Package 'jpinfect' reference manual

Title:	Acquiring and Processing Data from Japan Institute for Health Security
Description:	Download and post process the infectious disease case data from Japan Institute for Health Security. Also the package included ready-to-analyse datasets. See the data source website for further details <https://id-info.jihs.go.jp/>.
Authors:	Tomonori Hoshi [aut, cre], Erina Ishigaki [aut], Satoshi Kaneko [aut]
Maintainer:	Tomonori Hoshi <[email protected]>
License:	GPL (>= 3)
Version:	2024.2026.18
Built:	2026-05-17 09:18:37 UTC
Source:	https://github.com/tomonorihoshi/jpinfect

Bullet report Data

Description

This data set contains demographic information on bullet report based on prefecture, sourced from The Japan Institute for Health Security (JIHS).The specific date range provided are subject to updates.

Usage

bullet
bullet

Format

A data frame with 3360 rows and 180 columns.

prefecture: Case numbers for prefecture
year: Case numbers for year
week: Case numbers for week
date: Case numbers for date
Ebola hemorrhagic fever (weekly): Case numbers for Ebola hemorrhagic fever (weekly)
Ebola hemorrhagic fever (cumulative): Case numbers for Ebola hemorrhagic fever (cumulative)
Crimean-Congo hemorrhagic fever (weekly): Case numbers for Crimean-Congo hemorrhagic fever (weekly)
Crimean-Congo hemorrhagic fever (cumulative): Case numbers for Crimean-Congo hemorrhagic fever (cumulative)
Smallpox (weekly): Case numbers for Smallpox (weekly)
Smallpox (cumulative): Case numbers for Smallpox (cumulative)
South American hemorrhagic fever (weekly): Case numbers for South American hemorrhagic fever (weekly)
South American hemorrhagic fever (cumulative): Case numbers for South American hemorrhagic fever (cumulative)
Plague (weekly): Case numbers for Plague (weekly)
Plague (cumulative): Case numbers for Plague (cumulative)
Marburg disease (weekly): Case numbers for Marburg disease (weekly)
Marburg disease (cumulative): Case numbers for Marburg disease (cumulative)
Lassa fever (weekly): Case numbers for Lassa fever (weekly)
Lassa fever (cumulative): Case numbers for Lassa fever (cumulative)
Acute poliomyelitis (weekly): Case numbers for Acute poliomyelitis (weekly)
Acute poliomyelitis (cumulative): Case numbers for Acute poliomyelitis (cumulative)
Tuberculosis (weekly): Case numbers for Tuberculosis (weekly)
Tuberculosis (cumulative): Case numbers for Tuberculosis (cumulative)
Diphtheria (weekly): Case numbers for Diphtheria (weekly)
Diphtheria (cumulative): Case numbers for Diphtheria (cumulative)
Severe Acute Respiratory Syndrome (SARS) (weekly): Case numbers for Severe Acute Respiratory Syndrome (SARS) (weekly)
Severe Acute Respiratory Syndrome (SARS) (cumulative): Case numbers for Severe Acute Respiratory Syndrome (SARS) (cumulative)
Middle East Respiratory Syndrome Coronavirus (weekly): Case numbers for Middle East Respiratory Syndrome Coronavirus (weekly)
Middle East Respiratory Syndrome Coronavirus (cumulative): Case numbers for Middle East Respiratory Syndrome Coronavirus (cumulative)
Avian influenza H5N1 (weekly): Case numbers for Avian influenza H5N1 (weekly)
Avian influenza H5N1 (cumulative): Case numbers for Avian influenza H5N1 (cumulative)
Avian influenza H7N9 (weekly): Case numbers for Avian influenza H7N9 (weekly)
Avian influenza H7N9 (cumulative): Case numbers for Avian influenza H7N9 (cumulative)
Cholera (weekly): Case numbers for Cholera (weekly)
Cholera (cumulative): Case numbers for Cholera (cumulative)
Shigellosis (weekly): Case numbers for Shigellosis (weekly)
Shigellosis (cumulative): Case numbers for Shigellosis (cumulative)
Enterohemorrhagic Escherichia coli infection (weekly): Case numbers for Enterohemorrhagic Escherichia coli infection (weekly)
Enterohemorrhagic Escherichia coli infection (cumulative): Case numbers for Enterohemorrhagic Escherichia coli infection (cumulative)
Typhoid fever (weekly): Case numbers for Typhoid fever (weekly)
Typhoid fever (cumulative): Case numbers for Typhoid fever (cumulative)
Paratyphoid fever (weekly): Case numbers for Paratyphoid fever (weekly)
Paratyphoid fever (cumulative): Case numbers for Paratyphoid fever (cumulative)
Hepatitis E (weekly): Case numbers for Hepatitis E (weekly)
Hepatitis E (cumulative): Case numbers for Hepatitis E (cumulative)
West Nile fever (weekly): Case numbers for West Nile fever (weekly)
West Nile fever (cumulative): Case numbers for West Nile fever (cumulative)
Hepatitis A (weekly): Case numbers for Hepatitis A (weekly)
Hepatitis A (cumulative): Case numbers for Hepatitis A (cumulative)
Echinococcosis (weekly): Case numbers for Echinococcosis (weekly)
Echinococcosis (cumulative): Case numbers for Echinococcosis (cumulative)
Mpox (weekly): Case numbers for Mpox (weekly)
Mpox (cumulative): Case numbers for Mpox (cumulative)
Yellow fever (weekly): Case numbers for Yellow fever (weekly)
Yellow fever (cumulative): Case numbers for Yellow fever (cumulative)
Psittacosis (weekly): Case numbers for Psittacosis (weekly)
Psittacosis (cumulative): Case numbers for Psittacosis (cumulative)
Omsk hemorrhagic fever (weekly): Case numbers for Omsk hemorrhagic fever (weekly)
Omsk hemorrhagic fever (cumulative): Case numbers for Omsk hemorrhagic fever (cumulative)
Relapsing fever (weekly): Case numbers for Relapsing fever (weekly)
Relapsing fever (cumulative): Case numbers for Relapsing fever (cumulative)
Kyasanur forest disease (weekly): Case numbers for Kyasanur forest disease (weekly)
Kyasanur forest disease (cumulative): Case numbers for Kyasanur forest disease (cumulative)
Q fever (weekly): Case numbers for Q fever (weekly)
Q fever (cumulative): Case numbers for Q fever (cumulative)
Rabies (weekly): Case numbers for Rabies (weekly)
Rabies (cumulative): Case numbers for Rabies (cumulative)
Coccidioidomycosis (weekly): Case numbers for Coccidioidomycosis (weekly)
Coccidioidomycosis (cumulative): Case numbers for Coccidioidomycosis (cumulative)
Zika virus infection (weekly): Case numbers for Zika virus infection (weekly)
Zika virus infection (cumulative): Case numbers for Zika virus infection (cumulative)
Severe Fever with Thrombocytopenia Syndrome (SFTS) (weekly): Case numbers for Severe Fever with Thrombocytopenia Syndrome (SFTS) (weekly)
Severe Fever with Thrombocytopenia Syndrome (SFTS) (cumulative): Case numbers for Severe Fever with Thrombocytopenia Syndrome (SFTS) (cumulative)
Hemorrhagic fever with renal syndrome (weekly): Case numbers for Hemorrhagic fever with renal syndrome (weekly)
Hemorrhagic fever with renal syndrome (cumulative): Case numbers for Hemorrhagic fever with renal syndrome (cumulative)
Western equine encephalitis (weekly): Case numbers for Western equine encephalitis (weekly)
Western equine encephalitis (cumulative): Case numbers for Western equine encephalitis (cumulative)
Tick-borne encephalitis (weekly): Case numbers for Tick-borne encephalitis (weekly)
Tick-borne encephalitis (cumulative): Case numbers for Tick-borne encephalitis (cumulative)
Anthrax (weekly): Case numbers for Anthrax (weekly)
Anthrax (cumulative): Case numbers for Anthrax (cumulative)
Chikungunya fever (weekly): Case numbers for Chikungunya fever (weekly)
Chikungunya fever (cumulative): Case numbers for Chikungunya fever (cumulative)
Scrub typhus (Tsutsugamushi disease) (weekly): Case numbers for Scrub typhus (Tsutsugamushi disease) (weekly)
Scrub typhus (Tsutsugamushi disease) (cumulative): Case numbers for Scrub typhus (Tsutsugamushi disease) (cumulative)
Dengue fever (weekly): Case numbers for Dengue fever (weekly)
Dengue fever (cumulative): Case numbers for Dengue fever (cumulative)
Eastern equine encephalitis (weekly): Case numbers for Eastern equine encephalitis (weekly)
Eastern equine encephalitis (cumulative): Case numbers for Eastern equine encephalitis (cumulative)
Avian influenza (exclud. Avian influenza both H5N1 and H7N9) (weekly): Case numbers for Avian influenza (exclud. Avian influenza both H5N1 and H7N9) (weekly)
Avian influenza (exclud. Avian influenza both H5N1 and H7N9) (cumulative): Case numbers for Avian influenza (exclud. Avian influenza both H5N1 and H7N9) (cumulative)
Nipah virus infection (weekly): Case numbers for Nipah virus infection (weekly)
Nipah virus infection (cumulative): Case numbers for Nipah virus infection (cumulative)
Japanese spotted fever (weekly): Case numbers for Japanese spotted fever (weekly)
Japanese spotted fever (cumulative): Case numbers for Japanese spotted fever (cumulative)
Japanese encephalitis (weekly): Case numbers for Japanese encephalitis (weekly)
Japanese encephalitis (cumulative): Case numbers for Japanese encephalitis (cumulative)
Hantavirus pulmonary syndrome (weekly): Case numbers for Hantavirus pulmonary syndrome (weekly)
Hantavirus pulmonary syndrome (cumulative): Case numbers for Hantavirus pulmonary syndrome (cumulative)
Herpes B virus infection (weekly): Case numbers for Herpes B virus infection (weekly)
Herpes B virus infection (cumulative): Case numbers for Herpes B virus infection (cumulative)
Glanders (weekly): Case numbers for Glanders (weekly)
Glanders (cumulative): Case numbers for Glanders (cumulative)
Brucellosis (weekly): Case numbers for Brucellosis (weekly)
Brucellosis (cumulative): Case numbers for Brucellosis (cumulative)
Venezuelan equine encephalitis (weekly): Case numbers for Venezuelan equine encephalitis (weekly)
Venezuelan equine encephalitis (cumulative): Case numbers for Venezuelan equine encephalitis (cumulative)
Hendra virus infection (weekly): Case numbers for Hendra virus infection (weekly)
Hendra virus infection (cumulative): Case numbers for Hendra virus infection (cumulative)
Epidemic typhus (weekly): Case numbers for Epidemic typhus (weekly)
Epidemic typhus (cumulative): Case numbers for Epidemic typhus (cumulative)
Botulism (weekly): Case numbers for Botulism (weekly)
Botulism (cumulative): Case numbers for Botulism (cumulative)
Malaria (weekly): Case numbers for Malaria (weekly)
Malaria (cumulative): Case numbers for Malaria (cumulative)
Tularemia (weekly): Case numbers for Tularemia (weekly)
Tularemia (cumulative): Case numbers for Tularemia (cumulative)
Lyme disease (weekly): Case numbers for Lyme disease (weekly)
Lyme disease (cumulative): Case numbers for Lyme disease (cumulative)
Lyssavirus infection (excluding rabies) (weekly): Case numbers for Lyssavirus infection (excluding rabies) (weekly)
Lyssavirus infection (excluding rabies) (cumulative): Case numbers for Lyssavirus infection (excluding rabies) (cumulative)
Rift valley fever (weekly): Case numbers for Rift valley fever (weekly)
Rift valley fever (cumulative): Case numbers for Rift valley fever (cumulative)
Melioidosis (weekly): Case numbers for Melioidosis (weekly)
Melioidosis (cumulative): Case numbers for Melioidosis (cumulative)
Legionellosis (weekly): Case numbers for Legionellosis (weekly)
Legionellosis (cumulative): Case numbers for Legionellosis (cumulative)
Leptospirosis (weekly): Case numbers for Leptospirosis (weekly)
Leptospirosis (cumulative): Case numbers for Leptospirosis (cumulative)
Rocky mountain spotted fever (weekly): Case numbers for Rocky mountain spotted fever (weekly)
Rocky mountain spotted fever (cumulative): Case numbers for Rocky mountain spotted fever (cumulative)
Amebiasis (weekly): Case numbers for Amebiasis (weekly)
Amebiasis (cumulative): Case numbers for Amebiasis (cumulative)
Viral hepatitis (excluding hepatitis A and E) (weekly): Case numbers for Viral hepatitis (excluding hepatitis A and E) (weekly)
Viral hepatitis (excluding hepatitis A and E) (cumulative): Case numbers for Viral hepatitis (excluding hepatitis A and E) (cumulative)
Carbapenem-resistant Enterobacterales infection (weekly): Case numbers for Carbapenem-resistant Enterobacterales infection (weekly)
Carbapenem-resistant Enterobacterales infection (cumulative): Case numbers for Carbapenem-resistant Enterobacterales infection (cumulative)
Acute Flaccid Paralysis (excluding Acute poliomyelitis) (weekly): Case numbers for Acute Flaccid Paralysis (excluding Acute poliomyelitis) (weekly)
Acute Flaccid Paralysis (excluding Acute poliomyelitis) (cumulative): Case numbers for Acute Flaccid Paralysis (excluding Acute poliomyelitis) (cumulative)
Acute encephalitis (excluding JE and WNE) (weekly): Case numbers for Acute encephalitis (excluding JE and WNE) (weekly)
Acute encephalitis (excluding JE and WNE) (cumulative): Case numbers for Acute encephalitis (excluding JE and WNE) (cumulative)
Cryptosporidiosis (weekly): Case numbers for Cryptosporidiosis (weekly)
Cryptosporidiosis (cumulative): Case numbers for Cryptosporidiosis (cumulative)
Creutzfeldt-Jakob disease (weekly): Case numbers for Creutzfeldt-Jakob disease (weekly)
Creutzfeldt-Jakob disease (cumulative): Case numbers for Creutzfeldt-Jakob disease (cumulative)
Severe invasive streptococcal infections (TSLS) (weekly): Case numbers for Severe invasive streptococcal infections (TSLS) (weekly)
Severe invasive streptococcal infections (TSLS) (cumulative): Case numbers for Severe invasive streptococcal infections (TSLS) (cumulative)
Acquired immunodeficiency syndrome (AIDS) (weekly): Case numbers for Acquired immunodeficiency syndrome (AIDS) (weekly)
Acquired immunodeficiency syndrome (AIDS) (cumulative): Case numbers for Acquired immunodeficiency syndrome (AIDS) (cumulative)
Giardiasis (weekly): Case numbers for Giardiasis (weekly)
Giardiasis (cumulative): Case numbers for Giardiasis (cumulative)
Invasive haemophilus influenzae infection (weekly): Case numbers for Invasive haemophilus influenzae infection (weekly)
Invasive haemophilus influenzae infection (cumulative): Case numbers for Invasive haemophilus influenzae infection (cumulative)
Invasive meningococcal infection (weekly): Case numbers for Invasive meningococcal infection (weekly)
Invasive meningococcal infection (cumulative): Case numbers for Invasive meningococcal infection (cumulative)
Invasive streptococcal pneumoniae infection (weekly): Case numbers for Invasive streptococcal pneumoniae infection (weekly)
Invasive streptococcal pneumoniae infection (cumulative): Case numbers for Invasive streptococcal pneumoniae infection (cumulative)
Varicella (limited to hospiltalized case) (weekly): Case numbers for Varicella (limited to hospiltalized case) (weekly)
Varicella (limited to hospiltalized case) (cumulative): Case numbers for Varicella (limited to hospiltalized case) (cumulative)
Congenital rubella syndrome (weekly): Case numbers for Congenital rubella syndrome (weekly)
Congenital rubella syndrome (cumulative): Case numbers for Congenital rubella syndrome (cumulative)
Syphilis (weekly): Case numbers for Syphilis (weekly)
Syphilis (cumulative): Case numbers for Syphilis (cumulative)
Disseminated cryptococcal infection (weekly): Case numbers for Disseminated cryptococcal infection (weekly)
Disseminated cryptococcal infection (cumulative): Case numbers for Disseminated cryptococcal infection (cumulative)
Tetanus (weekly): Case numbers for Tetanus (weekly)
Tetanus (cumulative): Case numbers for Tetanus (cumulative)
Vancomycin-resistant S. aureus infection (weekly): Case numbers for Vancomycin-resistant S. aureus infection (weekly)
Vancomycin-resistant S. aureus infection (cumulative): Case numbers for Vancomycin-resistant S. aureus infection (cumulative)
Vancomycin-resistant Enterococcus infection (weekly): Case numbers for Vancomycin-resistant Enterococcus infection (weekly)
Vancomycin-resistant Enterococcus infection (cumulative): Case numbers for Vancomycin-resistant Enterococcus infection (cumulative)
Pertussis (weekly): Case numbers for Pertussis (weekly)
Pertussis (cumulative): Case numbers for Pertussis (cumulative)
Rubella (weekly): Case numbers for Rubella (weekly)
Rubella (cumulative): Case numbers for Rubella (cumulative)
Measles (weekly): Case numbers for Measles (weekly)
Measles (cumulative): Case numbers for Measles (cumulative)
Multiple drug-resistant Acinetobacter infection (weekly): Case numbers for Multiple drug-resistant Acinetobacter infection (weekly)
Multiple drug-resistant Acinetobacter infection (cumulative): Case numbers for Multiple drug-resistant Acinetobacter infection (cumulative)
Multi-drug-resistant Pseudomonas aeruginosa infection (weekly): Case numbers for Multi-drug-resistant Pseudomonas aeruginosa infection (weekly)
Multi-drug-resistant Pseudomonas aeruginosa infection (cumulative): Case numbers for Multi-drug-resistant Pseudomonas aeruginosa infection (cumulative)

