Package 'epitraxr'

Description

clear_old_reports deletes reports from previous runs and returns a list of the reports that were deleted.

Usage

clear_old_reports(internal, public)

Arguments

Value

The list of old reports that were cleared.

Examples

ireports_folder <- file.path(tempdir(), "internal")
preports_folder <- file.path(tempdir(), "public")
dir.create(ireports_folder)
dir.create(preports_folder)

clear_old_reports(ireports_folder, preports_folder)
unlink(c(ireports_folder, preports_folder), recursive = TRUE)

Description

'compute_trend' compares values of two columns and produces a new column containing the trend result. The trend is represented by one of three values:

• "Elevated": increase from baseline

• "Less Than Expected": decrease from baseline

• "Expected": no change from baseline

Usage

compute_trend(current, historical, threshold = 0)

Arguments

Value

Character vector containing the trend labels.

Examples

# Without threshold - any difference triggers trend
compute_trend(c(5, 10, 10), c(3, 10, 11))

# With 15% threshold - small changes are "Expected"
compute_trend(c(5, 10, 10), c(3, 10, 11), threshold = 0.15)

Description

'convert_counts_to_rate' converts case counts for a given population to an adjusted per population of size X and rounds to the given number of digits.

Usage

convert_counts_to_rate(counts, pop, digits, rate_adj_pop = 1e+05)

Arguments

Value

The count(s) as rates per rate_adj_pop.

Examples

convert_counts_to_rate(50, 200000, 2)
convert_counts_to_rate(c(10, 20), 100000, 1, 10000)

Description

create_epitrax_from_file reads an EpiTrax data file and creates a structured object containing the data along with commonly used metadata and empty report lists.

Usage

create_epitrax_from_file(filepath = NULL, num_yrs = 5)

Arguments

Value

An object of class epitrax containing:

• data: The validated and formatted EpiTrax data

• diseases: Vector of unique diseases in the dataset

• yrs: Vector of years in the dataset

• report_year: Most recent year in the dataset

• report_month: Most recent month in report_year

• internal_reports: Empty list to store internal reports

• public_reports: Empty list to store public reports

See Also

read_epitrax_data() which this function wraps and setup_epitrax() which wraps this function

Examples

if (interactive()) {
  # Interactive file chooser:
  create_epitrax_from_file()
}

# Using sample data included with package
data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
epitrax <- create_epitrax_from_file(data_file)

# Access components
head(epitrax$data)
epitrax$diseases
epitrax$report_year

Description

create_filesystem creates the given folders if they don't already exist.

Usage

create_filesystem(internal, public, settings)

Arguments

Value

NULL.

Examples

internal_folder = file.path(tempdir(), "internal")
public_folder = file.path(tempdir(), "public")
settings_folder = file.path(tempdir(), "settings")

create_filesystem(
  internal = internal_folder,
  public = public_folder,
  settings = settings_folder
)

unlink(c(internal_folder, public_folder, settings_folder), recursive = TRUE)

Description

'create_public_report_combined_month_ytd' creates a comprehensive public report that combines monthly case data with year-to-date statistics for the given month and year. This provides both current month context and cumulative year progress.

Usage

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

Arguments

Details

Uses the following config options:

• current_population

• avg_5yr_population

• rounding_decimals

• trend_threshold

Value

List containing the report name and combined monthly/YTD report data with columns for monthly cases/averages/trends and YTD statistics.

See Also

create_public_report_month(), create_report_ytd_counts() which this function uses and epitraxr_config() for config options

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
# Read in EpiTrax data
data <- read_epitrax_data(data_file)

diseases <- data.frame(
  EpiTrax_name = c("Influenza", "COVID-19", "Measles", "Syphilis"),
  Public_name = c("Influenza", "COVID-19", "Measles", "Syphilis")
)
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                          package = "epitraxr")
config <- get_report_config(config_file)
create_public_report_combined_month_ytd(
 data = data,
 diseases = diseases,
 y = 2024,
 m = 2,
 config = config
)

Description

'create_public_report_month' creates a public report for the given month.

Usage

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

Arguments

Details

Uses the following config options:

• current_population

• avg_5yr_population

• rounding_decimals

• trend_threshold

Value

List containing the report name and data.

See Also

get_month_counts(), create_report_monthly_avgs() which this function uses and epitraxr_config() for config options

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
# Read in EpiTrax data
data <- read_epitrax_data(data_file)

diseases <- data.frame(
  EpiTrax_name = c("Influenza", "COVID-19", "Measles", "Syphilis"),
  Public_name = c("Influenza", "COVID-19", "Measles", "Syphilis")
)
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                          package = "epitraxr")
config <- get_report_config(config_file)

create_public_report_month(
 data = data,
 diseases = diseases,
 y = 2024,
 m = 1,
 config = config
)

Description

'create_public_report_ytd' creates a public report for YTD rates.

