::gt_output("summarise_observation_period_gt") |> withSpinner()
)
)
)
),
# Codelist diagnostics -----
bslib::nav_menu(
title = "Codelist diagnostics",
icon = shiny::icon("list"),
## achilles code use -----
bslib::nav_panel(
title = "Achilles code use",
icon = shiny::icon("database"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "achilles_code_use_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "achilles_code_use_grouping_codelist_name",
label = "Codelist name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
div(style="display: flex; justify-content: space-between;",
div(style="flex: 1;", prettyCheckbox(inputId = "achilles_person_count",
label = "Person count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE)),
div(style="flex: 1;", prettyCheckbox(inputId = "achilles_record_count",
label = "Record count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE))
)
),
bslib::accordion_panel(
title = "Table formatting",
materialSwitch(inputId = "achilles_interactive",
value = TRUE,
label = "Interactive",
status = "primary"),
sortable::bucket_list(
header = NULL,
sortable::add_rank_list(
text = "none",
labels = c("codelist_name"),
input_id = "achilles_code_use_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name", "estimate_name"),
input_id = "achilles_code_use_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = character(),
input_id = "achilles_code_use_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = character(),
input_id = "achilles_code_use_hide"
)
)
)
)
),
bslib::nav_panel(
title = "achilles_code_use",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "achilles_code_use_download", label = ""),
class = "text-end"
),
uiOutput("achilles_code_use_tbl") |> withSpinner()
)
)
)
),
## unmapped concepts -----
# bslib::nav_panel(
# title = "Unmapped concepts",
# icon = shiny::icon("database"),
# bslib::layout_sidebar(
# sidebar = bslib::sidebar(width = 400, open = "closed",
# bslib::accordion(
# bslib::accordion_panel(
# title = "Settings",
# shinyWidgets::pickerInput(
# inputId = "unmapped_grouping_cdm_name",
# label = "Database",
# choices = NULL,
# selected = NULL,
# multiple = TRUE,
# options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
# ),
# shinyWidgets::pickerInput(
# inputId = "unmapped_grouping_codelist_name",
# label = "Codelist name",
# choices = NULL,
# selected = NULL,
# multiple = TRUE,
# options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
# )
# ),
# bslib::accordion_panel(
# title = "Table formatting",
# sortable::bucket_list(
# header = NULL,
# sortable::add_rank_list(
# text = "none",
# labels = c( "codelist_name"),
# input_id = "unmapped_none"
# ),
# sortable::add_rank_list(
# text = "header",
# labels = c("cdm_name", "estimate_name"),
# input_id = "unmapped_header"
# ),
# sortable::add_rank_list(
# text = "groupColumn",
# labels = NULL,
# input_id = "unmapped_groupColumn"
# ),
# sortable::add_rank_list(
# text = "hide",
# labels = character(),
# input_id = "unmapped_hide"
# )
# )
# )
# )
# ),
# bslib::nav_panel(
# title = "Unmapped",
# bslib::card(
# full_screen = TRUE,
# bslib::card_header(
# bslib::popover(
# shiny::icon("download"),
# shinyWidgets::pickerInput(
# inputId = "unmapped_formatted_download_type",
# label = "File type",
# selected = "docx",
# choices = c("docx", "png", "pdf", "html"),
# multiple = FALSE
# ),
# shiny::downloadButton(outputId = "unmapped_formatted_download", label = "Download")
# ),
# class = "text-end"
# ),
# gt::gt_output("unmapped_formatted") |> withSpinner()
# )
# )
# )
# ),
## Orphan codes -----
bslib::nav_panel(
title = "Orphan codes",
icon = shiny::icon("circle-half-stroke"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "orphan_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "orphan_grouping_codelist_name",
label = "Cohort name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
div(style="display: flex; justify-content: space-between;",
div(style="flex: 1;", prettyCheckbox(inputId = "orphan_person_count",
label = "Person count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE)),
div(style="flex: 1;", prettyCheckbox(inputId = "orphan_record_count",
label = "Record count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE))
)
),
bslib::accordion_panel(
title = "Table formatting",
materialSwitch(inputId = "orphan_interactive",
value = TRUE,
label = "Interactive",
status = "primary"),
sortable::bucket_list(
header = NULL,
sortable::add_rank_list(
text = "none",
labels = c("variable_name", "cohort_name", "variable_level"),
input_id = "orphan_codes_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name", "estimate_name"),
input_id = "orphan_codes_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = character(),
input_id = "orphan_codes_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = character(),
input_id = "orphan_codes_gt_hide"
)
)
)
)
),
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "orphan_codes_download", label = ""),
class = "text-end"
),
uiOutput("orphan_codes_tbl") |> withSpinner()
)
)
)
),
# Cohort diagnostics -----
bslib::nav_menu(
title = "Cohort diagnostics",
icon = shiny::icon("list"),
## Cohort code use -----
bslib::nav_panel(
title = "Cohort code use",
icon = shiny::icon("chart-column"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "cohort_code_use_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "cohort_code_use_grouping_cohort_name",
label = "Cohort name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "cohort_code_use_grouping_domain_id",
label = "Domain",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
div(style="display: flex; justify-content: space-between;",
div(style="flex: 1;", prettyCheckbox(inputId = "cohort_code_use_person_count",
label = "Person count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE)),
div(style="flex: 1;", prettyCheckbox(inputId = "cohort_code_use_record_count",
label = "Record count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE))
)
),
bslib::accordion_panel(
title = "Table formatting",
materialSwitch(inputId = "cohort_code_use_interactive",
value = TRUE,
label = "Interactive",
status = "primary"),
sortable::bucket_list(
header = NULL,
sortable::add_rank_list(
text = "none",
labels = c("cohort_name", "codelist_name", "source_concept_name", "source_concept_id", "domain_id", "variable_name", "variable_level"),