Source

The Japan Institute for Health Security (JIHS) (https://id-info.jihs.go.jp/index.html)

Download the bullet reports from the Japan Institute for Health Security (JIHS)

Description

This function downloads surveillance data from the Japan Institute for Health Security (JIHS) for a specified year and weeks, based on the chosen language (English or Japanese).

Usage

jpinfect_get_bullet(
  year = NULL,
  week = 1:53,
  language = "en",
  overwrite = FALSE,
  dest_dir = NULL
)
jpinfect_get_bullet(
  year = NULL,
  week = 1:53,
  language = "en",
  overwrite = FALSE,
  dest_dir = NULL
)

Arguments

year

An integer specifying the year of the data. Must be provided explicitly and must be greater than 2023.

week

A numeric vector specifying the weeks to download (default is 1:53). Week numbers should be between 1 and 53.

language

A character string specifying the language of the data ('en' for English, 'jp' for Japanese). Default is 'en'.

overwrite

A logical value indicating whether to overwrite existing files (default is FALSE). If FALSE, existing files are skipped, and only new files are downloaded.

dest_dir

Directory to save files. If NULL, uses tempdir() (files deleted when R session ends). Specify a permanent directory to keep downloaded data.

Details

- The function constructs a URL for JIHS data based on the year, week, and language using 'jpinfect_url_bullet'. - If the specified week is invalid (not between 1 and 53), an error is raised. - If the year is earlier than 2024, an error is raised, as the function only works for years after 2023. - Weeks without available data on the server are skipped, and a warning is displayed for each unavailable week. - If the requested file already exists and 'overwrite = FALSE', it is skipped. - A delay ('Sys.sleep(3)') is used between downloads to avoid overwhelming the server. - Progress updates are displayed in the console using 'message()'.

Value

No return value. The function downloads surveillance data files from JIHS and saves them to the specified directory ('dest_dir'). If the data is unavailable for certain weeks, those weeks are skipped, and an appropriate message is displayed.

Examples


# Download English data for weeks 1 to 2 in 2025
jpinfect_get_bullet(year = 2025, week = 1:2, language = "en")

# Download Japanese data for weeks 1 to 2 in 2025
jpinfect_get_bullet(year = 2025, week = 1:2, language = "jp")

# Overwrite existing files and download English data for week 2 in 2025
jpinfect_get_bullet(year = 2025, week = 2, language = "en",
                     overwrite = TRUE)


# Download English data for weeks 1 to 2 in 2025
jpinfect_get_bullet(year = 2025, week = 1:2, language = "en")

# Download Japanese data for weeks 1 to 2 in 2025
jpinfect_get_bullet(year = 2025, week = 1:2, language = "jp")

# Overwrite existing files and download English data for week 2 in 2025
jpinfect_get_bullet(year = 2025, week = 2, language = "en",
                     overwrite = TRUE)

Download the confirmed case datasets from the Japan Institute for Health Security (JIHS)

Description

This function downloads infectious disease data from the Japan Institute for Health Security (JIHS) for specified years and types.

Usage

jpinfect_get_confirmed(
  years = NULL,
  type = "sex",
  overwrite = FALSE,
  dest_dir = NULL
)
jpinfect_get_confirmed(
  years = NULL,
  type = "sex",
  overwrite = FALSE,
  dest_dir = NULL
)

Arguments

years

(numeric) A vector of years to download data for. If NULL, the most recent available year will be used. Available years range from 1999 to 2024.

type

(character) The type of data to download. Must be either "sex" or "place".

overwrite

(logical) Whether to overwrite existing files. Defaults to FALSE.

dest_dir

Directory to save files. If NULL, uses tempdir() (files deleted when R session ends). Specify a permanent directory to keep downloaded data.

Details

This function validates the input parameters, including the range of years and the type of data. It creates the destination directory if it does not already exist. For each year, the function attempts to download the corresponding file from JIHS. If a file already exists and overwrite = FALSE, the download is skipped.

Value

A named list mapping each requested year to its downloaded file path. Successful years contain a character path; failed years are NULL.

Examples


# Download data for 2020 and 2021
jpinfect_get_confirmed(years = c(2020, 2021), type = "sex")

# Download data for all available years
jpinfect_get_confirmed(type = "place")


# Download data for 2020 and 2021
jpinfect_get_confirmed(years = c(2020, 2021), type = "sex")

# Download data for all available years
jpinfect_get_confirmed(type = "place")

Merge multiple disease datasets into a unified data table

Description

This function merges multiple datasets ('dataset1', 'dataset2', and optionally 'dataset3') based on shared columns: 'prefecture', 'year', and 'week'. It also renames column names according to the dataset type ('sex', 'place', or 'bullet').

Usage

jpinfect_merge(
  dataset1 = sex_prefecture,
  dataset2 = place_prefecture,
  dataset3 = NULL
)
jpinfect_merge(
  dataset1 = sex_prefecture,
  dataset2 = place_prefecture,
  dataset3 = NULL
)

Arguments

dataset1

A data frame containing "sex" data to be merged.

dataset2

A data frame containing "place" data to be merged.

dataset3

(Optional) A third dataset containing "bullet" data to be added.

Value

A data frame that combines all input datasets and applies consistent column renaming.

Examples


# Example usage
bind_result <- jpinfect_merge(sex_prefecture, place_prefecture, bullet)


# Example usage
bind_result <- jpinfect_merge(sex_prefecture, place_prefecture, bullet)

Convert data from wide format to long format for easier analysis

Description

This function pivots a dataset between long and wide formats based on the column count. If the dataset has 5 or fewer columns, it is pivoted to a wide format, keeping 'prefecture', 'year', 'week' and 'date' as fixed identifiers. If the dataset has more than 5 columns, it is pivoted to a long format.

Usage

jpinfect_pivot(dataset)
jpinfect_pivot(dataset)

Arguments

dataset

A data frame containing the columns 'prefecture', 'year', 'week', 'date' and additional columns for diseases and their associated case counts.

Details

- If the dataset has 5 or fewer columns, the function uses 'pivot_wider()' to convert the dataset to a wide format. - If the dataset has more than 5 columns, the function uses 'pivot_longer()' to convert the dataset to a long format. - The function ensures that the columns 'prefecture', 'year', 'week' and 'date' are always present.

Value

A data frame that is pivoted either to a long or wide format, depending on the number of columns. If 'prefecture', 'year', 'week' or 'date' are missing from the dataset, the function stops with an error.

Examples


# Pivot the dataset
result <- jpinfect_pivot(place_prefecture)
print(result)


# Pivot the dataset
result <- jpinfect_pivot(place_prefecture)
print(result)

Import one week or more weeks of bullet reports

Description

This function imports and processes surveillance data files downloaded from the Japan Institute for Health Security (JIHS). The processed data for the specified year and weeks is combined into a single data frame, optionally saved to a file.