Usage

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

Arguments

Details

Uses the following config options:

• current_population

• avg_5yr_population

• rounding_decimals

• trend_threshold

Value

List containing the report name and data.

See Also

create_report_ytd_counts() which this function uses and epitraxr_config() for config options

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
# Read in EpiTrax data
data <- read_epitrax_data(data_file)

diseases <- data.frame(
  EpiTrax_name = c("Influenza", "COVID-19", "Measles", "Syphilis"),
  Public_name = c("Influenza", "COVID-19", "Measles", "Syphilis")
)
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                          package = "epitraxr")
config <- get_report_config(config_file)
create_public_report_ytd(
 data = data,
 diseases = diseases,
 y = 2024,
 m = 1,
 config = config
)

Description

'create_report_annual_counts' generates a data frame of annual case counts for each disease, with years as columns.

Usage

create_report_annual_counts(data, diseases)

Arguments

Value

Dataframe of annual counts with one row per disease and one column per year.

Examples

data <- data.frame(
  disease = c("A", "A", "B"),
  year = c(2020, 2021, 2020),
  counts = c(5, 7, 8)
)
create_report_annual_counts(data, diseases = c("A", "B", "C"))

Description

'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, is.public = FALSE)

Arguments

Details

Uses the following config options:

• current_population

• avg_5yr_population

• rounding_decimals

• trend_threshold

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

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)

Description

'create_report_monthly_avgs' generates a data frame of average monthly case counts for each disease across all years in the input data.

Usage

create_report_monthly_avgs(data, diseases, config)

Arguments

Details

Uses the following config options:

• rounding_decimals

Value

Dataframe of monthly averages with one row per disease and one column per month (Jan through Dec).

See Also

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)
)
config <- list(rounding_decimals = 1)
create_report_monthly_avgs(data, c("A", "B", "C"), config)

Description

'create_report_monthly_counts' generates a data frame of monthly case counts for each disease for a specific year, with months as columns.

Usage

create_report_monthly_counts(data, diseases, y)

Arguments

Value

Dataframe of monthly counts with one row per disease and one column per month (Jan through Dec).

Examples

data <- data.frame(
  disease = c("A", "A", "B", "B"),
  year = c(2024, 2024, 2024, 2023),
  month = c(1, 2, 1, 4),
  counts = c(5, 7, 8, 9)
)
create_report_monthly_counts(data, diseases = c("A", "B", "C"), y = 2024)

Description

'create_report_monthly_medians' generates a data frame of median monthly case counts for each disease across all years in the input data. This provides a more robust central tendency measure compared to averages for skewed data.

Usage

create_report_monthly_medians(data, diseases)

Arguments

Value

Dataframe of monthly medians with one row per disease and one column per month (Jan through Dec).

Examples

data <- data.frame(
  disease = c("A", "A", "A", "B", "B", "B"),
  year = c(2022, 2023, 2024, 2022, 2023, 2024),
  month = c(1, 1, 1, 2, 2, 2),
  counts = c(10, 20, 30, 5, 15, 25)
)
create_report_monthly_medians(data, c("A", "B", "C"))

Description

'create_report_ytd_counts' generates a data frame of year-to-date counts for each disease up to the given month, comparing the given year to the average of other years.

Usage

create_report_ytd_counts(data, diseases, y, m, config, as.rates = FALSE)

Arguments

Details

Uses the following config options:

• current_population

• avg_5yr_population

• rounding_decimals

Value

Dataframe with one row per disease and columns for current YTD and average YTD values (either counts or rates per 100k)

See Also

epitraxr_config() for config options

Examples

data <- data.frame(
  disease = c("A", "A", "B", "B"),
  year = c(2024, 2023, 2024, 2023),
  month = c(1, 1, 2, 2),
  counts = c(10, 20, 15, 25)
)
config <- list(
  current_population = 100000,
  avg_5yr_population = 100000,
  rounding_decimals = 1
)
create_report_ytd_counts(data, c("A", "B", "C"), 2024, 2, config)

Description

'create_report_ytd_medians' generates a data frame of median year-to-date counts for each disease up to the given month (months 1:m) across all years in the data. This provides a robust central tendency measure for YTD values.

Usage

create_report_ytd_medians(data, diseases, m)

Arguments

Value

Dataframe with one row per disease and columns for disease name and median YTD counts.

Examples

data <- data.frame(
  disease = c("A", "A", "A", "B", "B", "B"),
  year = c(2022, 2023, 2024, 2022, 2023, 2024),
  month = c(1, 1, 2, 2, 2, 3),
  counts = c(10, 15, 20, 5, 8, 12)
)
create_report_ytd_medians(data, c("A", "B", "C"), 2)

Description

epitrax_ireport_annual_counts generates an internal report of annual counts for each disease in the EpiTrax object data.

