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inst/shiny/ui.R
In PhenotypeR: Assess Study Cohorts Using a Common Data Model
ui <- fluidPage(
bslib::page_navbar(
theme = bs_theme(5, "pulse"),
navbar_options =list(class = "bg-dark", theme = "dark"),
title = "PhenotypeR",
bslib::nav_panel(title = "Background",
icon = shiny::icon("disease"),
shiny::includeMarkdown(path = "background.md")),
# databaseDiagnostics_start -----
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()
)
)
)
),
# databaseDiagnostics_end ----
# codelistDiagnostics_start -----
bslib::nav_menu(
title = "Codelist diagnostics",
icon = shiny::icon("list"),
## achilles_results_start
## achilles code use -----
bslib::nav_panel(
title = "Achilles code use",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "achilles_code_use_cdm_name",
label = NULL,
selected = selected$shared_cdm_name,
choices = choices$shared_cdm_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateAchillesCodeUse", "Update",
style = "simple"),
width = "100%"
)
)
)),
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_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_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_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",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"), # Explicitly use tags$label
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "orphan_code_use_cdm_name",
label = NULL,
selected = selected$shared_cdm_name,
choices = choices$shared_cdm_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateOrphanCodeUse", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("circle-half-stroke"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "orphan_code_use_codelist_name",
label = "Codelist name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
div(style="display: flex; justify-content: space-between;",
div(style="flex: 1;", prettyCheckbox(inputId = "orphan_person_count",
label = "Person count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE)),
div(style="flex: 1;", prettyCheckbox(inputId = "orphan_record_count",
label = "Record count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE))
)
),
bslib::accordion_panel(
title = "Table formatting",
materialSwitch(inputId = "orphan_interactive",
value = TRUE,
label = "Interactive",
status = "primary"),
sortable::bucket_list(
header = NULL,
sortable::add_rank_list(
text = "none",
labels = c("variable_name", "cohort_name", "variable_level"),
input_id = "orphan_codes_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name", "estimate_name"),
input_id = "orphan_codes_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = character(),
input_id = "orphan_codes_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = character(),
input_id = "orphan_codes_gt_hide"
)
)
)
)
),
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "orphan_codes_download", label = ""),
class = "text-end"
),
uiOutput("orphan_codes_tbl") |> withSpinner()
)
)
),
## achilles_results_end
## Cohort code use -----
bslib::nav_panel(
title = "Cohort code use",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "cohort_code_use_cdm_name",
label = NULL,
selected = selected$shared_cdm_name,
choices = choices$shared_cdm_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "cohort_code_use_cohort_name",
label = NULL,
selected = selected$shared_cohort_name,
choices = choices$shared_cohort_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateCohortCodeUse", "Update",
style = "simple"),
width = "100%"
)
)
)),
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_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()
)
)
)
),
## measurement_diagnostics_start
## Measurement code use -----
bslib::nav_panel(
title = "Measurements Code Use",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "measurement_timings_cdm_name",
label = NULL,
selected = selected$shared_cdm_name,
choices = choices$shared_cdm_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "measurement_timings_cohort_name",
label = NULL,
selected = selected$shared_cohort_name,
choices = choices$shared_cohort_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateMeasurementCodeUse", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("weight-scale"),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table Values (Concepts)",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "measurement_value_as_concept_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
sortable::bucket_list(
header = "Table formatting",
sortable::add_rank_list(
text = "none",
labels = c("cohort_name", "variable_level", "estimate_name"),
input_id = "measurement_value_as_concept_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name"),
input_id = "measurement_value_as_concepts_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = c("codelist_name"),
input_id = "measurement_value_as_concept_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = c("variable_name"),
input_id = "measurement_value_as_concept_gt_hide"
)
),
position = "right"
),
gt::gt_output("measurement_value_as_concept_tbl") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Plot Values (Concepts)",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "plot_measurement_value_as_concept_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "plot_measurement_value_as_concept_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "plot_measurement_value_as_concept_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "plot_measurement_value_as_concept_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "plot_measurement_value_as_concept_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shinyWidgets::pickerInput(
inputId = "measurement_value_as_concept_x",
label = "Horizontal axis",
selected = c("count"),
multiple = FALSE,
choices = c("count", "percentage"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_value_as_concept_y",
label = "Vertical axis",
selected = c("codelist_name"),
multiple = FALSE,
choices = c("count", "variable_level", "codelist_name", "concept_name", "cdm_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_value_as_concept_colour",
label = "Colour",
selected = c("concept_name", "variable_level"),
multiple = TRUE,
choices = c("count", "variable_level", "codelist_name", "concept_name", "cdm_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_value_as_concept_facet",
label = "Facet",
selected = c("cdm_name"),
multiple = TRUE,
choices = c("count", "variable_level", "codelist_name", "concept_name", "cdm_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
shiny::plotOutput("plot_measurement_value_as_concept")
)
)
),
bslib::nav_panel(
title = "Table Values (Numeric)",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "measurement_value_as_numeric_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
sortable::bucket_list(
header = "Table formatting",
sortable::add_rank_list(
text = "none",
labels = c("cohort_name", "estimate_name"),
