AlphaSimR (version 0.12.1)

SimParam: Simulation parameters

Description

Container for global simulation parameters. Saving this object as SP will allow it to be accessed by function defaults.

Public fields

nThreads

number of threads used on platforms with OpenMP support

snpChips

list of SNP chips

invalidQtl

list of segregating sites that aren't valid QTL

invalidSnp

list of segregating sites that aren't valid SNP

founderPop

founder population used for variance scaling

v

the crossover interference parameter for a gamma model of recombination. A value of 1 indicates no crossover interference (e.g. Haldane mapping function). A value of 2.6 approximates the degree of crossover interference implied by the Kosambi mapping function. (default is 1)

quadProb

the probability of quadrivalent pairing in an autopolyploid. (default is 0)

Active bindings

traits

list of traits

nChr

number of chromosomes

nTraits

number of traits

nSnpChips

number of SNP chips

segSites

segregating sites per chromosome

gender

is gender used for mating

sepMap

are there seperate genetic maps for males and females

genMap

"matrix" of chromosome genetic maps

femaleMap

"matrix" of chromosome genetic maps for females

maleMap

"matrix" of chromosome genetic maps for males

centromere

position of centromeres genetic map

femaleCentromere

position of centromeres on female genetic map

maleCentromere

position of centromeres on male genetic map

lastId

last ID number assigned

isTrackPed

is pedigree being tracked

pedigree

pedigree matrix for all individuals

isTrackRec

is recombination being tracked

recHist

list of historic recombination events

varA

additive genetic variance in founderPop

varG

total genetic variance in founderPop

varE

default error variance

version

the version of AlphaSimR used to generate this object

Methods

Public methods

• SimParam$new()

• SimParam$setTrackPed()

• SimParam$setTrackRec()

• SimParam$resetPed()

• SimParam$restrSegSites()

• SimParam$setGender()

• SimParam$addSnpChip()

• SimParam$addStructuredSnpChip()

• SimParam$addTraitA()

• SimParam$addTraitAD()

• SimParam$addTraitAG()

• SimParam$addTraitADG()

• SimParam$addTraitAE()

• SimParam$addTraitADE()

• SimParam$addTraitAEG()

• SimParam$addTraitADEG()

• SimParam$manAddTrait()

• SimParam$switchTrait()

• SimParam$removeTrait()

• SimParam$setVarE()

• SimParam$setCorE()

• SimParam$rescaleTraits()

• SimParam$setRecombRatio()

• SimParam$switchGenMap()

• SimParam$switchFemaleMap()

• SimParam$switchMaleMap()

• SimParam$addToRec()

• SimParam$updateLastId()

• SimParam$addToPed()

• SimParam$clone()

Method new()

Starts the process of building a new simulation by creating a new SimParam object and assigning a founder population to the class. It is recommended that you save the object with the name "SP", because subsequent functions will check your global enviroment for an object of this name if their simParam arguments are NULL. This allows you to call these functions without explicitly supplying a simParam argument with every call.

Usage

SimParam$new(founderPop)

Arguments

founderPop

an object of MapPop-class

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop)

Method setTrackPed()

Sets pedigree tracking for the simulation. By default pedigree tracking is turned off. When turned on, the pedigree of all individuals created will be tracked, except those created by hybridCross. Turning off pedigree tracking will turn off recombination tracking if it is turned on.

Usage

SimParam$setTrackPed(isTrackPed, force = FALSE)

Arguments

isTrackPed

should pedigree tracking be on.

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$setTrackPed(TRUE)

Method setTrackRec()

Sets recombination tracking for the simulation. By default recombination tracking is turned off. When turned on recombination tracking will also turn on pedigree tracking. Recombination tracking keeps records of all individuals created, except those created by hybridCross, because their pedigree is not tracked.

Usage

SimParam$setTrackRec(isTrackRec, force = FALSE)

Arguments

isTrackRec

should recombination tracking be on.

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$setTrackRec(TRUE)

Method resetPed()

Resets the internal lastId, the pedigree and recombination tracking (if in use) to the supplied lastId. Be careful using this function because it may introduce a bug if you use individuals from the deleted portion of the pedigree.

Usage

SimParam$resetPed(lastId = 0L)

Arguments

lastId

last ID to include in pedigree

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop)

#Create population pop = newPop(founderPop, simParam=SP) pop@id # 1:10

#Create another population after reseting pedigree SP$resetPed() pop2 = newPop(founderPop, simParam=SP) pop2@id # 1:10

Method restrSegSites()

Sets restrictions on which segregating sites can serve as SNP and/or QTL.

