Help for package denguedatahub

Title:

A Tidy Format Datasets of Dengue by Country

Version:

3.2.0

Description:

Provides a weekly, monthly, yearly summary of dengue cases by state/ province/ country.

License:

GPL-3

URL:

https://denguedatahub.netlify.app/

BugReports:

https://github.com/thiyangt/denguedatahub/issues

Encoding:

UTF-8

RoxygenNote:

7.3.2

Imports:

dplyr, tibble, tidyr, rvest, stringr, lifecycle, magrittr, here, utils, purrr, xml2, tabulapdf, rlang (≥ 0.4.11)

LazyData:

true

Suggests:

roxygen2, tsibble

SystemRequirements:

Java (>= 7.0): openjdk-11-jdk (deb), java-11-openjdk.x86_64 (rpm), openjdk@11 (brew)

Depends:

R (≥ 4.1.0)

NeedsCompilation:

Packaged:

2025-06-25 14:00:03 UTC; DELL

Author:

Thiyanga S. Talagala

[aut, cre]

Maintainer:

Thiyanga S. Talagala <ttalagala@sjp.ac.lk>

Repository:

CRAN

Date/Publication:

2025-06-25 14:50:02 UTC

Dengue and severe dengue cases and deaths for subregions of the Americas

Description

Region/Country-wise dengue and severe dengue cases and deaths since 1980 (Last accessed from the source on 30 January 2023).

Usage

americas_annual_data

Format

A tibble with 899134 rows and 5 variables:

region: Name of the affected region
country: Name of the country
type: An indicator for the type of cases (deaths, cases)
cases: cases
year: year

Source

https://www.paho.org/en/arbo-portal/dengue-data-and-analysis/dengue-analysis-subregions

Examples

head(americas_annual_data)

All dengue cases by week in US states and territories, 2010 - 2023

Description

All dengue cases by week in US states and territories, 2010 - 2023 published by the US Centers for Disease Control and Prevention (CDC)

Usage

cdc_casesby_week

Format

A tibble with 742 rows and 4 variables:

Year: Year
Travel.status: Travel status
Week: Week
Reported.cases: Number of reported dengue cases

Source

Accessed from https://www.cdc.gov/dengue/data-research/facts-stats/historic-data.html. Last accessed (Sep 3, 2024)

Examples

head(cdc_casesby_week)

All dengue cases by age group and sex in US states and territories, 2010 - 2023

Description

Annual dengue cases by age group and sex in US states and territories, 2010 - 2023 published by the US Centers for Disease Control and Prevention (CDC)

Usage

cdc_dengue_agesex

Format

A tibble with 3900 rows and 7 variables:

Year: Year
Travel.status: Travel status
Age: Age group
Male: Number of male dengue cases
Female: Number of female dengue cases

Source

Accessed from https://www.cdc.gov/dengue/data-research/facts-stats/historic-data.html. Last accessed (Sep 3, 2024)

Examples

head(cdc_dengue_agesex)

All dengue cases by jurisdiction of residence in US states and territories, 2010 - 2023

Description

All dengue cases by jurisdiction of residence in US states and territories, 2010 - 2023 published by the US Centers for Disease Control and Prevention (CDC)

Usage

cdc_dengue_casesbyjurisdiction

Format

A tibble with 742 rows and 4 variables:

Year: Year
Travel.status: Travel status
Jurisdiction: Jurisdiction
Count: Dengue counts
Legend: Categorization of counts for easy plotting
Notes: Additional notes regarding the observation record

Source

Accessed from https://www.cdc.gov/dengue/data-research/facts-stats/historic-data.html. Last accessed (Sep 3, 2024)

Examples

head(cdc_dengue_casesbyjurisdiction)

All dengue cases by county of residence in US states and territories, 2010 - 2023

Description

Annual dengue cases by county of residence in US states and territories, 2010 - 2023 published by the US Centers for Disease Control and Prevention (CDC)

Usage

cdc_dengue_countyyear

Format

A tibble with 3900 rows and 7 variables:

FullGeoName: Reporting Area
Year: Year
Travel.status: Travel status
County: County
Legend: Categorisation of counts for easy visualisations
Notes: Additional note about the area

Source

Accessed from https://www.cdc.gov/dengue/data-research/facts-stats/historic-data.html. Last accessed (Sep 3, 2024)

Examples

head(cdc_usa_dengue_infection)

Locally acquired dengue cases by year, 2010 - 2023

Description

Locally acquired dengue cases by year in the US, 2010 - 2023 published by the US Centers for Disease Control and Prevention (CDC)

Usage

cdc_local_dengue_cases

Format

A tibble with 14 rows and 3 variables:

Year: Year
Travel.status: Travel status
Reported.cases: Number of reported cases

Source

Accessed from https://www.cdc.gov/dengue/data-research/facts-stats/historic-data.html. Last accessed (Sep 3, 2024)