input_id = "measurement_value_as_numeric_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name"),
input_id = "measurement_value_as_numeric_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = c("codelist_name"),
input_id = "measurement_value_as_numeric_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = c("variable_name", "variable_level"),
input_id = "measurement_value_as_numeric_gt_hide"
)
),
position = "right"
),
gt::gt_output("measurement_value_as_numeric_tbl") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Plot Values (Numeric)",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "plot_measurement_value_as_numeric_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "plot_measurement_value_as_numeric_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "plot_measurement_value_as_numeric_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "plot_measurement_value_as_numeric_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "plot_measurement_value_as_numeric_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shinyWidgets::pickerInput(
inputId = "measurement_value_as_numeric_x",
label = "Horizontal axis",
selected = c("unit_concept_name"),
multiple = FALSE,
choices = c("unit_concept_name", "codelist_name", "concept_name", "cdm_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_value_as_numeric_plottype",
label = "Plot type",
selected = "boxplot",
multiple = FALSE,
choices = c("boxplot", "densityplot"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_value_as_numeric_colour",
label = "Colour",
selected = c("cdm_name"),
multiple = TRUE,
choices = c("unit_concept_name", "codelist_name", "concept_name", "cdm_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_value_as_numeric_facet",
label = "Facet",
selected = c("codelist_name", "concept_name"),
multiple = TRUE,
choices = c("unit_concept_name", "codelist_name", "concept_name", "cdm_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
shiny::plotOutput("plot_measurement_value_as_numeric")
)
)
),
bslib::nav_panel(
title = "Table Timings",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "measurement_timings_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
sortable::bucket_list(
header = "Table formatting",
sortable::add_rank_list(
text = "none",
labels = c("cohort_name", "variable_name", "estimate_name"),
input_id = "measurement_timings_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name"),
input_id = "measurement_timings_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = c("codelist_name"),
input_id = "measurement_timings_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = c("variable_level"),
input_id = "measurement_timings_gt_hide"
)
),
position = "right"
),
gt::gt_output("measurement_timings_tbl") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Plot timings",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "plot_measurement_timings_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "plot_measurement_timings_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "plot_measurement_timings_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "plot_measurement_timings_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "plot_measurement_timings_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shinyWidgets::pickerInput(
inputId = "measurement_timings_y",
label = "Vertical axis",
selected = c("time"),
multiple = FALSE,
choices = c("time", "measurements_per_subject"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_timings_time_scale",
label = "Time scale",
selected = c("days"),
multiple = FALSE,
choices = c("days", "years"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_timings_plottype",
label = "Plot type",
selected = "boxplot",
multiple = FALSE,
choices = c("boxplot", "densityplot"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_timings_colour",
label = "Colour",
selected = c("codelist_name"),
multiple = TRUE,
choices = c("cdm_name", "codelist_name", "cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_timings_facet",
label = "Facet",
selected = c("cdm_name"),
multiple = TRUE,
choices = c("cdm_name", "codelist_name", "cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
shiny::plotOutput("plot_measurement_timings")
)
)
)
)
)
## measurement_diagnostics_end
),
# codelistDiagnostics_end ----
# cohortDiagnostics_start -----
bslib::nav_menu(
title = "Cohort diagnostics",
icon = shiny::icon("list"),
## Cohort count ----
bslib::nav_panel(
title = "Cohort count",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_count_cdm_name",
label = NULL,
selected = selected$shared_cdm_name,
choices = choices$shared_cdm_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_count_cohort_name",
label = NULL,
selected = selected$shared_cohort_name,
choices = choices$shared_cohort_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateCohortCount", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("person"),
accordion(open = FALSE,
accordion_panel(
title = "Show cohort expectations",
value = "panel_ce_1",
reactable::reactableOutput("cohort_count_expectations")
)),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
div(style="display: flex; justify-content: space-between;",
div(style="flex: 1;", prettyCheckbox(inputId = "cohort_count_person_count",
label = "Person count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE)),
div(style="flex: 1;", prettyCheckbox(inputId = "cohort_count_record_count",
label = "Record count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE))
)
)
)
),
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"
),
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",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_characteristics_cdm_name",
label = NULL,
selected = selected$shared_cdm_names,
choices = choices$shared_cdm_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_characteristics_cohort_name",
label = NULL,
selected = selected$shared_cohort_names,
choices = choices$shared_cohort_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateCohortCharacteristics", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("users-gear"),
accordion(open = FALSE,
accordion_panel(
title = "Show cohort expectations",
value = "panel_ce_2",
reactable::reactableOutput("cohort_characteristics_expectations")
)),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
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 = "Table formatting",
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",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_cdm_name",
label = NULL,
selected = selected$shared_cdm_names,
choices = choices$shared_cdm_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_cohort_name",
label = NULL,
selected = selected$shared_cohort_names,
choices = choices$shared_cohort_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateLSC", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("arrow-up-right-dots"),
accordion(open = FALSE,
accordion_panel(
title = "Show cohort expectations",
