Simulate Pedigrees Ascertained for Rare Disease
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.
You can install SimRVPedigree from github with:
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.
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