Packages / splverse

A set of R packages developed to help solve problems that frequently occur when performing infectious disease surveillance. The splverse has been created by the Sykdomspulsen team (specialized in infectious disease surveillance), who use it every day to streamline and improve their pipelines and deliverables. The splverse has been used and improved throughout the COVID-19 pandemic, forming the basis of all of Sykdomspulsen’s products. To put it more succinctly: “All genuine knowledge originates in direct experience.”

Installation and Use

If you want to install the dev versions (or access packages that haven’t been released on CRAN), run usethis::edit_r_profile() to edit your .Rprofile.

Then write in:

options(
  repos = structure(c(
    SPLVERSE  = "https://docs.sykdomspulsen.no/drat/",
    CRAN      = "https://cran.rstudio.com"
  ))
)

Save the file and restart R.

You can now install splverse packages from our drat repository.

The splverse

attrib is designed to make the process of calculating attributable mortalities and incident risk ratios efficient and easy.

Go to docs…


nowcast helps you predict the present.

Go to docs…


org is a system to help you organize projects.

Go to docs…


plnr is a system to help you plan analyses.

Go to docs…


splalert helps create alerts from public health surveillance data.

Go to docs…


spldata contains preformatted structural data for Norway.

Go to docs…


splmaps contains preformatted maps of Norway that generally don’t need geolibraries.

Go to docs…


splshiny contains helpful functions for creating Shiny websites.

Go to docs…


splstyle contains helpful functions for creating outputs in the style(s) used by FHI and Sykdomspulsen.

Go to docs…


spltidy contains helpful functions for cleaning data.

Go to docs…


spltime contains helpful functions for working with time.

Go to docs…


splutil contains helpful functions to help with common base R problems.

Go to docs…


spread contains different infectious disease spread models.

Go to docs…

Corrections

If you see mistakes or want to suggest changes, please create an issue on the source repository.

Reuse

Text and figures are licensed under Creative Commons Attribution CC BY 4.0. Source code is available at https://github.com/sykdomspulsen-org/sykdomspulsen-org.github.io, unless otherwise noted. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".