Usage

jpinfect_read_bullet(
  year = NULL,
  week = 1:53,
  directory,
  language = "en",
  output_file = NULL
)
jpinfect_read_bullet(
  year = NULL,
  week = 1:53,
  directory,
  language = "en",
  output_file = NULL
)

Arguments

year

An integer specifying the year of the data files to process. If NULL, all years available in the directory are processed.

week

A numeric vector specifying the weeks to process (default is 1:53).

directory

A string specifying the directory containing the JIHS data files (required).

language

A character string specifying the language of the data ('en' for English, 'jp' for Japanese). Default is 'en'.

output_file

A string specifying the file name to save the combined data. If NULL, the combined data is not saved (default is NULL).

Details

- The function reads all files matching the specified 'year' and 'language' in the given 'directory'. - Files are filtered based on their naming patterns, which include '_zensu_en.csv' for English and '_zensu_jp.csv' for Japanese. - Each file is read and processed, including renaming columns, adding 'year' and 'week' information, and rearranging columns. - If no files matching the criteria are found, the function raises an error. - Processed data for all specified files is combined into a single data frame.

Value

A data frame containing the combined and processed JIHS surveillance data. If 'output_file' is specified, the data is also saved to a CSV file in the specified directory.

Examples


# Get path to example data files
data_dir <- system.file("extdata", package = "jpinfect")

# Process data for 2025, weeks 1 to 2, in English
combined_data <- jpinfect_read_bullet(year = 2025, week = 1:2,
                                         directory = data_dir,
                                         language = "en",
                                         output_file = tempfile("output.csv"))



# Get path to example data files
data_dir <- system.file("extdata", package = "jpinfect")

# Process data for 2025, weeks 1 to 2, in English
combined_data <- jpinfect_read_bullet(year = 2025, week = 1:2,
                                         directory = data_dir,
                                         language = "en",
                                         output_file = tempfile("output.csv"))

Read Confirmed Case Reports from File or Directory

Description

This function processes case reports either from a single file or from multiple files within a directory. The function is capable of handling data by "sex" or "place" types, and processes data accordingly based on file patterns.

Usage

jpinfect_read_confirmed(path, type = NULL, ..., skip_size_check = FALSE)
jpinfect_read_confirmed(path, type = NULL, ..., skip_size_check = FALSE)

Arguments

path

A character string specifying the path to a single file or directory containing multiple files.

type

A character string specifying the type of data to import. Must be either "sex" or "place".

...

Additional arguments passed to internal functions for further customization.

skip_size_check

A logical value indicating whether to skip the file size check. Defaults to FALSE.

Details

The function detects whether the path is a single file or a directory. If it is a single file, it processes the data using .jpinfect_read_excel. If it is a directory, it processes multiple files using .jpinfect_read_excels.

Supported file patterns:

"sex": Files with names containing "11.xls" or "Syu_01_1.xls".
"place": Files with names containing "Syu_02_1.xls".

Value

A data frame containing processed case reports for all rows and columns in the files.

Examples


# Process a single file
data_file <- system.file("extdata", "1999_Syu_11.xls", package = "jpinfect")
data_single <- jpinfect_read_confirmed(data_file, skip_size_check = TRUE)

# Process all files in a directory
data_dir <- system.file("extdata", package = "jpinfect")
data_multiple <- jpinfect_read_confirmed(data_dir, type = "place", skip_size_check = TRUE)


# Process a single file
data_file <- system.file("extdata", "1999_Syu_11.xls", package = "jpinfect")
data_single <- jpinfect_read_confirmed(data_file, skip_size_check = TRUE)

# Process all files in a directory
data_dir <- system.file("extdata", package = "jpinfect")
data_multiple <- jpinfect_read_confirmed(data_dir, type = "place", skip_size_check = TRUE)

Display Infectious Diseases Weekly Report (IDWR) URLs

Description

This function displays the URLs of Infectious Diseases Weekly Report (IDWR) from the Japan Institute for Health Security (JIHS) for a specified year and weeks, based on the chosen language (English or Japanese). See this webpage for further details: https://id-info.jihs.go.jp/

Usage

jpinfect_url_bullet(year = NULL, week = 1:53, language = "en")
jpinfect_url_bullet(year = NULL, week = 1:53, language = "en")

Arguments

year

An integer specifying the year of the data. Must be provided explicitly and should be after 2021.

week

A numeric vector specifying the weeks to display URLs for (default is 1:53). Week numbers should be between 1 and 53.

language

A character string specifying the language of the data ('en' for English, 'jp' for Japanese). Default is 'en'.

Details

- The function constructs URLs for each week using the IDWR data source for the specified language. - The year must be explicitly provided and must be greater than 2023. - Week numbers must be valid (1 to 53), otherwise an error is raised. - If the IDWR data is not available for a particular week, a warning is displayed, and that week is skipped. - Progress updates are provided in the console using 'message()'.

Value

A character vector of constructed URLs for the specified weeks and language. If the data is not available for certain weeks, a message is displayed, and those weeks are skipped.

Examples


# Display URLs for English data for weeks 1 to 5 in 2025
jpinfect_url_bullet(year = 2025, week = 1:5, language = "en")

# Display URLs for Japanese data for all weeks in 2025
jpinfect_url_bullet(year = 2025, language = "jp")

# Display URLs for English data for weeks 10 to 20 in 2024
jpinfect_url_bullet(year = 2024, week = 10:20, language = "en")


# Display URLs for English data for weeks 1 to 5 in 2025
jpinfect_url_bullet(year = 2025, week = 1:5, language = "en")

# Display URLs for Japanese data for all weeks in 2025
jpinfect_url_bullet(year = 2025, language = "jp")

# Display URLs for English data for weeks 10 to 20 in 2024
jpinfect_url_bullet(year = 2024, week = 10:20, language = "en")

Display dataset URLs of Confirmed Cases based on Infectious Diseases Weekly Report (IDWR)

Description

This function displays the URL for downloading Confirmed Cases based on Infectious Diseases Weekly Report (IDWR) from the Japan Institute for Health Security (JIHS) for a specified year. See this webpage for further details: https://id-info.jihs.go.jp/

Usage

jpinfect_url_confirmed(year = 2001, type = "sex")
jpinfect_url_confirmed(year = 2001, type = "sex")

Arguments

year

The year for which to generate the URL. Defaults to 2001.

type

The type of data to download. Must be either "sex" or "place". Defaults to "sex".

Value

A character string containing the URL for the specified year's data.

Examples


# Check URL for weekly cases by sex and prefecture in 2010
jpinfect_url_confirmed(2010)

# Check URL for weekly cases by suspected place of infection and prefecture in 2010
jpinfect_url_confirmed(2010, type = "place")

# Check URL for weekly cases by sex and prefecture in 2010
jpinfect_url_confirmed(2010)

# Check URL for weekly cases by suspected place of infection and prefecture in 2010
jpinfect_url_confirmed(2010, type = "place")

Place Prefecture Data

Description

This dataset contains information about the place of infection by prefecture, sourced from the Japan Institute for Health Security (JIHS). The data is between 2001 and 2024.

Usage

place_prefecture
place_prefecture

Format

A data frame with 60048 rows and 420 columns.