input_id = "cohort_code_use_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name", "estimate_name"),
input_id = "cohort_code_use_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = character(),
input_id = "cohort_code_use_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = character(),
input_id = "cohort_code_use_gt_hide"
)
)
)
)
),
bslib::nav_panel(
title = "Table cohort code use",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "cohort_code_use_download", label = ""),
class = "text-end"
),
uiOutput("cohort_code_use_tbl") |> withSpinner()
)
)
)
),
## Cohort count ----
bslib::nav_panel(
title = "Cohort count",
icon = shiny::icon("person"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_attrition_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_attrition_grouping_cohort_name",
label = "Cohort name",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Counts",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_cohort_count_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
shinyWidgets::pickerInput(
inputId = "summarise_cohort_count_variable_name",
label = "Variable name",
selected = c("Number records", "Number subjects"),
multiple = TRUE,
choices = c("Number records", "Number subjects"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
),
position = "right"
),
gt::gt_output("summarise_cohort_count_gt") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Attrition",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_cohort_attrition_gt_download", label = ""),
class = "text-end"
),
gt::gt_output("summarise_cohort_attrition_gt") |> withSpinner()
)
),
bslib::nav_panel(
title = "Flowchart",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "summarise_cohort_attrition_grViz_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "summarise_cohort_attrition_grViz_download_height",
label = "Height",
value = 10
),
shiny::downloadButton(outputId = "summarise_cohort_attrition_grViz_download", label = "Download")
),
class = "text-end"
),
DiagrammeR::grVizOutput("summarise_cohort_attrition_grViz") |> withSpinner()
)
)
)
)
),
## Cohort characteristics -----
bslib::nav_panel(
title = "Cohort characteristics",
icon = shiny::icon("users-gear"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_characteristics_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_characteristics_grouping_cohort_name",
label = "Cohort name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::prettyCheckbox(
inputId = "summarise_characteristics_include_matched",
label = "Show matched cohorts",
value = FALSE)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_characteristics_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
sortable::bucket_list(
header = NULL,
sortable::add_rank_list(
text = "none",
labels = c("variable_name", "variable_level", "estimate_name"),
input_id = "summarise_characteristics_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name", "cohort_name"),
input_id = "summarise_characteristics_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = NULL,
input_id = "summarise_characteristics_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = character(),
input_id = "summarise_characteristics_gt_hide"
)
),
position = "right"
),
gt::gt_output("summarise_characteristics_gt") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Age distribution",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "plot_age_pyramid_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "plot_age_pyramid_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "plot_age_pyramid_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "plot_age_pyramid_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "plot_age_pyramid_download", label = "Download")
),
class = "text-end",
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shiny::checkboxInput(
inputId = "summarise_characteristics_add_interquantile_range",
label = "Show interquantile range",
value = c(TRUE)
),
position = "right"
),
shiny::plotOutput("plot_age_pyramid")
)
)
)
)
)
),
## Large scale characteristics -----
bslib::nav_panel(
title = "Large scale characteristics",
icon = shiny::icon("arrow-up-right-dots"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_grouping_cohort_name",
label = "Cohort name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_grouping_domain",
label = "Domain",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_grouping_time_window",
label = "Time window",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_settings_analysis",
label = "Concept type",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "All concepts",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_large_scale_characteristics_tidy_download", label = ""),,
class = "text-end"
),
uiOutput("summarise_large_scale_characteristics_tidy") |> withSpinner()
)
),
bslib::nav_panel(
title = "Top concepts",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_large_scale_characteristics_gt_download", label = ""),
class = "text-end"
),
gt::gt_output("summarise_large_scale_characteristics_gt") |> withSpinner()
)
)
)
)
),
## Compare large scale characteristics -----
bslib::nav_panel(
title = "Compare large scale characteristics",
icon = shiny::icon("arrow-up-right-dots"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_grouping_cohort_1",
label = "Cohort 1",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_grouping_cohort_2",
label = "Cohort 2",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_grouping_time_window",
label = "Time window",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_grouping_domain",
label = "Domain",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_settings_analysis",
label = "Concept type",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::prettyCheckbox(
inputId = "compare_large_scale_characteristics_impute_missings",
label = "Impute missing values as 0",
value = TRUE)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "compare_large_scale_characteristics_tidy_download", label = ""),
class = "text-end"
),
reactable::reactableOutput("compare_large_scale_characteristics_tidy") |> withSpinner()
)
),
bslib::nav_panel(
title = "Plot",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "plot_compare_large_scale_characteristics_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "plot_compare_large_scale_characteristics_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "plot_compare_large_scale_characteristics_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "plot_compare_large_scale_characteristics_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "plot_compare_large_scale_characteristics_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_colour_1",