Usage

SimParam$restrSegSites(
  minQtlPerChr = NULL,
  minSnpPerChr = NULL,
  overlap = FALSE,
  minSnpFreq = NULL
)

Arguments

minQtlPerChr

the minimum number of segSites for QTLs. Can be a single value or a vector values for each chromosome.

minSnpPerChr

the minimum number of segSites for SNPs. Can be a single value or a vector values for each chromosome.

overlap

should SNP and QTL sites be allowed to overlap.

minSnpFreq

minimum allowable frequency for SNP loci. No minimum SNP frequency is used if value is NULL.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$restrSegSites(minQtlPerChr=5, minSnpPerChr=5)

Method setGender()

Changes how gender is used in the simulation. The default gender of a simulation is "no". To add gender to the simulation, run this function with "yes_sys" or "yes_rand". The value "yes_sys" will systematically assign gender to newly created individuals as first male, then female. Thus, odd numbers of individuals will have one more male than female. The value "yes_rand" will randomly assign gender to individuals.

Usage

SimParam$setGender(gender, force = FALSE)

Arguments

gender

acceptable value are "no", "yes_sys", or "yes_rand"

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$setGender("yes_sys")

Method addSnpChip()

Randomly assigns eligble SNPs to a SNP chip

Usage

SimParam$addSnpChip(nSnpPerChr, minSnpFreq = NULL, refPop = NULL)

Arguments

nSnpPerChr

number of SNPs per chromosome. Can be a single value or nChr values.

minSnpFreq

minimum allowable frequency for SNP loci. If NULL, no minimum frequency is used.

refPop

reference population for calculating SNP frequency. If NULL, the founder population is used.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$addSnpChip(10)

Method addStructuredSnpChip()

Randomly selects the number of snps in structure and then assigns them to chips based on structure

Usage

SimParam$addStructuredSnpChip(nSnpPerChr, structure, force = FALSE)

Arguments

nSnpPerChr

number of SNPs per chromosome. Can be a single value or nChr values.

structure

a matrix. Rows are snp chips, columns are chips. If value is true then that snp is on that chip.

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing.

Method addTraitA()

Randomly assigns eligble QTLs for one or more additive traits. If simulating more than one trait, all traits will be pleiotrophic with correlated additive effects.

Usage

SimParam$addTraitA(
  nQtlPerChr,
  mean = 0,
  var = 1,
  corA = NULL,
  gamma = FALSE,
  shape = 1,
  force = FALSE
)

Arguments

nQtlPerChr

number of QTLs per chromosome. Can be a single value or nChr values.

mean

a vector of desired mean genetic values for one or more traits

var

a vector of desired genetic variances for one or more traits

corA

a matrix of correlations between additive effects

gamma

should a gamma distribution be used instead of normal

shape

the shape parameter for the gamma distribution

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)

Method addTraitAD()

Randomly assigns eligble QTLs for one or more traits with dominance. If simulating more than one trait, all traits will be pleiotrophic with correlated effects.

Usage

SimParam$addTraitAD(
  nQtlPerChr,
  mean = 0,
  var = 1,
  meanDD = 0,
  varDD = 0,
  corA = NULL,
  corDD = NULL,
  useVarA = TRUE,
  gamma = FALSE,
  shape = 1,
  force = FALSE
)

Arguments

nQtlPerChr

number of QTLs per chromosome. Can be a single value or nChr values.

mean

a vector of desired mean genetic values for one or more traits

var

a vector of desired genetic variances for one or more traits

meanDD

mean dominance degree

varDD

variance of dominance degree

corA

a matrix of correlations between additive effects

corDD

a matrix of correlations between dominance degrees

useVarA

tune according to additive genetic variance if true. If FALSE, tuning is performed according to total genetic variance.

gamma

should a gamma distribution be used instead of normal

shape

the shape parameter for the gamma distribution

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5)

Method addTraitAG()

Randomly assigns eligble QTLs for one ore more additive GxE traits. If simulating more than one trait, all traits will be pleiotrophic with correlated effects.

Usage

SimParam$addTraitAG(
  nQtlPerChr,
  mean = 0,
  var = 1,
  varGxE = 1e-06,
  varEnv = 0,
  corA = NULL,
  corGxE = NULL,
  gamma = FALSE,
  shape = 1,
  force = FALSE
)

Arguments

nQtlPerChr

number of QTLs per chromosome. Can be a single value or nChr values.

mean

a vector of desired mean genetic values for one or more traits

var

a vector of desired genetic variances for one or more traits

varGxE

a vector of total genotype-by-environment variances for the traits

varEnv

a vector of environmental variances for one or more traits

corA

a matrix of correlations between additive effects

corGxE

a matrix of correlations between GxE effects

gamma

should a gamma distribution be used instead of normal

shape

the shape parameter for the gamma distribution

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAG(10, varGxE=2)

Method addTraitADG()

Randomly assigns eligble QTLs for a trait with dominance and GxE.

