Overview
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.
Installation
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')Usage
Auth
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.
Package conventions
- Most function begin with the prefix
get_followed by the screening areacervical,breast,colorectal, orlab. Auto-completion is your friend - Goal is to allow the download of data associated with the data of interest, e.g.
get_cervical_screened,get_cervical_positive, orget_cervical_treated - cancerscreening is “pipe-friendly” and, in-fact re-exports
%>%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: 689 × 10
#> value country element category period month year fiscal_year age_group
#> * <dbl> <chr> <fct> <fct> <date> <ord> <dbl> <fct> <fct>
#> 1 971 Kenya Pap Smear Initial… 2023-04-01 April 2023 2022/2023 25-49
#> 2 106 Kenya HPV Routine… 2024-01-01 Janu… 2024 2023/2024 25-49
#> 3 1060 Kenya Pap Smear Initial… 2023-05-01 May 2023 2022/2023 25-49
#> 4 1068 Kenya Pap Smear Initial… 2023-03-01 March 2023 2022/2023 25-49
#> 5 22 Kenya VIA Post-tr… 2022-08-01 Augu… 2022 2022/2023 <25
#> 6 464 Kenya HPV Routine… 2024-02-01 Febr… 2024 2023/2024 25-49
#> 7 1 Kenya VIA Post-tr… 2022-07-01 July 2022 2022/2023 <25
#> 8 638 Kenya Pap Smear Initial… 2023-08-01 Augu… 2023 2023/2024 25-49
#> 9 3 Kenya HPV Routine… 2022-07-01 July 2022 2022/2023 <25
#> 10 651 Kenya Pap Smear Initial… 2023-07-01 July 2023 2023/2024 25-49
#> # ℹ 679 more rows
#> # ℹ 1 more variable: source <fct>Aggregating Data
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 × 10
#> value country element category period month year fiscal_year age_group
#> * <dbl> <chr> <fct> <fct> <date> <ord> <dbl> <fct> <fct>
#> 1 5 Kenya HPV Post-tr… 2021-07-01 July 2021 2021/2022 <25
#> 2 106 Kenya VIA Routine… 2021-10-01 Octo… 2021 2021/2022 <25
#> 3 2227 Kenya VIA <NA> 2021-11-01 Nove… 2021 2021/2022 50+
#> 4 70 Kenya Pap Smear Initial… 2021-10-01 Octo… 2021 2021/2022 25-49
#> 5 872 Kenya Pap Smear <NA> 2021-10-01 Octo… 2021 2021/2022 50+
#> 6 455 Kenya Pap Smear <NA> 2021-12-01 Dece… 2021 2021/2022 50+
#> 7 109 Kenya VIA Routine… 2021-12-01 Dece… 2021 2021/2022 <25
#> 8 167 Kenya HPV <NA> 2021-11-01 Nove… 2021 2021/2022 <25
#> 9 1846 Kenya VIA <NA> 2021-12-01 Dece… 2021 2021/2022 50+
#> 10 132 Kenya HPV <NA> 2021-10-01 Octo… 2021 2021/2022 <25
#> # ℹ 171 more rows
#> # ℹ 1 more variable: 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 × 11
#> value county country element category period month year fiscal_year
#> * <dbl> <chr> <chr> <fct> <fct> <date> <ord> <dbl> <fct>
#> 1 1 Bomet Kenya HPV <NA> 2021-12-01 Dece… 2021 2021/2022
#> 2 5 Kakamega Kenya Suspic… <NA> 2021-11-01 Nove… 2021 2021/2022
#> 3 1 Bungoma Kenya Suspic… Initial… 2021-12-01 Dece… 2021 2021/2022
#> 4 2 Machakos Kenya VIA Routine… 2021-07-01 July 2021 2021/2022
#> 5 12 Kirinyaga Kenya VIA Initial… 2021-09-01 Sept… 2021 2021/2022
#> 6 3 Trans Nzoia Kenya Pap Sm… Initial… 2021-10-01 Octo… 2021 2021/2022
#> 7 1 Bomet Kenya Pap Sm… <NA> 2021-09-01 Sept… 2021 2021/2022
#> 8 6 Busia Kenya VIA <NA> 2021-09-01 Sept… 2021 2021/2022
#> 9 4 Nakuru Kenya Suspic… <NA> 2021-10-01 Octo… 2021 2021/2022
#> 10 12 Kisii Kenya VIA <NA> 2021-11-01 Nove… 2021 2021/2022
#> # ℹ 1,590 more rows
#> # ℹ 2 more variables: 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 × 12
#> 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 3 more variables: 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 × 12
#> value facility ward subcounty county element category period month year
#> <dbl> <chr> <chr> <chr> <chr> <fct> <fct> <date> <ord> <dbl>
#> 1 0 Spicas … Chep… Cheptais Bungo… CSF Total E… 2021-12-01 Dece… 2021
#> 2 0 Miriri … Gach… Masaba N… Nyami… Pleura… Maligna… 2021-07-01 July 2021
#> 3 0 Mvono C… Wund… Wundanyi Taita… Asciti… Total E… 2021-07-01 July 2021
#> 4 0 Machuru… Gesi… Masaba N… Nyami… CSF Total E… 2021-10-01 Octo… 2021
#> 5 0 Maungu … Maru… Voi Taita… CSF Maligna… 2021-09-01 Sept… 2021
#> 6 0 Spicas … Chep… Cheptais Bungo… CSF Total E… 2021-10-01 Octo… 2021
#> 7 0 Elgon V… Race… Kesses Uasin… CSF Total E… 2021-10-01 Octo… 2021
#> 8 0 Embu Le… Kiri… Manyatta Embu Urine Maligna… 2021-08-01 Augu… 2021
#> 9 0 Bunyore… Nort… Emuhaya Vihiga Asciti… Maligna… 2021-10-01 Octo… 2021
#> 10 0 Derkale… Derk… Banissa Mande… CSF Maligna… 2021-12-01 Dece… 2021
#> # ℹ 2,423 more rows
#> # ℹ 2 more variables: 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 × 12
#> value facility ward subcounty county element category period month year
#> <dbl> <chr> <chr> <chr> <chr> <fct> <fct> <date> <ord> <dbl>
#> 1 1 Aga Kha… Kiri… Manyatta Embu Skin Total E… 2021-12-01 Dece… 2021
#> 2 1 Imara M… Kiri… Manyatta Embu Ovary Total E… 2021-07-01 July 2021
#> 3 1 Outspan… Kiri… Manyatta Embu Oral Total E… 2021-07-01 July 2021
#> 4 1 Aga Kha… Kiri… Manyatta Embu Skin Maligna… 2021-12-01 Dece… 2021
#> 5 2 Aga Kha… Kiri… Manyatta Embu Breast… Maligna… 2021-11-01 Nove… 2021
#> 6 1 Focus C… Kiri… Manyatta Embu Ovary Total E… 2021-07-01 July 2021
#> 7 1 Aga Kha… Kiri… Manyatta Embu Breast… Maligna… 2021-12-01 Dece… 2021
#> 8 1 Aga Kha… Kiri… Manyatta Embu Soft t… Total E… 2021-10-01 Octo… 2021
#> 9 1 Outspan… Kiri… Manyatta Embu Breast… Total E… 2021-10-01 Octo… 2021
#> 10 13 Outspan… Kiri… Manyatta Embu Colore… Total E… 2021-09-01 Sept… 2021
#> # ℹ 55 more rows
#> # ℹ 2 more variables: fiscal_year <fct>, source <chr>Where to learn more
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.
Code of Conduct
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.