prefecture: Case numbers for prefecture
year: Case numbers for year
week: Case numbers for week
date: Case numbers for date
Ebola hemorrhagic fever (total): Case numbers for Ebola hemorrhagic fever (total)
Ebola hemorrhagic fever (Inside Japan): Case numbers for Ebola hemorrhagic fever (Inside Japan)
Ebola hemorrhagic fever (Others): Case numbers for Ebola hemorrhagic fever (Others)
Ebola hemorrhagic fever (Unknown): Case numbers for Ebola hemorrhagic fever (Unknown)
Crimean-Congo hemorrhagic fever (total): Case numbers for Crimean-Congo hemorrhagic fever (total)
Crimean-Congo hemorrhagic fever (Inside Japan): Case numbers for Crimean-Congo hemorrhagic fever (Inside Japan)
Crimean-Congo hemorrhagic fever (Others): Case numbers for Crimean-Congo hemorrhagic fever (Others)
Crimean-Congo hemorrhagic fever (Unknown): Case numbers for Crimean-Congo hemorrhagic fever (Unknown)
Plague (total): Case numbers for Plague (total)
Plague (Inside Japan): Case numbers for Plague (Inside Japan)
Plague (Others): Case numbers for Plague (Others)
Plague (Unknown): Case numbers for Plague (Unknown)
Marburg disease (total): Case numbers for Marburg disease (total)
Marburg disease (Inside Japan): Case numbers for Marburg disease (Inside Japan)
Marburg disease (Others): Case numbers for Marburg disease (Others)
Marburg disease (Unknown): Case numbers for Marburg disease (Unknown)
Lassa fever (total): Case numbers for Lassa fever (total)
Lassa fever (Inside Japan): Case numbers for Lassa fever (Inside Japan)
Lassa fever (Others): Case numbers for Lassa fever (Others)
Lassa fever (Unknown): Case numbers for Lassa fever (Unknown)
Cholera (total): Case numbers for Cholera (total)
Cholera (Inside Japan): Case numbers for Cholera (Inside Japan)
Cholera (Others): Case numbers for Cholera (Others)
Cholera (Unknown): Case numbers for Cholera (Unknown)
Shigellosis (total): Case numbers for Shigellosis (total)
Shigellosis (Inside Japan): Case numbers for Shigellosis (Inside Japan)
Shigellosis (Others): Case numbers for Shigellosis (Others)
Shigellosis (Unknown): Case numbers for Shigellosis (Unknown)
Typhoid fever (total): Case numbers for Typhoid fever (total)
Typhoid fever (Inside Japan): Case numbers for Typhoid fever (Inside Japan)
Typhoid fever (Others): Case numbers for Typhoid fever (Others)
Typhoid fever (Unknown): Case numbers for Typhoid fever (Unknown)
Paratyphoid fever (total): Case numbers for Paratyphoid fever (total)
Paratyphoid fever (Inside Japan): Case numbers for Paratyphoid fever (Inside Japan)
Paratyphoid fever (Others): Case numbers for Paratyphoid fever (Others)
Paratyphoid fever (Unknown): Case numbers for Paratyphoid fever (Unknown)
Poliomyelitis (total): Case numbers for Poliomyelitis (total)
Poliomyelitis (Inside Japan): Case numbers for Poliomyelitis (Inside Japan)
Poliomyelitis (Others): Case numbers for Poliomyelitis (Others)
Poliomyelitis (Unknown): Case numbers for Poliomyelitis (Unknown)
Diphtheria (total): Case numbers for Diphtheria (total)
Diphtheria (Inside Japan): Case numbers for Diphtheria (Inside Japan)
Diphtheria (Others): Case numbers for Diphtheria (Others)
Diphtheria (Unknown): Case numbers for Diphtheria (Unknown)
Enterohemorrhagic E. coli infection (total): Case numbers for Enterohemorrhagic E. coli infection (total)
Enterohemorrhagic E. coli infection (Inside Japan): Case numbers for Enterohemorrhagic E. coli infection (Inside Japan)
Enterohemorrhagic E. coli infection (Others): Case numbers for Enterohemorrhagic E. coli infection (Others)
Enterohemorrhagic E. coli infection (Unknown): Case numbers for Enterohemorrhagic E. coli infection (Unknown)
Amebiasis (total): Case numbers for Amebiasis (total)
Amebiasis (Inside Japan): Case numbers for Amebiasis (Inside Japan)
Amebiasis (Others): Case numbers for Amebiasis (Others)
Amebiasis (Unknown): Case numbers for Amebiasis (Unknown)
Echinococcosis (total): Case numbers for Echinococcosis (total)
Echinococcosis (Inside Japan): Case numbers for Echinococcosis (Inside Japan)
Echinococcosis (Others): Case numbers for Echinococcosis (Others)
Echinococcosis (Unknown): Case numbers for Echinococcosis (Unknown)
Yellow fever (total): Case numbers for Yellow fever (total)
Yellow fever (Inside Japan): Case numbers for Yellow fever (Inside Japan)
Yellow fever (Others): Case numbers for Yellow fever (Others)
Yellow fever (Unknown): Case numbers for Yellow fever (Unknown)
Psittacosis (total): Case numbers for Psittacosis (total)
Psittacosis (Inside Japan): Case numbers for Psittacosis (Inside Japan)
Psittacosis (Others): Case numbers for Psittacosis (Others)
Psittacosis (Unknown): Case numbers for Psittacosis (Unknown)
Relapsing fever (total): Case numbers for Relapsing fever (total)
Relapsing fever (Inside Japan): Case numbers for Relapsing fever (Inside Japan)
Relapsing fever (Others): Case numbers for Relapsing fever (Others)
Relapsing fever (Unknown): Case numbers for Relapsing fever (Unknown)
Acute viral hepatitis (total): Case numbers for Acute viral hepatitis (total)
Acute viral hepatitis (Inside Japan): Case numbers for Acute viral hepatitis (Inside Japan)
Acute viral hepatitis (Others): Case numbers for Acute viral hepatitis (Others)
Acute viral hepatitis (Unknown): Case numbers for Acute viral hepatitis (Unknown)
Q fever (total): Case numbers for Q fever (total)
Q fever (Inside Japan): Case numbers for Q fever (Inside Japan)
Q fever (Others): Case numbers for Q fever (Others)
Q fever (Unknown): Case numbers for Q fever (Unknown)
Rabies (total): Case numbers for Rabies (total)
Rabies (Inside Japan): Case numbers for Rabies (Inside Japan)
Rabies (Others): Case numbers for Rabies (Others)
Rabies (Unknown): Case numbers for Rabies (Unknown)
Cryptosporidiosis (total): Case numbers for Cryptosporidiosis (total)
Cryptosporidiosis (Inside Japan): Case numbers for Cryptosporidiosis (Inside Japan)
Cryptosporidiosis (Others): Case numbers for Cryptosporidiosis (Others)
Cryptosporidiosis (Unknown): Case numbers for Cryptosporidiosis (Unknown)
Creutzfeldt-Jakob disease (total): Case numbers for Creutzfeldt-Jakob disease (total)
Creutzfeldt-Jakob disease (Inside Japan): Case numbers for Creutzfeldt-Jakob disease (Inside Japan)
Creutzfeldt-Jakob disease (Others): Case numbers for Creutzfeldt-Jakob disease (Others)
Creutzfeldt-Jakob disease (Unknown): Case numbers for Creutzfeldt-Jakob disease (Unknown)
Severe invasive streptococcal infections (total): Case numbers for Severe invasive streptococcal infections (total)
Severe invasive streptococcal infections (Inside Japan): Case numbers for Severe invasive streptococcal infections (Inside Japan)
Severe invasive streptococcal infections (Others): Case numbers for Severe invasive streptococcal infections (Others)
Severe invasive streptococcal infections (Unknown): Case numbers for Severe invasive streptococcal infections (Unknown)
AIDS (total): Case numbers for AIDS (total)
AIDS (Inside Japan): Case numbers for AIDS (Inside Japan)
AIDS (Others): Case numbers for AIDS (Others)
AIDS (Unknown): Case numbers for AIDS (Unknown)
Coccidioidomycosis (total): Case numbers for Coccidioidomycosis (total)
Coccidioidomycosis (Inside Japan): Case numbers for Coccidioidomycosis (Inside Japan)
Coccidioidomycosis (Others): Case numbers for Coccidioidomycosis (Others)
Coccidioidomycosis (Unknown): Case numbers for Coccidioidomycosis (Unknown)
Giardiasis (total): Case numbers for Giardiasis (total)
Giardiasis (Inside Japan): Case numbers for Giardiasis (Inside Japan)
Giardiasis (Others): Case numbers for Giardiasis (Others)
Giardiasis (Unknown): Case numbers for Giardiasis (Unknown)
Hemorrhagic fever with renal syndrome (total): Case numbers for Hemorrhagic fever with renal syndrome (total)
Hemorrhagic fever with renal syndrome (Inside Japan): Case numbers for Hemorrhagic fever with renal syndrome (Inside Japan)
Hemorrhagic fever with renal syndrome (Others): Case numbers for Hemorrhagic fever with renal syndrome (Others)
Hemorrhagic fever with renal syndrome (Unknown): Case numbers for Hemorrhagic fever with renal syndrome (Unknown)
Meningococcal meningitis (total): Case numbers for Meningococcal meningitis (total)
Meningococcal meningitis (Inside Japan): Case numbers for Meningococcal meningitis (Inside Japan)
Meningococcal meningitis (Others): Case numbers for Meningococcal meningitis (Others)
Meningococcal meningitis (Unknown): Case numbers for Meningococcal meningitis (Unknown)
Congenital rubella syndrome (total): Case numbers for Congenital rubella syndrome (total)
Congenital rubella syndrome (Inside Japan): Case numbers for Congenital rubella syndrome (Inside Japan)
Congenital rubella syndrome (Others): Case numbers for Congenital rubella syndrome (Others)
Congenital rubella syndrome (Unknown): Case numbers for Congenital rubella syndrome (Unknown)
Anthrax (total): Case numbers for Anthrax (total)
Anthrax (Inside Japan): Case numbers for Anthrax (Inside Japan)
Anthrax (Others): Case numbers for Anthrax (Others)
Anthrax (Unknown): Case numbers for Anthrax (Unknown)
Scrub typhus (total): Case numbers for Scrub typhus (total)
Scrub typhus (Inside Japan): Case numbers for Scrub typhus (Inside Japan)
Scrub typhus (Others): Case numbers for Scrub typhus (Others)
Scrub typhus (Unknown): Case numbers for Scrub typhus (Unknown)
Dengue fever (total): Case numbers for Dengue fever (total)
Dengue fever (Inside Japan): Case numbers for Dengue fever (Inside Japan)
Dengue fever (Others): Case numbers for Dengue fever (Others)
Dengue fever (Unknown): Case numbers for Dengue fever (Unknown)
Japanese spotted fever (total): Case numbers for Japanese spotted fever (total)
Japanese spotted fever (Inside Japan): Case numbers for Japanese spotted fever (Inside Japan)
Japanese spotted fever (Others): Case numbers for Japanese spotted fever (Others)
Japanese spotted fever (Unknown): Case numbers for Japanese spotted fever (Unknown)
Japanese encephalitis (total): Case numbers for Japanese encephalitis (total)
Japanese encephalitis (Inside Japan): Case numbers for Japanese encephalitis (Inside Japan)
Japanese encephalitis (Others): Case numbers for Japanese encephalitis (Others)
Japanese encephalitis (Unknown): Case numbers for Japanese encephalitis (Unknown)
Infant botulism (total): Case numbers for Infant botulism (total)
Infant botulism (Inside Japan): Case numbers for Infant botulism (Inside Japan)
Infant botulism (Others): Case numbers for Infant botulism (Others)
Infant botulism (Unknown): Case numbers for Infant botulism (Unknown)
Syphilis (total): Case numbers for Syphilis (total)
Syphilis (Inside Japan): Case numbers for Syphilis (Inside Japan)
Syphilis (Others): Case numbers for Syphilis (Others)
Syphilis (Unknown): Case numbers for Syphilis (Unknown)
Tetanus (total): Case numbers for Tetanus (total)
Tetanus (Inside Japan): Case numbers for Tetanus (Inside Japan)
Tetanus (Others): Case numbers for Tetanus (Others)
Tetanus (Unknown): Case numbers for Tetanus (Unknown)
VRE infection (total): Case numbers for VRE infection (total)
VRE infection (Inside Japan): Case numbers for VRE infection (Inside Japan)
VRE infection (Others): Case numbers for VRE infection (Others)
VRE infection (Unknown): Case numbers for VRE infection (Unknown)
Hantavirus pulmonary syndrome (total): Case numbers for Hantavirus pulmonary syndrome (total)
Hantavirus pulmonary syndrome (Inside Japan): Case numbers for Hantavirus pulmonary syndrome (Inside Japan)
Hantavirus pulmonary syndrome (Others): Case numbers for Hantavirus pulmonary syndrome (Others)
Hantavirus pulmonary syndrome (Unknown): Case numbers for Hantavirus pulmonary syndrome (Unknown)
B virus disease (total): Case numbers for B virus disease (total)
B virus disease (Inside Japan): Case numbers for B virus disease (Inside Japan)
B virus disease (Others): Case numbers for B virus disease (Others)
B virus disease (Unknown): Case numbers for B virus disease (Unknown)
Brucellosis (total): Case numbers for Brucellosis (total)
Brucellosis (Inside Japan): Case numbers for Brucellosis (Inside Japan)
