Package: hiphop
Title: Parentage Assignment using Bi-Allelic Genetic Markers
Version: 0.0.1
Authors@R: c(
    person(given = "Martijn",
           family = "van de Pol",
           role = c("aut", "cre"),
           email = "martijn@myscience.eu",
           comment = c(ORCID = "0000-0003-4102-4079")),
      person(given = "Lyanne",
           family = "Brouwer",
           role = c("aut"),
           email = "lyanne@myscience.eu",
           comment = c(ORCID = "0000-0001-6728-4851")),
      person(given = "Andrew",
           family = "Cockburn",
           role = c("aut"),
           email = "andrew.cockburn@anu.edu.au",
           comment = c(ORCID = "0000-0002-8531-3350")))
Description: Can be used for paternity and maternity assignment and outperforms 
  conventional methods where closely related individuals occur in the pool of 
  possible parents. The method compares the genotypes of offspring with any 
  combination of potentials parents and scores the number of mismatches of these 
  individuals at bi-allelic genetic markers (e.g. Single Nucleotide Polymorphisms). 
  It elaborates on a prior exclusion method based on the Homozygous Opposite Test 
  (HOT; Huisman 2017 <doi:10.1111/1755-0998.12665>) by introducing the 
  additional exclusion criterion HIPHOP (Homozygous Identical Parents, 
  Heterozygous Offspring are Precluded; Cockburn et al., in revision). Potential 
  parents are excluded if they have more mismatches than can 
  be expected due to genotyping error and mutation, and thereby one can identify the 
  true genetic parents and detect situations where one (or both) of the true 
  parents is not sampled. Package 'hiphop' can deal with (a) the case where there 
  is contextual information about parentage of the mother (i.e. a female has been 
  seen to be involved in reproductive tasks such as nest building), but paternity 
  is unknown (e.g. due to promiscuity), (b) where both parents need to be assigned, 
  because there is no contextual information on which female laid eggs and which 
  male fertilized them (e.g. polygynandrous mating system where multiple females 
  and males deposit young in a common nest, or organisms with external fertilisation 
  that breed in aggregations).
    For details: Cockburn, A., Penalba, J.V.,Jaccoud, D.,Kilian, A., Brouwer, L.,
       Double, M.C., Margraf, N., Osmond, H.L., van de Pol, M. and Kruuk, L.E.B. 
       (in revision). HIPHOP: improved paternity assignment among close relatives 
       using a simple exclusion method for bi-allelic markers. 
       Molecular Ecology Resources, DOI to be added upon acceptance.
Depends: R (>= 3.6)
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
URL: https://groups.google.com/d/forum/r-hiphop
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-08-12 10:13:11 UTC; marti
Author: Martijn van de Pol [aut, cre] (<https://orcid.org/0000-0003-4102-4079>),
  Lyanne Brouwer [aut] (<https://orcid.org/0000-0001-6728-4851>),
  Andrew Cockburn [aut] (<https://orcid.org/0000-0002-8531-3350>)
Maintainer: Martijn van de Pol <martijn@myscience.eu>
Repository: CRAN
Date/Publication: 2020-08-19 09:30:03 UTC
Built: R 4.6.0; ; 2026-04-25 19:31:53 UTC; unix