value = "panel_ce_3",
reactable::reactableOutput("large_scale_characteristics_expectations")
)),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_table_name",
label = "Domain",
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_variable_level",
label = "Time window",
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_analysis",
label = "Analysis",
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"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shiny::numericInput(
min = 1,
step = 1,
inputId = "summarise_large_scale_characteristics_top_concepts",
label = "Top concepts",
value = 10
),
position = "right"
),
gt::gt_output("summarise_large_scale_characteristics_gt") |> withSpinner()
)
)
)
)
)
),
## Compare large scale characteristics -----
bslib::nav_panel(
title = "Compare large scale characteristics",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_cdm_name",
label = NULL,
selected = selected$shared_cdm_names,
choices = choices$shared_cdm_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%",
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_cohort_name",
label = NULL,
selected = selected$shared_cohort_names,
choices = choices$shared_cohort_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateCompareLSC", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("people-arrows"),
accordion(open = FALSE,
accordion_panel(
title = "Show cohort expectations",
value = "panel_ce_4",
reactable::reactableOutput("compare_large_scale_characteristics_expectations")
)),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_cohort_compare",
label = "Comparator cohort",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shiny::fluidRow(
shiny::column(width = 5, offset = 1,
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_cohort_1",
label = "Cohort type (reference)",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
tags$style(HTML("
label[for='compare_large_scale_characteristics_cohort_1'] {
text-align: center;
width: 100%;
display: block;
}"))
),
shiny::column(width = 5,
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_cohort_2",
label = "Cohort type (comparator)",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
tags$style(HTML("
label[for='compare_large_scale_characteristics_cohort_2'] {
text-align: center;
width: 100%;
display: block;
}"))
)
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_table_name",
label = "Domain",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_analysis",
label = "Analysis",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_variable_level",
label = "Time window",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::prettyCheckbox(
inputId = "compare_large_scale_characteristics_impute_missings",
label = "Impute missing values as 0",
value = TRUE)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "compare_large_scale_characteristics_tidy_download", label = ""),
class = "text-end"
),
htmltools::tags$p(style = "font-size: 0.75em;", msgMatchedSample),
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",
htmltools::tags$p(style = "font-size: 0.75em;", msgMatchedSample),
plotly::plotlyOutput("plotly_compare_lsc") |> withSpinner()
)
)
)
)
)
),
## Compare cohorts -----
bslib::nav_panel(
title = "Compare cohorts",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_cdm_name",
label = NULL,
selected = selected$shared_cdm_names,
choices = choices$shared_cdm_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_cohort_name_reference",
label = NULL,
selected = selected$shared_cohort_names,
choices = choices$shared_cohort_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateCompareCohorts", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("yin-yang"),
accordion(open = FALSE,
accordion_panel(
title = "Show cohort expectations",
value = "panel_ce_5",
reactable::reactableOutput("compare_cohorts_expectations")
)),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_cohort_comparator",
label = "Cohort comparator",
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 = "Cohort Overlap (Table)",
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",
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")
),
shiny::checkboxInput(
inputId = "summarise_cohort_overlap_gt_uniqueCombinations",
label = "uniqueCombinations",
value = c(TRUE)
),
sortable::bucket_list(
header = "Table formatting",
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"
)
),
position = "right"
),
gt::gt_output("summarise_cohort_overlap_gt") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Cohort Overlap (Plot)",
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_variable_name",
label = "Variable name",
choices = c("Only in reference cohort", "In both cohorts", "Only in comparator cohort"),
selected = c("Only in reference cohort", "In both cohorts", "Only in comparator cohort"),
multiple = TRUE,
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)
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_plot_colour",
label = "Colour",
selected = c("variable_name"),
multiple = TRUE,
choices = c("cdm_name", "cohort_name_reference", "cohort_name_comparator", "variable_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
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"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
plotly::plotlyOutput("summarise_cohort_overlap_plot")
)
)
),
bslib::nav_panel(
title = "Cohort Timing (Table)",
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",
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)
),
sortable::bucket_list(
header = "Table formatting",
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"
)
),
position = "right"
),
gt::gt_output("summarise_cohort_timing_gt") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Cohort Timing (Plot)",
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_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_plot_uniqueCombinations",
label = "uniqueCombinations",
value = c(TRUE)
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_plot_colour",
label = "Colour",
selected = c("cohort_name_comparator"),
multiple = TRUE,
choices = c("cdm_name", "cohort_name_reference", "cohort_name_comparator", "variable_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
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"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
plotly::plotlyOutput("summarise_cohort_timing_plot")
)
)
)
)
)
),
## cohort_survival_start
## Cohort survival -----
bslib::nav_panel(
title = "Cohort survival",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "survival_probability_cdm_name",
label = NULL,
selected = selected$shared_cdm_names,
choices = choices$shared_cdm_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "survival_probability_cohort_name",
label = NULL,
selected = selected$shared_cohort_names,
choices = choices$shared_cohort_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateCohortSurvival", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("chart-gantt"),
