sbi - package

sbi - R functions for the course "Statistical Bioinformatics" and the Summer school of the University of Potsdam "Statistics for Human Biology and Public Health".

library(sbi)        ### load the library into your session
ls(sbi)             ### what methods are available
library(help="sbi") ### lookup the package help

Package with functions for the course Statistical Bioinformatics at the University of Potsdam. The course takes place as a mandatory course for the Master Bioinformatics program every Winter semester. There are as well some functions added which are used in the Summer school Human Biology and Public Health of the University of Potsdam.

The package comes as a single file R script. You can either just source the latest version of that script directly from Github like this:

$ R    # start R from a terminal or via start menu
> source("https://raw.githubusercontent.com/mittelmark/sbi/refs/heads/main/sbi-src.R")
> ls(sbi)  ## list all methods
> vignette("sbi-examples")  ## load the vignette

Or you install the latest release as a normal package:

$ R
> install.packages("https://github.com/mittelmark/sbi/releases/download/v0.8.0/sbi_0.8.0.tar.gz",repos=NULL)
> library(sbi)
> ls(sbi)
> vignette("sbi-examples")

Or you install the latest release from a Unix Terminal like this:

wget https://github.com/mittelmark/sbi/releases/download/v0.8.0/sbi_0.8.0.tar.gz
R CMD INSTALL --library=~/R sbi_0.8.0.tar.gz

Installation as a package has the advantage that you have the documentation and the package vignette available as usually for R packages.

Or you can install the latest development version directly from Github like this:

• fetch the package code from github
• extract all individual files from the master file sbi-src.R into the package structure
• build the package
• check the package
• install the package

Here the commands:

wget -O sbi-src.R https://github.com/mittelmark/sbi/raw/main/sbi-src.R
Rscript sbi-src.R --process    sbi-src.R         # extract all files
Rscript sbi-src.R --vignettex  sbi-src.R         # extract examples as vignette
Rscript sbi-src.R --build      sbi               # build package tar-gz file
Rscript sbi-src.R --check      sbi_0.8.0.tar.gz  # check package tar-gz file
Rscript sbi-src.R --install    sbi_0.8.0.tar.gz  # install from local tar-gz file

The single file R package approach is described in the rsfp project.

• 2026-08-17: version 0.8.0
  • function sbi_moranI for network clustering detection
  • function es_plot for barplot of effect size values
  • function ts_data to create to related time series data vectors
  • function ts_plot to plot time series data with time points on top
  • argument palette for sbi_pastel function with spectral palette
  • little typo and code issue fixes with the aid of Agnes 2.5 Flash model
• 2026-07-24: version 0.7.0 - package - vignette
  • Update nach Summerschool 2026
  • function sbi_pssim - for pattern similarity to arbitrary patterns
  • function sbi_ia_plot - for interactions in a linear model
  • function sbi_conf_plot - for plotting a set of means and confidence intervals
  • function sbi_ba_plot Bland-Altman - coherence plot
  • function sbi_angles_triangle - calculate the angles for a given triangle
  • function sbi_series_trend - calculate the trend for the values of a vector
  • data set conscripts for Germany from 1885 to 1995 and additional socioeconomic data for that period
  • typo fixes with aid of Big Pickel model
• 2026-07-10: version 0.6.0 - package - vignette
  • adding transform and untransform methods to support signed log and Yeo-Johnson transformation
  • removed mtex function and local use of graphviz dot and plantuml etc
• 2026-01-17: version 0.4.2 - package - vignette
  • adding doc, ellipse and cylinder shape to flow charts and shape function
  • adding fstart, fnext, fend shapes for process charts
• 2025-10-15: version 0.4.1
  • fix for kroki service not working by using local installs of GraphViz dot, plantuml and ditaa first before using kroki
  • fix for background color in vignette in code sections
• 2025-10-09: version 0.4.0
  • new function KL divergence sbi_kl
• 2025-09-23: version 0.3.0
  • new function sbi_error_plot
  • new function sbi_mtex to display LaTeX equations
• 2025-09-18: version 0.2.1
  • fix main.cex to cex.main in vignette
• 2025-09-17: Version 0.2.0
  • new commands nfig, rfig, ntab, rtab for figure and table numbering and referencing
  • new command mtex for create LaTeX equations as png documents
  • switching from extrafont in vignette to showtext
  • adding timetable functions tt_plot and tt_item
• 2025-09-01: Version 0.1.2
  • fixing issue with girls / boys order in ref_table
• 2025-07-12:
  • adding cdc references for weight
• 2025-07-10: Version 0.1.0
  • adding methods qr_plot and randomize
  • adding new MUAC references from Ado et. al. 2017
• 2024-08-28: Version 0.0.1 - Initial Release

• Detlef Groth (2024-2026), University of Potsdam (Author and Maintainer)
• Laura Schander (2024), University of Potsdam (Contributor)

MIT License see file LICENSE.