README.md

In JayAchar/hisreportr: hisreportr: Automating MSF OCA EMR reporting

hisreportr

Generate standardised reports from the MSF OCA HIS EMR.

Introduction

This package is designed to provide reporting functionality for the MSF OCA EMR being released in 2019. Functions for connecting to the PostgreSQL data base, data reformatting and R-markdown templates are all included. The package has been designed with automated workflows in mind rather than interactive use since this is likely to be the most frequent use-case.

Installation

You can install the released version of hisreportr from Github with:

# installing packages from Github requires devtools
  require(devtools)

# install package  
  devtools::install_github("JayAchar/hisreportr")

# load package
  library(hisreportr)

PostgreSQL server credentials

The access_postgresql() has been configured to access the MSF OCA PostgreSQL server instance using the credentials provided by system administrators. The following environment variables are accessed by the render_report() function to access the server for data retrieval:

• PGRES_HOST
• PGRES_USER
• PGRES_PWD_OCA
• PGRES_DBNAME

To generate reports using render_report(), these environment variables should be defined, or R markdown parameters passed during the function call. Please see the render_report() documentation about how this can be done.

The code below gives an example of how to include add a R environment variable:

# add PostgreSQL server password to R environment
  Sys.setenv(PGRES_PWD_OCA = "testpwd1234")

This will add the environment variable and password to the .Renviron file, which is executed when R starts up.

Generating reports

Report templates are saved in the inst/rmarkdown folder. Current plans are for the following report templates to be developed:

• TB monthly cohort report
• HIV monthly cohort report
• HCV monthly cohort report

Future development time may focus on data quality reports, annualised reports, more detailed cohort reports or interactive data visualisation through the use of Shiny.

To generate a report using this package to connect to the current PostgreSQL server instance, use the render_report() function. A suggested function call is described:

# generate a TB monthly cohort report including data from October 2019
  render_report(report_name = "tb_month",
                output_dir = "~/Documents",
                params = list(reporting_month = 10,
                              reporting_year = 2019))

The argument output_dir can be used to define the local output directory. In the example above, the .html file will be saved to the user’s Documents folder.

The parameters reporting_month and reporting_year have been included within each monthly template to allow users to re-generate historical reports. If they are not defined in the function call, values from the current local date will be substituted.

Using docker for running reports

Building the Image

Run below command :

  docker build -f docker/Dockerfile -t reportsserver .

Running reports using docker

Update config/rconfig file to include values for

• PGRES_HOST
• PGRES_USER
• PGRES_PWD_OCA
• PGRES_DBNAME

Run below command :

  docker run -v /tmp/reports:/reports --env-file=config/rconfig reportsserver

/tmp/reports is the location on the host [which should be manually created] which is mounted on /reports in the container. This is customizable, you could mount any directory on host to get the reports.

Note - runreport.sh has hardcoded values for month, year , report name. It would be made parameterized as part of other Jira cards.

JayAchar/hisreportr documentation built on March 18, 2020, 5:57 a.m.