Examples

head(cdc_local_dengue_cases)

Travel associated dengue cases by year, 2010 - 2023

Description

Travel associated dengue cases by year, 2010 - 2023 in the US, 2010 - 2023 published by the US Centers for Disease Control and Prevention (CDC)

Usage

cdc_travel_associated_dengue_cases

Format

A tibble with 14 rows and 3 variables:

Year: Year
Travel.status: Travel status
Reported.cases: Number of reported cases

Source

Accessed from https://www.cdc.gov/dengue/data-research/facts-stats/historic-data.html. Last accessed (Sep 3, 2024)

Examples

head(cdc_travel_associated_dengue_cases)

Annual number of dengue fever infections in the USA

Description

Annual cases of dengue in different areas of the USA

Usage

cdc_usa_dengue_infection

Format

A tibble with 9170 rows and 38 variables:

area: Reporting Area
year: Year
week: Week
dengue_cases: Dengue cases in the current week
dengue_like_illness: Dengue like illness cases in the current week
severe_dengue: Severe dengue cases in the current week

Source

https://data.cdc.gov/browse.php?federation_filter=85&format=php&sortBy=alpha&tags=dengue

Examples

head(cdc_usa_dengue_infection)

Dengue related data in China

Description

Annual indigenous and imported dengue cases in mainland China, 2005-2020

Usage

china_annual_data

Format

A tibble with 16 rows and 5 variables:

year: Year
dengue.cases.indigenous: Number of indigenous dengue cases
dengue.cases.imported: Number of imported dengue cases
counties.with.dengue.fever.indigenous: Number of counties with dengue fever - indigenous cases
counties.with.dengue.fever.imported: Number of counties with dengue fever - imported cases

Source

https://pmc.ncbi.nlm.nih.gov/articles/PMC8997546/table/ijerph-19-03910-t001/?report=objectonly

Examples

head(china_annual_data)

Read weekly epidemiological reports and convert dengue data into tidy format

Description

Read weekly epidemiological reports and convert dengue data into tidy format

Usage

convert_slwer_to_tidy(
  year,
  reports.url,
  start.date.first,
  end.date.first,
  start.date.last,
  end.date.last,
  week.no
)

Arguments

year

year

reports.url

URL address vector obtained from get_pdflinks_srilanka

start.date.first

starting date of the first report week (format "2006-12-23")

end.date.first

endinging date of the first report week (format "2006-12-23")

start.date.last

starting date of the last report week (format "2006-12-23")

end.date.last

endinging date of the first report week (format "2006-12-23")

week.no

report number vector

Read weekly epidemiological reports and convert dengue data into tidy format

Description

Read weekly epidemiological reports and convert dengue data into tidy format

Usage

convert_srilanka_wer_to_tidy(
  year,
  url.part1 = "https://www.epid.gov.lk",
  url.part2,
  start.date.first,
  end.date.first,
  start.date.last,
  end.date.last,
  week.no
)

Arguments

year

year

url.part1

first part of the URL, by default "https://www.epid.gov.lk"

url.part2

URL address vector obtained from filter_year_wer_link

start.date.first

starting date of the first report week (format "2006-12-23")

end.date.first

endinging date of the first report week (format "2006-12-23")

start.date.last

starting date of the last report week (format "2006-12-23")

end.date.last

endinging date of the first report week (format "2006-12-23")

week.no

report number vector

Download and save weekly epidemiological reports from Epidemiology Unit, Ministry of Health, Sri Lanka (url https://www.epid.gov.lk/weekly-epidemiological-report/weekly-epidemiological-report)

Description

Download and save weekly epidemiological reports from Epidemiology Unit, Ministry of Health, Sri Lanka (url https://www.epid.gov.lk/weekly-epidemiological-report/weekly-epidemiological-report)

Usage

download_pdfwer_srilanka(
  url =
    "https://www.epid.gov.lk/weekly-epidemiological-report/weekly-epidemiological-report",
  folder.name,
  volume.number
)

Arguments

url

url of the webpage that you intend to download files. The default is URL of the weekly epidemiological reports page

folder.name

create a folder with this name and save the pdf file inside this folder

volume.number

Volume number of the epidemiological reports (Volumes corresponds to year)

Value

Pdf files corresponds to the volume number you specified inside the folder.name

Author(s)

Thiyanga S Talagala

Filter links corresponds to a specific year using the function output get_address

Description

Filter links corresponds to a specific year using the function output get_address

Usage

filter_year_wer(year, address)

Arguments

year

year that you want to extract the reports

address

list or the outout from get_addess function

Author(s)

Thiyanga S Talagala

Extract links of all downloadable files on a webpage

Description

Extract links of all downloadable files on a webpage

Usage

get_addresses(url)

Arguments

url

url of the webpage that you intend to download files.

