## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
# avoid warnings about the different heading
options(rmarkdown.html_vignette.check_title = FALSE)

# load the package library
library(cvdprevent)

## -----------------------------------------------------------------------------
cvd_time_period_list() |>
  dplyr::filter(IndicatorTypeName == 'Standard') |>
  dplyr::slice_max(order_by = TimePeriodID, n = 4) |>
  dplyr::select(TimePeriodID, TimePeriodName) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_time_period_list(indicator_type_id = 2) |>
  dplyr::slice_max(order_by = TimePeriodID, n = 4) |>
  dplyr::select(
    IndicatorTypeID,
    IndicatorTypeName,
    TimePeriodID,
    TimePeriodName
  ) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_time_period_system_levels() |>
  dplyr::slice_max(order_by = TimePeriodID) |>
  dplyr::select(TimePeriodID, TimePeriodName, SystemLevelID, SystemLevelName) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_area_system_level(time_period_id = 17) |>
  dplyr::select(SystemLevelID, SystemLevelName) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_area_system_level_time_periods() |>
  dplyr::filter(SystemLevelName == 'Practice') |>
  dplyr::slice_max(order_by = TimePeriodID, n = 4) |>
  dplyr::select(SystemLevelID, SystemLevelName, TimePeriodID, TimePeriodName) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_area_list(time_period_id = 17, system_level_id = 4) |>
  dplyr::select(SystemLevelName, AreaID, AreaCode, AreaName) |>
  dplyr::slice_head(n = 4) |>
  gt::gt()

## -----------------------------------------------------------------------------
# get the list from the function
returned_list <- cvd_area_details(time_period_id = 17, area_id = 7922)

## -----------------------------------------------------------------------------
returned_list$area_details |>
  dplyr::select(AreaCode, AreaName, SystemLevelID) |>
  gt::gt()

## -----------------------------------------------------------------------------
returned_list$area_parent_details |>
  dplyr::select(AreaID, AreaName, SystemLevelID) |>
  gt::gt()

## -----------------------------------------------------------------------------
returned_list$area_child_details |>
  dplyr::select(AreaID, AreaName, SystemLevelID) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_area_unassigned(time_period_id = 17, system_level_id = 5) |>
  dplyr::slice_head(n = 4) |>
  dplyr::select(SystemLevelName, AreaID, AreaName) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_area_unassigned(time_period_id = 17, system_level_id = 1) |>
  dplyr::select(SystemLevelName, AreaID, AreaName) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_area_search(partial_area_name = 'foo', time_period_id = 17) |>
  dplyr::select(AreaID, AreaName, AreaCode) |>
  gt::gt()

## -----------------------------------------------------------------------------
return_list <- cvd_area_nested_subsystems(area_id = 8030)
return_list |> summary()

## -----------------------------------------------------------------------------
return_list$level_1 |>
  gt::gt()

## -----------------------------------------------------------------------------
return_list$level_2 |>
  dplyr::slice_head(n = 4) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_area_flat_subsystems(area_id = 5) |>
  dplyr::glimpse()

## -----------------------------------------------------------------------------
cvd_indicator_list(time_period_id = 17, system_level_id = 5) |>
  dplyr::select(IndicatorID, IndicatorCode, IndicatorShortName) |>
  dplyr::slice_head(n = 4) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_indicator_metric_list(time_period_id = 17, system_level_id = 1) |>
  dplyr::filter(IndicatorID == 1, MetricCategoryName == '40-59') |>
  dplyr::count(
    IndicatorID,
    IndicatorShortName,
    MetricID,
    MetricCategoryName,
    CategoryAttribute
  ) |>
  dplyr::select(-n) |>
  gt::gt()

## -----------------------------------------------------------------------------
returned_list <- cvd_indicator(time_period_id = 17, area_id = 1103)
returned_list |> summary()

## -----------------------------------------------------------------------------
returned_list$indicators |>
  dplyr::select(IndicatorID, IndicatorCode, IndicatorShortName) |>
  dplyr::arrange(IndicatorID) |>
  dplyr::slice_head(n = 4) |>
  gt::gt()