accordion(open = FALSE,
accordion_panel(
title = "Show cohort expectations",
value = "panel_ce_6",
reactable::reactableOutput("cohort_survival_expectations")
)),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shiny::checkboxInput(
inputId = "survival_porbability_include_matches",
label = "Show matched cohorts",
value = c(TRUE)
),
shinyWidgets::pickerInput(
inputId = "survival_probability_time_scale",
label = "Time scale",
choices = c("days", "months", "years"),
selected = "days",
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_cohort_survival_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
sortable::bucket_list(
header = "Table formatting",
sortable::add_rank_list(
text = "none",
labels = c("cdm_name", "target_cohort"),
input_id = "survival_table_none"
),
sortable::add_rank_list(
text = "header",
labels = "estimate_name",
input_id = "survival_table_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = character(),
input_id = "survival_table_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = character(),
input_id = "survival_table_hide"
)
),
position = "right"
),
gt::gt_output("summarise_cohort_survival_gt") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Plot",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "summarise_cohort_survival_plot_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "summarise_cohort_survival_plot_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_survival_plot_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "summarise_cohort_survival_plot_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "summarise_cohort_survival_plot_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
materialSwitch(inputId = "survival_plot_interactive",
value = TRUE,
label = "Interactive",
status = "primary"),
shiny::checkboxInput(
inputId = "survival_plot_ribbon",
label = "Ribbon",
value = c(TRUE)
),
shiny::checkboxInput(
inputId = "survival_plot_cf",
label = "Plot cumulative failure",
value = FALSE
),
shiny::checkboxInput(
inputId = "survival_plot_log_log",
label = "Plot LogLog",
value = FALSE
),
shinyWidgets::pickerInput(
inputId = "survival_plot_colour",
label = "Colour",
selected = c("target_cohort"),
multiple = TRUE,
choices = c("cdm_name", "target_cohort"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "survival_plot_facet",
label = "Facet",
selected = c("cdm_name"),
multiple = TRUE,
choices = c("cdm_name", "target_cohort"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
uiOutput("summarise_cohort_survival_plot") |> withSpinner()
)
)
)
)
)
)
## cohort_survival_end
),
# cohortDiagnostics_end ----
# populationDiagnostics_start -----
bslib::nav_menu(
title = "Population diagnostics",
icon = shiny::icon("list"),
## Incidence -----
bslib::nav_panel(
title = "Incidence",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "incidence_cdm_name",
label = NULL,
selected = selected$shared_cdm_names,
choices = choices$shared_cdm_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "incidence_outcome_cohort_name",
label = NULL,
selected = selected$shared_cohort_names,
choices = choices$shared_cohort_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateIncidence", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("shower"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "incidence_analysis_interval",
label = "Time interval",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_denominator_age_group",
label = "Denominator age group",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_denominator_sex",
label = "Denominator sex",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_denominator_days_prior_observation",
label = "Denominator days prior observation",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table incidence",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "incidence_gt_download", label = ""),
class = "text-end"
),
htmltools::tags$p(style = "font-size: 0.75em;", msgPopulationDiag),
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 = "outcome_cohort_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")
),
position = "right"
),
htmltools::tags$p(style = "font-size: 0.75em;", msgPopulationDiag),
uiOutput("incidence_plot") |> withSpinner()
)
)
)
)
)
),
## Prevalence -----
bslib::nav_panel(
title = "Prevalence",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "prevalence_cdm_name",
label = NULL,
selected = selected$shared_cdm_names,
choices = choices$shared_cdm_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "prevalence_outcome_cohort_name",
label = NULL,
selected = selected$shared_cohort_names,
choices = choices$shared_cohort_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updatePrevalence", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("bath"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "prevalence_analysis_interval",
label = "Time interval",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_denominator_age_group",
label = "Denominator age group",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_denominator_sex",
label = "Denominator sex",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_denominator_days_prior_observation",
label = "Denominator days prior observation",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table prevalence",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "prevalence_gt_download", label = ""),
class = "text-end"
),
htmltools::tags$p(style = "font-size: 0.75em;", gsub("Incidence", "Prevalence", msgPopulationDiag)),
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 = "outcome_cohort_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")
),
position = "right"
),
htmltools::tags$p(style = "font-size: 0.75em;", gsub("Incidence", "Prevalence", msgPopulationDiag)),
uiOutput("prevalence_plot") |> withSpinner()
)
)
)
)
)
)
),
# populationDiagnostics_end ----
nav_spacer(),
bslib::nav_item(
bslib::popover(
shiny::icon("circle-info"),
shiny::tags$img(
src = "phenotyper_logo.png",
class = "logo-img",
alt = "Logo",
height = "auto",
width = "30%",
style = "float:right"
),
"This shiny app was generated with ",
shiny::a(
"PhenotypeR",
href = "https://github.com/OHDSI/PhenotypeR",
target = "_blank"
),
shiny::strong(phenotyper_version)
)
),
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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ui <- fluidPage(
bslib::page_navbar(
theme = bs_theme(5, "pulse"),
navbar_options =list(class = "bg-dark", theme = "dark"),
title = "PhenotypeR",
bslib::nav_panel(title = "Background",
icon = shiny::icon("disease"),
shiny::includeMarkdown(path = "background.md")),
# databaseDiagnostics_start -----
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()
)
)
)
),
# databaseDiagnostics_end ----
# codelistDiagnostics_start -----
bslib::nav_menu(
title = "Codelist diagnostics",
icon = shiny::icon("list"),
## achilles_results_start
## achilles code use -----
bslib::nav_panel(
