Description Usage Arguments Details Value Author(s) References Examples

The user provides input needed to define a locus (also called system or forensic marker) to be used for pedigree calculations.
The input is checked and if no errors are found a list with class `FamiliasLocus`

is returned containing
the information.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
FamiliasLocus(frequencies, allelenames, name,
MutationModel = "Stepwise",
MutationRate = 0,
MutationRange = 0.5,
MutationRate2 = 0,
MutationMatrix,
Stabilization = "None",
MaxStabilizedMutrate = 1,
femaleMutationModel,
femaleMutationRate,
femaleMutationRange,
femaleMutationRate2,
femaleMutationMatrix,
maleMutationModel,
maleMutationRate,
maleMutationRange,
maleMutationRate2,
maleMutationMatrix)
``` |

`frequencies` |
The first input of FamiliasLocus may be either a vector containing allele frequencies, or a previously created FamiliasLocus object. In the first case, the vector may include a possible silent allele; that it is silent is indicated in the allelenames. The frequencies must sum to 1. In the second case, the new object will be identical to the old object in terms of frequencies, names of alleles, and name of locus, so the 'allelenames' and 'name' parameters must be missing. However, at least one Mutation parameter or the Stabilization parameter must be non-missing, and new mutation matrices will be constructed based on these. If all Mutation parameters are missing, stabilized mutation matrices will be produced based on the mutation matrices of the old object. |

`allelenames` |
Names of the alleles, like |

`name` |
Characters like 'D3S1358', used to identify the locus (marker). The default is to use the name of the frequencies argument to this function. |

`MutationModel` |
The mutation model, used to create the mutation matrix. It may be 'Equal', 'Proportional', 'Stepwise', or 'Custom', see Details. |

`MutationRate` |
The mutation rate; for the 'Stepwise' model the rate of integer-step mutations. It is not used when the MutationModel is 'Custom'. |

`MutationRange` |
Only used when the MutationModel is 'Stepwise'. It then indicates the relative probability of mutating n+1 steps versus mutating n steps. |

`MutationRate2` |
Only used when the MutationModel is 'Stepwise'. It then indicates the rate of non-integer-step mutations, e.g., mutations from an allele with an integer name to alleles with decimal names indicating microvariants. |

`MutationMatrix` |
Only used when the MutationModel is 'Custom'. It then directly specifies the mutation matrix. |

`Stabilization` |
The possible values are 'None', 'DP', 'RM', and 'PM', with 'None' being the default. The other values adjust the mutation matrices so that allele frequencies after one or more generations of mutations will be equal to the original allele frequencies. See Details. |

`MaxStabilizedMutrate` |
Not used when stabilization is 'None'. Otherwise it indicates an upper bound for the specific mutation rate for each allele allowed in the mutation matrices after stabilization. |

`femaleMutationModel` |
Specifies a separate female value for MutationModel; defaults to MutationModel. |

`femaleMutationRate` |
Specifies a separate female value for MutationRate; defaults to MutationRate. |

`femaleMutationRange` |
Specifies a separate female value for MutationRange; defaults to MutationRange. |

`femaleMutationRate2` |
Specifies a separate female value for MutationRate2; defaults to MutationRate2. |

`femaleMutationMatrix` |
Specifies a separate female value for MutationMatrix; defaults to MutationMatrix. |

`maleMutationModel` |
Specifies a separate male value for MutationModel; defaults to MutationModel. |

`maleMutationRate` |
Specifies a separate male value for MutationRate; defaults to MutationRate. |

`maleMutationRange` |
Specifies a separate male value for MutationRange; defaults to MutationRange. |

`maleMutationRate2` |
Specifies a separate male value for MutationRate2; defaults to MutationRate2. |

`maleMutationMatrix` |
Specifies a separate male value for MutationMatrix; defaults to MutationMatrix. |

