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Create grouped disease statistics report

Source: R/reports.R
create_report_grouped_stats.Rd

'create_report_grouped_stats' generates a comprehensive report with current and historical statistics for diseases organized by group. The report includes monthly counts/rates, year-to-date counts, and trend analysis.

Usage

create_report_grouped_stats(data, diseases, y, m, config)

Arguments

data

Dataframe. Input data with columns:

  • disease (character)

  • year (integer)

  • month (integer)

  • counts (integer)

diseases

Dataframe. Diseases to include in the report. Must have column EpiTrax_name (character) with diseases to include. Optionally may have column Group_name (character) to define disease groupings. If Group_name is missing, all diseases will be grouped under "Uncategorized".

y

Integer. Report year

m

Integer. Report month (1-12)

config

List. Report settings

Value

Dataframe with one row per disease containing:

  • Group: Disease group name

  • Disease: Disease name

  • Monthly counts and rates for current year/month

  • Historical monthly averages and medians

  • Year-to-date counts and historical averages and medians

  • YTD trend indicators

Details

Uses the following config options:

  • current_population

  • avg_5yr_population

  • rounding_decimals

  • trend_threshold

See also

create_report_monthly_counts(), create_report_monthly_avgs(), create_report_monthly_medians(), create_report_ytd_counts(), create_report_ytd_medians() which this function uses and epitraxr_config() for config options

Examples

data <- data.frame(
  disease = c("A", "A", "B", "B"),
  year = c(2023, 2024, 2023, 2024),
  month = c(1, 1, 2, 2),
  counts = c(10, 20, 15, 25)
)
diseases <- data.frame(
  EpiTrax_name = c("A", "B", "C"),
  Group_name = c("Group1", "Group1", "Group2")
)
config <- list(
  current_population = 100000,
  avg_5yr_population = 100000,
  rounding_decimals = 1,
  trend_threshold = 0.15
)
create_report_grouped_stats(data, diseases, 2024, 2, config)
#>    Group Disease February 2024 February 2024 Rate Historical February Avg
#> 1 Group1       A             0                  0                       0
#> 2 Group1       B            25                 25                      15
#> 3 Group2       C             0                  0                       0
#>   Historical February Median 2024 YTD Historical 2024 YTD Avg
#> 1                          0       20                      10
#> 2                         15       25                      15
#> 3                          0        0                       0
#>   Historical 2024 YTD Median YTD Trend
#> 1                         10  Elevated
#> 2                         15  Elevated
#> 3                          0  Expected