Usage

epitrax_ireport_annual_counts(epitrax)

Arguments

Value

Updated EpiTrax object with annual_counts added to the internal_reports field.

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                           package = "epitraxr")
disease_lists <- list(
  internal = "use_defaults",
  public = "use_defaults"
)

epitrax <- setup_epitrax(
  filepath = data_file,
  config_file = config_file,
  disease_list_files = disease_lists
) |>
 epitrax_ireport_annual_counts()

epitrax$internal_reports$annual_counts

Description

epitrax_ireport_monthly_avgs generates an internal report of monthly averages for all years in the EpiTrax object data, with the option to exclude the current report year.

Usage

epitrax_ireport_monthly_avgs(epitrax, exclude.report.year = FALSE)

Arguments

Value

Updated EpiTrax object with monthly averages report added to the internal_reports field.

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                           package = "epitraxr")
disease_lists <- list(
  internal = "use_defaults",
  public = "use_defaults"
)

epitrax <- setup_epitrax(
  filepath = data_file,
  config_file = config_file,
  disease_list_files = disease_lists
) |>
 epitrax_ireport_monthly_avgs()

names(epitrax$internal_reports)

Description

epitrax_ireport_monthly_counts_all_yrs generates internal reports of monthly counts for each year in the EpiTrax object data.

Usage

epitrax_ireport_monthly_counts_all_yrs(epitrax)

Arguments

Value

Updated EpiTrax object with monthly counts reports for each year added to the internal_reports field.

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                           package = "epitraxr")
disease_lists <- list(
  internal = "use_defaults",
  public = "use_defaults"
)

epitrax <- setup_epitrax(
  filepath = data_file,
  config_file = config_file,
  disease_list_files = disease_lists
) |>
 epitrax_ireport_monthly_counts_all_yrs()

names(epitrax$internal_reports)

Description

epitrax_ireport_ytd_counts_for_month generates an internal report of year-to-date counts up to a specific month in the EpiTrax object data.

Usage

epitrax_ireport_ytd_counts_for_month(epitrax, as.rates = FALSE)

Arguments

Value

Updated EpiTrax object with report added to the internal_reports field.

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                           package = "epitraxr")
disease_lists <- list(
  internal = "use_defaults",
  public = "use_defaults"
)

epitrax <- setup_epitrax(
  filepath = data_file,
  config_file = config_file,
  disease_list_files = disease_lists
) |>
 epitrax_ireport_ytd_counts_for_month(as.rates = TRUE)

names(epitrax$internal_reports)

Description

epitrax_preport_combined_month_ytd generates a public report of monthly and year-to-date (YTD) disease statistics for the report month in the EpiTrax object data.

Usage

epitrax_preport_combined_month_ytd(epitrax)

Arguments

Value

Updated EpiTrax object with YTD rates report added to the public_reports field.

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                           package = "epitraxr")
disease_lists <- list(
  internal = "use_defaults",
  public = "use_defaults"
)

epitrax <- setup_epitrax(
  filepath = data_file,
  config_file = config_file,
  disease_list_files = disease_lists
) |>
 epitrax_preport_combined_month_ytd()

names(epitrax$public_reports)

Description

epitrax_preport_month_crosssections generates monthly cross-section reports. These compare the counts for a given month against the monthly averages for the same month across previous years.

Usage

epitrax_preport_month_crosssections(epitrax, month_offsets = 0:3)

Arguments

Value

Updated EpiTrax object with monthly cross-section reports added to the public_reports field.

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                           package = "epitraxr")
disease_lists <- list(
  internal = "use_defaults",
  public = "use_defaults"
)

epitrax <- setup_epitrax(
  filepath = data_file,
  config_file = config_file,
  disease_list_files = disease_lists
) |>
 epitrax_preport_month_crosssections(month_offsets = 0:1)

names(epitrax$public_reports)

Description

epitrax_preport_ytd_rates generates a public report of year-to-date rates for the current month in the EpiTrax object data.

Usage

epitrax_preport_ytd_rates(epitrax)

Arguments

Value

Updated EpiTrax object with YTD rates report added to the public_reports field.

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                           package = "epitraxr")
disease_lists <- list(
  internal = "use_defaults",
  public = "use_defaults"
)

epitrax <- setup_epitrax(
  filepath = data_file,
  config_file = config_file,
  disease_list_files = disease_lists
) |>
 epitrax_preport_ytd_rates()

names(epitrax$public_reports)

Description

epitrax_report_grouped_stats generates a comprehensive report with current and historical statistics for diseases organized by group. The report includes monthly counts/rates, historical averages and medians, year-to-date counts, and trend analysis. It can be run for either internal or public reports.

Usage

epitrax_report_grouped_stats(epitrax, is.public = FALSE)

Arguments

Value

Updated EpiTrax object with grouped statistics report added to either the internal_reports or public_reports field, depending on the is.public parameter.