label = "Colour",
selected = c("table"),
multiple = TRUE,
choices = c("table", "database", "time_window"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_facet_1",
label = "Facet",
selected = c("database"),
multiple = TRUE,
choices = c("table", "database", "time_window"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
position = "right"
),
plotly::plotlyOutput("plotly_compare_lsc") |> withSpinner()
)
)
)
)
),
## Cohort overlap -----
bslib::nav_panel(
title = "Cohort overlap",
icon = shiny::icon("circle-half-stroke"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_grouping_cohort_name_reference",
label = "Cohort name reference",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_grouping_cohort_name_comparator",
label = "Cohort name comparator",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
),
bslib::accordion_panel(
title = "Variables",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_variable_name",
label = "Variable name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
),
bslib::accordion_panel(
title = "Estimates",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_estimate_name",
label = "Estimate name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table cohort overlap",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_cohort_overlap_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
# materialSwitch(inputId = "overlap_plot_interactive",
# value = TRUE,
# label = "Interactive",
# status = "primary"),
sortable::bucket_list(
header = NULL,
sortable::add_rank_list(
text = "none",
labels = c("cohort_name_reference", "cohort_name_comparator", "estimate_name"),
input_id = "summarise_cohort_overlap_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = "variable_name",
input_id = "summarise_cohort_overlap_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = "cdm_name",
input_id = "summarise_cohort_overlap_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = "variable_level",
input_id = "summarise_cohort_overlap_gt_hide"
)
),
shiny::checkboxInput(
inputId = "summarise_cohort_overlap_gt_uniqueCombinations",
label = "uniqueCombinations",
value = c(TRUE)
),
position = "right"
),
gt::gt_output("summarise_cohort_overlap_gt") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Plot cohort overlap",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "summarise_cohort_overlap_plot_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "summarise_cohort_overlap_plot_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_plot_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "summarise_cohort_overlap_plot_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "summarise_cohort_overlap_plot_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_plot_facet",
label = "facet",
selected = c("cdm_name", "cohort_name_reference"),
multiple = TRUE,
choices = c("cdm_name", "cohort_name_reference", "cohort_name_comparator", "variable_name", "variable_level", "estimate_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shiny::checkboxInput(
inputId = "summarise_cohort_overlap_plot_uniqueCombinations",
label = "uniqueCombinations",
value = c(TRUE)
),
position = "right"
),
plotly::plotlyOutput("summarise_cohort_overlap_plot")
)
)
)
)
)
),
## Cohort timing -----
bslib::nav_panel(
title = "Cohort timing",
icon = shiny::icon("hourglass-half"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_grouping_cohort_name_reference",
label = "Cohort name reference",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_grouping_cohort_name_comparator",
label = "Cohort name comparator",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
),
bslib::accordion_panel(
title = "Estimates",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_estimate_name",
label = "Estimate name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table cohort timing",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_cohort_timing_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
sortable::bucket_list(
header = NULL,
sortable::add_rank_list(
text = "none",
labels = c("cohort_name_reference", "cohort_name_comparator", "estimate_name"),
input_id = "summarise_cohort_timing_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = "variable_name",
input_id = "summarise_cohort_timing_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = "cdm_name",
input_id = "summarise_cohort_timing_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = "variable_level",
input_id = "summarise_cohort_timing_gt_hide"
)
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_gt_time_scale",
label = "Time scale",
choices = c("days", "years"),
selected = "days",
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shiny::checkboxInput(
inputId = "summarise_cohort_timing_gt_uniqueCombinations",
label = "uniqueCombinations",
value = c(TRUE)
),
position = "right"
),
gt::gt_output("summarise_cohort_timing_gt") |> withSpinner()
)
)
),
# Cohort timing ----
bslib::nav_panel(
title = "Plot cohort timing",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "summarise_cohort_timing_plot_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "summarise_cohort_timing_plot_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_plot_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "summarise_cohort_timing_plot_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "summarise_cohort_timing_plot_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_plot_facet",
label = "facet",
selected = c("cdm_name", "cohort_name_reference"),
multiple = TRUE,
choices = c("cdm_name", "cohort_name_reference", "cohort_name_comparator", "variable_name", "variable_level", "estimate_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shiny::checkboxInput(
inputId = "summarise_cohort_timing_plot_uniqueCombinations",
label = "uniqueCombinations",
value = c(TRUE)
),
position = "right"
),
plotly::plotlyOutput("summarise_cohort_timing_plot")
)
)
)
)
)
)
),
# Population diagnostics -----
bslib::nav_menu(
title = "Population diagnostics",
icon = shiny::icon("list"),
## Incidence -----
bslib::nav_panel(
title = "Incidence",
