In publichealthengland/hcaidcs: R functions for the mandatory surveillance of bacteraemia and C. difficile infection

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

This is a collection of functions to make working with data from the HCAI DCS easier.

Installation

The quickest way to install the package is to use install_git from the devtools package.

# install devtools if necessary
install.packages("devtools")

# then install the hcaidcs package
devtools::install_github(repo = 'publichealthengland/hcaidcs', ref = "master")

Github installation problems

The above command may return the following error:

Installation failed: Error in 'git2r_clone': failed to send request: A connection with the server could not be established

This is likely to happen if you are installing it in a work environment, where local IT have set up a proxy server to connect to the internet. You may be able to get around this by telling R to use your proxy settings.

To determine your proxy settings go to 'Internet options' and select the 'Connections' tab. Choose the 'LAN settings' button and make a note of the address and port number.

then, in R do the following:

install.packages("httr")# only if you don't already have it installed
library(httr)
set_config(
  use_proxy(url="ddd.ddd.ddd.dd", port=dddd, username="windowsuser.name", 
            password="windows_pwdtext")
)
devtools::install_github(repo = 'publichealthengland/hcaidcs', ref = "master")

where d is a digit, url is the address you recorded above and port is the port, commonly 8080.

Alternative installation

If you are unable to identify your local proxy settings, one can download the zip file from github and do the following:

1. Save the zip file to a local drive (normally C:, but often H: if you are at PHE)` but do not unzip
2. Open RStudio
3. Run the following line: install.packages(file.choose(), repos=NULL)
4. This will launch a file chooser where you can select the zip file you have just downloaded.

This should install the package to the R package library.

If installation is successful you will then be able to load the package with library(hcaidcs)

Use

Please see the online documentation for descriptions of functions. Vignettes on the use of the package will follow soon.

Functions that begin aec_ are intended for producing tables or plots for the annual epidemiologic commentary.

Functions beginning ann_tab_ are intended for the production of the annual tables.

Functions prefixed kh03_ indicate functions for use in the preparation of the kh03 denominator data.

Functions prefixed mf_ indicate functions for use in the preparation of the HCAI monthly factsheet for the department of health.

Copyright notice

This package was developed at Public Health England and carries the Open Government Licence as a result. However, it also includes geographic data from Office for National Statistics (ONS) and so the following copyright statement also applies. Contains National Statistics data © Crown copyright and database right 2018

Contains OS data © Crown copyright and database right 2018

Contributions

Contributions to this package are welcome. Please see the Contribution guidelines. Please also see the Code of Conduct

publichealthengland/hcaidcs documentation built on Jan. 17, 2024, 1:34 p.m.