Sanger Tools was born out of necessity.
It is the formal aggregation of a set of coding solutions employed regularly to carry out Population Health Management Analytics; rapidly and consistently. It has has been created specifically for Gloucestershire CCG and wider National Health Service (NHS) staff working with patient level population health data.
However, we hope Sanger Tools aids analytical workers around to world who work with similar datasets.
Currently this will be best suited to CCG and CSU staff.
If you are using this package outside of the NHS we would be very keen to hear from you!
The package draws its name from Sanger House; the office in which NHS Gloucestershire CCG's analytical team are based.
The tools in this package have been created to assist in every-day tasks undertaken by most NHS analysts. Functions have been created to provide an easy-to-use interface for common tasks where analysts are working between R, SQL and Excel. Many of the functions are created to work with datasets which contain 1 Row Per Patient in tidy data format; where each row is an observation and columns are variables pertaining to the patient. This format is commonly seen across the NHS; often referred to as Master Patient Index (MPI).
Many of the functions are written in Tidyverse; as such there will be performance limitations on larger datasets. Please take care to read to the documentation and included examples as the functions in this package use a combination of Standard Evalutation (Base R) and Non-Standard Evalutation (Tidyverse).
SangerTools is still under construction and we will be incrementally adding new features with another release to CRAN in Q1 2022.
You can install the package using the following commands
# install.packages("remotes") # if not already installed
remotes::install_github("https://github.com/ald0405/SangerTools")
library(SangerTools)
# install.packages("SangerTools")
library(SangerTools)
To learn how to use the package, check out the vignette on RPubs.