icon = shiny::icon("chart-line"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "incidence_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_grouping_outcome_cohort_name",
label = "Outcome cohort name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_settings_analysis_interval",
label = "Time interval",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_settings_denominator_age_group",
label = "Denominator age group",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_settings_denominator_sex",
label = "Denominator sex",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_settings_denominator_days_prior_observation",
label = "Denominator days prior observation",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table incidence",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "incidence_gt_download", label = ""),
class = "text-end"
),
gt::gt_output("incidence_gt") |> withSpinner()
)
),
bslib::nav_panel(
title = "Plot incidence",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "incidence_plot_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "incidence_plot_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "incidence_plot_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "incidence_plot_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "incidence_plot_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
materialSwitch(inputId = "incidence_plot_interactive",
value = TRUE,
label = "Interactive",
status = "primary"),
shinyWidgets::pickerInput(
inputId = "incidence_plot_y",
label = "Vertical axis",
selected = "Incidence",
multiple = FALSE,
choices = c("Incidence", "Denominator count", "Denominator person years", "Outcome count"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_plot_x",
label = "Horizontal axis",
selected = "incidence_start_date",
multiple = FALSE,
choices = c("cdm_name",
"incidence_start_date",
"analysis_outcome_washout",
"denominator_age_group",
"denominator_sex",
"denominator_days_prior_observation",
"outcome_cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_plot_facet",
label = "Facet",
selected = "cdm_name",
multiple = TRUE,
choices = c("cdm_name",
"incidence_start_date",
"analysis_outcome_washout",
"denominator_age_group",
"denominator_sex",
"denominator_days_prior_observation",
"outcome_cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shiny::checkboxInput(
inputId = "incidence_plot_facet_free",
label = "Free scales",
value = c(FALSE)
),
shinyWidgets::pickerInput(
inputId = "incidence_plot_colour",
label = "Colour",
selected = NULL,
multiple = TRUE,
choices = c("cdm_name",
"incidence_start_date",
"analysis_outcome_washout",
"denominator_age_group",
"denominator_sex",
"denominator_days_prior_observation",
"outcome_cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
uiOutput("incidence_plot") |> withSpinner()
)
)
)
)
)
),
## Prevalence -----
bslib::nav_panel(
title = "Prevalence",
icon = shiny::icon("chart-line"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "prevalence_grouping_cdm_name",
label = "CDM",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_grouping_outcome_cohort_name",
label = "Outcome cohort name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_settings_analysis_interval",
label = "Time interval",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_settings_denominator_age_group",
label = "Denominator age group",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_settings_denominator_sex",
label = "Denominator sex",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_settings_denominator_days_prior_observation",
label = "Denominator days prior observation",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table prevalence",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "prevalence_gt_download", label = ""),
class = "text-end"
),
gt::gt_output("prevalence_gt") |> withSpinner()
)
),
bslib::nav_panel(
title = "Plot prevalence",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "prevalence_plot_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "prevalence_plot_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "prevalence_plot_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "prevalence_plot_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "prevalence_plot_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
materialSwitch(inputId = "prevalence_plot_interactive",
value = TRUE,
label = "Interactive",
status = "primary"),
shinyWidgets::pickerInput(
inputId = "prevalence_plot_y",
label = "Vertical axis",
selected = "Prevalence",
multiple = FALSE,
choices = c("Prevalence", "Denominator count", "Outcome count"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_plot_x",
label = "Horizontal axis",
selected = "prevalence_start_date",
multiple = FALSE,
choices = c("cdm_name",
"prevalence_start_date",
"denominator_age_group",
"denominator_sex",
"denominator_days_prior_observation",
"outcome_cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_plot_facet",
label = "Facet",
selected = "cdm_name",
multiple = TRUE,
choices = c("cdm_name",
"prevalence_start_date",
"denominator_age_group",
"denominator_sex",
"denominator_days_prior_observation",
"outcome_cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shiny::checkboxInput(
inputId = "prevalence_plot_facet_free",
label = "Free scales",
value = c(FALSE)
),
shinyWidgets::pickerInput(
inputId = "prevalence_plot_colour",
label = "Colour",
selected = NULL,
multiple = TRUE,
choices = c("cdm_name",
"prevalence_start_date",
"denominator_age_group",
"denominator_sex",
"denominator_days_prior_observation",
"outcome_cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
uiOutput("prevalence_plot") |> withSpinner()
)
)
)
)
)
)
),
# end ------
bslib::nav_spacer(),
bslib::nav_item(
bslib::popover(
shiny::icon("download"),
shiny::downloadButton(
outputId = "download_raw",
label = "Download raw data",
icon = shiny::icon("download")
)
)
)
)
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# Generated by OmopViewer 0.1.0
# Be careful editing this file
ui <- bslib::page_navbar(
theme = bs_theme(bootswatch = "pulse"),
# zephyr
title = "PhenotypeR",
bslib::nav_panel(
title = "Background",
icon = shiny::icon("disease"),
shiny::includeMarkdown(path = "background.md")
),
# Database diagnostics -----
bslib::nav_menu(
title = "Database diagnostics",
icon = shiny::icon("list"),
## snapshot -----
bslib::nav_panel(
title = "Snapshot",
icon = shiny::icon("clipboard-list"),