title = "Achilles code use",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "achilles_code_use_cdm_name",
label = NULL,
selected = selected$shared_cdm_name,
choices = choices$shared_cdm_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateAchillesCodeUse", "Update",
style = "simple"),
width = "100%"
)
)
)),
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_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_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_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",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"), # Explicitly use tags$label
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "orphan_code_use_cdm_name",
label = NULL,
selected = selected$shared_cdm_name,
choices = choices$shared_cdm_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateOrphanCodeUse", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("circle-half-stroke"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "orphan_code_use_codelist_name",
label = "Codelist name",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
div(style="display: flex; justify-content: space-between;",
div(style="flex: 1;", prettyCheckbox(inputId = "orphan_person_count",
label = "Person count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE)),
div(style="flex: 1;", prettyCheckbox(inputId = "orphan_record_count",
label = "Record count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE))
)
),
bslib::accordion_panel(
title = "Table formatting",
materialSwitch(inputId = "orphan_interactive",
value = TRUE,
label = "Interactive",
status = "primary"),
sortable::bucket_list(
header = NULL,
sortable::add_rank_list(
text = "none",
labels = c("variable_name", "cohort_name", "variable_level"),
input_id = "orphan_codes_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name", "estimate_name"),
input_id = "orphan_codes_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = character(),
input_id = "orphan_codes_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = character(),
input_id = "orphan_codes_gt_hide"
)
)
)
)
),
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "orphan_codes_download", label = ""),
class = "text-end"
),
uiOutput("orphan_codes_tbl") |> withSpinner()
)
)
),
## achilles_results_end
## Cohort code use -----
bslib::nav_panel(
title = "Cohort code use",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "cohort_code_use_cdm_name",
label = NULL,
selected = selected$shared_cdm_name,
choices = choices$shared_cdm_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "cohort_code_use_cohort_name",
label = NULL,
selected = selected$shared_cohort_name,
choices = choices$shared_cohort_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateCohortCodeUse", "Update",
style = "simple"),
width = "100%"
)
)
)),
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_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()
)
)
)
),
## measurement_diagnostics_start
## Measurement code use -----
bslib::nav_panel(
title = "Measurements Code Use",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "measurement_timings_cdm_name",
label = NULL,
selected = selected$shared_cdm_name,
choices = choices$shared_cdm_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "measurement_timings_cohort_name",
label = NULL,
selected = selected$shared_cohort_name,
choices = choices$shared_cohort_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateMeasurementCodeUse", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("weight-scale"),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table Values (Concepts)",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "measurement_value_as_concept_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
sortable::bucket_list(
header = "Table formatting",
sortable::add_rank_list(
text = "none",
labels = c("cohort_name", "variable_level", "estimate_name"),
input_id = "measurement_value_as_concept_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name"),
input_id = "measurement_value_as_concepts_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = c("codelist_name"),
input_id = "measurement_value_as_concept_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = c("variable_name"),
input_id = "measurement_value_as_concept_gt_hide"
)
),
position = "right"
),
gt::gt_output("measurement_value_as_concept_tbl") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Plot Values (Concepts)",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "plot_measurement_value_as_concept_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "plot_measurement_value_as_concept_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "plot_measurement_value_as_concept_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "plot_measurement_value_as_concept_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "plot_measurement_value_as_concept_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shinyWidgets::pickerInput(
inputId = "measurement_value_as_concept_x",
label = "Horizontal axis",
selected = c("count"),
multiple = FALSE,
choices = c("count", "percentage"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_value_as_concept_y",
label = "Vertical axis",
selected = c("codelist_name"),
multiple = FALSE,
choices = c("count", "variable_level", "codelist_name", "concept_name", "cdm_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_value_as_concept_colour",
label = "Colour",
selected = c("concept_name", "variable_level"),
multiple = TRUE,
choices = c("count", "variable_level", "codelist_name", "concept_name", "cdm_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_value_as_concept_facet",
label = "Facet",
selected = c("cdm_name"),
multiple = TRUE,
choices = c("count", "variable_level", "codelist_name", "concept_name", "cdm_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
shiny::plotOutput("plot_measurement_value_as_concept")
)
)
),
bslib::nav_panel(
title = "Table Values (Numeric)",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "measurement_value_as_numeric_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
sortable::bucket_list(
header = "Table formatting",
sortable::add_rank_list(
text = "none",
labels = c("cohort_name", "estimate_name"),
input_id = "measurement_value_as_numeric_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name"),
input_id = "measurement_value_as_numeric_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = c("codelist_name"),
input_id = "measurement_value_as_numeric_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = c("variable_name", "variable_level"),
input_id = "measurement_value_as_numeric_gt_hide"
)
),
position = "right"
),
gt::gt_output("measurement_value_as_numeric_tbl") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Plot Values (Numeric)",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "plot_measurement_value_as_numeric_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "plot_measurement_value_as_numeric_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "plot_measurement_value_as_numeric_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "plot_measurement_value_as_numeric_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "plot_measurement_value_as_numeric_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shinyWidgets::pickerInput(