Brucellosis (Others): Case numbers for Brucellosis (Others)
Brucellosis (Unknown): Case numbers for Brucellosis (Unknown)
Epidemic louse-borne typhus (total): Case numbers for Epidemic louse-borne typhus (total)
Epidemic louse-borne typhus (Inside Japan): Case numbers for Epidemic louse-borne typhus (Inside Japan)
Epidemic louse-borne typhus (Others): Case numbers for Epidemic louse-borne typhus (Others)
Epidemic louse-borne typhus (Unknown): Case numbers for Epidemic louse-borne typhus (Unknown)
Malaria (total): Case numbers for Malaria (total)
Malaria (Inside Japan): Case numbers for Malaria (Inside Japan)
Malaria (Others): Case numbers for Malaria (Others)
Malaria (Unknown): Case numbers for Malaria (Unknown)
Lyme disease (total): Case numbers for Lyme disease (total)
Lyme disease (Inside Japan): Case numbers for Lyme disease (Inside Japan)
Lyme disease (Others): Case numbers for Lyme disease (Others)
Lyme disease (Unknown): Case numbers for Lyme disease (Unknown)
Legionellosis (total): Case numbers for Legionellosis (total)
Legionellosis (Inside Japan): Case numbers for Legionellosis (Inside Japan)
Legionellosis (Others): Case numbers for Legionellosis (Others)
Legionellosis (Unknown): Case numbers for Legionellosis (Unknown)
Severe Acute Respiratory Syndrome (SARS) (total): Case numbers for Severe Acute Respiratory Syndrome (SARS) (total)
Severe Acute Respiratory Syndrome (SARS) (Inside Japan): Case numbers for Severe Acute Respiratory Syndrome (SARS) (Inside Japan)
Severe Acute Respiratory Syndrome (SARS) (Others): Case numbers for Severe Acute Respiratory Syndrome (SARS) (Others)
Severe Acute Respiratory Syndrome (SARS) (Unknown): Case numbers for Severe Acute Respiratory Syndrome (SARS) (Unknown)
Smallpox (total): Case numbers for Smallpox (total)
Smallpox (Inside Japan): Case numbers for Smallpox (Inside Japan)
Smallpox (Others): Case numbers for Smallpox (Others)
Smallpox (Unknown): Case numbers for Smallpox (Unknown)
Acute poliomyelitis (total): Case numbers for Acute poliomyelitis (total)
Acute poliomyelitis (Inside Japan): Case numbers for Acute poliomyelitis (Inside Japan)
Acute poliomyelitis (Others): Case numbers for Acute poliomyelitis (Others)
Acute poliomyelitis (Unknown): Case numbers for Acute poliomyelitis (Unknown)
Enterohemorrhagic Escherichia coli infection (total): Case numbers for Enterohemorrhagic Escherichia coli infection (total)
Enterohemorrhagic Escherichia coli infection (Inside Japan): Case numbers for Enterohemorrhagic Escherichia coli infection (Inside Japan)
Enterohemorrhagic Escherichia coli infection (Others): Case numbers for Enterohemorrhagic Escherichia coli infection (Others)
Enterohemorrhagic Escherichia coli infection (Unknown): Case numbers for Enterohemorrhagic Escherichia coli infection (Unknown)
Hepatitis E (total): Case numbers for Hepatitis E (total)
Hepatitis E (Inside Japan): Case numbers for Hepatitis E (Inside Japan)
Hepatitis E (Others): Case numbers for Hepatitis E (Others)
Hepatitis E (Unknown): Case numbers for Hepatitis E (Unknown)
West Nile fever (including West Nile encephalitis) (total): Case numbers for West Nile fever (including West Nile encephalitis) (total)
West Nile fever (including West Nile encephalitis) (Inside Japan): Case numbers for West Nile fever (including West Nile encephalitis) (Inside Japan)
West Nile fever (including West Nile encephalitis) (Others): Case numbers for West Nile fever (including West Nile encephalitis) (Others)
West Nile fever (including West Nile encephalitis) (Unknown): Case numbers for West Nile fever (including West Nile encephalitis) (Unknown)
Hepatitis A (total): Case numbers for Hepatitis A (total)
Hepatitis A (Inside Japan): Case numbers for Hepatitis A (Inside Japan)
Hepatitis A (Others): Case numbers for Hepatitis A (Others)
Hepatitis A (Unknown): Case numbers for Hepatitis A (Unknown)
Avian influenza virus infection (total): Case numbers for Avian influenza virus infection (total)
Avian influenza virus infection (Inside Japan): Case numbers for Avian influenza virus infection (Inside Japan)
Avian influenza virus infection (Others): Case numbers for Avian influenza virus infection (Others)
Avian influenza virus infection (Unknown): Case numbers for Avian influenza virus infection (Unknown)
Monkeypox (total): Case numbers for Monkeypox (total)
Monkeypox (Inside Japan): Case numbers for Monkeypox (Inside Japan)
Monkeypox (Others): Case numbers for Monkeypox (Others)
Monkeypox (Unknown): Case numbers for Monkeypox (Unknown)
Scrub typhus (Tsutsugamushi disease) (total): Case numbers for Scrub typhus (Tsutsugamushi disease) (total)
Scrub typhus (Tsutsugamushi disease) (Inside Japan): Case numbers for Scrub typhus (Tsutsugamushi disease) (Inside Japan)
Scrub typhus (Tsutsugamushi disease) (Others): Case numbers for Scrub typhus (Tsutsugamushi disease) (Others)
Scrub typhus (Tsutsugamushi disease) (Unknown): Case numbers for Scrub typhus (Tsutsugamushi disease) (Unknown)
Nipah virus infection (total): Case numbers for Nipah virus infection (total)
Nipah virus infection (Inside Japan): Case numbers for Nipah virus infection (Inside Japan)
Nipah virus infection (Others): Case numbers for Nipah virus infection (Others)
Nipah virus infection (Unknown): Case numbers for Nipah virus infection (Unknown)
Herpes B virus infection (total): Case numbers for Herpes B virus infection (total)
Herpes B virus infection (Inside Japan): Case numbers for Herpes B virus infection (Inside Japan)
Herpes B virus infection (Others): Case numbers for Herpes B virus infection (Others)
Herpes B virus infection (Unknown): Case numbers for Herpes B virus infection (Unknown)
Epidemic typhus (total): Case numbers for Epidemic typhus (total)
Epidemic typhus (Inside Japan): Case numbers for Epidemic typhus (Inside Japan)
Epidemic typhus (Others): Case numbers for Epidemic typhus (Others)
Epidemic typhus (Unknown): Case numbers for Epidemic typhus (Unknown)
Botulism (total): Case numbers for Botulism (total)
Botulism (Inside Japan): Case numbers for Botulism (Inside Japan)
Botulism (Others): Case numbers for Botulism (Others)
Botulism (Unknown): Case numbers for Botulism (Unknown)
Tularemia (total): Case numbers for Tularemia (total)
Tularemia (Inside Japan): Case numbers for Tularemia (Inside Japan)
Tularemia (Others): Case numbers for Tularemia (Others)
Tularemia (Unknown): Case numbers for Tularemia (Unknown)
Lyssavirus infection (excluding rabies) (total): Case numbers for Lyssavirus infection (excluding rabies) (total)
Lyssavirus infection (excluding rabies) (Inside Japan): Case numbers for Lyssavirus infection (excluding rabies) (Inside Japan)
Lyssavirus infection (excluding rabies) (Others): Case numbers for Lyssavirus infection (excluding rabies) (Others)
Lyssavirus infection (excluding rabies) (Unknown): Case numbers for Lyssavirus infection (excluding rabies) (Unknown)
Leptospirosis (total): Case numbers for Leptospirosis (total)
Leptospirosis (Inside Japan): Case numbers for Leptospirosis (Inside Japan)
Leptospirosis (Others): Case numbers for Leptospirosis (Others)
Leptospirosis (Unknown): Case numbers for Leptospirosis (Unknown)
Viral hepatitis (excluding hepatitis A and E) (total): Case numbers for Viral hepatitis (excluding hepatitis A and E) (total)
Viral hepatitis (excluding hepatitis A and E) (Inside Japan): Case numbers for Viral hepatitis (excluding hepatitis A and E) (Inside Japan)
Viral hepatitis (excluding hepatitis A and E) (Others): Case numbers for Viral hepatitis (excluding hepatitis A and E) (Others)
Viral hepatitis (excluding hepatitis A and E) (Unknown): Case numbers for Viral hepatitis (excluding hepatitis A and E) (Unknown)
Acute encephalitis (excluding JE and WNE) (total): Case numbers for Acute encephalitis (excluding JE and WNE) (total)
Acute encephalitis (excluding JE and WNE) (Inside Japan): Case numbers for Acute encephalitis (excluding JE and WNE) (Inside Japan)
Acute encephalitis (excluding JE and WNE) (Others): Case numbers for Acute encephalitis (excluding JE and WNE) (Others)
Acute encephalitis (excluding JE and WNE) (Unknown): Case numbers for Acute encephalitis (excluding JE and WNE) (Unknown)
Infectious CJD (total): Case numbers for Infectious CJD (total)
Infectious CJD (Inside Japan): Case numbers for Infectious CJD (Inside Japan)
Infectious CJD (Others): Case numbers for Infectious CJD (Others)
Infectious CJD (Unknown): Case numbers for Infectious CJD (Unknown)
Severe invasive streptococcal infections (TSLS) (total): Case numbers for Severe invasive streptococcal infections (TSLS) (total)
Severe invasive streptococcal infections (TSLS) (Inside Japan): Case numbers for Severe invasive streptococcal infections (TSLS) (Inside Japan)
Severe invasive streptococcal infections (TSLS) (Others): Case numbers for Severe invasive streptococcal infections (TSLS) (Others)
Severe invasive streptococcal infections (TSLS) (Unknown): Case numbers for Severe invasive streptococcal infections (TSLS) (Unknown)
Acquired immunodeficiency syndrome (AIDS) (total): Case numbers for Acquired immunodeficiency syndrome (AIDS) (total)
Acquired immunodeficiency syndrome (AIDS) (Inside Japan): Case numbers for Acquired immunodeficiency syndrome (AIDS) (Inside Japan)
Acquired immunodeficiency syndrome (AIDS) (Others): Case numbers for Acquired immunodeficiency syndrome (AIDS) (Others)
Acquired immunodeficiency syndrome (AIDS) (Unknown): Case numbers for Acquired immunodeficiency syndrome (AIDS) (Unknown)
Vancomycin-resistant S. aureus infection (total): Case numbers for Vancomycin-resistant S. aureus infection (total)
Vancomycin-resistant S. aureus infection (Inside Japan): Case numbers for Vancomycin-resistant S. aureus infection (Inside Japan)
Vancomycin-resistant S. aureus infection (Others): Case numbers for Vancomycin-resistant S. aureus infection (Others)
Vancomycin-resistant S. aureus infection (Unknown): Case numbers for Vancomycin-resistant S. aureus infection (Unknown)
Vancomycin-resistant Enterococcus infection (total): Case numbers for Vancomycin-resistant Enterococcus infection (total)
Vancomycin-resistant Enterococcus infection (Inside Japan): Case numbers for Vancomycin-resistant Enterococcus infection (Inside Japan)
Vancomycin-resistant Enterococcus infection (Others): Case numbers for Vancomycin-resistant Enterococcus infection (Others)
Vancomycin-resistant Enterococcus infection (Unknown): Case numbers for Vancomycin-resistant Enterococcus infection (Unknown)
South American hemorrhagic fever (total): Case numbers for South American hemorrhagic fever (total)
South American hemorrhagic fever (Inside Japan): Case numbers for South American hemorrhagic fever (Inside Japan)
South American hemorrhagic fever (Others): Case numbers for South American hemorrhagic fever (Others)
South American hemorrhagic fever (Unknown): Case numbers for South American hemorrhagic fever (Unknown)
Tuberculosis (total): Case numbers for Tuberculosis (total)
Tuberculosis (Inside Japan): Case numbers for Tuberculosis (Inside Japan)
Tuberculosis (Others): Case numbers for Tuberculosis (Others)
Tuberculosis (Unknown): Case numbers for Tuberculosis (Unknown)
West Nile fever (total): Case numbers for West Nile fever (total)
West Nile fever (Inside Japan): Case numbers for West Nile fever (Inside Japan)
West Nile fever (Others): Case numbers for West Nile fever (Others)
West Nile fever (Unknown): Case numbers for West Nile fever (Unknown)
Omsk hemorrhagic fever (total): Case numbers for Omsk hemorrhagic fever (total)
Omsk hemorrhagic fever (Inside Japan): Case numbers for Omsk hemorrhagic fever (Inside Japan)
Omsk hemorrhagic fever (Others): Case numbers for Omsk hemorrhagic fever (Others)
Omsk hemorrhagic fever (Unknown): Case numbers for Omsk hemorrhagic fever (Unknown)
Kyasanur forest disease (total): Case numbers for Kyasanur forest disease (total)
Kyasanur forest disease (Inside Japan): Case numbers for Kyasanur forest disease (Inside Japan)