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                           package = "epitraxr")
disease_lists <- list(
  internal = "use_defaults",
  public = "use_defaults"
)

epitrax <- setup_epitrax(
  filepath = data_file,
  config_file = config_file,
  disease_list_files = disease_lists
) |>
 epitrax_report_grouped_stats()

names(epitrax$internal_reports)

Description

epitrax_report_monthly_medians generates a report of monthly medians for all years in the EpiTrax object data, with the option to exclude the current report year. It can be run for either internal or public reports.

Usage

epitrax_report_monthly_medians(
  epitrax,
  is.public = FALSE,
  exclude.report.year = FALSE
)

Arguments

Value

Updated EpiTrax object with monthly medians report added to either the internal_reports or public_reports field, depending on the is.public parameter.

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                           package = "epitraxr")
disease_lists <- list(
  internal = "use_defaults",
  public = "use_defaults"
)

epitrax <- setup_epitrax(
  filepath = data_file,
  config_file = config_file,
  disease_list_files = disease_lists
) |>
 epitrax_report_monthly_medians()

names(epitrax$internal_reports)

Description

epitrax_report_ytd_medians generates a report of median year-to-date counts for each disease up to the current report month across all years in the EpiTrax object data, with the option to exclude the current report year. It can be run for either internal or public reports.

Usage

epitrax_report_ytd_medians(
  epitrax,
  is.public = FALSE,
  exclude.report.year = FALSE
)

Arguments

Value

Updated EpiTrax object with YTD medians report added to either the internal_reports or public_reports field, depending on the is.public parameter.

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                           package = "epitraxr")
disease_lists <- list(
  internal = "use_defaults",
  public = "use_defaults"
)

epitrax <- setup_epitrax(
  filepath = data_file,
  config_file = config_file,
  disease_list_files = disease_lists
) |>
 epitrax_report_ytd_medians()

names(epitrax$internal_reports)

Description

epitrax_set_config_from_file reads a report configuration file and adds it to the EpiTrax object.

Usage

epitrax_set_config_from_file(epitrax, filepath)

Arguments

Value

Updated EpiTrax object with config field set.

See Also

epitrax_set_config_from_list() and the convenience function setup_epitrax() which wraps this function

Examples

config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                           package = "epitraxr")
epitrax <- structure(
  list(data = c(1,2,3)),
  class = "epitrax"
)
epitrax <- epitrax_set_config_from_file(epitrax, config_file)

Description

epitrax_set_config_from_list sets the report configuration from the given list.

Usage

epitrax_set_config_from_list(epitrax, config = NULL)

Arguments

Value

Updated EpiTrax object with config field set.

See Also

epitrax_set_config_from_file() and the convenience function setup_epitrax() which wraps this function

Examples

config <- list(
 current_population = 56000,
 avg_5yr_population = 57000,
 rounding_decimals = 3,
 generate_csvs = FALSE
)
epitrax <- structure(
  list(data = c(1,2,3)),
  class = "epitrax"
)
epitrax <- epitrax_set_config_from_list(epitrax, config)

Description

epitrax_set_report_diseases reads internal and public disease lists and adds them to the EpiTrax object.

Usage

epitrax_set_report_diseases(epitrax, disease_list_files = NULL)

Arguments

Value

Updated EpiTrax object with report_diseases field set.

See Also

setup_epitrax() the convenience function which wraps this function

Examples

i_file <- system.file("tinytest/test_files/disease_lists/internal_list.csv",
                       package = "epitraxr")
p_file <- system.file("tinytest/test_files/disease_lists/public_list.csv",
                       package = "epitraxr")

epitrax <- structure(
  list(data = c(1,2,3)),
  class = "epitrax"
)

epitrax <- epitrax_set_report_diseases(
  epitrax,
  disease_list_files = list(
    internal = i_file,
    public = p_file
  )
)

Description

epitrax_write_csvs writes the internal and public reports from an EpiTrax object to CSV files in the specified filesystem. Doesn't write files if the EpiTrax config setting generate_csvs is set to false.

Usage

epitrax_write_csvs(epitrax, fsys)

Arguments

Value

The original EpiTrax object, unchanged.

Examples

fsys <- list(
  internal = file.path(tempdir(), "internal_reports"),
  public = file.path(tempdir(), "public_reports"),
  settings = file.path(tempdir(), "report_settings")
)
data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                           package = "epitraxr")
disease_lists <- list(
  internal = "use_defaults",
  public = "use_defaults"
)

epitrax <- setup_epitrax(
  filepath = data_file,
  config_file = config_file,
  disease_list_files = disease_lists
) |>
 epitrax_preport_ytd_rates() |>
 epitrax_write_csvs(fsys = fsys)

# Cleanup
unlink(unlist(fsys, use.names = FALSE), recursive = TRUE)

Description

epitrax_write_pdf_grouped_stats writes the grouped statistics reports from an EpiTrax object to PDF files using a formatted template. It processes both internal and public grouped statistics reports.

