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hiphop  

Parentage Assignment using Bi-Allelic Genetic Markers
View on CRAN: Click here


Download and install hiphop package within the R console
Install from CRAN:
install.packages("hiphop")

Install from Github:
library("remotes")
install_github("cran/hiphop")

Install by package version:
library("remotes")
install_version("hiphop", "0.0.1")



Attach the package and use:
library("hiphop")
Maintained by
Martijn van de Pol
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-08-19
Latest Update: 2020-08-19
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 ) 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.
How to cite:
Martijn van de Pol (2020). hiphop: Parentage Assignment using Bi-Allelic Genetic Markers. R package version 0.0.1, https://cran.r-project.org/web/packages/hiphop. Accessed 05 Jun. 2026.
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Other packages that cited hiphop R package
View hiphop citation profile
Other R packages that hiphop depends, imports, suggests or enhances
Complete documentation for hiphop
Functions, R codes and Examples using the hiphop R package
Some associated functions: combinations . genotypes . hothiphop . individuals . inspect . topmatch . 
Some associated R codes: hothiphop.R . inspect.R . topmatch.R .  Full hiphop package functions and examples
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