inputId = "measurement_value_as_numeric_x",
label = "Horizontal axis",
selected = c("unit_concept_name"),
multiple = FALSE,
choices = c("unit_concept_name", "codelist_name", "concept_name", "cdm_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_value_as_numeric_plottype",
label = "Plot type",
selected = "boxplot",
multiple = FALSE,
choices = c("boxplot", "densityplot"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_value_as_numeric_colour",
label = "Colour",
selected = c("cdm_name"),
multiple = TRUE,
choices = c("unit_concept_name", "codelist_name", "concept_name", "cdm_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_value_as_numeric_facet",
label = "Facet",
selected = c("codelist_name", "concept_name"),
multiple = TRUE,
choices = c("unit_concept_name", "codelist_name", "concept_name", "cdm_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
shiny::plotOutput("plot_measurement_value_as_numeric")
)
)
),
bslib::nav_panel(
title = "Table Timings",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "measurement_timings_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
sortable::bucket_list(
header = "Table formatting",
sortable::add_rank_list(
text = "none",
labels = c("cohort_name", "variable_name", "estimate_name"),
input_id = "measurement_timings_gt_none"
),
sortable::add_rank_list(
text = "header",
labels = c("cdm_name"),
input_id = "measurement_timings_gt_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = c("codelist_name"),
input_id = "measurement_timings_gt_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = c("variable_level"),
input_id = "measurement_timings_gt_hide"
)
),
position = "right"
),
gt::gt_output("measurement_timings_tbl") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Plot timings",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "plot_measurement_timings_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "plot_measurement_timings_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "plot_measurement_timings_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "plot_measurement_timings_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "plot_measurement_timings_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shinyWidgets::pickerInput(
inputId = "measurement_timings_y",
label = "Vertical axis",
selected = c("time"),
multiple = FALSE,
choices = c("time", "measurements_per_subject"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_timings_time_scale",
label = "Time scale",
selected = c("days"),
multiple = FALSE,
choices = c("days", "years"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_timings_plottype",
label = "Plot type",
selected = "boxplot",
multiple = FALSE,
choices = c("boxplot", "densityplot"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_timings_colour",
label = "Colour",
selected = c("codelist_name"),
multiple = TRUE,
choices = c("cdm_name", "codelist_name", "cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "measurement_timings_facet",
label = "Facet",
selected = c("cdm_name"),
multiple = TRUE,
choices = c("cdm_name", "codelist_name", "cohort_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
shiny::plotOutput("plot_measurement_timings")
)
)
)
)
)
## measurement_diagnostics_end
),
# codelistDiagnostics_end ----
# cohortDiagnostics_start -----
bslib::nav_menu(
title = "Cohort diagnostics",
icon = shiny::icon("list"),
## Cohort count ----
bslib::nav_panel(
title = "Cohort count",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_count_cdm_name",
label = NULL,
selected = selected$shared_cdm_name,
choices = choices$shared_cdm_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_count_cohort_name",
label = NULL,
selected = selected$shared_cohort_name,
choices = choices$shared_cohort_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateCohortCount", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("person"),
accordion(open = FALSE,
accordion_panel(
title = "Show cohort expectations",
value = "panel_ce_1",
reactable::reactableOutput("cohort_count_expectations")
)),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
div(style="display: flex; justify-content: space-between;",
div(style="flex: 1;", prettyCheckbox(inputId = "cohort_count_person_count",
label = "Person count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE)),
div(style="flex: 1;", prettyCheckbox(inputId = "cohort_count_record_count",
label = "Record count",
value = TRUE,
status = "primary",
shape = "curve",
outline = TRUE))
)
)
)
),
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"
),
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",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_characteristics_cdm_name",
label = NULL,
selected = selected$shared_cdm_names,
choices = choices$shared_cdm_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_characteristics_cohort_name",
label = NULL,
selected = selected$shared_cohort_names,
choices = choices$shared_cohort_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateCohortCharacteristics", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("users-gear"),
accordion(open = FALSE,
accordion_panel(
title = "Show cohort expectations",
value = "panel_ce_2",
reactable::reactableOutput("cohort_characteristics_expectations")
)),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
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 = "Table formatting",
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",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_cdm_name",
label = NULL,
selected = selected$shared_cdm_names,
choices = choices$shared_cdm_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_cohort_name",
label = NULL,
selected = selected$shared_cohort_names,
choices = choices$shared_cohort_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateLSC", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("arrow-up-right-dots"),
accordion(open = FALSE,
accordion_panel(
title = "Show cohort expectations",
value = "panel_ce_3",
reactable::reactableOutput("large_scale_characteristics_expectations")
)),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_large_scale_characteristics_table_name",
label = "Domain",
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_variable_level",
label = "Time window",
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_analysis",
label = "Analysis",
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"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
shiny::numericInput(
min = 1,
step = 1,
inputId = "summarise_large_scale_characteristics_top_concepts",
label = "Top concepts",
value = 10
),
position = "right"
),
