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mbend - Matrix Bending

Bending non-positive-definite (symmetric) matrices to positive-definite, using weighted and unweighted methods. Jorjani, H., et al. (2003) <doi:10.3168/jds.S0022-0302(03)73646-7>. Schaeffer, L. R. (2014) <http://animalbiosciences.uoguelph.ca/~lrs/ELARES/PDforce.pdf>.

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6.12 score 3 stars 3 dependents 21 scripts 4.6k downloads

FnR - Inbreeding and Numerator Relationship Coefficients

Compute inbreeding coefficients using the method of Meuwissen and Luo (1992) <doi:10.1186/1297-9686-24-4-305>, and numerator relationship coefficients between individuals using the method of Van Vleck (2007) <https://pubmed.ncbi.nlm.nih.gov/18050089/>.

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4.18 score 3 stars 2 scripts 563 downloads

pedMermaid - Pedigree Mermaid Syntax

Generate Mermaid syntax for a pedigree flowchart from a pedigree data frame. Mermaid syntax is commonly used to generate plots, charts, diagrams, and flowcharts. It is a textual syntax for creating reproducible illustrations. This package generates Mermaid syntax from a pedigree data frame to visualize a pedigree flowchart. The Mermaid syntax can be embedded in a Markdown or R Markdown file, or viewed on Mermaid editors and renderers. Links' shape, style, and orientation can be customized via function arguments, and nodes' shapes and styles can be customized via optional columns in the pedigree data frame.

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4.00 score 2 stars 159 downloads

pedSimulate - Pedigree, Genetic Merit, Phenotype, and Genotype Simulation

Simulate pedigree, genetic merits and phenotypes with random/non-random matings followed by random/non-random selection with different intensities and patterns in males and females. Genotypes can be simulated for a given pedigree, or an appended pedigree to an existing pedigree with genotypes. Mrode, R. A. (2005) <ISBN:9780851989969, 0851989969>; Nilforooshan, M.A. (2022) <doi:10.37496/rbz5120210131>.

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3.18 score 3 stars 220 downloads

ggroups - Pedigree and Genetic Groups

Calculates additive and dominance genetic relationship matrices and their inverses, in matrix and tabular-sparse formats. It includes functions for checking and processing pedigree, calculating inbreeding coefficients (Meuwissen & Luo, 1992 <doi:10.1186/1297-9686-24-4-305>), as well as functions to calculate the matrix of genetic group contributions (Q), and adding those contributions to the genetic merit of animals (Quaas (1988) <doi:10.3168/jds.S0022-0302(88)79691-5>). Calculation of Q is computationally extensive. There are computationally optimized functions to calculate Q.

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3.00 score 2 stars 3 scripts 239 downloads