Usage

epitrax_write_pdf_grouped_stats(epitrax, params, fsys, trend.only = FALSE)

Arguments

Value

The original EpiTrax object, unchanged.

Examples

## Not run: 
  # Example not run because it requires LaTeX installation

  fsys <- list(
    internal = file.path(tempdir(), "internal_reports"),
    public = file.path(tempdir(), "public_reports"),
    settings = file.path(tempdir(), "report_settings")
  )
  fsys <- setup_filesystem(fsys)

  data_file <- system.file("sample_data/sample_epitrax_data.csv",
                          package = "epitraxr")
  config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                            package = "epitraxr")
  disease_lists <- list(
    internal = "use_defaults",
    public = "use_defaults"
  )

  params <- list(
    title = "Monthly Grouped Disease Statistics"
  )

  epitrax <- setup_epitrax(
    filepath = data_file,
    config_file = config_file,
    disease_list_files = disease_lists
  ) |>
    epitrax_report_grouped_stats() |>
    epitrax_write_pdf_grouped_stats(params = params, fsys = fsys)

  # Cleanup
  unlink(unlist(fsys, use.names = FALSE), recursive = TRUE)

## End(Not run)

Description

epitrax_write_pdf_public_reports writes a PDF report for each public report, excluding grouped stats reports (which are handled by epitrax_write_pdf_grouped_stats). The PDF uses pretty formatting and adds a header and footer.

Usage

epitrax_write_pdf_public_reports(epitrax, fsys, trend.only = FALSE)

Arguments

Value

The original EpiTrax object, unchanged.

Examples

## Not run: 
  # Example not run because it requires LaTeX installation

  fsys <- list(
    internal = file.path(tempdir(), "internal_reports"),
    public = file.path(tempdir(), "public_reports"),
    settings = file.path(tempdir(), "report_settings")
  )
  fsys <- setup_filesystem(fsys)

  data_file <- system.file("sample_data/sample_epitrax_data.csv",
                          package = "epitraxr")
  config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                            package = "epitraxr")
  disease_lists <- list(
    internal = "use_defaults",
    public = "use_defaults"
  )

  epitrax <- setup_epitrax(
    filepath = data_file,
    config_file = config_file,
    disease_list_files = disease_lists
  ) |>
    epitrax_preport_month_crosssections(month_offsets = 0) |>
    epitrax_write_pdf_public_reports(fsys = fsys)

  # Cleanup
  unlink(unlist(fsys, use.names = FALSE), recursive = TRUE)

## End(Not run)

Description

epitrax_write_xlsxs writes the internal and public reports from an EpiTrax object to Excel files in the specified filesystem. Combines all internal reports into one Excel file with separate sheets for each report. Likewise with public reports.

Usage

epitrax_write_xlsxs(epitrax, fsys)

Arguments

Value

The original EpiTrax object, unchanged.

Examples

fsys <- list(
  internal = file.path(tempdir(), "internal_reports"),
  public = file.path(tempdir(), "public_reports"),
  settings = file.path(tempdir(), "report_settings")
)
fsys <- setup_filesystem(fsys)

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                           package = "epitraxr")
disease_lists <- list(
  internal = "use_defaults",
  public = "use_defaults"
)

epitrax <- setup_epitrax(
  filepath = data_file,
  config_file = config_file,
  disease_list_files = disease_lists
) |>
 epitrax_preport_ytd_rates() |>
 epitrax_write_xlsxs(fsys = fsys)

# Cleanup
unlink(unlist(fsys, use.names = FALSE), recursive = TRUE)

Description

epitraxr_config creates a list of configuration options used for generating reports.

Usage

epitraxr_config(
  current_population = 1e+05,
  avg_5yr_population = 1e+05,
  rounding_decimals = 2,
  generate_csvs = TRUE,
  trend_threshold = 0.15
)

Arguments

Value

A named list with 'keys' corresponding to config options.

Examples

epitraxr_config(
  current_population = 56000,
  avg_5yr_population = 57000,
  rounding_decimals = 3,
  generate_csvs = FALSE,
  trend_threshold = 0.2
)

Description

format_epitrax_data prepares the input EpiTrax data for use by report generation functions in the package. It adds the counts column, renames columns to standard names used by the package ("disease", "month", "year", "counts"), and rearranges columns for consistency.

Usage

format_epitrax_data(data)

Arguments

Value

A standardized data frame with columns "disease", "month", "year", and "counts".

