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
You can install SimRVPedigree from github with:
# install.packages("devtools") devtools::install_github("cnieuwoudt/SimRVPedigree")
SimRVPedigree provides routines to simulate and manipulate pedigrees
ascertained to contain multiple family members affected by a rare
To simulate pedigrees or to simulate life events for an individual we
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
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[], ref_year = 2017, cex = 0.75)
# Obtain summary information for the ascertained pedigree. summary(ex_ped[]) #> $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
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