Description

Streamline Access to Cancer Screening Data.

Description

Retrieve cancer screening data for cervical, breast and colorectal cancers from the Kenya Health Information System <https://hiskenya.org> in a consistent way.

README.md

cran.r-project.org

cancerscreening

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

Load cancerscreening package

library("cancerscreening")

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 area cervical, breast, colorectal, or lab. 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, or get_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: 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>

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 × 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>

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.

r-cancerscreening

cancerscreening

Overview

Installation

Usage

Load cancerscreening package

Auth

Package conventions

Aggregating Data

Where to learn more

Code of Conduct

Version

License

Status

Source

Homepage

Platforms (75)

cancerscreening

Overview

Installation

Usage

Load cancerscreening package

Auth

Package conventions

Aggregating Data

Where to learn more

Code of Conduct

Version

License

Status

Source

Homepage

Platforms75 (75)

Platforms (75)