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_omop_snapshot_gt_download", label = ""),
class = "text-end"
),
gt::gt_output("summarise_omop_snapshot_gt") |> withSpinner()
)
),
## observation periods -----
bslib::nav_panel(
title = "Observation periods",
icon = shiny::icon("eye"),
bslib::nav_panel(
title = "Table observation period",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_observation_period_gt_download", label = ""),
class = "text-end"
),
gt::gt_output("summarise_observation_period_gt") |> withSpinner()
)
)
)
),
# Codelist diagnostics -----
bslib::nav_menu(
title = "Codelist diagnostics",
icon = shiny::icon("list"),
## achilles code use -----
bslib::nav_panel(
title = "Achilles code use",
icon = shiny::icon("database"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "achilles_code_use_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "achilles_code_use_grouping_codelist_name",
label = "Codelist name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
div(style="display: flex; justify-content: space-between;",
div(style="flex: 1;", prettyCheckbox(inputId = "achilles_person_count",
label = "Person count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE)),
div(style="flex: 1;", prettyCheckbox(inputId = "achilles_record_count",
label = "Record count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE))
)
),
bslib::accordion_panel(
title = "Table formatting",
materialSwitch(inputId = "achilles_interactive",
value = TRUE,
label = "Interactive",
status = "primary"),
sortable::bucket_list(
header = NULL,
sortable::add_rank_list(
text = "none",
labels = c("codelist_name"),
input_id = "achilles_code_use_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name", "estimate_name"),
input_id = "achilles_code_use_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = character(),
input_id = "achilles_code_use_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = character(),
input_id = "achilles_code_use_hide"
)
)
)
)
),
bslib::nav_panel(
title = "achilles_code_use",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "achilles_code_use_download", label = ""),
class = "text-end"
),
uiOutput("achilles_code_use_tbl") |> withSpinner()
)
)
)
),
## unmapped concepts -----
# bslib::nav_panel(
# title = "Unmapped concepts",
# icon = shiny::icon("database"),
# bslib::layout_sidebar(
# sidebar = bslib::sidebar(width = 400, open = "closed",
# bslib::accordion(
# bslib::accordion_panel(
# title = "Settings",
# shinyWidgets::pickerInput(
# inputId = "unmapped_grouping_cdm_name",
# label = "Database",
# choices = NULL,
# selected = NULL,
# multiple = TRUE,
# options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
# ),
# shinyWidgets::pickerInput(
# inputId = "unmapped_grouping_codelist_name",
# label = "Codelist name",
# choices = NULL,
# selected = NULL,
# multiple = TRUE,
# options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
# )
# ),
# bslib::accordion_panel(
# title = "Table formatting",
# sortable::bucket_list(
# header = NULL,
# sortable::add_rank_list(
# text = "none",
# labels = c( "codelist_name"),
# input_id = "unmapped_none"
# ),
# sortable::add_rank_list(
# text = "header",
# labels = c("cdm_name", "estimate_name"),
# input_id = "unmapped_header"
# ),
# sortable::add_rank_list(
# text = "groupColumn",
# labels = NULL,
# input_id = "unmapped_groupColumn"
# ),
# sortable::add_rank_list(
# text = "hide",
# labels = character(),
# input_id = "unmapped_hide"
# )
# )
# )
# )
# ),
# bslib::nav_panel(
# title = "Unmapped",
# bslib::card(
# full_screen = TRUE,
# bslib::card_header(
# bslib::popover(
# shiny::icon("download"),
# shinyWidgets::pickerInput(
# inputId = "unmapped_formatted_download_type",
# label = "File type",
# selected = "docx",
# choices = c("docx", "png", "pdf", "html"),
# multiple = FALSE
# ),
# shiny::downloadButton(outputId = "unmapped_formatted_download", label = "Download")
# ),
# class = "text-end"
# ),
# gt::gt_output("unmapped_formatted") |> withSpinner()
# )
# )
# )
# ),
## Orphan codes -----
bslib::nav_panel(
title = "Orphan codes",
icon = shiny::icon("circle-half-stroke"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "orphan_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "orphan_grouping_codelist_name",
label = "Cohort name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
div(style="display: flex; justify-content: space-between;",
div(style="flex: 1;", prettyCheckbox(inputId = "orphan_person_count",
label = "Person count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE)),
div(style="flex: 1;", prettyCheckbox(inputId = "orphan_record_count",
label = "Record count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE))
)
),
bslib::accordion_panel(
title = "Table formatting",
materialSwitch(inputId = "orphan_interactive",
value = TRUE,
label = "Interactive",
status = "primary"),
sortable::bucket_list(
header = NULL,
sortable::add_rank_list(
text = "none",
labels = c("variable_name", "cohort_name", "variable_level"),
input_id = "orphan_codes_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name", "estimate_name"),
input_id = "orphan_codes_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = character(),
input_id = "orphan_codes_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = character(),
input_id = "orphan_codes_gt_hide"
)
)
)
)
),
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "orphan_codes_download", label = ""),
class = "text-end"
),
uiOutput("orphan_codes_tbl") |> withSpinner()
)
)
)
),
# Cohort diagnostics -----
bslib::nav_menu(
title = "Cohort diagnostics",
icon = shiny::icon("list"),
## Cohort code use -----
bslib::nav_panel(
title = "Cohort code use",
icon = shiny::icon("chart-column"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "cohort_code_use_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "cohort_code_use_grouping_cohort_name",
label = "Cohort name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "cohort_code_use_grouping_domain_id",
label = "Domain",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
div(style="display: flex; justify-content: space-between;",
div(style="flex: 1;", prettyCheckbox(inputId = "cohort_code_use_person_count",
label = "Person count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE)),
div(style="flex: 1;", prettyCheckbox(inputId = "cohort_code_use_record_count",
label = "Record count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE))