Usage

SimParam$addTraitADG(
  nQtlPerChr,
  mean = 0,
  var = 1,
  varEnv = 1e-06,
  varGxE = 1e-06,
  meanDD = 0,
  varDD = 0,
  corA = NULL,
  corDD = NULL,
  corGxE = NULL,
  useVarA = TRUE,
  gamma = FALSE,
  shape = 1,
  force = FALSE
)

Arguments

nQtlPerChr

number of QTLs per chromosome. Can be a single value or nChr values.

mean

a vector of desired mean genetic values for one or more traits

var

a vector of desired genetic variances for one or more traits

varEnv

a vector of environmental variances for one or more traits

varGxE

a vector of total genotype-by-environment variances for the traits

meanDD

mean dominance degree

varDD

variance of dominance degree

corA

a matrix of correlations between additive effects

corDD

a matrix of correlations between dominance degrees

corGxE

a matrix of correlations between GxE effects

useVarA

tune according to additive genetic variance if true

gamma

should a gamma distribution be used instead of normal

shape

the shape parameter for the gamma distribution

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitADG(10, meanDD=0.5, varGxE=2)

Method addTraitAE()

Randomly assigns eligble QTLs for one or more additive and epistasis traits. If simulating more than one trait, all traits will be pleiotrophic with correlated additive effects.

Usage

SimParam$addTraitAE(
  nQtlPerChr,
  mean = 0,
  var = 1,
  relAA = 0,
  corA = NULL,
  corAA = NULL,
  useVarA = TRUE,
  gamma = FALSE,
  shape = 1,
  force = FALSE
)

Arguments

nQtlPerChr

number of QTLs per chromosome. Can be a single value or nChr values.

mean

a vector of desired mean genetic values for one or more traits

var

a vector of desired genetic variances for one or more traits

relAA

the relative value of additive-by-additive variance compared to additive variance in a diploid organism with allele frequency 0.5

corA

a matrix of correlations between additive effects

corAA

a matrix of correlations between additive-by-additive effects

useVarA

tune according to additive genetic variance if true. If FALSE, tuning is performed according to total genetic variance.

gamma

should a gamma distribution be used instead of normal

shape

the shape parameter for the gamma distribution

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

Method addTraitADE()

Randomly assigns eligble QTLs for one or more traits with dominance and epistasis. If simulating more than one trait, all traits will be pleiotrophic with correlated effects.

Usage

SimParam$addTraitADE(
  nQtlPerChr,
  mean = 0,
  var = 1,
  meanDD = 0,
  varDD = 0,
  relAA = 0,
  corA = NULL,
  corDD = NULL,
  corAA = NULL,
  useVarA = TRUE,
  gamma = FALSE,
  shape = 1,
  force = FALSE
)

Arguments

nQtlPerChr

number of QTLs per chromosome. Can be a single value or nChr values.

mean

a vector of desired mean genetic values for one or more traits

var

a vector of desired genetic variances for one or more traits

meanDD

mean dominance degree

varDD

variance of dominance degree

relAA

the relative value of additive-by-additive variance compared to additive variance in a diploid organism with allele frequency 0.5

corA

a matrix of correlations between additive effects

corDD

a matrix of correlations between dominance degrees

corAA

a matrix of correlations between additive-by-additive effects

useVarA

tune according to additive genetic variance if true. If FALSE, tuning is performed according to total genetic variance.

gamma

should a gamma distribution be used instead of normal

shape

the shape parameter for the gamma distribution

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitADE(10)

Method addTraitAEG()

Randomly assigns eligble QTLs for one or more additive and epistasis GxE traits. If simulating more than one trait, all traits will be pleiotrophic with correlated effects.

Usage

SimParam$addTraitAEG(
  nQtlPerChr,
  mean = 0,
  var = 1,
  relAA = 0,
  varGxE = 1e-06,
  varEnv = 0,
  corA = NULL,
  corAA = NULL,
  corGxE = NULL,
  useVarA = TRUE,
  gamma = FALSE,
  shape = 1,
  force = FALSE
)

Arguments

nQtlPerChr

number of QTLs per chromosome. Can be a single value or nChr values.

mean

a vector of desired mean genetic values for one or more traits

var

a vector of desired genetic variances for one or more traits

relAA

the relative value of additive-by-additive variance compared to additive variance in a diploid organism with allele frequency 0.5

varGxE

a vector of total genotype-by-environment variances for the traits

varEnv

a vector of environmental variances for one or more traits

corA

a matrix of correlations between additive effects

corAA

a matrix of correlations between additive-by-additive effects

corGxE

a matrix of correlations between GxE effects

useVarA

tune according to additive genetic variance if true. If FALSE, tuning is performed according to total genetic variance.

gamma

should a gamma distribution be used instead of normal

shape

the shape parameter for the gamma distribution

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAEG(10, varGxE=2)

Method addTraitADEG()

Randomly assigns eligble QTLs for a trait with dominance, epistasis and GxE.

