README.md
In pedsuite: Easy Installation of the 'ped suite' Packages for Pedigree Analysis

The ped suite: R packages for pedigree analysis

The ped suite 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.

At the centre of the ped suite 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: Textual descriptions of pedigree relationships

The following packages are devoted to special applications:

ibdsim2: Simulation of identity-by-descent sharing by family members
dvir: Disaster victim identification
pedbuildr: Pedigree reconstruction
paramlink2: Parametric linkage analysis
pedmut: Mutation models for pedigree likelihood computations
segregatr: Segregation analysis for clinical variant interpretation

These packages have been superseded by other packages and are no longer compatible with the rest of the ped suite. They are maintained only for legacy purposes and should not be used in new projects.

paramlink: This package marked the birth of the ped suite. 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).)

kinship2: All pedigree plots in the ped suite are internally made by importing the plotting feature of kinship2 (Sinnwell, Therneau & Schaid). Creating nice pedigree plots is a highly non-trivial matter, so if you use the ped suite to make pedigree plots for publications, please also credit kinship2.

In addition to the R packages, the ped suite also includes QuickPed, a free interactive program for creating and exploring pedigrees. Read more about it here, or simply try it out: https://magnusdv.shinyapps.io/quickped.