SimRVPedigree

Simulate Pedigrees Ascertained for Rare Disease

Under Construction

Please note: this version of SimRVPedigree may be under construction. For the latest stable version of SimRVPedigree please visit https://CRAN.R-project.org/package=SimRVPedigree.

Installation

You can install SimRVPedigree from github with:

# install.packages("devtools")
devtools::install_github("cnieuwoudt/SimRVPedigree")

Overview

SimRVPedigree provides routines to simulate and manipulate pedigrees ascertained to contain multiple family members affected by a rare disease.

To simulate pedigrees or to simulate life events for an individual we provide: * sim_RVped() to simulate pedigrees ascertained for multiple disease-affected relatives, * sim_ped() to simulate pedigrees, and * sim_life() to simulate life events until a specified stop-year.

To manipulate pedigrees we provide: * plot.ped() to plot pedigrees, * summary.ped() to obtain summary information for a pedigree or a collection of pedigrees, * censor_ped() to censor a pedigree after a specified year, and * reassign_gen() to reassign generation number based on the most recent common ancestor of all disease-affected relatives.

Example

library(SimRVPedigree)

#Load example age-specific hazard rates data.
data(AgeSpecific_Hazards)

#Create an object of class hazard.
HRates <- hazard(hazardDF = AgeSpecific_Hazards)

#Simulate a pedigree ascertained for multiple disease-affected relatives
set.seed(5444)
ex_ped <- sim_RVped(hazard_rates = HRates,
                    GRR = 20,
                    RVfounder = TRUE,
                    FamID = 1,
                    founder_byears = c(1900, 1950),
                    ascertain_span = c(1995, 2015),
                    num_affected = 2,
                    stop_year = 2017,
                    recall_probs = c(1, 1, 0.25, 0))

# Plot the ascertained pedigree
plot(ex_ped[[2]], ref_year = 2017, cex = 0.75)

# Obtain summary information for the ascertained pedigree.
summary(ex_ped[[2]])
#> $family_info
#>   FamID totalRelatives numAffected aveOnsetAge aveIBD ascertainYear segRV
#> 1     1             15           2          56    0.5          2015  TRUE
#> 
#> $affected_info
#>   FamID ID birthYr onsetYr deathYr proband RVstatus
#> 1     1  4    1936    1996    1998   FALSE        1
#> 2     1  7    1963    2015      NA    TRUE        1