See Also

mmwr_week_to_month()

Examples

df <- data.frame(
  patient_mmwr_year = c(2020L, 2020L),
  month = c(1, 2),
  patient_disease = c("A", "B")
)
df <- format_epitrax_data(df)

Description

get_month_counts aggregates disease counts by month and year. This is a helper function used internally by report generation functions to summarize monthly disease counts.

Usage

get_month_counts(data)

Arguments

Value

A dataframe with the aggregated monthly counts

Examples

df <- data.frame(
  disease = c("Flu", "Flu", "Measles"),
  year = c(2020, 2020, 2020),
  month = c(1, 1, 2),
  counts = c(5, 3, 2)
)
get_month_counts(df)

Description

'get_report_config' reads in the config YAML file. Missing fields will be set to default values and a warning will be issued. The config file can have the following fields:

• current_population: Integer. Current population size.

• avg_5yr_population: Integer. Average population over the last 5 years.

• rounding_decimals: Integer. Number of decimals to round report values to.

• generate_csvs: Logical. Whether to generate CSV files.

• trend_threshold: Numeric. Threshold for trend calculations.

Usage

get_report_config(filepath)

Arguments

Details

See the example config file here: system.file("sample_data/sample_config.yml", package = "epitraxr").

Value

A named list with an attribute of 'keys' from the file.

Examples

config_file <- system.file("sample_data/sample_config.yml",
                          package = "epitraxr")
report_config <- get_report_config(config_file)

Description

get_report_diseases is a convenience function that combines get_report_diseases_internal and get_report_diseases_public.

Usage

get_report_diseases(internal, public, defaults)

Arguments

Value

A list with two elements:

• internal: Dataframe with EpiTrax_name column

• public: Dataframe with EpiTrax_name and Public_name columns

See Also

get_report_diseases_internal(), get_report_diseases_public() which this function wraps.

Examples

# Using default lists (when files don't exist)
default_list <- c("Measles", "Chickenpox")
disease_lists <- get_report_diseases("", "", default_list)

# Using disease list files
i_file <- system.file("tinytest/test_files/disease_lists/internal_list.csv",
                       package = "epitraxr")
p_file <- system.file("tinytest/test_files/disease_lists/public_list.csv",
                       package = "epitraxr")
disease_lists <- get_report_diseases(
  internal = i_file,
  public = p_file,
  defaults = default_list
)

Description

'get_report_diseases_internal' reads the internal list from a given CSV file or uses the default diseases, if the file doesn't exist.

Usage

get_report_diseases_internal(filepath, defaults)

Arguments

Details

The provided internal disease list file must contain at least a column named EpiTrax_name which contains EpiTrax disease names to include in the report. The file can optionally contain a column named Group_name, which maps the diseases in EpiTrax_name to a disease group. This is only used for reports that include disease groupings.

See the example file here: system.file("sample_data/sample_disease_list.csv", package = "epitraxr")

Value

A dataframe containing the diseases to include in the internal report and possibly the disease groupings.

Examples

# Using default list (when file doesn't exist)
default_list <- c("Measles", "Chickenpox")
disease_list <- get_report_diseases_internal("", default_list)

# Using a disease list file
list_file <- system.file("sample_data/sample_disease_list.csv",
                        package = "epitraxr")
disease_list <- get_report_diseases_internal(list_file, default_list)

Description

'get_report_diseases_public' reads the public list from a given CSV file or uses the default diseases if the file doesn't exist.

Usage

get_report_diseases_public(filepath, defaults)

Arguments

Details

The provided public disease list file must contain two columns named EpiTrax_name and Public_name which map EpiTrax disease names to a public-facing name for the public report. The file can optionally contain a column named Group_name, which maps the diseases in EpiTrax_name to a disease group. This is only used for reports that include disease groupings.

See the example file here: system.file("sample_data/sample_disease_list.csv", package = "epitraxr")

Value

A dataframe containing the diseases to include in the public report and the name to use for each disease in the public report. It may also contain the disease groupings.

Examples

# Using default list (when file doesn't exist)
default_list <- c("Measles", "Chickenpox")
disease_list <- get_report_diseases_public("", default_list)

# Using a disease list file
list_file <- system.file("sample_data/sample_disease_list.csv",
                        package = "epitraxr")
disease_list <- get_report_diseases_public(list_file, default_list)

Description

'get_yrs' extracts and returns the sorted unique years from the 'year' column of a data frame.

Usage

get_yrs(data)

Arguments

Value

Integer vector of sorted unique years present in the data.

Examples

df <- data.frame(year = c(2020, 2021, 2020, 2022))
get_yrs(df)

Description

mmwr_week_to_month calculates the calendar month from the patient_mmwr_week and patient_mmwr_year fields of the EpiTrax data. The result is stored in the month column and the patient_mmwr_week column is removed.

Usage

mmwr_week_to_month(data)

Arguments

Value

The input data frame with an added "month" column (integer 1-12) and removed patient_mmwr_week column.