Usage

SimParam$addTraitADEG(
  nQtlPerChr,
  mean = 0,
  var = 1,
  varEnv = 1e-06,
  varGxE = 1e-06,
  meanDD = 0,
  varDD = 0,
  relAA = 0,
  corA = NULL,
  corDD = NULL,
  corAA = NULL,
  corGxE = NULL,
  useVarA = TRUE,
  gamma = FALSE,
  shape = 1,
  force = FALSE
)

Arguments

nQtlPerChr

number of QTLs per chromosome. Can be a single value or nChr values.

mean

a vector of desired mean genetic values for one or more traits

var

a vector of desired genetic variances for one or more traits

varEnv

a vector of environmental variances for one or more traits

varGxE

a vector of total genotype-by-environment variances for the traits

meanDD

mean dominance degree

varDD

variance of dominance degree

relAA

the relative value of additive-by-additive variance compared to additive variance in a diploid organism with allele frequency 0.5

corA

a matrix of correlations between additive effects

corDD

a matrix of correlations between dominance degrees

corAA

a matrix of correlations between additive-by-additive effects

corGxE

a matrix of correlations between GxE effects

useVarA

tune according to additive genetic variance if true

gamma

should a gamma distribution be used instead of normal

shape

the shape parameter for the gamma distribution

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitADEG(10, meanDD=0.5, varGxE=2)

Method manAddTrait()

Manually add a new trait to the simulation.

Usage

SimParam$manAddTrait(
  lociMap,
  varA = NA_real_,
  varG = NA_real_,
  varE = NA_real_,
  force = FALSE
)

Arguments

lociMap

a new object descended from LociMap-class

varA

the value for varA in the base population, optional

varG

the value for varG in the base population, optional

varE

default error variance for phenotype, optional

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing

Method switchTrait()

Switch a trait in the simulation.

Usage

SimParam$switchTrait(
  traitPos,
  lociMap,
  varA = NA_real_,
  varG = NA_real_,
  varE = NA_real_,
  force = FALSE
)

Arguments

traitPos

an integer indicate which trait to switch

lociMap

a new object descended from LociMap-class

varA

the value for varA in the base population, optional

varG

the value for varG in the base population, optional

varE

default error variance for phenotype, optional

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing

Method removeTrait()

Remove a trait from the simulation

Usage

SimParam$removeTrait(traits, force = FALSE)

Arguments

traits

an integer vector indicating which traits to remove

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing

Method setVarE()

Defines a default value for error variances in the simulation.

Usage

SimParam$setVarE(h2 = NULL, H2 = NULL, varE = NULL)

Arguments

h2

a vector of desired narrow-sense heritabilities

H2

a vector of desired broad-sense heritabilities

varE

a vector of error variances

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10) SP$setVarE(h2=0.5)

Method setCorE()

Defines a correlation structure for default error variances. You must call setVarE first to define the default error variances.

Usage

SimParam$setCorE(corE)

Arguments

corE

a correlation matrix for the error variances

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10, mean=c(0,0), var=c(1,1), corA=diag(2)) SP$setVarE(varE=c(1,1)) E = 0.5*diag(2)+0.5 #Positively correlated error SP$setCorE(E)

Method rescaleTraits()

Linearly scales all traits to achieve desired values of means and variances in the founder population.

Usage

SimParam$rescaleTraits(
  mean = 0,
  var = 1,
  varEnv = 0,
  varGxE = 1e-06,
  useVarA = TRUE
)

Arguments

mean

a vector of new trait means

var

a vector of new trait variances

varEnv

a vector of new environmental variances

varGxE

a vector of new GxE variances

useVarA

tune according to additive genetic variance if true

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)

#Create population pop = newPop(founderPop, simParam=SP) meanG(pop)

#Change mean to 1 SP$rescaleTraits(mean=1) #Run resetPop for change to take effect pop = resetPop(pop, simParam=SP) meanG(pop)

Method setRecombRatio()

Set the relative recombination rates between males and females. This allows for gender specific recombination rates, under the assumption of equivalent recombination landscapes.

