Easy Installation of the 'pedsuite' Packages for Pedigree Analysis

The 'pedsuite' is a collection of packages for pedigree analysis, covering applications in forensic genetics, medical genetics and more. A detailed presentation of the 'pedsuite' is given in the book 'Pedigree Analysis in R' (Vigeland, 2021, ISBN: 9780128244302).

The pedsuite: R packages for pedigree analysis

The pedsuite is a collection of R packages for pedigree analysis, covering a variety of applications across several fields. The packages are designed to work harmoniously together, often allowing complex tasks to be solved in a few lines of code.

Core packages

At the centre of the pedsuite we find the package pedtools, on which all the others depend. In addition, several packages contain basic features often needed in many types of analysis. These are the core packages:

pedtools: Creating and working with pedigrees and marker data
forrel: Forensic pedigree analysis and relatedness analysis
pedprobr: Marker probabilities and pedigree likelihoods
ribd: Computation of pedigree-based relatedness coefficients
verbalisr: Verbal descriptions of pedigree relationships

Specialised packages

The following packages are devoted to special applications:

ibdsim2: Simulation of identity-by-descent sharing by family members
dvir: Disaster victim identification
ibdfindr: Inferring identical-by-descent genomic segments from SNP Genotypes
norSTR: Data package with STR allele frequencies
paramlink2: Parametric linkage analysis
pedbuildr: Pedigree reconstruction
pedFamilias: Import and export .fam files used by the Familias software
pedmut: Mutation models for pedigree likelihood computations
segregatr: Segregation analysis for clinical variant interpretation

Retired packages

These packages have been superseded by other packages and are no longer compatible with the rest of the pedsuite.

paramlink: This package marked the birth of the pedsuite. Originally intended for parametric linkage analysis, it also contained the seeds of the current packages pedtools, pedprobr, ribd and forrel.
IBDsim: This is replaced by ibdsim2. (Regrettably, the name ‘IBDsim’ is very similar to that of the unrelated (non-R) software ‘IBDSim’ (Leblois, Estoup & Rousset).)