Value

web addresses of all downloadable files

Author(s)

Thiyanga S Talagala

Get URLs of weekly epidemiological reports from Epidemiology Unit, Ministry of Health, Sri Lanka (url https://www.epid.gov.lk/weekly-epidemiological-report/weekly-epidemiological-report)

Description

Get URLs of weekly epidemiological reports from Epidemiology Unit, Ministry of Health, Sri Lanka (url https://www.epid.gov.lk/weekly-epidemiological-report/weekly-epidemiological-report)

Usage

get_pdflinks_srilanka(
  url =
    "https://www.epid.gov.lk/weekly-epidemiological-report/weekly-epidemiological-report",
  volume.number
)

Arguments

url

url of the webpage that you intend to download files. The default is URL of the weekly epidemiological reports page

volume.number

Volume number of the epidemiological reports (Volumes corresponds to year)

Value

URLS of PDF files corresponds to the volume number

Author(s)

Thiyanga S Talagala

DENGUE/DHF situation in India since 2017

Description

State/Union Territory(UT)-wise dengue/DHF annual deaths and cases since 2017 (Last accessed from the source on 30 January 2023).

Usage

india_annual_data

Format

A tibble with 432 rows and 5 variables:

area: Name of the affected states/UTs
type: An indicator for the type of cases (deaths, cases)
year: Year
additional_information: Additional information regarding collected year period
value: Cases

Source

National Center for Vector Borne Disease Control, Directorate General of Health Services, Ministry of Health and Family Welfare, Government of India.

Examples

head(india_annual_data)

Imported dengue cases in Korea

Description

Data for imported dengue cases were collected from Korea Centers for Disease Control and Prevention (KCDC)

Usage

korea_dengue

Format

A tibble with 33 rows and 7 variables:

Country: Country
Region: Region
2011: Year 2011
2012: Year 2012
2013: Year 2013
2014: Year 2014
2015: Year 2015

Source

Je, Sungmo, Wonjun Bae, Jiyeon Kim, Seung Hyeok Seok, and Eung-Soo Hwang. "Epidemiological characteristics and risk factors of dengue infection in Korean travelers." Journal of Korean Medical Science 31, no. 12 (2016): 1863-1873.

Examples

head(korea_dengue)

Level of Dengue risk around the world

Description

Country-wise dengue risk levels (Last accessed from the source on 18 January 2023).

Usage

level_of_risk

Format

A tibble with 293 rows and 4 variables:

country: factor Name of the country
level_of_risk': factor Dengue risk level. There are three categories: Frequent or continuous, Sporadic or uncertain, Varies by region. Frequent/continuous risk: evidence of more than 10 dengue cases in at least 3 of the previous 10 years. Sporadic/uncertain risk: evidence of at least 1 locally acquired dengue case during the last 10 years.
region: factor Region
last_accessed: information last accessed date

Source

The 2024 data accessed from https://www.cdc.gov/dengue/areas-with-risk/index.html.

Examples

head(level_of_risk)

Apply min-max transformation

Description

Apply min-max transformation

Usage

min_max(data, variable.to.minmax, local = FALSE, group.var)

Arguments

data

tibble that contains cases, groups

variable.to.minmax

the variable that we want to tranform using the min-max transformation

local

TRUE if you need to apply local minmax transformation

group.var

variables that you need to create group-wise

Value

tibble with minmax transformed applied

Daily number of dengue fever infections in Philippines

Description

Daily cases of dengue in Philippines

Usage

philippines_daily_data

Format

A tibble with 32701 rows and 5 variables:

location: location
affected_and_infected: affected and infected number of cases
affected_and_killed: affected and killed number of cases
date: date of the week
region: region name

Source

https://data.humdata.org/dataset/philippine-dengue-cases-and-deaths?

Examples

head(philippines_daily_data)

Weekly number of dengue fever infections in Sri Lanka

Description

Weekly cases of dengue in Sri Lanka

Usage

singapore_weekly_data

Format

A tibble with 18772 rows and 6 variables:

year: year
week: week number
cases: Number of dengue cases

Source

https://www.straitstimes.com/multimedia/graphics/2022/06/singapore-dengue-cases/index.html?shell#:~:text=Singapore%20is%20currently%20seeing%2030,lower%20than%20the%202020%20surge

Examples

head(singapore_weekly_data)

Annual reported dengue cases in Sri Lanka

Description

Annual reported dengue cases in Sri Lanka 1989-2021

Usage

sl_annual

Format

A tibble with 35 rows and 3 variables:

year: Year
dengue.cases: Number of dengue cases
epidemic: Epidemic: 1 if the year is classified as an epidemic year, 0 otherwise

Source

Source 1: World Health Organization. Dengue Fact Sheet and Situation Report, Sri Lanka. 22 July 2022. Available at: https://cdn.who.int/media/docs/default-source/sri-lanka-documents/dengue-fact-sheet_7-2022-srl.pdf?sfvrsn=49021bd_1. (Accessed: 4 September 2024), Source 2: Weekly Dengue Updates, National Dengue Control Unit, Ministry of Health

Examples

head(sl_annual)

Identification of dengue serotypes circulating in Sri Lanka

Description

History of dengue dengue serotypes circulating in Sri Lanka.

