Steven H. French [ctb], Navdeep Singh [ctb]
Description: Performs iterative extrapolation of species' haplotype accumulation curves using a nonparametric stochastic (Monte Carlo) optimization method for assessment of specimen sampling completeness based on the approach of Phillips et al. (2015) <doi:10.1515/dna-2015-0008>, Phillips et al. (2019) <doi:10.1002/ece3.4757> and Phillips et al. (2020) <doi: 10.7717/peerj-cs.243>. 'HACSim' outputs a number of useful summary statistics of sampling coverage ("Measures of Sampling Closeness"), including an estimate of the likely required sample size (along with desired level confidence intervals) necessary to recover a given number/proportion of observed unique species' haplotypes. Any genomic marker can be targeted to assess likely required specimen sample sizes for genetic diversity assessment. The method is particularly well-suited to assess sampling sufficiency for DNA barcoding initiatives. Users can also simulate their own DNA sequences according to various models of nucleotide substitution. A Shiny app is also available.
Packaged: 2022-06-13 00:18:40 UTC; jarrettphillips

Packaged: 2022-05-26 02:40:25 UTC; jarrettphillips

Description: Functions to perform ROR for sequence-based association

Description: The package provides a set of functions whose aim is to propose 4 methods of QTL detection and fine mapping.HAPIM LD is an interval-mapping method designed for unrelated individuals with no family information and is based on a maximum-likelihood calculation.HAPIM LDL is an interval-mapping method which uses family information of individuals and combines linkage and linkage disequilibrium.It is based on a maximum-likelihood calculation.HAPLOMAX gives an analysis of variance with a sire effect and a haplotype effect. HAPLOMAX HS gives an analysis of variance with a sire effect and a haplotype effect in half-sire design.
Packaged: Mon Jul  7 09:15:08 2008; sdejean

Author: S. Dejean, N. Oumouhou, D. Estivals, B. Mangin
Description:  The package provides a set of functions whose aim is to propose 4 methods of QTL detection. HAPimLD is an interval-mapping method designed for unrelated individuals with no family information that makes use of linkage disequilibrium. HAPimLDL is an interval-mapping method for design of half-sib families. It combines linkage analysis and linkage disequilibrium. HaploMax is  based on an analysis of variance with a dose haplotype effect. HaploMaxHS is based on an analysis of variance with a sire effect and a dose haplotype effect in half-sib family design.   Fundings for the package development were provided to the LDLmapQTL project by the ANR GENANIMAL program and APIS-GENE.
Packaged: Mon Aug 25 15:12:59 2008; mangin