gt::gt_output("summarise_large_scale_characteristics_gt") |> withSpinner()
)
)
)
)
)
),
## Compare large scale characteristics -----
bslib::nav_panel(
title = "Compare large scale characteristics",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_cdm_name",
label = NULL,
selected = selected$shared_cdm_names,
choices = choices$shared_cdm_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%",
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_cohort_name",
label = NULL,
selected = selected$shared_cohort_names,
choices = choices$shared_cohort_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateCompareLSC", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("people-arrows"),
accordion(open = FALSE,
accordion_panel(
title = "Show cohort expectations",
value = "panel_ce_4",
reactable::reactableOutput("compare_large_scale_characteristics_expectations")
)),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_cohort_compare",
label = "Comparator cohort",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shiny::fluidRow(
shiny::column(width = 5, offset = 1,
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_cohort_1",
label = "Cohort type (reference)",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
tags$style(HTML("
label[for='compare_large_scale_characteristics_cohort_1'] {
text-align: center;
width: 100%;
display: block;
}"))
),
shiny::column(width = 5,
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_cohort_2",
label = "Cohort type (comparator)",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
tags$style(HTML("
label[for='compare_large_scale_characteristics_cohort_2'] {
text-align: center;
width: 100%;
display: block;
}"))
)
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_table_name",
label = "Domain",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_analysis",
label = "Analysis",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "compare_large_scale_characteristics_variable_level",
label = "Time window",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::prettyCheckbox(
inputId = "compare_large_scale_characteristics_impute_missings",
label = "Impute missing values as 0",
value = TRUE)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "compare_large_scale_characteristics_tidy_download", label = ""),
class = "text-end"
),
htmltools::tags$p(style = "font-size: 0.75em;", msgMatchedSample),
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",
htmltools::tags$p(style = "font-size: 0.75em;", msgMatchedSample),
plotly::plotlyOutput("plotly_compare_lsc") |> withSpinner()
)
)
)
)
)
),
## Compare cohorts -----
bslib::nav_panel(
title = "Compare cohorts",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_cdm_name",
label = NULL,
selected = selected$shared_cdm_names,
choices = choices$shared_cdm_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_cohort_name_reference",
label = NULL,
selected = selected$shared_cohort_names,
choices = choices$shared_cohort_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateCompareCohorts", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("yin-yang"),
accordion(open = FALSE,
accordion_panel(
title = "Show cohort expectations",
value = "panel_ce_5",
reactable::reactableOutput("compare_cohorts_expectations")
)),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_cohort_comparator",
label = "Cohort comparator",
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 = "Cohort Overlap (Table)",
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",
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")
),
shiny::checkboxInput(
inputId = "summarise_cohort_overlap_gt_uniqueCombinations",
label = "uniqueCombinations",
value = c(TRUE)
),
sortable::bucket_list(
header = "Table formatting",
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"
)
),
position = "right"
),
gt::gt_output("summarise_cohort_overlap_gt") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Cohort Overlap (Plot)",
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_variable_name",
label = "Variable name",
choices = c("Only in reference cohort", "In both cohorts", "Only in comparator cohort"),
selected = c("Only in reference cohort", "In both cohorts", "Only in comparator cohort"),
multiple = TRUE,
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)
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_overlap_plot_colour",
label = "Colour",
selected = c("variable_name"),
multiple = TRUE,
choices = c("cdm_name", "cohort_name_reference", "cohort_name_comparator", "variable_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
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"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
plotly::plotlyOutput("summarise_cohort_overlap_plot")
)
)
),
bslib::nav_panel(
title = "Cohort Timing (Table)",
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",
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)
),
sortable::bucket_list(
header = "Table formatting",
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"
)
),
position = "right"
),
gt::gt_output("summarise_cohort_timing_gt") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Cohort Timing (Plot)",
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_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_plot_uniqueCombinations",
label = "uniqueCombinations",
value = c(TRUE)
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_timing_plot_colour",
label = "Colour",
selected = c("cohort_name_comparator"),
multiple = TRUE,
choices = c("cdm_name", "cohort_name_reference", "cohort_name_comparator", "variable_name"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
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"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
plotly::plotlyOutput("summarise_cohort_timing_plot")
)
)
)
)
)
),
## cohort_survival_start
## Cohort survival -----
bslib::nav_panel(
title = "Cohort survival",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "survival_probability_cdm_name",
label = NULL,
selected = selected$shared_cdm_names,
choices = choices$shared_cdm_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "survival_probability_cohort_name",
label = NULL,
selected = selected$shared_cohort_names,
choices = choices$shared_cohort_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateCohortSurvival", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("chart-gantt"),
accordion(open = FALSE,
accordion_panel(
title = "Show cohort expectations",
value = "panel_ce_6",
reactable::reactableOutput("cohort_survival_expectations")
)),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shiny::checkboxInput(
inputId = "survival_porbability_include_matches",
label = "Show matched cohorts",
value = c(TRUE)
),
shinyWidgets::pickerInput(
inputId = "survival_probability_time_scale",
label = "Time scale",
choices = c("days", "months", "years"),
selected = "days",
multiple = FALSE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "summarise_cohort_survival_gt_download", label = ""),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
