countGen
(Package: pedigree) :
Count generation number for each individual in a pedigree.
Counts generation number for individuals in a pedigreee.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: countGen
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calcG
(Package: pedigree) :
Function to calculate a relationship matrix from marker data
Function to calculate a relationship matrix from marker data. Option to return the inverse of matrix. Inverse calculated using Matrix package.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: calcG
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gblup
(Package: pedigree) :
Function to calculate breeding values using an animal model and a
Fit an animal model to data, use a given variance ratio (α = frac{σ^2_e}{σ^ 2_a}). Calculate genetic relationship matrix using the function calcG of this package.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: gblup
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makeA
(Package: pedigree) :
Makes the A matrix for a part of a pedigree
Makes the A matrix for a part of a pedigree and stores it in a file called A.txt.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: makeA
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add.Inds
(Package: pedigree) :
Function to add missing individuals to a pedigree
Function add.Inds() adds missing individuals to a pedigree and returns the complete pedigree as a data.frame with the same headers as the original pedigree. Remeber to check for errors beforehand with function errors.ped. Unknown parents should be coded as NA.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: add.Inds
●
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blup
(Package: pedigree) :
Function to calculate breeding values using an animal model
Fit an animal model to data, use a given variance ratio (α = frac{σ^2_e}{σ^ 2_a}). Calculate inverse of the additive genetic relationship matrix using function makeInv() of this package.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: blup
●
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calcInbreeding
(Package: pedigree) :
Calculates inbreeding coefficients for individuals in a pedigree.
Calculates inbreeding coefficients of individuals in a pedigree.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: calcInbreeding
●
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makeAinv
(Package: pedigree) :
Makes inverted A matrix for a pedigree
Makes inverted A matrix for a pedigree and stores it in a file called Ainv.txt.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: makeAinv
●
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Package with functions to analyse and transform pedigree data. A pedigree is a data.frame where the first column contains an ID, and the second and third columns contain ID of first and second parent.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: pedigree, pedigree-package
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trimPed
(Package: pedigree) :
Function to trim a pedigree based on available data
Trims a pedigree given a vector of data. Branches without data are trimmed off the pedigree.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: trimPed
●
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