)
),
bslib::accordion_panel(
title = "Table formatting",
materialSwitch(inputId = "cohort_code_use_interactive",
value = TRUE,
label = "Interactive",
status = "primary"),
sortable::bucket_list(
header = NULL,
sortable::add_rank_list(
text = "none",
labels = c("cohort_name", "codelist_name", "source_concept_name", "source_concept_id", "domain_id", "variable_name", "variable_level"),
input_id = "cohort_code_use_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name", "estimate_name"),
input_id = "cohort_code_use_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = character(),
input_id = "cohort_code_use_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = character(),
input_id = "cohort_code_use_gt_hide"
)
)
)
)
),
bslib::nav_panel(
title = "Table cohort code use",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "cohort_code_use_download", label = ""),
class = "text-end"
),
uiOutput("cohort_code_use_tbl") |> withSpinner()
)
)
)
),
## Cohort count ----
bslib::nav_panel(
title = "Cohort count",
icon = shiny::icon("person"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_attrition_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_attrition_grouping_cohort_name",
label = "Cohort name",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Counts",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_cohort_count_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
shinyWidgets::pickerInput(
inputId = "summarise_cohort_count_variable_name",
label = "Variable name",
selected = c("Number records", "Number subjects"),
multiple = TRUE,
choices = c("Number records", "Number subjects"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
),
position = "right"
),
gt::gt_output("summarise_cohort_count_gt") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Attrition",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_cohort_attrition_gt_download", label = ""),
class = "text-end"
),
gt::gt_output("summarise_cohort_attrition_gt") |> withSpinner()
)
),
bslib::nav_panel(
title = "Flowchart",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "summarise_cohort_attrition_grViz_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "summarise_cohort_attrition_grViz_download_height",
label = "Height",
value = 10
),
shiny::downloadButton(outputId = "summarise_cohort_attrition_grViz_download", label = "Download")
),
class = "text-end"
),
DiagrammeR::grVizOutput("summarise_cohort_attrition_grViz") |> withSpinner()
)
)
)
)
),
## Cohort characteristics -----
bslib::nav_panel(
title = "Cohort characteristics",
icon = shiny::icon("users-gear"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_characteristics_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_characteristics_grouping_cohort_name",
label = "Cohort name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::prettyCheckbox(
inputId = "summarise_characteristics_include_matched",
label = "Show matched cohorts",
value = FALSE)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_characteristics_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
sortable::bucket_list(
header = NULL,
sortable::add_rank_list(
text = "none",
labels = c("variable_name", "variable_level", "estimate_name"),
input_id = "summarise_characteristics_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name", "cohort_name"),
input_id = "summarise_characteristics_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = NULL,
input_id = "summarise_characteristics_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = character(),
input_id = "summarise_characteristics_gt_hide"
)
),
position = "right"
),
gt::gt_output("summarise_characteristics_gt") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Age distribution",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "plot_age_pyramid_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "plot_age_pyramid_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "plot_age_pyramid_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "plot_age_pyramid_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "plot_age_pyramid_download", label = "Download")
),
class = "text-end",
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shiny::checkboxInput(
inputId = "summarise_characteristics_add_interquantile_range",
label = "Show interquantile range",
value = c(TRUE)
),
position = "right"
),
shiny::plotOutput("plot_age_pyramid")
)
)
)
)
)
),
## Large scale characteristics -----
bslib::nav_panel(
title = "Large scale characteristics",
icon = shiny::icon("arrow-up-right-dots"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_grouping_cohort_name",
label = "Cohort name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_grouping_domain",
label = "Domain",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_grouping_time_window",
label = "Time window",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_settings_analysis",
label = "Concept type",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "All concepts",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_large_scale_characteristics_tidy_download", label = ""),,
class = "text-end"
),
uiOutput("summarise_large_scale_characteristics_tidy") |> withSpinner()
)
),
bslib::nav_panel(
title = "Top concepts",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_large_scale_characteristics_gt_download", label = ""),
class = "text-end"
),
gt::gt_output("summarise_large_scale_characteristics_gt") |> withSpinner()
)
)
)
)
),
## Compare large scale characteristics -----
bslib::nav_panel(
title = "Compare large scale characteristics",
icon = shiny::icon("arrow-up-right-dots"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_grouping_cohort_1",
label = "Cohort 1",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_grouping_cohort_2",
label = "Cohort 2",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_grouping_time_window",
label = "Time window",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_grouping_domain",
label = "Domain",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_settings_analysis",
label = "Concept type",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::prettyCheckbox(
inputId = "compare_large_scale_characteristics_impute_missings",
label = "Impute missing values as 0",
value = TRUE)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "compare_large_scale_characteristics_tidy_download", label = ""),