## -----------------------------------------------------------------------------
returned_list$metric_categories |>
  dplyr::filter(IndicatorID == 7, MetricCategoryID %in% c(7, 8)) |>
  dplyr::select(
    IndicatorID,
    MetricCategoryTypeName,
    CategoryAttribute,
    MetricCategoryName,
    MetricID
  ) |>
  gt::gt()

## -----------------------------------------------------------------------------
returned_list$metric_data |>
  dplyr::filter(MetricID %in% c(126, 132)) |>
  dplyr::select(MetricID, Value, Numerator, Denominator) |>
  gt::gt()

## -----------------------------------------------------------------------------
returned_list$timeseries_data |>
  dplyr::filter(MetricID %in% c(126, 132), !is.na(Value)) |>
  # prepare for plotting
  dplyr::mutate(
    EndDate = as.Date(EndDate, format = '%a, %d %b %Y 00:00:00 GMT'),
    MetricID = MetricID |> as.factor()
  ) |>
  ggplot2::ggplot(ggplot2::aes(
    x = EndDate,
    y = Value,
    group = MetricID,
    colour = MetricID
  )) +
  ggplot2::geom_point() +
  ggplot2::geom_line()

## -----------------------------------------------------------------------------
returned_list <-
  cvd_indicator(time_period_id = 17, area_id = 3, tag_id = c(3, 4))

## -----------------------------------------------------------------------------
if (!is.null(returned_list$indicators)) {
  returned_list$indicators |>
    dplyr::select(IndicatorID, IndicatorCode, IndicatorShortName) |>
    dplyr::arrange(IndicatorID) |>
    dplyr::slice_head(n = 4) |>
    gt::gt()
}

## -----------------------------------------------------------------------------
cvd_indicator_tags() |>
  dplyr::arrange(IndicatorTagID) |>
  dplyr::slice_head(n = 5) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_indicator_details(indicator_id = 7) |>
  dplyr::select(IndicatorID, MetaDataTitle, MetaData) |>
  dplyr::slice_head(n = 5) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_indicator_sibling(time_period_id = 17, area_id = 1103, metric_id = 126) |>
  dplyr::select(
    AreaID,
    AreaName,
    Value,
    LowerConfidenceLimit,
    UpperConfidenceLimit
  ) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_indicator_child_data(time_period_id = 17, area_id = 74, metric_id = 126) |>
  dplyr::select(
    AreaID,
    AreaName,
    Value,
    LowerConfidenceLimit,
    UpperConfidenceLimit
  ) |>
  gt::gt()

## -----------------------------------------------------------------------------
returned_list <- cvd_indicator_data(
  time_period_id = 17,
  indicator_id = 7,
  area_id = 701
)
returned_list |> summary()

## -----------------------------------------------------------------------------
if ("indicator_metrics" %in% names(returned_list)) {
  returned_list$indicator_metrics |> dplyr::glimpse()
}

## -----------------------------------------------------------------------------
if ("area_data" %in% names(returned_list)) {
  returned_list$area_data |>
    dplyr::filter(MetricCategoryTypeName == "Sex") |>
    dplyr::select(
      AreaID,
      CategoryAttribute,
      Value,
      LowerConfidenceLimit,
      UpperConfidenceLimit
    ) |>
    gt::gt()
}

## -----------------------------------------------------------------------------
if ("national_data" %in% names(returned_list)) {
  returned_list$national_data |>
    dplyr::filter(MetricCategoryTypeName == "Sex") |>
    dplyr::select(
      AreaID,
      CategoryAttribute,
      Value,
      LowerConfidenceLimit,
      UpperConfidenceLimit
    ) |>
    gt::gt()
}

## -----------------------------------------------------------------------------
cvd_indicator_raw_data(
  indicator_id = 7,
  time_period_id = 17,
  system_level_id = 5
) |>
  dplyr::slice_head(n = 5) |>
  dplyr::select(AreaCode, AreaName, Value) |>
  gt::gt()

## -----------------------------------------------------------------------------
returned_list <- cvd_indicator_nationalarea_metric_data(
  metric_id = 150,
  time_period_id = 17,
  area_id = 553
)

returned_list |> summary()

## -----------------------------------------------------------------------------
area_data <- returned_list$area
area_data |> gt::gt()

## -----------------------------------------------------------------------------
target_data <- returned_list$target
target_data |> gt::gt()