Kyasanur forest disease (Others): Case numbers for Kyasanur forest disease (Others)
Kyasanur forest disease (Unknown): Case numbers for Kyasanur forest disease (Unknown)
Western equine encephalitis (total): Case numbers for Western equine encephalitis (total)
Western equine encephalitis (Inside Japan): Case numbers for Western equine encephalitis (Inside Japan)
Western equine encephalitis (Others): Case numbers for Western equine encephalitis (Others)
Western equine encephalitis (Unknown): Case numbers for Western equine encephalitis (Unknown)
Tick-borne encephalitis (total): Case numbers for Tick-borne encephalitis (total)
Tick-borne encephalitis (Inside Japan): Case numbers for Tick-borne encephalitis (Inside Japan)
Tick-borne encephalitis (Others): Case numbers for Tick-borne encephalitis (Others)
Tick-borne encephalitis (Unknown): Case numbers for Tick-borne encephalitis (Unknown)
Eastern equine encephalitis (total): Case numbers for Eastern equine encephalitis (total)
Eastern equine encephalitis (Inside Japan): Case numbers for Eastern equine encephalitis (Inside Japan)
Eastern equine encephalitis (Others): Case numbers for Eastern equine encephalitis (Others)
Eastern equine encephalitis (Unknown): Case numbers for Eastern equine encephalitis (Unknown)
Glanders (total): Case numbers for Glanders (total)
Glanders (Inside Japan): Case numbers for Glanders (Inside Japan)
Glanders (Others): Case numbers for Glanders (Others)
Glanders (Unknown): Case numbers for Glanders (Unknown)
Venezuelan equine encephalitis (total): Case numbers for Venezuelan equine encephalitis (total)
Venezuelan equine encephalitis (Inside Japan): Case numbers for Venezuelan equine encephalitis (Inside Japan)
Venezuelan equine encephalitis (Others): Case numbers for Venezuelan equine encephalitis (Others)
Venezuelan equine encephalitis (Unknown): Case numbers for Venezuelan equine encephalitis (Unknown)
Hendra virus infection (total): Case numbers for Hendra virus infection (total)
Hendra virus infection (Inside Japan): Case numbers for Hendra virus infection (Inside Japan)
Hendra virus infection (Others): Case numbers for Hendra virus infection (Others)
Hendra virus infection (Unknown): Case numbers for Hendra virus infection (Unknown)
Rift valley fever (total): Case numbers for Rift valley fever (total)
Rift valley fever (Inside Japan): Case numbers for Rift valley fever (Inside Japan)
Rift valley fever (Others): Case numbers for Rift valley fever (Others)
Rift valley fever (Unknown): Case numbers for Rift valley fever (Unknown)
Melioidosis (total): Case numbers for Melioidosis (total)
Melioidosis (Inside Japan): Case numbers for Melioidosis (Inside Japan)
Melioidosis (Others): Case numbers for Melioidosis (Others)
Melioidosis (Unknown): Case numbers for Melioidosis (Unknown)
Rocky mountain spotted fever (total): Case numbers for Rocky mountain spotted fever (total)
Rocky mountain spotted fever (Inside Japan): Case numbers for Rocky mountain spotted fever (Inside Japan)
Rocky mountain spotted fever (Others): Case numbers for Rocky mountain spotted fever (Others)
Rocky mountain spotted fever (Unknown): Case numbers for Rocky mountain spotted fever (Unknown)
Avian influenza H5N1 (total): Case numbers for Avian influenza H5N1 (total)
Avian influenza H5N1 (Inside Japan): Case numbers for Avian influenza H5N1 (Inside Japan)
Avian influenza H5N1 (Others): Case numbers for Avian influenza H5N1 (Others)
Avian influenza H5N1 (Unknown): Case numbers for Avian influenza H5N1 (Unknown)
Avian influenza (exclud. Avian influenza H5N1) (total): Case numbers for Avian influenza (exclud. Avian influenza H5N1) (total)
Avian influenza (exclud. Avian influenza H5N1) (Inside Japan): Case numbers for Avian influenza (exclud. Avian influenza H5N1) (Inside Japan)
Avian influenza (exclud. Avian influenza H5N1) (Others): Case numbers for Avian influenza (exclud. Avian influenza H5N1) (Others)
Avian influenza (exclud. Avian influenza H5N1) (Unknown): Case numbers for Avian influenza (exclud. Avian influenza H5N1) (Unknown)
Rubella (total): Case numbers for Rubella (total)
Rubella (Inside Japan): Case numbers for Rubella (Inside Japan)
Rubella (Others): Case numbers for Rubella (Others)
Rubella (Unknown): Case numbers for Rubella (Unknown)
Measles (total): Case numbers for Measles (total)
Measles (Inside Japan): Case numbers for Measles (Inside Japan)
Measles (Others): Case numbers for Measles (Others)
Measles (Unknown): Case numbers for Measles (Unknown)
Pandemic influenza (A/H1N1) (total): Case numbers for Pandemic influenza (A/H1N1) (total)
Pandemic influenza (A/H1N1) (Inside Japan): Case numbers for Pandemic influenza (A/H1N1) (Inside Japan)
Pandemic influenza (A/H1N1) (Others): Case numbers for Pandemic influenza (A/H1N1) (Others)
Pandemic influenza (A/H1N1) (Unknown): Case numbers for Pandemic influenza (A/H1N1) (Unknown)
Chikungunya fever (total): Case numbers for Chikungunya fever (total)
Chikungunya fever (Inside Japan): Case numbers for Chikungunya fever (Inside Japan)
Chikungunya fever (Others): Case numbers for Chikungunya fever (Others)
Chikungunya fever (Unknown): Case numbers for Chikungunya fever (Unknown)
Avian influenza H7N9 (total): Case numbers for Avian influenza H7N9 (total)
Avian influenza H7N9 (Inside Japan): Case numbers for Avian influenza H7N9 (Inside Japan)
Avian influenza H7N9 (Others): Case numbers for Avian influenza H7N9 (Others)
Avian influenza H7N9 (Unknown): Case numbers for Avian influenza H7N9 (Unknown)
Severe Fever with Thrombocytopenia Syndrome (total): Case numbers for Severe Fever with Thrombocytopenia Syndrome (total)
Severe Fever with Thrombocytopenia Syndrome (Inside Japan): Case numbers for Severe Fever with Thrombocytopenia Syndrome (Inside Japan)
Severe Fever with Thrombocytopenia Syndrome (Others): Case numbers for Severe Fever with Thrombocytopenia Syndrome (Others)
Severe Fever with Thrombocytopenia Syndrome (Unknown): Case numbers for Severe Fever with Thrombocytopenia Syndrome (Unknown)
Invasive haemophilus influenzae infection (total): Case numbers for Invasive haemophilus influenzae infection (total)
Invasive haemophilus influenzae infection (Inside Japan): Case numbers for Invasive haemophilus influenzae infection (Inside Japan)
Invasive haemophilus influenzae infection (Others): Case numbers for Invasive haemophilus influenzae infection (Others)
Invasive haemophilus influenzae infection (Unknown): Case numbers for Invasive haemophilus influenzae infection (Unknown)
Invasive meningococcal infection (total): Case numbers for Invasive meningococcal infection (total)
Invasive meningococcal infection (Inside Japan): Case numbers for Invasive meningococcal infection (Inside Japan)
Invasive meningococcal infection (Others): Case numbers for Invasive meningococcal infection (Others)
Invasive meningococcal infection (Unknown): Case numbers for Invasive meningococcal infection (Unknown)
Invasive streptococcal pneumoniae infection (total): Case numbers for Invasive streptococcal pneumoniae infection (total)
Invasive streptococcal pneumoniae infection (Inside Japan): Case numbers for Invasive streptococcal pneumoniae infection (Inside Japan)
Invasive streptococcal pneumoniae infection (Others): Case numbers for Invasive streptococcal pneumoniae infection (Others)
Invasive streptococcal pneumoniae infection (Unknown): Case numbers for Invasive streptococcal pneumoniae infection (Unknown)
Middle East Respiratory Syndrome (MERS) (total): Case numbers for Middle East Respiratory Syndrome (MERS) (total)
Middle East Respiratory Syndrome (MERS) (Inside Japan): Case numbers for Middle East Respiratory Syndrome (MERS) (Inside Japan)
Middle East Respiratory Syndrome (MERS) (Others): Case numbers for Middle East Respiratory Syndrome (MERS) (Others)
Middle East Respiratory Syndrome (MERS) (Unknown): Case numbers for Middle East Respiratory Syndrome (MERS) (Unknown)
Carbapenem-resistant enterobacteriaceae infection (total): Case numbers for Carbapenem-resistant enterobacteriaceae infection (total)
Carbapenem-resistant enterobacteriaceae infection (Inside Japan): Case numbers for Carbapenem-resistant enterobacteriaceae infection (Inside Japan)
Carbapenem-resistant enterobacteriaceae infection (Others): Case numbers for Carbapenem-resistant enterobacteriaceae infection (Others)
Carbapenem-resistant enterobacteriaceae infection (Unknown): Case numbers for Carbapenem-resistant enterobacteriaceae infection (Unknown)
Varicella (limited to hospiltalized case) (total): Case numbers for Varicella (limited to hospiltalized case) (total)
Varicella (limited to hospiltalized case) (Inside Japan): Case numbers for Varicella (limited to hospiltalized case) (Inside Japan)
Varicella (limited to hospiltalized case) (Others): Case numbers for Varicella (limited to hospiltalized case) (Others)
Varicella (limited to hospiltalized case) (Unknown): Case numbers for Varicella (limited to hospiltalized case) (Unknown)
Disseminated cryptococcal infection (total): Case numbers for Disseminated cryptococcal infection (total)
Disseminated cryptococcal infection (Inside Japan): Case numbers for Disseminated cryptococcal infection (Inside Japan)
Disseminated cryptococcal infection (Others): Case numbers for Disseminated cryptococcal infection (Others)
Disseminated cryptococcal infection (Unknown): Case numbers for Disseminated cryptococcal infection (Unknown)
Multidrug-resistant Acinetobacter infection (total): Case numbers for Multidrug-resistant Acinetobacter infection (total)
Multidrug-resistant Acinetobacter infection (Inside Japan): Case numbers for Multidrug-resistant Acinetobacter infection (Inside Japan)
Multidrug-resistant Acinetobacter infection (Others): Case numbers for Multidrug-resistant Acinetobacter infection (Others)
Multidrug-resistant Acinetobacter infection (Unknown): Case numbers for Multidrug-resistant Acinetobacter infection (Unknown)
Zika virus infection (total): Case numbers for Zika virus infection (total)
Zika virus infection (Inside Japan): Case numbers for Zika virus infection (Inside Japan)
Zika virus infection (Others): Case numbers for Zika virus infection (Others)
Zika virus infection (Unknown): Case numbers for Zika virus infection (Unknown)
Acute Flaccid Paralysis (excluding Acute poliomyelitis) (total): Case numbers for Acute Flaccid Paralysis (excluding Acute poliomyelitis) (total)
Acute Flaccid Paralysis (excluding Acute poliomyelitis) (Inside Japan): Case numbers for Acute Flaccid Paralysis (excluding Acute poliomyelitis) (Inside Japan)
Acute Flaccid Paralysis (excluding Acute poliomyelitis) (Others): Case numbers for Acute Flaccid Paralysis (excluding Acute poliomyelitis) (Others)
Acute Flaccid Paralysis (excluding Acute poliomyelitis) (Unknown): Case numbers for Acute Flaccid Paralysis (excluding Acute poliomyelitis) (Unknown)
Pertussis (total): Case numbers for Pertussis (total)
Pertussis (Inside Japan): Case numbers for Pertussis (Inside Japan)
Pertussis (Others): Case numbers for Pertussis (Others)
Pertussis (Unknown): Case numbers for Pertussis (Unknown)
Mpox (total): Case numbers for Mpox (total)
Mpox (Inside Japan): Case numbers for Mpox (Inside Japan)
Mpox (Others): Case numbers for Mpox (Others)
Mpox (Unknown): Case numbers for Mpox (Unknown)
HIV/AIDS (total): Case numbers for HIV/AIDS (total)
HIV/AIDS (Inside Japan): Case numbers for HIV/AIDS (Inside Japan)
HIV/AIDS (Others): Case numbers for HIV/AIDS (Others)
HIV/AIDS (Unknown): Case numbers for HIV/AIDS (Unknown)
Carbapenem-resistant Enterobacterales infection (total): Case numbers for Carbapenem-resistant enterobacteriaceae infection (total)
Carbapenem-resistant Enterobacterales infection (Inside Japan): Case numbers for Carbapenem-resistant enterobacteriaceae infection (Inside Japan)
Carbapenem-resistant Enterobacterales infection (Others): Case numbers for Carbapenem-resistant enterobacteriaceae infection (Others)
Carbapenem-resistant Enterobacterales infection (Unknown): Case numbers for Carbapenem-resistant enterobacteriaceae infection (Unknown)