class = "text-end"
),
reactable::reactableOutput("compare_large_scale_characteristics_tidy") |> withSpinner()
)
),
bslib::nav_panel(
title = "Plot",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "plot_compare_large_scale_characteristics_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "plot_compare_large_scale_characteristics_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "plot_compare_large_scale_characteristics_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "plot_compare_large_scale_characteristics_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "plot_compare_large_scale_characteristics_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_colour_1",
label = "Colour",
selected = c("table"),
multiple = TRUE,
choices = c("table", "database", "time_window"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_facet_1",
label = "Facet",
selected = c("database"),
multiple = TRUE,
choices = c("table", "database", "time_window"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
position = "right"
),
plotly::plotlyOutput("plotly_compare_lsc") |> withSpinner()
)
)
)
)
),
## Cohort overlap -----
bslib::nav_panel(
title = "Cohort overlap",
icon = shiny::icon("circle-half-stroke"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_grouping_cohort_name_reference",
label = "Cohort name reference",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_grouping_cohort_name_comparator",
label = "Cohort name comparator",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
),
bslib::accordion_panel(
title = "Variables",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_variable_name",
label = "Variable name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
),
bslib::accordion_panel(
title = "Estimates",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_estimate_name",
label = "Estimate name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table cohort overlap",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_cohort_overlap_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
# materialSwitch(inputId = "overlap_plot_interactive",
# value = TRUE,
# label = "Interactive",
# status = "primary"),
sortable::bucket_list(
header = NULL,
sortable::add_rank_list(
text = "none",
labels = c("cohort_name_reference", "cohort_name_comparator", "estimate_name"),
input_id = "summarise_cohort_overlap_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = "variable_name",
input_id = "summarise_cohort_overlap_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = "cdm_name",
input_id = "summarise_cohort_overlap_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = "variable_level",
input_id = "summarise_cohort_overlap_gt_hide"
)
),
shiny::checkboxInput(
inputId = "summarise_cohort_overlap_gt_uniqueCombinations",
label = "uniqueCombinations",
value = c(TRUE)
),
position = "right"
),
gt::gt_output("summarise_cohort_overlap_gt") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Plot cohort overlap",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "summarise_cohort_overlap_plot_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "summarise_cohort_overlap_plot_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_plot_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "summarise_cohort_overlap_plot_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "summarise_cohort_overlap_plot_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_plot_facet",
label = "facet",
selected = c("cdm_name", "cohort_name_reference"),
multiple = TRUE,
choices = c("cdm_name", "cohort_name_reference", "cohort_name_comparator", "variable_name", "variable_level", "estimate_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shiny::checkboxInput(
inputId = "summarise_cohort_overlap_plot_uniqueCombinations",
label = "uniqueCombinations",
value = c(TRUE)
),
position = "right"
),
plotly::plotlyOutput("summarise_cohort_overlap_plot")
)
)
)
)
)
),
## Cohort timing -----
bslib::nav_panel(
title = "Cohort timing",
icon = shiny::icon("hourglass-half"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_grouping_cohort_name_reference",
label = "Cohort name reference",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_grouping_cohort_name_comparator",
label = "Cohort name comparator",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
),
bslib::accordion_panel(
title = "Estimates",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_estimate_name",
label = "Estimate name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table cohort timing",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_cohort_timing_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
sortable::bucket_list(
header = NULL,
sortable::add_rank_list(
text = "none",
labels = c("cohort_name_reference", "cohort_name_comparator", "estimate_name"),
input_id = "summarise_cohort_timing_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = "variable_name",
input_id = "summarise_cohort_timing_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = "cdm_name",
input_id = "summarise_cohort_timing_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = "variable_level",
input_id = "summarise_cohort_timing_gt_hide"
)
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_gt_time_scale",
label = "Time scale",
choices = c("days", "years"),
selected = "days",
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shiny::checkboxInput(
inputId = "summarise_cohort_timing_gt_uniqueCombinations",
label = "uniqueCombinations",
value = c(TRUE)
),
position = "right"
),
gt::gt_output("summarise_cohort_timing_gt") |> withSpinner()
)
)
),
# Cohort timing ----
bslib::nav_panel(
title = "Plot cohort timing",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "summarise_cohort_timing_plot_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "summarise_cohort_timing_plot_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_plot_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "summarise_cohort_timing_plot_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "summarise_cohort_timing_plot_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_plot_facet",
label = "facet",
selected = c("cdm_name", "cohort_name_reference"),
multiple = TRUE,
choices = c("cdm_name", "cohort_name_reference", "cohort_name_comparator", "variable_name", "variable_level", "estimate_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shiny::checkboxInput(
