knitr::opts_chunk$set(echo = TRUE)
Draft R code for extracting data from DHIS 2 and populating a bulletin template.
Make sure that your computer is connected to the Internet and that you have previously followed the Prerequisites and Installing steps below to install everything required.
Create a new folder in a location of your choice. Then open RStudio and create a new RStudio Project in this folder using the RStudio menu: File -> New Project -> Existing Directory -> Browse to the new folder just created.
You can then create the weekly surveillance bulletin Markdown document with the following steps in RStudio:
library(dhis2bulletin) draft_bulletin()
Make any necessary amendments to the Markdown template (DHIS 2 federal bulletin.Rmd
) that opens.
Click "Knit with Parameters" at the top of the Markdown template. You will be asked for your DHIS 2 user name and password. These are used to extract data from DHIS 2 for the charts and tables but are not saved anywhere.
The draft bulletin will then open as a Word document (DHIS 2 federal bulletin.docx by default). Make any necessary amendments to the text and footer of the Word document. Note that there is a Style called "Table" which will need to be applied manually to each table. Save the Word file with a file name of your choice.
Note that two folders will have been created in the project folder: figs
(containing the charts generated) and data
(containing the raw data files for reference).
Once the above steps have been done once, then to re-run the bulletin requires only the following steps.
Open the project folder and double-click the .Rproj
file to open RStudio.
Open the Markdown template and make any necessary amendments.
Click "Knit with Parameters" and enter your DHIS 2 user name and password.
Make the necessary amendments to the Word document that opens.
You first need to install R and RStudio.
Then run RStudio. To prepare for installation of the dhis2bulletin
package you need to run the following lines of code:
update.packages(ask = FALSE) install.packages('devtools', dep = TRUE) devtools::install_github('ukgovdatascience/govstyle')
dhis2bulletin
packageTo install the package from GitHub use the command:
devtools::install_github('prcleary/dhis2bulletin')
To update to the latest versions of packages in future you can use the following lines of code:
update.packages(ask = FALSE) devtools::install_github('ukgovdatascience/govstyle') devtools::install_github('prcleary/dhis2bulletin')
One final step: as the script obtains data by using your user name and password, this code will not work if you are using 2-Factor Authentication to log into DHIS 2. You should temporarily disable this in your Settings before running this code.
Paul Cleary: email me with any queries.
This project is licensed under the MIT License.
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