cancerscreening provides an R interface to Kenya Health Information System (KHIS)
via the DHIS
2 API. The goal of cancerscreening is to provide a easy
way to download cancer screening data from the KHIS using the khisr package.
You can install the released version of cancerscreening from CRAN with:
install.packages("cancerscreening")And the development version of from Github with:
# install.packages("pak")
pak::pak('damurka/cancerscreening')library("cancerscreening")cancerscreening will, by default, help you interact with KHIS as an authenticated user. Before calling any function that makes an API call you need credentials to KHIS. You will be expected to set this credential to download the data. See the article set you credentials for more
# Set the credentials using username and password
khis_cred(username = 'KHIS username', password = 'KHIS password')
# Set credentials using configuration path
khis_cred(config_path = 'path/to/secret.json')After setting the credential you can invoke any function to download data from the API.
For this overview, we’ve logged into KHIS as a specific user in a hidden chunk.
get_ followed by
the screening area cervical, breast,
colorectal, or lab. Auto-completion is your
friendget_cervical_screened,
get_cervical_positive, or
get_cervical_treated%>% but does not require its use.This is a basic example which shows you how to solve a common problem:
# Download the cervical cancer screening data for country
cacx_screened <- get_cervical_screened('2022-07-01')
cacx_screened
#> # A tibble: 758 × 11
#> value country element category period month year quarter fiscal_year
#> <dbl> <chr> <fct> <fct> <date> <ord> <dbl> <fct> <fct>
#> 1 1 Kenya HPV Post-trea… 2024-05-01 May 2024 Q4 2023/2024
#> 2 971 Kenya Pap Smear Initial S… 2023-04-01 April 2023 Q4 2022/2023
#> 3 106 Kenya HPV Routine S… 2024-01-01 Janu… 2024 Q3 2023/2024
#> 4 1060 Kenya Pap Smear Initial S… 2023-05-01 May 2023 Q4 2022/2023
#> 5 1068 Kenya Pap Smear Initial S… 2023-03-01 March 2023 Q3 2022/2023
#> 6 22 Kenya VIA Post-trea… 2022-08-01 Augu… 2022 Q1 2022/2023
#> 7 464 Kenya HPV Routine S… 2024-02-01 Febr… 2024 Q3 2023/2024
#> 8 1 Kenya VIA Post-trea… 2022-07-01 July 2022 Q1 2022/2023
#> 9 638 Kenya Pap Smear Initial S… 2023-08-01 Augu… 2023 Q1 2023/2024
#> 10 3 Kenya HPV Routine S… 2022-07-01 July 2022 Q1 2022/2023
#> # ℹ 748 more rows
#> # ℹ 2 more variables: age_group <fct>, source <fct>These functions are designed to efficiently download cancer screening data at various aggregation levels (e.g., country, county). By specifying the desired level, you can retrieve only the data you need, reducing download times and optimizing transfer efficiency.
# Download cervical cancer screening data aggregated to country
cacx_screened <- get_cervical_screened('2021-07-01',
end_date = '2021-12-31',
level = 'country')
cacx_screened
#> # A tibble: 181 × 11
#> value country element category period month year quarter fiscal_year
#> <dbl> <chr> <fct> <fct> <date> <ord> <dbl> <fct> <fct>
#> 1 5 Kenya HPV Post-trea… 2021-07-01 July 2021 Q1 2021/2022
#> 2 106 Kenya VIA Routine S… 2021-10-01 Octo… 2021 Q2 2021/2022
#> 3 2227 Kenya VIA <NA> 2021-11-01 Nove… 2021 Q2 2021/2022
#> 4 70 Kenya Pap Smear Initial S… 2021-10-01 Octo… 2021 Q2 2021/2022
#> 5 872 Kenya Pap Smear <NA> 2021-10-01 Octo… 2021 Q2 2021/2022
#> 6 455 Kenya Pap Smear <NA> 2021-12-01 Dece… 2021 Q2 2021/2022
#> 7 109 Kenya VIA Routine S… 2021-12-01 Dece… 2021 Q2 2021/2022
#> 8 167 Kenya HPV <NA> 2021-11-01 Nove… 2021 Q2 2021/2022
#> 9 1846 Kenya VIA <NA> 2021-12-01 Dece… 2021 Q2 2021/2022
#> 10 132 Kenya HPV <NA> 2021-10-01 Octo… 2021 Q2 2021/2022
#> # ℹ 171 more rows
#> # ℹ 2 more variables: age_group <fct>, source <fct>
# Download cervical cancer screening positives aggregated by county
cacx_positive <- get_cervical_positive('2021-07-01',
end_date = '2021-12-31',
level = 'county')
cacx_positive
#> # A tibble: 1,600 × 12
#> value county country element category period month year quarter
#> <dbl> <chr> <chr> <fct> <fct> <date> <ord> <dbl> <fct>
#> 1 1 Bomet Kenya HPV <NA> 2021-12-01 Dece… 2021 Q2
#> 2 5 Kakamega Kenya Suspicious… <NA> 2021-11-01 Nove… 2021 Q2
#> 3 1 Bungoma Kenya Suspicious… Initial… 2021-12-01 Dece… 2021 Q2
#> 4 2 Machakos Kenya VIA Routine… 2021-07-01 July 2021 Q1