Source

The Japan Institute for Health Security (JIHS) (https://id-info.jihs.go.jp/index.html)

English Names of Prefectures in Japan

Description

This vector contains the English names of all 47 prefectures in Japan, listed in geographical order, starting from Hokkaido in the north to Okinawa in the south.

Usage

prefecture_en
prefecture_en

Format

A character vector of length 47.

Hokkaido: The northernmost prefecture.
Aomori: Located in the Tohoku region.
...: Other prefectures follow in geographical order.
Okinawa: The southernmost prefecture.

Examples

# Access the first prefecture
prefecture_en[1]  # "Hokkaido"

# Print all prefectures
print(prefecture_en)

# Access the first prefecture
prefecture_en[1]  # "Hokkaido"

# Print all prefectures
print(prefecture_en)

Sex Prefecture Data

Description

This dataset contains demographic information on sex by prefecture, sourced from the Japan Institute for Health Security (JIHS). The data ranges between 1999 and 2024.

Usage

sex_prefecture
sex_prefecture

Format

A data frame with 64416 rows and 319 columns.

prefecture: Case numbers for prefecture
year: Case numbers for year
week: Case numbers for week
date: Case numbers for date
Ebola hemorrhagic fever (total): Case numbers for Ebola hemorrhagic fever (total)
Ebola hemorrhagic fever (male): Case numbers for Ebola hemorrhagic fever (male)
Ebola hemorrhagic fever (female): Case numbers for Ebola hemorrhagic fever (female)
Crimean-Congo hemorrhagic fever (total): Case numbers for Crimean-Congo hemorrhagic fever (total)
Crimean-Congo hemorrhagic fever (male): Case numbers for Crimean-Congo hemorrhagic fever (male)
Crimean-Congo hemorrhagic fever (female): Case numbers for Crimean-Congo hemorrhagic fever (female)
Plague (total): Case numbers for Plague (total)
Plague (male): Case numbers for Plague (male)
Plague (female): Case numbers for Plague (female)
Marburg disease (total): Case numbers for Marburg disease (total)
Marburg disease (male): Case numbers for Marburg disease (male)
Marburg disease (female): Case numbers for Marburg disease (female)
Lassa fever (total): Case numbers for Lassa fever (total)
Lassa fever (male): Case numbers for Lassa fever (male)
Lassa fever (female): Case numbers for Lassa fever (female)
Cholera (total): Case numbers for Cholera (total)
Cholera (male): Case numbers for Cholera (male)
Cholera (female): Case numbers for Cholera (female)
Shigellosis (total): Case numbers for Shigellosis (total)
Shigellosis (male): Case numbers for Shigellosis (male)
Shigellosis (female): Case numbers for Shigellosis (female)
Typhoid fever (total): Case numbers for Typhoid fever (total)
Typhoid fever (male): Case numbers for Typhoid fever (male)
Typhoid fever (female): Case numbers for Typhoid fever (female)
Paratyphoid fever (total): Case numbers for Paratyphoid fever (total)
Paratyphoid fever (male): Case numbers for Paratyphoid fever (male)
Paratyphoid fever (female): Case numbers for Paratyphoid fever (female)
Acute poliomyelitis (total): Case numbers for Acute poliomyelitis (total)
Acute poliomyelitis (male): Case numbers for Acute poliomyelitis (male)
Acute poliomyelitis (female): Case numbers for Acute poliomyelitis (female)
Diphtheria (total): Case numbers for Diphtheria (total)
Diphtheria (male): Case numbers for Diphtheria (male)
Diphtheria (female): Case numbers for Diphtheria (female)
Enterohemorrhagic E. coli infection (total): Case numbers for Enterohemorrhagic E. coli infection (total)
Enterohemorrhagic E. coli infection (male): Case numbers for Enterohemorrhagic E. coli infection (male)
Enterohemorrhagic E. coli infection (female): Case numbers for Enterohemorrhagic E. coli infection (female)
Amebiasis (total): Case numbers for Amebiasis (total)
Amebiasis (male): Case numbers for Amebiasis (male)
Amebiasis (female): Case numbers for Amebiasis (female)
Echinococcosis (total): Case numbers for Echinococcosis (total)
Echinococcosis (male): Case numbers for Echinococcosis (male)
Echinococcosis (female): Case numbers for Echinococcosis (female)
Yellow fever (total): Case numbers for Yellow fever (total)
Yellow fever (male): Case numbers for Yellow fever (male)
Yellow fever (female): Case numbers for Yellow fever (female)
Psittacosis (total): Case numbers for Psittacosis (total)
Psittacosis (male): Case numbers for Psittacosis (male)
Psittacosis (female): Case numbers for Psittacosis (female)
Relapsing fever (total): Case numbers for Relapsing fever (total)
Relapsing fever (male): Case numbers for Relapsing fever (male)
Relapsing fever (female): Case numbers for Relapsing fever (female)
Acute viral hepatitis (total): Case numbers for Acute viral hepatitis (total)
Acute viral hepatitis (male): Case numbers for Acute viral hepatitis (male)
Acute viral hepatitis (female): Case numbers for Acute viral hepatitis (female)
Q fever (total): Case numbers for Q fever (total)
Q fever (male): Case numbers for Q fever (male)
Q fever (female): Case numbers for Q fever (female)
Rabies (total): Case numbers for Rabies (total)
Rabies (male): Case numbers for Rabies (male)
Rabies (female): Case numbers for Rabies (female)
Cryptosporidiosis (total): Case numbers for Cryptosporidiosis (total)
Cryptosporidiosis (male): Case numbers for Cryptosporidiosis (male)
Cryptosporidiosis (female): Case numbers for Cryptosporidiosis (female)
Creutzfeldt-Jakob disease (total): Case numbers for Creutzfeldt-Jakob disease (total)
Creutzfeldt-Jakob disease (male): Case numbers for Creutzfeldt-Jakob disease (male)
Creutzfeldt-Jakob disease (female): Case numbers for Creutzfeldt-Jakob disease (female)
Severe invasive streptococcal infections (total): Case numbers for Severe invasive streptococcal infections (total)
Severe invasive streptococcal infections (male): Case numbers for Severe invasive streptococcal infections (male)
Severe invasive streptococcal infections (female): Case numbers for Severe invasive streptococcal infections (female)
AIDS (total): Case numbers for AIDS (total)
AIDS (male): Case numbers for AIDS (male)
AIDS (female): Case numbers for AIDS (female)
Coccidioidomycosis (total): Case numbers for Coccidioidomycosis (total)
Coccidioidomycosis (male): Case numbers for Coccidioidomycosis (male)
Coccidioidomycosis (female): Case numbers for Coccidioidomycosis (female)
Giardiasis (total): Case numbers for Giardiasis (total)
Giardiasis (male): Case numbers for Giardiasis (male)
Giardiasis (female): Case numbers for Giardiasis (female)
Hemorrhagic fever with renal syndrome (total): Case numbers for Hemorrhagic fever with renal syndrome (total)
Hemorrhagic fever with renal syndrome (male): Case numbers for Hemorrhagic fever with renal syndrome (male)
Hemorrhagic fever with renal syndrome (female): Case numbers for Hemorrhagic fever with renal syndrome (female)
Meningococcal meningitis (total): Case numbers for Meningococcal meningitis (total)
Meningococcal meningitis (male): Case numbers for Meningococcal meningitis (male)
Meningococcal meningitis (female): Case numbers for Meningococcal meningitis (female)
Congenital rubella syndrome (total): Case numbers for Congenital rubella syndrome (total)
Congenital rubella syndrome (male): Case numbers for Congenital rubella syndrome (male)
Congenital rubella syndrome (female): Case numbers for Congenital rubella syndrome (female)
Anthrax (total): Case numbers for Anthrax (total)
Anthrax (male): Case numbers for Anthrax (male)
Anthrax (female): Case numbers for Anthrax (female)
Tsutsugamushi disease (total): Case numbers for Tsutsugamushi disease (total)
Tsutsugamushi disease (male): Case numbers for Tsutsugamushi disease (male)
Tsutsugamushi disease (female): Case numbers for Tsutsugamushi disease (female)
Dengue fever (total): Case numbers for Dengue fever (total)
Dengue fever (male): Case numbers for Dengue fever (male)
Dengue fever (female): Case numbers for Dengue fever (female)
Japanese spotted fever (total): Case numbers for Japanese spotted fever (total)
Japanese spotted fever (male): Case numbers for Japanese spotted fever (male)
Japanese spotted fever (female): Case numbers for Japanese spotted fever (female)
Japanese encephalitis (total): Case numbers for Japanese encephalitis (total)
Japanese encephalitis (male): Case numbers for Japanese encephalitis (male)
Japanese encephalitis (female): Case numbers for Japanese encephalitis (female)
Infant botulism (total): Case numbers for Infant botulism (total)
Infant botulism (male): Case numbers for Infant botulism (male)
Infant botulism (female): Case numbers for Infant botulism (female)
Syphilis (total): Case numbers for Syphilis (total)
Syphilis (male): Case numbers for Syphilis (male)
Syphilis (female): Case numbers for Syphilis (female)
Tetanus (total): Case numbers for Tetanus (total)
Tetanus (male): Case numbers for Tetanus (male)
Tetanus (female): Case numbers for Tetanus (female)
VRE infection (total): Case numbers for VRE infection (total)
VRE infection (male): Case numbers for VRE infection (male)
VRE infection (female): Case numbers for VRE infection (female)
Hantavirus pulmonary syndrome (total): Case numbers for Hantavirus pulmonary syndrome (total)
Hantavirus pulmonary syndrome (male): Case numbers for Hantavirus pulmonary syndrome (male)
Hantavirus pulmonary syndrome (female): Case numbers for Hantavirus pulmonary syndrome (female)
B virus disease (total): Case numbers for B virus disease (total)
B virus disease (male): Case numbers for B virus disease (male)
B virus disease (female): Case numbers for B virus disease (female)
Brucellosis (total): Case numbers for Brucellosis (total)
Brucellosis (male): Case numbers for Brucellosis (male)
Brucellosis (female): Case numbers for Brucellosis (female)
Epidemic typhus (total): Case numbers for Epidemic typhus (total)
Epidemic typhus (male): Case numbers for Epidemic typhus (male)
Epidemic typhus (female): Case numbers for Epidemic typhus (female)
Malaria (total): Case numbers for Malaria (total)
Malaria (male): Case numbers for Malaria (male)
Malaria (female): Case numbers for Malaria (female)
Lyme disease (total): Case numbers for Lyme disease (total)
Lyme disease (male): Case numbers for Lyme disease (male)
Lyme disease (female): Case numbers for Lyme disease (female)
Legionellosis (total): Case numbers for Legionellosis (total)
Legionellosis (male): Case numbers for Legionellosis (male)
Legionellosis (female): Case numbers for Legionellosis (female)
Poliomyelitis (total): Case numbers for Poliomyelitis (total)
Poliomyelitis (male): Case numbers for Poliomyelitis (male)
Poliomyelitis (female): Case numbers for Poliomyelitis (female)
Scrub typhus (total): Case numbers for Scrub typhus (total)
Scrub typhus (male): Case numbers for Scrub typhus (male)
Scrub typhus (female): Case numbers for Scrub typhus (female)
Epidemic louse-borne typhus (total): Case numbers for Epidemic louse-borne typhus (total)
Epidemic louse-borne typhus (male): Case numbers for Epidemic louse-borne typhus (male)
Epidemic louse-borne typhus (female): Case numbers for Epidemic louse-borne typhus (female)
Severe Acute Respiratory Syndrome (SARS) (total): Case numbers for Severe Acute Respiratory Syndrome (SARS) (total)
Severe Acute Respiratory Syndrome (SARS) (male): Case numbers for Severe Acute Respiratory Syndrome (SARS) (male)
Severe Acute Respiratory Syndrome (SARS) (female): Case numbers for Severe Acute Respiratory Syndrome (SARS) (female)
Smallpox (total): Case numbers for Smallpox (total)
Smallpox (male): Case numbers for Smallpox (male)
Smallpox (female): Case numbers for Smallpox (female)
Enterohemorrhagic Escherichia coli infection (total): Case numbers for Enterohemorrhagic Escherichia coli infection (total)
Enterohemorrhagic Escherichia coli infection (male): Case numbers for Enterohemorrhagic Escherichia coli infection (male)
Enterohemorrhagic Escherichia coli infection (female): Case numbers for Enterohemorrhagic Escherichia coli infection (female)
Hepatitis E (total): Case numbers for Hepatitis E (total)
Hepatitis E (male): Case numbers for Hepatitis E (male)
Hepatitis E (female): Case numbers for Hepatitis E (female)
West Nile fever (including West Nile encephalitis) (total): Case numbers for West Nile fever (including West Nile encephalitis) (total)
West Nile fever (including West Nile encephalitis) (male): Case numbers for West Nile fever (including West Nile encephalitis) (male)
West Nile fever (including West Nile encephalitis) (female): Case numbers for West Nile fever (including West Nile encephalitis) (female)
Hepatitis A (total): Case numbers for Hepatitis A (total)
Hepatitis A (male): Case numbers for Hepatitis A (male)
Hepatitis A (female): Case numbers for Hepatitis A (female)
Avian influenza virus infection (total): Case numbers for Avian influenza virus infection (total)
Avian influenza virus infection (male): Case numbers for Avian influenza virus infection (male)
Avian influenza virus infection (female): Case numbers for Avian influenza virus infection (female)
Monkeypox (total): Case numbers for Monkeypox (total)
Monkeypox (male): Case numbers for Monkeypox (male)
Monkeypox (female): Case numbers for Monkeypox (female)
Scrub typhus (Tsutsugamushi disease) (total): Case numbers for Scrub typhus (Tsutsugamushi disease) (total)
Scrub typhus (Tsutsugamushi disease) (male): Case numbers for Scrub typhus (Tsutsugamushi disease) (male)
Scrub typhus (Tsutsugamushi disease) (female): Case numbers for Scrub typhus (Tsutsugamushi disease) (female)
Nipah virus infection (total): Case numbers for Nipah virus infection (total)
Nipah virus infection (male): Case numbers for Nipah virus infection (male)
Nipah virus infection (female): Case numbers for Nipah virus infection (female)
Herpes B virus infection (total): Case numbers for Herpes B virus infection (total)
Herpes B virus infection (male): Case numbers for Herpes B virus infection (male)
Herpes B virus infection (female): Case numbers for Herpes B virus infection (female)
Botulism (total): Case numbers for Botulism (total)
Botulism (male): Case numbers for Botulism (male)
Botulism (female): Case numbers for Botulism (female)
Tularemia (total): Case numbers for Tularemia (total)