Examples

df <- data.frame(
  patient_mmwr_year = 2020L,
  patient_mmwr_week = 1L,
  patient_disease = "A"
)
mmwr_week_to_month(df)

Description

'read_epitrax_data' reads EpiTrax data from a CSV, validates, and formats it. It also filters rows older than given number of years. The input file must contain the columns:

• patient_mmwr_year (integer)

• patient_mmwr_week (integer)

• patient_disease (character)

Usage

read_epitrax_data(filepath = NULL, num_yrs = 5)

Arguments

Details

See the example file here: system.file("sample_data/sample_epitrax_data.csv", package = "epitraxr")

Value

The validated and formatted EpiTrax data from the input file.

Examples

if(interactive()) {
  # Interactive file chooser:
  read_epitrax_data()
}

# Using a file path:
data <- read_epitrax_data(
  filepath = system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr"),
  num_yrs = 3
)
head(data)

Description

'reshape_annual_wide' reshapes a given data frame with diseases for rows and years for columns.

Usage

reshape_annual_wide(data)

Arguments

Value

The reshaped data frame.

Examples

df <- data.frame(
  disease = c("A", "A", "B"),
  year = c(2020, 2021, 2020),
  counts = c(5, 7, 8)
)
reshape_annual_wide(df)

Description

'reshape_monthly_wide' reshapes a given data frame with diseases for rows and months for columns.

Usage

reshape_monthly_wide(data)

Arguments

Value

The reshaped data frame.

Examples

df <- data.frame(
  disease = c("A", "B"),
  month = c(1, 2),
  counts = c(5, 6)
)
reshape_monthly_wide(df)

Description

run_app launches the interactive Shiny web application for EpiTrax data analysis and report generation. The app provides a user-friendly interface for uploading data, configuring reports, and generating various types of disease surveillance reports.

Usage

run_app(...)

Arguments

Value

Starts the execution of the app, printing the port to the console.

Examples

if (interactive() & requireNamespace("shiny")) {
  run_app()
}

Description

'set_na_0' sets NA values to 0 in a data frame.

Usage

set_na_0(df)

Arguments

Value

Dataframe with NA values replaced by 0.

Examples

df <- data.frame(year = c(2020, NA, 2022))
set_na_0(df)

Description

setup_epitrax initializes an EpiTrax object with configuration and report disease lists. It is a convenience function that combines create_epitrax_from_file(), epitrax_set_config_from_file(), and epitrax_set_report_diseases().

Usage

setup_epitrax(
  filepath = NULL,
  num_yrs = 5,
  disease_list_files = NULL,
  config_list = NULL,
  config_file = NULL
)

Arguments

Value

An EpiTrax object with configuration and report diseases set.

See Also

create_epitrax_from_file(), epitrax_set_config_from_file(), epitrax_set_config_from_list(), and epitrax_set_report_diseases() which this function wraps.

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
disease_lists <- list(
  internal = system.file("tinytest/test_files/disease_lists/internal_list.csv",
                         package = "epitraxr"),
  public = system.file("tinytest/test_files/disease_lists/public_list.csv",
                       package = "epitraxr")
)

epitrax <- setup_epitrax(
  filepath = data_file,
  disease_list_files = disease_lists
)

Description

setup_filesystem creates the necessary folder structure and optionally clears old reports. This is a convenience function that combines create_filesystem and clear_old_reports.

Usage

setup_filesystem(folders, clear.reports = FALSE)

Arguments

Value

The input folders list, unchanged.

See Also

create_filesystem(), clear_old_reports() which this function wraps.

Examples

# Create folders in a temporary directory
folders <- list(
  internal = file.path(tempdir(), "internal"),
  public = file.path(tempdir(), "public"),
  settings = file.path(tempdir(), "settings")
)
setup_filesystem(folders)
unlink(unlist(folders, use.names = FALSE), recursive = TRUE)

Description

'standardize_report_diseases' removes rows from the data that shouldn't appear in the report and adds rows for diseases that should be in the report, but weren't in the input dataset. Added rows are filled with 0s.

Usage

standardize_report_diseases(data, diseases)

Arguments

Value

Report data with rows for all diseases to report.

Examples

df <- data.frame(disease=c("A","B","D"), counts=c(5,7,8))
standardize_report_diseases(df, c("A","C"))

Description

validate_config checks the values of the given config list. If any values are missing or invalid, they are set to default values and a warning is issued.

Usage

validate_config(config)

Arguments

Value

A named list with 'keys' corresponding to config options.

Examples

validate_config(config = list())

Description

'validate_data' checks the data for expected columns and data types, removes unneeded columns, and returns the resulting data. Missing or NA values will be removed with a warning. Valid data must include the following columns (and types):

• patient_mmwr_year (integer)

• patient_mmwr_week (integer)

• patient_disease (character)

Usage

validate_data(data)

Arguments

Value

The validated data with all unneeded columns removed.