## -----------------------------------------------------------------------------
cvd_indicator_priority_groups() |>
  dplyr::select(
    PriorityGroup,
    PathwayGroupName,
    PathwayGroupID,
    IndicatorID,
    IndicatorName
  ) |>
  dplyr::slice_head(by = PathwayGroupID) |>
  gt::gt(row_group_as_column = T)

## -----------------------------------------------------------------------------
cvd_indicator_pathway_group(pathway_group_id = 9) |>
  dplyr::select(
    PathwayGroupName,
    PathwayGroupID,
    IndicatorCode,
    IndicatorID,
    IndicatorName
  ) |>
  dplyr::group_by(PathwayGroupName) |>
  gt::gt(row_group_as_column = T)

## -----------------------------------------------------------------------------
cvd_indicator_group(indicator_group_id = 13) |>
  dplyr::select(
    IndicatorGroupID,
    IndicatorGroupName,
    IndicatorGroupTypeName,
    IndicatorID,
    IndicatorName
  ) |>
  dplyr::group_by(IndicatorGroupID, IndicatorGroupName) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_indicator_metric_timeseries(metric_id = 130, area_id = 705) |>
  # prepare for plotting
  dplyr::mutate(
    TimePeriodName = stats::reorder(TimePeriodName, TimePeriodID)
  ) |>
  ggplot2::ggplot(ggplot2::aes(
    x = TimePeriodName,
    y = Value,
    group = AreaName,
    colour = AreaName
  )) +
  ggplot2::geom_point() +
  ggplot2::geom_line() +
  ggplot2::theme(
    axis.text.x = ggplot2::element_text(angle = 45, hjust = 1)
  )

## -----------------------------------------------------------------------------
cvd_indicator_metric_timeseries(metric_id = 130, area_id = 705) |>
  dplyr::select(AreaName, TimePeriodName, TimePeriodID, Value) |>
  tidyr::pivot_wider(
    names_from = AreaName,
    values_from = Value
  ) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_indicator_person_timeseries(indicator_id = 7, area_id = 705) |>
  dplyr::filter(
    MetricCategoryTypeName == 'Age group',
    !is.na(Value)
  ) |>
  dplyr::mutate(
    TimePeriodName = stats::reorder(TimePeriodName, TimePeriodID)
  ) |>
  ggplot2::ggplot(
    ggplot2::aes(
      x = TimePeriodName,
      y = Value,
      group = MetricCategoryName,
      colour = MetricCategoryName
    )
  ) +
  ggplot2::geom_point() +
  ggplot2::geom_line() +
  ggplot2::theme(
    axis.text.x = ggplot2::element_text(angle = 45, hjust = 1)
  )

## -----------------------------------------------------------------------------
cvd_indicator_person_timeseries(indicator_id = 7, area_id = 705) |>
  dplyr::filter(
    MetricCategoryTypeName == 'Age group',
    !is.na(Value)
  ) |>
  dplyr::select(MetricCategoryName, TimePeriodName, TimePeriodID, Value) |>
  tidyr::pivot_wider(
    names_from = MetricCategoryName,
    values_from = Value
  ) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_indicator_metric_systemlevel_comparison(
  metric_id = 1270,
  time_period_id = 17,
  area_id = 705
) |>
  dplyr::filter(AreaID %in% c(705:709), !is.na(Value)) |>
  dplyr::select(SystemLevelName, AreaID, AreaName, Value) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_indicator_metric_area_breakdown(
  metric_id = 128,
  time_period_id = 17,
  area_id = 705
) |>
  dplyr::select(SystemLevelName, AreaID, AreaName, Value) |>
  gt::gt()

## -----------------------------------------------------------------------------
cvd_external_resource() |>
  dplyr::filter(ExternalResourceID < 10) |>
  dplyr::select(
    ExternalResourceCategory,
    ExternalResourceSource,
    ExternalResourceTitle
  ) |>
  dplyr::group_by(ExternalResourceCategory) |>
  gt::gt(row_group_as_column = T)

## -----------------------------------------------------------------------------
cvd_data_availability(time_period_id = 6, system_level_id = 5) |>
  dplyr::select(
    IndicatorShortName,
    IsAvailable,
    SystemLevelName,
    MetricCategoryTypeID
  ) |>
  dplyr::slice_head(n = 5) |>
  gt::gt()