Usage

sl_dengue_serotype

Format

A tibble with 35 rows and 3 variables:

year: Year
dengue.cases: Number of dengue cases

Source

Ali, Shahid, Abdul Waheed Khan, Andrew W. Taylor-Robinson, Muhammad Adnan, Shahana Malik, and Saba Gul. "The unprecedented magnitude of the 2017 dengue outbreak in Sri Lanka provides lessons for future mosquito-borne infection control and prevention." Infection, Disease & Health 23, no. 2 (2018): 114-120.

Examples

head(sl_dengue_serotype)

Provinces and Districts of Sri Lanka

Description

Sri Lanka is divided into 9 provinces, each comprising several districts. Here is a list of the districts and the provinces to which they belong.

province: Name of the province
district: Name of the district

Usage

sl_province_districts

Format

An object of class tbl_df (inherits from tbl, data.frame) with 26 rows and 2 columns.

Source

https://moe.gov.lk/ministry-2/provinces/

Examples

sl_province_districts

Type and proportion of breeding habitats positive for Aedes aegypti mosquitoes, across provinces in Sri Lanka, 2017.

Description

Total number of premises inspected: 279,728; Total number of premises inspected: 279,728; total Ae. aegypti–positive containers: 9,699. Other miscellaneous items include refrigerator trays, nonfunctional cisterns, pet feeding cups, gutters, concrete slabs, and any other water-collecting containers. (Last accessed from the source on 3 September 2024).

Usage

sl_sites

Format

A tibble with 9 rows and 7 variables:

Province: Province
Discarded_items: Percentage of water-retaining containers positive for discarded items
Water_storage_containers_and_tanks: Percentage of water-retaining containers positive for water storage containers and tanks
Ponds_and_ornamental_items: Percentage of water-retaining containers positive for ponds and ornamental items
Wells_and_tube_wells: Percentage of water-retaining containers positive for wells and tube wells
Natural_water_collections: Percentage of water-retaining containers positive for natural water collections
Other_miscellaneous_items: Percentage of water-retaining containers positive for other miscellaneous items

Source

Tissera, H.A., Jayamanne, B.D., Raut, R., Janaki, S.M., Tozan, Y., Samaraweera, P.C., Liyanage, P., Ghouse, A., Rodrigo, C., de Silva, A.M. and Fernando, S.D., 2020. Severe dengue epidemic, Sri Lanka, 2017. Emerging infectious diseases, 26(4), p.682. head(sl_sites)

Weekly number of dengue fever infections in Sri Lanka

Description

Weekly cases of dengue in Sri Lanka

Usage

srilanka_weekly_data

Format

A tibble with 23815 rows and 6 variables:

year: year
week: week number
start.date: starting date of the week
end.date: ending date of the week
district: district name
cases: Number of dengue cases

Source

Weekly Epidemiological Reports, Epidemiology Unit, Ministry of Health, Sri Lanka.

Examples

head(srilanka_weekly_data)

Indigenous and imported dengue cases in Taiwan, 1987-2023.

Description

Annual indigenous and imported dengue cases in Taiwan, 1987-2023.

Usage

taiwan_dengue

Format

A tibble with 37 rows and 3 variables:

year: Year
indigenous.dengue: Number of indigenous dengue cases
imported.dengue: Number of imported dengue

Source

Taiwan Centres for Disease Control, Available at: https://www.cdc.gov.tw/En/Category/ListContent/bg0g_VU_Ysrgkes_KRUDgQ?uaid=9_Oq7OYHa-l8B05iUwyVvQ. (Accessed: 4 September 2024), Source 2: Weekly Dengue Updates, National Dengue Control Unit, Ministry of Health

Examples

head(taiwan_dengue)

Annual number of dengue fever infections around the world

Description

Annual incidence of dengue around the world

Usage

world_annual

Format

A tibble with 6750 rows and 4 variables:

longitude: Longitude
latitude: Latitude
group: group variable
order: collect in order
region: regions
subregion: subregions
code: Country or area code
year: year
incidence: Number of dengue incidence across all ages

dengue.present: whetherdengue cases present or not

Source

https://ourworldindata.org/grapher/dengue-incidence

Examples

head(world_annual)