#> 5 12 Kirinyaga Kenya VIA Initial… 2021-09-01 Sept… 2021 Q1
#> 6 3 Trans Nzoia Kenya Pap Smear Initial… 2021-10-01 Octo… 2021 Q2
#> 7 1 Bomet Kenya Pap Smear <NA> 2021-09-01 Sept… 2021 Q1
#> 8 6 Busia Kenya VIA <NA> 2021-09-01 Sept… 2021 Q1
#> 9 4 Nakuru Kenya Suspicious… <NA> 2021-10-01 Octo… 2021 Q2
#> 10 12 Kisii Kenya VIA <NA> 2021-11-01 Nove… 2021 Q2
#> # ℹ 1,590 more rows
#> # ℹ 3 more variables: fiscal_year <fct>, age_group <fct>, source <fct>
# Download Breast mammogram screening aggregated by subcounty
breast_mammogram <- get_breast_mammogram('2021-07-01',
end_date = '2021-12-31',
level = 'subcounty')
breast_mammogram
#> # A tibble: 21 × 13
#> value subcounty county country element age_group period month year
#> <dbl> <chr> <chr> <chr> <fct> <fct> <date> <ord> <dbl>
#> 1 15 Starehe Nairo… Kenya BIRADS… 25-34 2021-07-01 July 2021
#> 2 1 Lurambi Kakam… Kenya BIRADS… 56-74 2021-09-01 Sept… 2021
#> 3 3 Mvita Momba… Kenya BIRADS… 40-55 2021-10-01 Octo… 2021
#> 4 1 Starehe Nairo… Kenya BIRADS… 56-74 2021-12-01 Dece… 2021
#> 5 1 Kirinyaga South Kirin… Kenya BIRADS… 25-34 2021-12-01 Dece… 2021
#> 6 1 Starehe Nairo… Kenya BIRADS… 40-55 2021-09-01 Sept… 2021
#> 7 1 Laikipia East Laiki… Kenya BIRADS… 40-55 2021-11-01 Nove… 2021
#> 8 1 Kangundo Macha… Kenya BIRADS… 40-55 2021-11-01 Nove… 2021
#> 9 2 Mvita Momba… Kenya BIRADS… 40-55 2021-10-01 Octo… 2021
#> 10 1 Laikipia East Laiki… Kenya BIRADS… 35-39 2021-11-01 Nove… 2021
#> # ℹ 11 more rows
#> # ℹ 4 more variables: quarter <fct>, fiscal_year <fct>, source <chr>,
#> # category <fct>
# Download Fluid cytology data aggregated by facility
fluid_cytology <- get_lab_fluid_cytology('2021-07-01',
end_date = '2021-12-31',
level = 'facility')
fluid_cytology
#> # A tibble: 2,433 × 14
#> value facility ward subcounty county country element category period
#> <dbl> <chr> <chr> <chr> <chr> <chr> <fct> <fct> <date>
#> 1 0 Spicas Medi… Chep… Cheptais Bungo… Kenya CSF Total E… 2021-12-01
#> 2 0 Miriri Disp… Gach… Masaba N… Nyami… Kenya Pleura… Maligna… 2021-07-01
#> 3 0 Mvono Clinic Wund… Wundanyi Taita… Kenya Asciti… Total E… 2021-07-01
#> 4 0 Machururiat… Gesi… Masaba N… Nyami… Kenya CSF Total E… 2021-10-01
#> 5 0 Maungu Mode… Maru… Voi Taita… Kenya CSF Maligna… 2021-09-01
#> 6 0 Spicas Medi… Chep… Cheptais Bungo… Kenya CSF Total E… 2021-10-01
#> 7 0 Elgon View … Race… Kesses Uasin… Kenya CSF Total E… 2021-10-01
#> 8 0 Embu Level … Kiri… Manyatta Embu Kenya Urine Maligna… 2021-08-01
#> 9 0 Bunyore Med… Nort… Emuhaya Vihiga Kenya Asciti… Maligna… 2021-10-01
#> 10 0 Derkale Dis… Derk… Banissa Mande… Kenya CSF Maligna… 2021-12-01
#> # ℹ 2,423 more rows
#> # ℹ 5 more variables: month <ord>, year <dbl>, quarter <fct>,
#> # fiscal_year <fct>, source <chr>
# Download histology data for Embu county (id PFu8alU2KWG)
histology <- get_lab_tissue_histology('2021-07-01',
end_date = '2021-12-31',
level = 'facility',
organisations = 'PFu8alU2KWG')
histology
#> # A tibble: 65 × 14
#> value facility ward subcounty county country element category period
#> <dbl> <chr> <chr> <chr> <chr> <chr> <fct> <fct> <date>
#> 1 1 Aga Khan Un… Kiri… Manyatta Embu Kenya Skin Total E… 2021-12-01
#> 2 1 Imara Medip… Kiri… Manyatta Embu Kenya Ovary Total E… 2021-07-01
#> 3 1 Outspan Hos… Kiri… Manyatta Embu Kenya Oral Total E… 2021-07-01
#> 4 1 Aga Khan Un… Kiri… Manyatta Embu Kenya Skin Maligna… 2021-12-01
#> 5 2 Aga Khan Un… Kiri… Manyatta Embu Kenya Breast… Maligna… 2021-11-01
#> 6 1 Focus Clini… Kiri… Manyatta Embu Kenya Ovary Total E… 2021-07-01
#> 7 1 Aga Khan Un… Kiri… Manyatta Embu Kenya Breast… Maligna… 2021-12-01
#> 8 1 Aga Khan Un… Kiri… Manyatta Embu Kenya Soft t… Total E… 2021-10-01
#> 9 1 Outspan Hos… Kiri… Manyatta Embu Kenya Breast… Total E… 2021-10-01
#> 10 13 Outspan Hos… Kiri… Manyatta Embu Kenya Colore… Total E… 2021-09-01
#> # ℹ 55 more rows
#> # ℹ 5 more variables: month <ord>, year <dbl>, quarter <fct>,
#> # fiscal_year <fct>, source <chr>Get Started is a more extensive general introduction to cancerscreening.
Browse the articles index to find articles that cover various topics in more depth.
See the function index for an organized, exhaustive listing.
Please note that the cancerscreening project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.