Usage

SimParam$setRecombRatio(femaleRatio)

Arguments

femaleRatio

relative ratio of recombination in females compared to males. A value of 2 indicate twice as much recombination in females. The value must be greater than 0. (default is 1)

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters SP = SimParam$new(founderPop) SP$setRecombRatio(2) #Twice as much recombination in females

Method switchGenMap()

Replaces existing genetic map.

Usage

SimParam$switchGenMap(genMap, centromere = NULL)

Arguments

genMap

a list of length nChr containing numeric vectors for the position of each segregating site on a chromosome.

centromere

a numeric vector of centromere positions. If NULL, the centromere are assumed to be metacentric.

Method switchFemaleMap()

Replaces existing female genetic map.

Usage

SimParam$switchFemaleMap(genMap, centromere = NULL)

Arguments

genMap

a list of length nChr containing numeric vectors for the position of each segregating site on a chromosome.

centromere

a numeric vector of centromere positions. If NULL, the centromere are assumed to be metacentric.

Method switchMaleMap()

Replaces existing male genetic map.

Usage

SimParam$switchMaleMap(genMap, centromere = NULL)

Arguments

genMap

a list of length nChr containing numeric vectors for the position of each segregating site on a chromosome.

centromere

a numeric vector of centromere positions. If NULL, the centromere are assumed to be metacentric.

Method addToRec()

For internal use only.

Usage

SimParam$addToRec(hist)

Arguments

hist

new recombination history

Method updateLastId()

For internal use only.

Usage

SimParam$updateLastId(lastId)

Arguments

lastId

last ID assigned

Method addToPed()

For internal use only.

Usage

SimParam$addToPed(lastId, mother, father, isDH)

Arguments

lastId

ID of last individual

mother

vector of mother IDs

father

vector of father IDs

isDH

vector of DH indicators

Method clone()

The objects of this class are cloneable with this method.

Usage

SimParam$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# NOT RUN {
## ------------------------------------------------
## Method `SimParam$new`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)

## ------------------------------------------------
## Method `SimParam$setTrackPed`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$setTrackPed(TRUE)

## ------------------------------------------------
## Method `SimParam$setTrackRec`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$setTrackRec(TRUE)

## ------------------------------------------------
## Method `SimParam$resetPed`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)

#Create population
pop = newPop(founderPop, simParam=SP)
pop@id # 1:10

#Create another population after reseting pedigree
SP$resetPed()
pop2 = newPop(founderPop, simParam=SP)
pop2@id # 1:10

## ------------------------------------------------
## Method `SimParam$restrSegSites`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$restrSegSites(minQtlPerChr=5, minSnpPerChr=5)

## ------------------------------------------------
## Method `SimParam$setGender`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$setGender("yes_sys")

## ------------------------------------------------
## Method `SimParam$addSnpChip`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addSnpChip(10)

## ------------------------------------------------
## Method `SimParam$addTraitA`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitA(10)

## ------------------------------------------------
## Method `SimParam$addTraitAD`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitAD(10, meanDD=0.5)

## ------------------------------------------------
## Method `SimParam$addTraitAG`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitAG(10, varGxE=2)

## ------------------------------------------------
## Method `SimParam$addTraitADG`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitADG(10, meanDD=0.5, varGxE=2)

## ------------------------------------------------
## Method `SimParam$addTraitAE`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

## ------------------------------------------------
## Method `SimParam$addTraitADE`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitADE(10)

## ------------------------------------------------
## Method `SimParam$addTraitAEG`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitAEG(10, varGxE=2)

## ------------------------------------------------
## Method `SimParam$addTraitADEG`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitADEG(10, meanDD=0.5, varGxE=2)

## ------------------------------------------------
## Method `SimParam$setVarE`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitA(10)
SP$setVarE(h2=0.5)

## ------------------------------------------------
## Method `SimParam$setCorE`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitA(10, mean=c(0,0), var=c(1,1), corA=diag(2))
SP$setVarE(varE=c(1,1))
E = 0.5*diag(2)+0.5 #Positively correlated error
SP$setCorE(E)

## ------------------------------------------------
## Method `SimParam$rescaleTraits`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitA(10)

#Create population
pop = newPop(founderPop, simParam=SP)
meanG(pop)

#Change mean to 1
SP$rescaleTraits(mean=1)
#Run resetPop for change to take effect
pop = resetPop(pop, simParam=SP) 
meanG(pop)

## ------------------------------------------------
## Method `SimParam$setRecombRatio`
## ------------------------------------------------

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$setRecombRatio(2) #Twice as much recombination in females
# }