inputId = "summarise_cohort_timing_plot_uniqueCombinations",
label = "uniqueCombinations",
value = c(TRUE)
),
position = "right"
),
plotly::plotlyOutput("summarise_cohort_timing_plot")
)
)
)
)
)
)
),
# Population diagnostics -----
bslib::nav_menu(
title = "Population diagnostics",
icon = shiny::icon("list"),
## Incidence -----
bslib::nav_panel(
title = "Incidence",
icon = shiny::icon("chart-line"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "incidence_grouping_cdm_name",
label = "CDM name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_grouping_outcome_cohort_name",
label = "Outcome cohort name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_settings_analysis_interval",
label = "Time interval",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_settings_denominator_age_group",
label = "Denominator age group",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_settings_denominator_sex",
label = "Denominator sex",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_settings_denominator_days_prior_observation",
label = "Denominator days prior observation",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table incidence",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "incidence_gt_download", label = ""),
class = "text-end"
),
gt::gt_output("incidence_gt") |> withSpinner()
)
),
bslib::nav_panel(
title = "Plot incidence",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "incidence_plot_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "incidence_plot_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "incidence_plot_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "incidence_plot_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "incidence_plot_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
materialSwitch(inputId = "incidence_plot_interactive",
value = TRUE,
label = "Interactive",
status = "primary"),
shinyWidgets::pickerInput(
inputId = "incidence_plot_y",
label = "Vertical axis",
selected = "Incidence",
multiple = FALSE,
choices = c("Incidence", "Denominator count", "Denominator person years", "Outcome count"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_plot_x",
label = "Horizontal axis",
selected = "incidence_start_date",
multiple = FALSE,
choices = c("cdm_name",
"incidence_start_date",
"analysis_outcome_washout",
"denominator_age_group",
"denominator_sex",
"denominator_days_prior_observation",
"outcome_cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_plot_facet",
label = "Facet",
selected = "cdm_name",
multiple = TRUE,
choices = c("cdm_name",
"incidence_start_date",
"analysis_outcome_washout",
"denominator_age_group",
"denominator_sex",
"denominator_days_prior_observation",
"outcome_cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shiny::checkboxInput(
inputId = "incidence_plot_facet_free",
label = "Free scales",
value = c(FALSE)
),
shinyWidgets::pickerInput(
inputId = "incidence_plot_colour",
label = "Colour",
selected = NULL,
multiple = TRUE,
choices = c("cdm_name",
"incidence_start_date",
"analysis_outcome_washout",
"denominator_age_group",
"denominator_sex",
"denominator_days_prior_observation",
"outcome_cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
uiOutput("incidence_plot") |> withSpinner()
)
)
)
)
)
),
## Prevalence -----
bslib::nav_panel(
title = "Prevalence",
icon = shiny::icon("chart-line"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "prevalence_grouping_cdm_name",
label = "CDM",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_grouping_outcome_cohort_name",
label = "Outcome cohort name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_settings_analysis_interval",
label = "Time interval",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_settings_denominator_age_group",
label = "Denominator age group",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_settings_denominator_sex",
label = "Denominator sex",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_settings_denominator_days_prior_observation",
label = "Denominator days prior observation",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table prevalence",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "prevalence_gt_download", label = ""),
class = "text-end"
),
gt::gt_output("prevalence_gt") |> withSpinner()
)
),
bslib::nav_panel(
title = "Plot prevalence",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "prevalence_plot_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "prevalence_plot_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "prevalence_plot_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "prevalence_plot_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "prevalence_plot_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
materialSwitch(inputId = "prevalence_plot_interactive",
value = TRUE,
label = "Interactive",
status = "primary"),
shinyWidgets::pickerInput(
inputId = "prevalence_plot_y",
label = "Vertical axis",
selected = "Prevalence",
multiple = FALSE,
choices = c("Prevalence", "Denominator count", "Outcome count"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_plot_x",
label = "Horizontal axis",
selected = "prevalence_start_date",
multiple = FALSE,
choices = c("cdm_name",
"prevalence_start_date",
"denominator_age_group",
"denominator_sex",
"denominator_days_prior_observation",
"outcome_cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_plot_facet",
label = "Facet",
selected = "cdm_name",
multiple = TRUE,
choices = c("cdm_name",
"prevalence_start_date",
"denominator_age_group",
"denominator_sex",
"denominator_days_prior_observation",
"outcome_cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shiny::checkboxInput(
inputId = "prevalence_plot_facet_free",
label = "Free scales",
value = c(FALSE)
),
shinyWidgets::pickerInput(
inputId = "prevalence_plot_colour",
label = "Colour",
selected = NULL,
multiple = TRUE,
choices = c("cdm_name",
"prevalence_start_date",
"denominator_age_group",
"denominator_sex",
"denominator_days_prior_observation",
"outcome_cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
uiOutput("prevalence_plot") |> withSpinner()
)
)
)
)
)
)
),
# end ------
bslib::nav_spacer(),
bslib::nav_item(
bslib::popover(
shiny::icon("download"),
shiny::downloadButton(
outputId = "download_raw",
label = "Download raw data",
icon = shiny::icon("download")
)
)
)
)
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