To test the desk review, load sirfunctions as an .Rproject and then devtools::load_all(). A desk review starts by first defining the following parameters at the minimum:
country_name: name of the country to perform a desk review
local_dr_folder: absolute path in the local machine where to store the desk review at.
The following parameters are optional:
iss_data_path: file path where the ISS data is stored locally
lab_data_path: file parh where the lab data is stored locally
Until the desk review code is loaded to dev or main, please pass branch="59-dr-modularization-data-loading" in init_dr(). The purpose of the branch parameter is to point to the right GitHub repository to download the various desk review functions. The default is "main", with the expectation that the desk review functions will be included in the release of sirfunctions v1.1.
Once the parameters are defined, run the following to assign ctry.data with the polio data of a specific country:
ctry.data <- init_dr(country_name, local_dr_folder = local_folder_path, branch="59-dr-modularization-data-loading")
Upon initialization, it will create a folder structure for the desk review within the local DR folder. It will also automatically set up helpful global environment variables, such as paths to the data folder, figure folder, etc... A parameter file will be created that records the start and end date of the desk review.
Within the year folder of the country folder, a desk review template in the form of an RMarkdown will also be downloaded. After initializing ctry.data, you may proceed with the steps as outlined in the desk review template file.
SPECIFIC ASK: At the minimum please, test 1 country from AFRO, 1 country from EMRO, and 1 country outside of the two regions. ISS Data is available for specific countries, shoot me an email to test out that functionality.
To test the desk review, load
sirfunctionsas an .Rproject and thendevtools::load_all(). A desk review starts by first defining the following parameters at the minimum:country_name: name of the country to perform a desk reviewlocal_dr_folder: absolute path in the local machine where to store the desk review at.The following parameters are optional:
iss_data_path: file path where the ISS data is stored locallylab_data_path: file parh where the lab data is stored locallyUntil the desk review code is loaded to
devormain, please passbranch="59-dr-modularization-data-loading"ininit_dr(). The purpose of thebranchparameter is to point to the right GitHub repository to download the various desk review functions. The default is"main", with the expectation that the desk review functions will be included in the release ofsirfunctions v1.1.Once the parameters are defined, run the following to assign
ctry.datawith the polio data of a specific country:ctry.data <- init_dr(country_name, local_dr_folder = local_folder_path, branch="59-dr-modularization-data-loading")Upon initialization, it will create a folder structure for the desk review within the local DR folder. It will also automatically set up helpful global environment variables, such as paths to the data folder, figure folder, etc... A parameter file will be created that records the start and end date of the desk review.
Within the year folder of the country folder, a desk review template in the form of an RMarkdown will also be downloaded. After initializing
ctry.data, you may proceed with the steps as outlined in the desk review template file.SPECIFIC ASK: At the minimum please, test 1 country from AFRO, 1 country from EMRO, and 1 country outside of the two regions. ISS Data is available for specific countries, shoot me an email to test out that functionality.