Tularemia (male): Case numbers for Tularemia (male)
Tularemia (female): Case numbers for Tularemia (female)
Lyssavirus infection (excluding rabies) (total): Case numbers for Lyssavirus infection (excluding rabies) (total)
Lyssavirus infection (excluding rabies) (male): Case numbers for Lyssavirus infection (excluding rabies) (male)
Lyssavirus infection (excluding rabies) (female): Case numbers for Lyssavirus infection (excluding rabies) (female)
Leptospirosis (total): Case numbers for Leptospirosis (total)
Leptospirosis (male): Case numbers for Leptospirosis (male)
Leptospirosis (female): Case numbers for Leptospirosis (female)
Viral hepatitis (excluding hepatitis A and E) (total): Case numbers for Viral hepatitis (excluding hepatitis A and E) (total)
Viral hepatitis (excluding hepatitis A and E) (male): Case numbers for Viral hepatitis (excluding hepatitis A and E) (male)
Viral hepatitis (excluding hepatitis A and E) (female): Case numbers for Viral hepatitis (excluding hepatitis A and E) (female)
Acute encephalitis (excluding JE and WNE) (total): Case numbers for Acute encephalitis (excluding JE and WNE) (total)
Acute encephalitis (excluding JE and WNE) (male): Case numbers for Acute encephalitis (excluding JE and WNE) (male)
Acute encephalitis (excluding JE and WNE) (female): Case numbers for Acute encephalitis (excluding JE and WNE) (female)
Severe invasive streptococcal infections (TSLS) (total): Case numbers for Severe invasive streptococcal infections (TSLS) (total)
Severe invasive streptococcal infections (TSLS) (male): Case numbers for Severe invasive streptococcal infections (TSLS) (male)
Severe invasive streptococcal infections (TSLS) (female): Case numbers for Severe invasive streptococcal infections (TSLS) (female)
Acquired immunodeficiency syndrome (AIDS) (total): Case numbers for Acquired immunodeficiency syndrome (AIDS) (total)
Acquired immunodeficiency syndrome (AIDS) (male): Case numbers for Acquired immunodeficiency syndrome (AIDS) (male)
Acquired immunodeficiency syndrome (AIDS) (female): Case numbers for Acquired immunodeficiency syndrome (AIDS) (female)
Vancomycin-resistant S. aureus infection (total): Case numbers for Vancomycin-resistant S. aureus infection (total)
Vancomycin-resistant S. aureus infection (male): Case numbers for Vancomycin-resistant S. aureus infection (male)
Vancomycin-resistant S. aureus infection (female): Case numbers for Vancomycin-resistant S. aureus infection (female)
Vancomycin-resistant Enterococcus infection (total): Case numbers for Vancomycin-resistant Enterococcus infection (total)
Vancomycin-resistant Enterococcus infection (male): Case numbers for Vancomycin-resistant Enterococcus infection (male)
Vancomycin-resistant Enterococcus infection (female): Case numbers for Vancomycin-resistant Enterococcus infection (female)
South American hemorrhagic fever (total): Case numbers for South American hemorrhagic fever (total)
South American hemorrhagic fever (male): Case numbers for South American hemorrhagic fever (male)
South American hemorrhagic fever (female): Case numbers for South American hemorrhagic fever (female)
Tuberculosis (total): Case numbers for Tuberculosis (total)
Tuberculosis (male): Case numbers for Tuberculosis (male)
Tuberculosis (female): Case numbers for Tuberculosis (female)
West Nile fever (total): Case numbers for West Nile fever (total)
West Nile fever (male): Case numbers for West Nile fever (male)
West Nile fever (female): Case numbers for West Nile fever (female)
Omsk hemorrhagic fever (total): Case numbers for Omsk hemorrhagic fever (total)
Omsk hemorrhagic fever (male): Case numbers for Omsk hemorrhagic fever (male)
Omsk hemorrhagic fever (female): Case numbers for Omsk hemorrhagic fever (female)
Kyasanur forest disease (total): Case numbers for Kyasanur forest disease (total)
Kyasanur forest disease (male): Case numbers for Kyasanur forest disease (male)
Kyasanur forest disease (female): Case numbers for Kyasanur forest disease (female)
Western equine encephalitis (total): Case numbers for Western equine encephalitis (total)
Western equine encephalitis (male): Case numbers for Western equine encephalitis (male)
Western equine encephalitis (female): Case numbers for Western equine encephalitis (female)
Tick-borne encephalitis (total): Case numbers for Tick-borne encephalitis (total)
Tick-borne encephalitis (male): Case numbers for Tick-borne encephalitis (male)
Tick-borne encephalitis (female): Case numbers for Tick-borne encephalitis (female)
Eastern equine encephalitis (total): Case numbers for Eastern equine encephalitis (total)
Eastern equine encephalitis (male): Case numbers for Eastern equine encephalitis (male)
Eastern equine encephalitis (female): Case numbers for Eastern equine encephalitis (female)
Glanders (total): Case numbers for Glanders (total)
Glanders (male): Case numbers for Glanders (male)
Glanders (female): Case numbers for Glanders (female)
Venezuelan equine encephalitis (total): Case numbers for Venezuelan equine encephalitis (total)
Venezuelan equine encephalitis (male): Case numbers for Venezuelan equine encephalitis (male)
Venezuelan equine encephalitis (female): Case numbers for Venezuelan equine encephalitis (female)
Hendra virus infection (total): Case numbers for Hendra virus infection (total)
Hendra virus infection (male): Case numbers for Hendra virus infection (male)
Hendra virus infection (female): Case numbers for Hendra virus infection (female)
Rift valley fever (total): Case numbers for Rift valley fever (total)
Rift valley fever (male): Case numbers for Rift valley fever (male)
Rift valley fever (female): Case numbers for Rift valley fever (female)
Melioidosis (total): Case numbers for Melioidosis (total)
Melioidosis (male): Case numbers for Melioidosis (male)
Melioidosis (female): Case numbers for Melioidosis (female)
Rocky mountain spotted fever (total): Case numbers for Rocky mountain spotted fever (total)
Rocky mountain spotted fever (male): Case numbers for Rocky mountain spotted fever (male)
Rocky mountain spotted fever (female): Case numbers for Rocky mountain spotted fever (female)
Avian influenza H5N1 (total): Case numbers for Avian influenza H5N1 (total)
Avian influenza H5N1 (male): Case numbers for Avian influenza H5N1 (male)
Avian influenza H5N1 (female): Case numbers for Avian influenza H5N1 (female)
Avian influenza (exclud. Avian influenza H5N1) (total): Case numbers for Avian influenza (exclud. Avian influenza H5N1) (total)
Avian influenza (exclud. Avian influenza H5N1) (male): Case numbers for Avian influenza (exclud. Avian influenza H5N1) (male)
Avian influenza (exclud. Avian influenza H5N1) (female): Case numbers for Avian influenza (exclud. Avian influenza H5N1) (female)
Rubella (total): Case numbers for Rubella (total)
Rubella (male): Case numbers for Rubella (male)
Rubella (female): Case numbers for Rubella (female)
Measles (total): Case numbers for Measles (total)
Measles (male): Case numbers for Measles (male)
Measles (female): Case numbers for Measles (female)
Pandemic influenza (A/H1N1) (total): Case numbers for Pandemic influenza (A/H1N1) (total)
Pandemic influenza (A/H1N1) (male): Case numbers for Pandemic influenza (A/H1N1) (male)
Pandemic influenza (A/H1N1) (female): Case numbers for Pandemic influenza (A/H1N1) (female)
Chikungunya fever (total): Case numbers for Chikungunya fever (total)
Chikungunya fever (male): Case numbers for Chikungunya fever (male)
Chikungunya fever (female): Case numbers for Chikungunya fever (female)
Avian influenza H7N9 (total): Case numbers for Avian influenza H7N9 (total)
Avian influenza H7N9 (male): Case numbers for Avian influenza H7N9 (male)
Avian influenza H7N9 (female): Case numbers for Avian influenza H7N9 (female)
Severe Fever with Thrombocytopenia Syndrome (total): Case numbers for Severe Fever with Thrombocytopenia Syndrome (total)
Severe Fever with Thrombocytopenia Syndrome (male): Case numbers for Severe Fever with Thrombocytopenia Syndrome (male)
Severe Fever with Thrombocytopenia Syndrome (female): Case numbers for Severe Fever with Thrombocytopenia Syndrome (female)
Invasive haemophilus influenzae infection (total): Case numbers for Invasive haemophilus influenzae infection (total)
Invasive haemophilus influenzae infection (male): Case numbers for Invasive haemophilus influenzae infection (male)
Invasive haemophilus influenzae infection (female): Case numbers for Invasive haemophilus influenzae infection (female)
Invasive meningococcal infection (total): Case numbers for Invasive meningococcal infection (total)
Invasive meningococcal infection (male): Case numbers for Invasive meningococcal infection (male)
Invasive meningococcal infection (female): Case numbers for Invasive meningococcal infection (female)
Invasive streptococcal pneumoniae infection (total): Case numbers for Invasive streptococcal pneumoniae infection (total)
Invasive streptococcal pneumoniae infection (male): Case numbers for Invasive streptococcal pneumoniae infection (male)
Invasive streptococcal pneumoniae infection (female): Case numbers for Invasive streptococcal pneumoniae infection (female)
Middle East Respiratory Syndrome (MERS) (total): Case numbers for Middle East Respiratory Syndrome (MERS) (total)
Middle East Respiratory Syndrome (MERS) (male): Case numbers for Middle East Respiratory Syndrome (MERS) (male)
Middle East Respiratory Syndrome (MERS) (female): Case numbers for Middle East Respiratory Syndrome (MERS) (female)
Carbapenem-resistant enterobacteriaceae infection (total): Case numbers for Carbapenem-resistant enterobacteriaceae infection (total)
Carbapenem-resistant enterobacteriaceae infection (male): Case numbers for Carbapenem-resistant enterobacteriaceae infection (male)
Carbapenem-resistant enterobacteriaceae infection (female): Case numbers for Carbapenem-resistant enterobacteriaceae infection (female)
Varicella (limited to hospiltalized case) (total): Case numbers for Varicella (limited to hospiltalized case) (total)
Varicella (limited to hospiltalized case) (male): Case numbers for Varicella (limited to hospiltalized case) (male)
Varicella (limited to hospiltalized case) (female): Case numbers for Varicella (limited to hospiltalized case) (female)
Disseminated cryptococcal infection (total): Case numbers for Disseminated cryptococcal infection (total)
Disseminated cryptococcal infection (male): Case numbers for Disseminated cryptococcal infection (male)
Disseminated cryptococcal infection (female): Case numbers for Disseminated cryptococcal infection (female)
Multidrug-resistant Acinetobacter infection (total): Case numbers for Multidrug-resistant Acinetobacter infection (total)
Multidrug-resistant Acinetobacter infection (male): Case numbers for Multidrug-resistant Acinetobacter infection (male)
Multidrug-resistant Acinetobacter infection (female): Case numbers for Multidrug-resistant Acinetobacter infection (female)
Zika virus infection (total): Case numbers for Zika virus infection (total)
Zika virus infection (male): Case numbers for Zika virus infection (male)
Zika virus infection (female): Case numbers for Zika virus infection (female)
Acute Flaccid Paralysis (excluding Acute poliomyelitis) (total): Case numbers for Acute Flaccid Paralysis (excluding Acute poliomyelitis) (total)
Acute Flaccid Paralysis (excluding Acute poliomyelitis) (male): Case numbers for Acute Flaccid Paralysis (excluding Acute poliomyelitis) (male)
Acute Flaccid Paralysis (excluding Acute poliomyelitis) (female): Case numbers for Acute Flaccid Paralysis (excluding Acute poliomyelitis) (female)
Pertussis (total): Case numbers for Pertussis (total)
Pertussis (male): Case numbers for Pertussis (male)
Pertussis (female): Case numbers for Pertussis (female)
Mpox (total): Case numbers for Mpox (total)
Mpox (male): Case numbers for Mpox (male)
Mpox (female): Case numbers for Mpox (female)
Carbapenem-resistant Enterobacterales infection (total): Case numbers for Carbapenem-resistant Enterobacterales infection (total)
Carbapenem-resistant Enterobacterales infection (male): Case numbers for Carbapenem-resistant Enterobacterales infection (male)
Carbapenem-resistant Enterobacterales infection (female): Case numbers for Carbapenem-resistant Enterobacterales infection (female)
HIV/AIDS (total): Case numbers for HIV/AIDS (total)
HIV/AIDS (male): Case numbers for HIV/AIDS (male)
HIV/AIDS (female): Case numbers for HIV/AIDS (female)

Source

The Japan Institute for Health Security (JIHS) (https://id-info.jihs.go.jp/index.html)

Package 'jpinfect'

Help Index

Bullet report Data

Description

Usage

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Download the bullet reports from the Japan Institute for Health Security (JIHS)

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Download the confirmed case datasets from the Japan Institute for Health Security (JIHS)

Description

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Merge multiple disease datasets into a unified data table

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Value

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Convert data from wide format to long format for easier analysis

Description

Usage

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Value

Examples

Import one week or more weeks of bullet reports

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Read Confirmed Case Reports from File or Directory

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Display Infectious Diseases Weekly Report (IDWR) URLs

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Usage

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Display dataset URLs of Confirmed Cases based on Infectious Diseases Weekly Report (IDWR)

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Value

Examples

Place Prefecture Data

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Usage

Format

Source

English Names of Prefectures in Japan

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Usage

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Examples

Sex Prefecture Data

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