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:
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.
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')
To install the package from GitHub use the command:
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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