buildMixtureDomains {DNAmixturesLite}

Create RHugin domains for computation.

Description

The function is intended for internal use in DNAmixture, and it creates one network per marker.

IMPORTANT: This is the DNAmixturesLite package, which is intended as a service to enable users to try DNAmixtures without purchasing a commercial licence for Hugin. When at all possible, we strongly recommend the use of DNAmixtures rather than this lite-version. See https://dnamixtures.r-forge.r-project.org/ for details on both packages.

While the lite-version seeks to provide the full functionality of DNAmixtures, note that computations are much less efficient and that there are some differences in available functionality. Be aware that the present documentation is copied from DNAmixtures and thus may not accurately describe the implementation of this lite-version.

Usage

buildMixtureDomains(
  n.unknown,
  data,
  domainnamelist,
  write,
  dir = NULL,
  ntraces = 1,
  triangulate = TRUE,
  compile = TRUE,
  compress = TRUE,
  use.order = TRUE
)

Arguments

n.unknown

Number of unknown contributors

data

A list of data.frames on the form returned by DNAmixtureData.

domainnamelist

List of names for networkfiles.

write

[not available in lite-version] Save networkfiles? Defaults to FALSE.

dir

Path to the networkfiles.

ntraces

Number of traces (EPG's)

triangulate

Triangulate the networks? Default is to triangulate the network using a good elimination order.

compile

Compile the networks? Defaults to TRUE.

compress

Compress the network? Defaults to TRUE and is strongly recommended for models with a large number of contributors.

use.order

Should the default elimination order be used for triangulation? Otherwise the "total.weight" heuristic for triangulation in HUGIN is used.

Details

For one marker, the network contains variables

n_i_a

The number of alleles a that unknown contributor Ui possesses.

S_i_a

Cumulative allele counts, summarising how many alleles amongst types 1, ..., a that contributor i possesses.

O_r_a

Binary variable representing observed peak height for allele a in EPG r. See setCPT.O for details.

D_r_a

Binary variable representing the event of a peak for allele a falling below threshold in EPG r.

Q_r_a

Binary variable representing the event of a peak for allele a being smaller than the peak observed in EPG r.

The network is by default triangulated, compiled, compressed, and, optionally, saved as a hkb-file. If the networks are large – if there are many unknown contributors – it is worth considering saving the networks rather than re-building them every time DNAmixture is called.

Value

A list containing a list of pointers for RHugin domains. Additionally a list of the total size of the compressed junction tree in percent of the uncompressed size.

Note

If amelogenin is included as a marker, use integer codes for the alleles with X preceding Y, e.g. X=0, Y=1.

Author(s)

Therese Graversen