# contLikINT

### Description

contLikINT marginalizes the likelihood of the STR DNA mixture given some assumed a bayesian model by numerical integration.

### Usage

1 2 3 4 |

### Arguments

`nC` |
Number of contributors in model. |

`samples` |
A List with samples which for each samples has locus-list elements with list elements adata and hdata. 'adata' is a qualitative (allele) data vector and 'hdata' is a quantitative (peak heights) data vector. |

`popFreq` |
A list of allele frequencies for a given population. |

`lower` |
Lower bounds of parameters. Must be in following order: mx1,..,mx_(nC-1),mu,sigma,beta,xi. |

`upper` |
Upper bounds of parameters. Must be in following order: mx1,..,mx_(nC-1),mu,sigma,beta,xi. |

`refData` |
Reference objects has locus-list element [[i]] with a list element 'r' which contains a 2 long vector with alleles for each references. |

`condOrder` |
Specify conditioning references from refData (must be consistent order). For instance condOrder=(0,2,1,0) means that we restrict the model such that Ref2 and Ref3 are respectively conditioned as 2. contributor and 1. contributor in the model. |

`knownRef` |
Specify known non-contributing references from refData (index). For instance knownRef=(1,2) means that reference 1 and 2 is known non-contributor in the hypothesis. This affectes coancestry correction. |

`xi` |
A numeric giving stutter-ratio if it is known. Default is NULL, meaning it is integrated out. |

`prC` |
A numeric for allele drop-in probability. Default is 0. |

`reltol` |
Required relative tolerance error of evaluations in integration routine. Default is 0.001. |

`threshT` |
The detection threshold given. Used when considering probability of allele drop-outs. |

`fst` |
is the coancestry coeffecient. Default is 0. |

`lambda` |
Parameter in modeled peak height shifted exponential model. Default is 0. |

`pXi` |
Prior function for xi-parameter (stutter). Flat prior on [0,1] is default. |

`kit` |
shortname of kit: "ESX17","ESI17","ESI17Fast","ESX17Fast","Y23","Identifiler","NGM","ESSPlex","ESSplexSE","NGMSElect","SGMPlus","ESX16", "Fusion","GlobalFiler" |

`scale` |
used to make integrale calculateable for small numbers. For scale!=0, integrale must be scaled afterwards with exp(-scale) to be correct. |

`maxEval` |
Maximum number of evaluations in the adaptIntegrate function. Default is 0 which gives an infinite limit. |

### Details

The procedure are doing numerical integration to approximate the marginal probability over the noisance parameters. Mixture proportions have flat prior.

Function calls procedure in c++ by using the package Armadillo and Boost.

### Value

ret A list(margL,deviation,nEvals) where margL is Marginalized likelihood for hypothesis (model) given observed evidence, deviation is the confidence-interval of margL, nEvals is number of evaluations.

### Author(s)

Oyvind Bleka <Oyvind.Bleka.at.fhi.no>

### References

Hahn,T. (2005). CUBA - a library for multidimensional numerical integration. Computer Physics Communications, 168(2),78-95.

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