sortable::bucket_list(
header = "Table formatting",
sortable::add_rank_list(
text = "none",
labels = c("cdm_name", "target_cohort"),
input_id = "survival_table_none"
),
sortable::add_rank_list(
text = "header",
labels = "estimate_name",
input_id = "survival_table_header"
),
sortable::add_rank_list(
text = "groupColumn",
labels = character(),
input_id = "survival_table_groupColumn"
),
sortable::add_rank_list(
text = "hide",
labels = character(),
input_id = "survival_table_hide"
)
),
position = "right"
),
gt::gt_output("summarise_cohort_survival_gt") |> withSpinner()
)
)
),
bslib::nav_panel(
title = "Plot",
bslib::card(
full_screen = TRUE,
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::numericInput(
inputId = "summarise_cohort_survival_plot_download_width",
label = "Width",
value = 15
),
shiny::numericInput(
inputId = "summarise_cohort_survival_plot_download_height",
label = "Height",
value = 10
),
shinyWidgets::pickerInput(
inputId = "summarise_cohort_survival_plot_download_units",
label = "Units",
selected = "cm",
choices = c("px", "cm", "inch"),
multiple = FALSE
),
shiny::numericInput(
inputId = "summarise_cohort_survival_plot_download_dpi",
label = "dpi",
value = 300
),
shiny::downloadButton(outputId = "summarise_cohort_survival_plot_download", label = "Download")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
materialSwitch(inputId = "survival_plot_interactive",
value = TRUE,
label = "Interactive",
status = "primary"),
shiny::checkboxInput(
inputId = "survival_plot_ribbon",
label = "Ribbon",
value = c(TRUE)
),
shiny::checkboxInput(
inputId = "survival_plot_cf",
label = "Plot cumulative failure",
value = FALSE
),
shiny::checkboxInput(
inputId = "survival_plot_log_log",
label = "Plot LogLog",
value = FALSE
),
shinyWidgets::pickerInput(
inputId = "survival_plot_colour",
label = "Colour",
selected = c("target_cohort"),
multiple = TRUE,
choices = c("cdm_name", "target_cohort"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "survival_plot_facet",
label = "Facet",
selected = c("cdm_name"),
multiple = TRUE,
choices = c("cdm_name", "target_cohort"),
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
position = "right"
),
uiOutput("summarise_cohort_survival_plot") |> withSpinner()
)
)
)
)
)
)
## cohort_survival_end
),
# cohortDiagnostics_end ----
# populationDiagnostics_start -----
bslib::nav_menu(
title = "Population diagnostics",
icon = shiny::icon("list"),
## Incidence -----
bslib::nav_panel(
title = "Incidence",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "incidence_cdm_name",
label = NULL,
selected = selected$shared_cdm_names,
choices = choices$shared_cdm_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "incidence_outcome_cohort_name",
label = NULL,
selected = selected$shared_cohort_names,
choices = choices$shared_cohort_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updateIncidence", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("shower"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "incidence_analysis_interval",
label = "Time interval",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_denominator_age_group",
label = "Denominator age group",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_denominator_sex",
label = "Denominator sex",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "incidence_denominator_days_prior_observation",
label = "Denominator days prior observation",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table incidence",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "incidence_gt_download", label = ""),
class = "text-end"
),
htmltools::tags$p(style = "font-size: 0.75em;", msgPopulationDiag),
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 = "outcome_cohort_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")
),
position = "right"
),
htmltools::tags$p(style = "font-size: 0.75em;", msgPopulationDiag),
uiOutput("incidence_plot") |> withSpinner()
)
)
)
)
)
),
## Prevalence -----
bslib::nav_panel(
title = "Prevalence",
bslib::accordion(
bslib::accordion_panel(
title = "Shared inputs",
tags$div(
style = "background-color: #750075; color: white; padding: 10px; font-weight: bold; display: flex; flex-wrap: wrap; gap: 10px; gap: 10px; height: auto; align-items: center;",
tags$label("Select Database(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "prevalence_cdm_name",
label = NULL,
selected = selected$shared_cdm_names,
choices = choices$shared_cdm_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$label("Select Cohort(s):"),
tags$div(
style = "width: 225px;",
tags$div(
style = "margin-top: 15px;",
shinyWidgets::pickerInput(
inputId = "prevalence_outcome_cohort_name",
label = NULL,
selected = selected$shared_cohort_names,
choices = choices$shared_cohort_names,
multiple = TRUE,
options = list(`actions-box` = TRUE, `selected-text-format` = "count > 1",
`deselect-all-text` = "None", `select-all-text` = "All"),
width = "100%"
)
)
),
tags$div(
style = "width: 225px;",
actionBttn("updatePrevalence", "Update",
style = "simple"),
width = "100%"
)
)
)),
icon = shiny::icon("bath"),
bslib::layout_sidebar(
sidebar = bslib::sidebar(width = 400, open = "closed",
bslib::accordion(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "prevalence_analysis_interval",
label = "Time interval",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_denominator_age_group",
label = "Denominator age group",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_denominator_sex",
label = "Denominator sex",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "prevalence_denominator_days_prior_observation",
label = "Denominator days prior observation",
choices = NULL,
selected = NULL,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
)
)
),
bslib::navset_card_tab(
bslib::nav_panel(
title = "Table prevalence",
bslib::card(
full_screen = TRUE,
bslib::card_header(
shiny::downloadButton(outputId = "prevalence_gt_download", label = ""),
class = "text-end"
),
htmltools::tags$p(style = "font-size: 0.75em;", gsub("Incidence", "Prevalence", msgPopulationDiag)),
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 = "outcome_cohort_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")
),
position = "right"
),
htmltools::tags$p(style = "font-size: 0.75em;", gsub("Incidence", "Prevalence", msgPopulationDiag)),
uiOutput("prevalence_plot") |> withSpinner()
)
)
)
)
)
)
),
# populationDiagnostics_end ----
nav_spacer(),
bslib::nav_item(
bslib::popover(
shiny::icon("circle-info"),
shiny::tags$img(
src = "phenotyper_logo.png",
class = "logo-img",
alt = "Logo",
height = "auto",
width = "30%",
style = "float:right"
),
"This shiny app was generated with ",
shiny::a(
"PhenotypeR",
href = "https://github.com/OHDSI/PhenotypeR",
target = "_blank"
),
shiny::strong(phenotyper_version)
)
),
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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