Code chunks will not be evaluated, because:
Set credential unsuccessful.This article takes a quick tour of the main features of cancerscreening.
Remember to see the articles for more detailed treatment of all these topics and more.
These functions directly call the KHIS server to download the data
require the setting of KHIS credentials. See setting
the credentials for more information. The get analytics call is
supported by three metadata functions that help make the data complete
and these include the get_organisation_units_metadata() to
show where the data is from and
get_data_elements_metadata() to show what the data is about
and group the data into various categories.
The cancer screening data that are being tracked breast cancer, cervical cancer, colorectal cancer and laboratory diagnostic data.
get_cervical_screened(): Downloads data on women
screened for cervical cancer.get_cervical_positive(): Retrieves data on women who
tested positive for cervical pre-cancer or cancer.get_cervical_treated(): Accesses data on women who
received treatment for cervical pre-cancer or cancer.get_breast_cbe(): Downloads data on women who received
CBE for breast cancer screening.get_breast_ultrasound(): Downloads data on women who
received ultrasound for breast cancer screening.get_breast_mammogram(): Downloads data on women who
received mammograms for breast cancer screening.get_colorectal_fobt(): Retrieves data on individuals
who receive FOBT for colorectal cancer screening tests.get_colorectal_colonoscopy(): Retrieves data on
individuals who receive colonoscopy for colorectal cancer screening
tests.get_lab_fluid_cytology(): Retrieve data on fluid
cytology done in the lab. They include Ascitic fluid, cerebral spinal
fluid, pleural fluid and urine.get_lab_tissue_histology(): Retrieve data on tissue
histology done in the lab. They include Breast, colorectal, oesphageal,
head & neck, hepatobiliary, lymph nodes, oral, ovary, prostate, skin
and uterine tissues;get_lab_bone_marrow(): Retrieve data on bone marrow
done in the lab.get_lab_fna(): Retrieve data on fine-needle aspiration
done in the lab. They include breast, liver, lymph node and
thyroid.get_lab_smears()Retrieve data on smears done in the
lab. They include pap smear, tissue impressions, and touch
preparation.To get the data the following calls can be made
# Get data for those screening for cervical cancer
cervical_screened <- get_cervical_screened('2022-01-01', end_date = '2022-06-30')
cervical_screened
# Get data for those screening for colorectal cancer using FOBT
colorectal_screened <- get_colorectal_fobt('2022-01-01', end_date = '2022-06-30')
colorectal_screened
# Get data for those screening for breast cancer using mammogram
breast_screened <- get_breast_mammogram('2022-01-01', end_date = '2022-06-30')
breast_screenedThese functions do not require to access the KHIS server the project and calculate the target population guided the Kenya housing and population census 2019 and the Kenya National Cancer Screening guidelines 2019.
The functions include: get_cervical_target_population(),
get_colorectal_target_population(),
get_breast_cbe_target_population() and
get_breast_mammogram_target_population().
If these function do not meet your criteria you can make your target
population using the get_filtered_population().
# Get the cervical screening target population for 2022
cervical_target_population <- get_cervical_target_population(2022)
cervical_target_population
# Get the colorectal cancer screening target population for 20223 by county
colorectal_target_population <- get_colorectal_target_population(2023, level = 'county')
colorectal_target_population
# Get the population of women 15-49 year for the year 2024
wra_pop <- get_filtered_population(year = 2024, min_age = 15, max_age = 49, pop_sex = 'female')
wra_pop