Package: breedR 0.12-7

breedR: Statistical Methods for Forest Genetic Resources Analysts

Statistical tools to build predictive models for the breeders community. It aims to assess the genetic value of individuals under a number of situations, including spatial autocorrelation, genetic/environment interaction and competition. It is under active development as part of the Trees4Future project, particularly developed having forest genetic trials in mind. But can be used for animals or other situations as well.

Authors:Facundo Muñoz with libraries by Ignacy Misztal

breedR_0.12-7.tar.gz
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breedR_0.12-7.tgz(r-4.4-emscripten)breedR_0.12-7.tgz(r-4.3-emscripten)
breedR.pdf |breedR.html✨
breedR/json (API)
NEWS

# Install 'breedR' in R:
install.packages('breedR', repos = c('https://famuvie.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/famuvie/breedr/issues

Datasets:
  • douglas - Multi-site Douglas-fir dataset
  • globulus - Eucalyptus Globulus dataset
  • larix - Longitudinal Larix dataset
  • m1 - A small Metagene synthesized dataset
  • m4 - Metagene synthesized dataset with four generations

On CRAN:

5.42 score 31 stars 24 scripts 31 exports 40 dependencies

Last updated 4 months agofrom:bf52f982aa. Checks:ERROR: 9. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 01 2024
R-4.5-win-x86_64ERRORNov 01 2024
R-4.5-linux-x86_64ERRORNov 01 2024
R-4.4-win-x86_64ERRORNov 01 2024
R-4.4-mac-x86_64ERRORNov 01 2024
R-4.4-mac-aarch64ERRORNov 01 2024
R-4.3-win-x86_64ERRORNov 01 2024
R-4.3-mac-x86_64ERRORNov 01 2024
R-4.3-mac-aarch64ERRORNov 01 2024

Exports:b.valuesbreedR.getOptionbreedR.qdelbreedR.qgetbreedR.qnukebreedR.qstatbreedR.remote_loadbreedR.sample.ARbreedR.sample.BVbreedR.sample.phenotypebreedR.sample.splinesbreedR.setOptionbuild_pedigreecheck_pedigreecheck_progsf90compare.plotscoordinatescoordinates<-fixefget_ntraitsget_pedigreeinstall_progsf90ngenerationsnindividualsprint.breedR.qranefread.metageneremlf90sim.spatialsummary.breedR.qvariogram

Dependencies:bootclicolorspacefansifarverggplot2gluegtableHaploSimisobandlabelinglatticelifecyclelme4magrittrMASSMatrixmgcvminqamunsellnlmenloptrpedigreepedigreemmpillarpkgconfigplyrR6RColorBrewerRcppRcppEigenreshaperlangscalessptibbleutf8vctrsviridisLitewithr

Additive Genetic Models in Mixed Populations

Facundo Muñoz

Rendered fromAdditive-Genetic-Models-in-Mixed-Populations.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2020-06-10
Started: 2015-05-03

BreedR Overview

Facundo Muñoz

Rendered fromOverview.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2017-04-15
Started: 2014-09-04

Computing heritability

Facundo Muñoz

Rendered fromHeritability.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2017-01-10
Started: 2015-11-25

General and Specific Combining Abilities

Facundo Muñoz

Rendered fromGeneral-and-Specific-Combining-Abilities.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2015-12-24
Started: 2015-02-06

Handling pedigrees

Facundo Muñoz

Rendered fromHandling-pedigrees.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2017-04-28
Started: 2015-02-06

Heterogeneous variances and weighting

Facundo Muñoz

Rendered fromHeterogeneous-variances.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2017-03-22
Started: 2017-01-09

Missing values

Facundo Muñoz

Rendered fromMissing-values.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2017-04-12
Started: 2015-11-25