Examples

df <- data.frame(
  patient_mmwr_year = 2020L,
  patient_mmwr_week = 1L,
  patient_disease = "A"
)
validate_data(df)

Description

validate_epitrax checks that the EpiTrax object is valid.

Usage

validate_epitrax(epitrax, report.check = TRUE)

Arguments

Value

NULL if valid, otherwise throws an error.

Examples

epitrax <- structure(
  list(
    data = c(1,2,3),
    config = list(rounding_decimals = 2, generate_csvs = TRUE),
    report_diseases = list(internal = "internal_list", public = "public_list")
  ),
  class = "epitrax"
)
validate_epitrax(epitrax, report.check = TRUE)

Description

validate_filesystem checks that the filesystem structure is valid.

Usage

validate_filesystem(fsys)

Arguments

Value

NULL if valid, otherwise throws an error.

Examples

fsys <- list(
  internal = "internal_reports",
  public = "public_reports"
)
validate_filesystem(fsys)

Description

write_report_csv writes the given data to the specified folder with the given filename.

Usage

write_report_csv(data, filename, folder)

Arguments

Value

NULL.

Examples

# Create sample data
r_data <- data.frame(
  Disease = c("Measles", "Chickenpox"),
  Counts = c(20, 43)
)

# Write to temporary directory
write_report_csv(r_data, "report.csv", tempdir())
unlink(file.path(tempdir(), "report.csv"), recursive = TRUE)

Description

write_report_pdf renders a report as a PDF using a R Markdown template. It is relatively flexible and can be used for various types of report.

Usage

write_report_pdf(data, params, filename, folder, trend.only = FALSE)

Arguments

Value

NULL (called for side effects - creates the report file).

Examples

## Not run: 
  # Example not run because it requires LaTeX installation

  # Create sample report data
  r_data <- data.frame(
    Disease = c("COVID", "Flu", "Measles"),
    `March 2024` = c(0, 25, 5),
    `Historical March Avg` = c(0, 15, 8),
    `Trend` = compute_trend(c(0, 25, 5), c(0, 15, 8)),
    check.names = FALSE
  )

  # Set report parameters
  params <- list(
    title = "Monthly Disease Surveillance Report",
    report_year = 2024,
    report_month = 3,
    trend_threshold = 0.20
  )

  # Write to temporary directory
  write_report_pdf(
    data = r_data,
    params = params,
    filename = "monthly_disease_report.pdf",
    folder = tempdir()
  )

## End(Not run)

Description

write_report_pdf_grouped renders a grouped disease statistics report as a PDF using a R Markdown template. The report includes comprehensive disease statistics organized by groups with current and historical data.

Usage

write_report_pdf_grouped(data, params, filename, folder, trend.only = FALSE)

Arguments

Value

NULL (called for side effects - creates the report file).

Examples

## Not run: 
  # Example not run because it requires LaTeX installation

  # Create sample grouped report data
  r_data <- data.frame(
    Group = c("Respiratory", "Respiratory", "Vaccine-Preventable"),
    Disease = c("COVID", "Flu", "Measles"),
    `March 2024` = c(0, 25, 5),
    `March 2024 Rate` = c(0, 25, 5),
    `Historical March Avg` = c(0, 15, 8),
    `Historical March Median` = c(0, 15, 8),
    `2024 YTD` = c(0, 37, 9),
    `Historical 2024 YTD Avg` = c(20, 25, 14),
    `Historical 2024 YTD Median` = c(20, 25, 14),
    `YTD Trend` = compute_trend(c(0, 37, 9), c(20, 25, 14)),
    check.names = FALSE
  )

  # Set report parameters
  params <- list(
    title = "Grouped Disease Surveillance Report",
    report_year = 2024,
    report_month = 3,
    trend_threshold = 0.20
  )

  # Write to temporary directory
  write_report_pdf_grouped(
    data = r_data,
    params = params,
    filename = "grouped_disease_report.pdf",
    folder = tempdir()
  )

## End(Not run)

Description

write_report_xlsx writes the given data to the specified folder with the given filename in Excel (.xlsx) format.

Usage

write_report_xlsx(data, filename, folder)

Arguments

Value

NULL.

Examples

# Create sample data with multiple sheets
r_data1 <- data.frame(
  Disease = c("Measles", "Chickenpox"),
  Counts = c(20, 43)
)
r_data2 <- data.frame(
  Disease = c("Measles", "Chickenpox"),
  Rate = c(10.5, 22.7)
)
r_xl <- list(
  counts = r_data1,
  rates = r_data2
)

# Write to temporary directory
write_report_xlsx(r_xl, "report.xlsx", tempdir())
unlink(file.path(tempdir(), "report.xlsx"), recursive = TRUE)