In JayAchar/tbreportr: Tools for Reporting TB Data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE
)

Accessing instructions

This instruction vignette is available either online at Github or through emailing the author. Alternatively, you may ask your medical manager since they may also have a copy. For the most up to date version, it's recommended to visit the online repository linked.

Purpose

This R package has been designed to support MSF field staff using Koch 6 to collect programmatic data for TB activities. It will take exported Koch 6 files formatted as .xls, and generate a pre-formatted HTML report. The package will be updated if bugs are discovered, if new features are requested, or reporting needs change. Medical co-ordinators can ask the developer for customisation of the report via email.

Requirements

To use this automated reporting tool for Koch 6, your computer will require the following:

A working version of R (a programming language),
Authority to install R-packages,
Export epidemio files from Koch 6 saved as .xls files

To check whether R is installed on your computer:

open Command Prompt through your Start Menu
type the letter "r" and press Enter

If R has been installed, the resultant text will start by describing the version number and date of release (see image below). If R has not been installed, this tool cannot currently be used. A staff member with administrator rights for this computer will need to install the open-source (free) programme by downloading it from a trusted website on the internet. See this online site for further details.

Preparation

Internet access will be required during the preparation process since additional files need to be downloaded. In Command Prompt, ensure that R is running - the icon at the start of the line will look like this >. If you cannot see this, then simply type the letter "r" to start R running.

Copy the code immediately below, one line at a time and press enter. You may be asked to pick a country from where to download the files - choose a country close to your location.

install.packages("devtools")
install_github("JayAchar/tbreportr")

The computer will download a number of files required by R to use this function. Wait for it to finish, then close Command Prompt.

Using Windows Explorer, navigate to My Documents, then add a new empty folder called koch6. Inside this folder, add two empty folders called reports and scripts. The names need to be typed exactly this way in all lower letters.

The koch6 folder is where your Export Epidemio files must be saved for the report to be generated. The reports folder will be where generated reports are saved. The scripts folder is where you will need to save the file you are about to download. After reports are produced, they can be moved but you must ensure the folder remains in place.

Generating report

Open Koch 6 and export epidemio, ensuring that you save all the export files in the koch6 folder in My Documents.
Open Command Prompt and start R (type "r" at the command line).
Type the following:

setwd("~/koch6")
library(tbreportr)
mmr_outputer()

Wait for the start of the line to change back to > then check your reports folder where you should find a date and time stamped .html report.
Close Command Prompt.