The probabilities for when and how mutations happen can be specified in mutation matrices, where the row corresponding to an allele indicates the probabilities that the allele is transferred as the allele indicated by the column. Mutation matrices may be specified directly in the MutationMatrix parameters by setting the value of the MutationModel parameter to 'Custom'. Otherwise they are computed based on the values of the MutationModel, MutationRate, MutationRate2, and MutationRange parameters. If MutationModel is 'Equal', there is an equal probability of mutating to any non-silent allele, given that a mutation happens. This model is referred to as 'Equal probability (simple and fast)' in Familias 2.0. If MutationModel is 'Proportional', the probability of mutating to any non-silent allele is proportional to its frequency. It is referred to as 'Probability proportional to frequency (stable)' in Familias 2.0. If MutationModel is 'Stepwise', it is required that the names of all non-silent alleles are positive integers, indicating the number of sequence repetitions of an STR marker, or decimal numbers with a single decimal, such as '15.2', indicating a microvariant. Mutations are then divided into two types: Those that add or subtract an integer to the allele, and those that add or subtract some fractional amount. The rate of these two types of mutations are given separately as MutationRate and MutationRate2, respectively. Relative probabilities of different mutaitons of the first type are specified using the MutationRange parameter. The model with only integer alleles is referred to as 'Probability decreasing with range (equal)' in Familias 2.0, while the more general model is called 'Extended stepwise' in Familias 3.0. Note that the probability of mutations to or from silent alleles is set to zero in all models except the 'Custom' model.

The 'Stabilization' parameter may be used to change the mutation matrices so that they become stationary relative to the frequencies vector. See the references. When the 'PM' setting is used together with the 'Stepwise' MutationModel and all allele names are integers, the resulting model is referred to as 'Probability decreasing with range (stable)' in Familias 2.0.

A list of class `FamiliasLocus`

containing

`locusname` |
The name of the locus |

`alleles` |
The frequencies of the alleles. The names of the alleles are included as the vector names. |

`femaleMutationType` |
A string specifying the type of the female mutations. |

`femaleMutationMatrix` |
The mutation matrix used for female transfer. |

`maleMutationType` |
A string specifying the type of the male mutations. |

`maleMutationMatrix` |
The mutation matrix used for male transfer. |

`simpleMutationMatrices` |
Indicates whether the probability of mutating to an allele is always independent of which allele the mutation happens from. If this is true, some likelihood computations can be done faster. |

`Stabilization` |
The stabilization method used. |

Petter Mostad mostad@chalmers.se, Thore Egeland Thore.Egeland@gmail.com, and Ivar Simonsson Ivar simonssi@chalmers.se

Egeland, Kling, Mostad: Relationship Inference with Familias and R. 2016. Simonsson, Mostad: Stationary Mutation models. (Submitted)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | ```
#Simple examples
FamiliasLocus(1:4/10)
FamiliasLocus(frequencies=c(0.1, 0.2, 0.3, 0.4),
allelenames= c("A", "B", "C", "D"), name="locus1")
#Modified to include a silent frequency
FamiliasLocus(frequencies=c(0.1, 0.2, 0.3, 0.3, 0.1),
allelenames= c("8", "9", "10", "11", "silent"), name="locus1")
#Mutation rates added
FamiliasLocus(frequencies=c(0.1, 0.2, 0.3, 0.4),
allelenames= c("8", "9", "10", "11"), name="locus1",
femaleMutationRate=0.001, maleMutationRate=0.005)
#Mutation matrices specified directly
MM <- matrix(c(0.99, 0.005, 0.003, 0.002, 0.005, 0.99, 0.005, 0,
0, 0.005, 0.99, 0.005, 0.002, 0.003, 0.005, 0.99), 4, 4, byrow=TRUE)
FamiliasLocus(frequencies=c(0.1, 0.2, 0.3, 0.4),
allelenames= c("08", "09", "10", "11"), name="locus1",
MutationModel = "Custom", MutationMatrix = MM)
#A locus is first created, and then edited
loc <- FamiliasLocus(c(0.2, 0.5, 0.3))
loc2 <- FamiliasLocus(loc, maleMutationRate = 0.001)
FamiliasLocus(loc2, Stabilization = "PM")
#A locus using standard Norwegian frequencies is created
data(NorwegianFrequencies)
FamiliasLocus(NorwegianFrequencies$TH01)
``` |

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