Readme and manuals

Help Manual

Help pageTopics
Frequentist and Bayesian methods for breeders, quantitative geneticists and forest genetic resources analysts.breedR-package breedR
Build an additive_genetic modeladditive_genetic
Build an additive-genetic animal modeladditive_genetic_animal
Build an additive-genetic competition modeladditive_genetic_competition
Represent a symmetric matrix in triplet formatas.triplet
Breeding valuesb.values
Incidence Matrix of Bidimensional Splinesbispline_incidence
Build an autoregressive modelbreedr_ar
Build a blocks modelbreedr_blocks
Constructor for a generic breedR effectbreedr_effect dim.breedr_effect
Default repository for PROGSF90 binariesbreedr_progsf90_repo
Build a splines modelbreedr_splines
Determine the user's home directorybreedR.get.HOME
Determine the user namebreedR.get.USER
Set and get global options for breedRbreedR.getOption breedR.option breedR.options breedR.setOption
Check host OSbreedR.os
test 32/64 bits architecturebreedR.os.32or64bit
Return platform stringbreedR.os.type
Perform a job remotelybreedR.remote
Build an encompassing gridbuild_grid
Build pedigreeas.data.frame.pedigree build_pedigree
Check the rules for a well-formed pedigreecheck_pedigree
Checks installation of PROGSF90 binariescheck_progsf90
Check initial variances specificationcheck_var.ini
Compare two or more ggplots of the same kindcompare.plots
Build a virtual competition modelcompetition
breedR coordinates methodscoordinates,breedR-method coordinates,effect_group-method coordinates,metagene-method coordinates,spatial-method coordinates<-,breedR-method coordinates<-,metagene-method coordinates_breedR
Default initial value for variance componentsdefault_initial_variance
Determine a sensible number of knotsdetermine.n.knots
Constructor for a diagonal random effectdiagonal
Distribute knots uniformly in a griddistribute_knots_uniformgrid
Multi-site Douglas-fir datasetdouglas
Constructor for a group of effectsdim.effect_group effect_group
Type of a (group of) effect(s)effect_type effect_type.breedr_effect effect_type.effect_group
Extract a block of lines from a section of the REML logextract_block
Extract or replace data in a metagene object$.metagene $<-.metagene Extract.metagene [.metagene
Find and fill all the holes in a vectorfill_holes
Constructor for a fixed effectfixed
Extract fixed-effects estimatesfixed.effects fixef fixef.breedR fixef.remlf90
Build a generic modelgeneric
Build an genetic modelgenetic
Get names of effectsget_efnames
Extract the number of traitsget_ntraits
Parameters of a breedR componentget_param get_param.breedr_modelframe get_param.effect_group get_param.remlf90 get_param.spatial
Get the Pedigree from an objectget_pedigree get_pedigree.breedr_modelframe get_pedigree.effect_group get_pedigree.genetic get_pedigree.metagene get_pedigree.remlf90
Covariance structure of a breedR componentget_structure get_structure.breedR get_structure.breedr_effect get_structure.effect_group
Eucalyptus Globulus datasetglobulus
Install PROGSF90 binary dependenciesinstall_progsf90
Test whether a string from a REML log is numericis_numericlog
Longitudinal Larix datasetlarix
Lattice of spatial locationsloc_grid
A small Metagene synthesized datasetm1
Metagene synthesized dataset with four generationsm4
'move' an arrangement in a given directionneighbours.at neighbours.at.list neighbours.at.matrix
Number of generationsngenerations
Number of individualsnindividuals
Define mapping between a lattice and nodesnode2lattice_mapping
Normalise coordinates specificationnormalise_coordinates
Parse a matrix from a text output robustlyparse.txtmat
Build an permanent-environmental competition modelpermanent_environmental_competition
Determine a numeric code for missing observationspf90_code_missing
Default formula for heritabilitypf90_default_heritability
Spatial plot of a model's fit componentsplot.remlf90
progsf90 classprogsf90
Constructor for a random effectrandom
Extract the modes of the random effectsranef ranef.breedR ranef.remlf90
Metagene Data Inputas.data.frame.metagene get_ntraits.metagene metagene ngenerations.metagene nindividuals.metagene plot.metagene print.summary.metagene read.metagene summary.metagene
Inference with REMLF90remlf90
Control and view a remote breedR-queue of submitted jobsbreedR.qdel breedR.qget breedR.qnuke breedR.qstat breedR.remote_load print.breedR.q remote submit summary.breedR.q
Render a progsf90 effectrenderpf90 renderpf90.additive_genetic_animal renderpf90.additive_genetic_competition renderpf90.ar renderpf90.blocks renderpf90.breedr_modelframe renderpf90.default renderpf90.diagonal renderpf90.effect_group renderpf90.fixed renderpf90.generic renderpf90.permanent_environmental_competition renderpf90.splines
Render a sparse matrix into non-zero values and column indicesrenderpf90.matrix
Retrieve results stored in some remote directoryretrieve_remote
Simulate a spatial structuresim.spatial
Simulation of phenotypes and model componentsbreedR.sample.AR breedR.sample.BV breedR.sample.pedigree breedR.sample.phenotype breedR.sample.ranef breedR.sample.splines simulation
Build a spatial modelspatial
Plot an spatially arranged continuous variablespatial.plot
'Splat' arguments to a functionsplat
Check properties for a covariance matrixvalidate_variance
Empirical variograms of residualsprint.breedR.variogram variogram
Covariance matrix of a fitted remlf90 objectvcov.remlf90
Variogram of a matrixvgram.matrix