Simulate Pedigrees This function simulates

Simulate Pedigrees This function simulates "balanced" pedigrees based on a group of parameters: 1) k - Kids per couple; 2) G - Number of generations; 3) p - Proportion of males in offspring; 4) r - Mating rate.

Usage

simulatePedigree(
  kpc = 3,
  Ngen = 4,
  sexR = 0.5,
  marR = 2/3,
  rd_kpc = FALSE,
  balancedSex = TRUE,
  balancedMar = TRUE,
  verbose = FALSE,
  personID = "ID",
  momID = "momID",
  dadID = "dadID",
  spouseID = "spouseID",
  code_male = "M",
  code_female = "F"
)

SimPed(...)

Arguments

kpc: Number of kids per couple. An integer >= 2 that determines how many kids each fertilized mated couple will have in the pedigree. Default value is 3. Returns an error when kpc equals 1.
Ngen: Number of generations. An integer >= 2 that determines how many generations the simulated pedigree will have. The first generation is always a fertilized couple. The last generation has no mated individuals.
sexR: Sex ratio of offspring. A numeric value ranging from 0 to 1 that determines the proportion of males in all offspring in this pedigree. For instance, 0.4 means 40 percent of the offspring will be male.
marR: Mating rate. A numeric value ranging from 0 to 1 which determines the proportion of mated (fertilized) couples in the pedigree within each generation. For instance, marR = 0.5 suggests 50 percent of the offspring in a specific generation will be mated and have their offspring.
rd_kpc: logical. If TRUE, the number of kids per mate will be randomly generated from a poisson distribution with mean kpc. If FALSE, the number of kids per mate will be fixed at kpc.
balancedSex: Not fully developed yet. Always TRUE in the current version.
balancedMar: Not fully developed yet. Always TRUE in the current version.
verbose: logical If TRUE, message progress through stages of algorithm
personID: character. Name of the column in ped for the person ID variable
momID: character. Name of the column in ped for the mother ID variable
dadID: character. Name of the column in ped for the father ID variable
spouseID: The name of the column that will contain the spouse ID in the output data frame. Default is "spID".
code_male: The value to use for males. Default is "M"
code_female: The value to use for females. Default is "F"
...: Additional arguments to be passed to other functions.

Value

A data.frame with each row representing a simulated individual. The columns are as follows:

fam: The family id of each simulated individual. It is 'fam1' in a single simulated pedigree.
ID: The unique personal ID of each simulated individual. The first digit is the fam id; the fourth digit is the generation the individual is in; the following digits represent the order of the individual within their pedigree. For example, 100411 suggests this individual has a family id of 1, is in the 4th generation, and is the 11th individual in the 4th generation.
gen: The generation the simulated individual is in.
dadID: Personal ID of the individual's father.
momID: Personal ID of the individual's mother.
spID: Personal ID of the individual's mate.
sex: Biological sex of the individual. F - female; M - male.

Examples

set.seed(5)
df_ped <- simulatePedigree(
  kpc = 4,
  Ngen = 4,
  sexR = .5,
  marR = .7
)
summary(df_ped)
#>      fam                  ID              gen            dadID       
#>  Length:57          Min.   : 10011   Min.   :1.000   Min.   : 10012  
#>  Class :character   1st Qu.: 10036   1st Qu.:3.000   1st Qu.: 10024  
#>  Mode  :character   Median :100312   Median :3.000   Median : 10037  
#>                     Mean   : 59171   Mean   :3.298   Mean   : 42859  
#>                     3rd Qu.:100416   3rd Qu.:4.000   3rd Qu.:100311  
#>                     Max.   :100432   Max.   :4.000   Max.   :100320  
#>                                                      NA's   :13      
#>      momID             spID            sex           
#>  Min.   : 10011   Min.   : 10011   Length:57         
#>  1st Qu.: 10022   1st Qu.: 10025   Class :character  
#>  Median : 10036   Median : 10036   Mode  :character  
#>  Mean   : 42859   Mean   : 40124                     
#>  3rd Qu.:100316   3rd Qu.:100311                     
#>  Max.   :100318   Max.   :100320                     
#>  NA's   :13       NA's   :33