BMTME v1.0.4

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by Luna-V<c3><a1>zquez Francisco J. View Source

Bayesian Multi-Trait Multi-Environment for Genomic Selection Analysis

Genomic selection and prediction models with the capacity to use multiple traits and environments, through ready-to-use Bayesian models. It consists a group of functions that help to create regression models for some genomic models proposed by Montesinos-L<c3><b3>pez, et al. (2016) <doi:10.1534/g3.116.032359> also in Montesinos-L<c3><b3>pez et al. (2018) <doi:10.1534/g3.118.200728> and Montesinos-L<c3><b3>pez et al. (2018) <doi:10.2134/agronj2018.06.0362>.

Functions in BMTME

Name	Description
barplot.BMORSENV	barplot BMORSENV graph
WheatMadaToy	Wheat Mada Data
summary.BMORSCV	summary.BMORSCV
print.BMORSCV	Print BMORSCV information object
print.BMORSENV	Print BMORSENV information object
summary.BMECV	summary.BMECV
genoMaizeToy	Genomic values of Maize dataset.
genoWheatToy	Genomic values of Wheat toy dataset.
WheatToy	Phenotypic values and Genetic values of Wheat toy dataset.
cholesky	Cholesky
boxplot.BMECV	boxplot.BMECV
print.BMTME	Print BMTME information object
genoJapa50	Genomic values of Japa dataset.
genoMada	Genomic values of Mada dataset.
BMORS	Bayesian Multi-Output Regression Stacking (BMORS)
phenoIranianToy	Phenotypic values of Iranian toy dataset.
detectCores	Detect number of cores
genoIranianToy	Genomic values of Iranian toy dataset.
print.BMTMECV	Print BMTMECV information object
plot.BME	plot.BME
print.BMECV	Print BMECV information object
phenoJapa30	Phenotypic values of Japa dataset.
plot.BMORSCV	Plot BMORSCV Simple scatter plot comparing the observed values against the predicted values.
boxplot.BMORSCV	boxplot.BMORSCV
print.BMORS	Print BMORS information object
summary.BMORSENV	summary.BMORSENV
boxplot.BMTMECV	boxplot.BMTMECV
summary.BMTMECV	summary.BMTMECV
residuals.BME	residuals.BME
residuals.BMTME	residuals.BMTME
genoJapa30	Genomic values of Japa dataset.
phenoJapa50	Phenotypic values of Japa dataset.
phenoMada	Phenotypic values of Mada dataset.
phenoMaizeToy	Phenotypic values of Maize dataset.
plot.BMTME	plot.BMTME Simple scatter plot comparing the observed values against the predicted values.
phenoWheatToy	Phenotypic values of Wheat toy dataset.
print.BME	Print BME information object
BMORS_Env	Bayesian Multi-Output regression stacking for specific environment estimations
BMTME	Bayes Multi-Trait Milti-Environment Model (BMTME)
CV.KFold	Cross-Validation with K Folds
CV.RandomPart	Cross-Validation with Random Partitions
MaizeToy	Maize Data
WheatIranianToy	Wheat Iranian Toy Data
WheatJapa30	Wheat Japa 30 Data
WheatJapa50	Wheat Japa 50 Data
BME	Bayesian Multi-Environment Model (BME)
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Vignettes of BMTME

Name
bme.Rmd
bmors.Rmd
bmorsenv.Rmd
bmtme.Rmd
No Results!

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Details

Date	2018-12-25
Language	en-US
License	LGPL-3
Encoding	UTF-8
LazyData	true
Type	Package
RoxygenNote	6.1.1
URL	https://github.com/frahik/BMTME
BugReports	https://github.com/frahik/BMTME/issues/new
NeedsCompilation	yes
Collate	BME.R BMTME.R BMTME_Package.R BMORS.R BMORSEnv.R cholesky.R datasets.R detectCore.R RandomPartition.R RcppExports.R utils.R
LinkingTo	Rcpp, RcppArmadillo
SystemRequirements	C++11
VignetteBuilder	knitr
Packaged	2019-01-06 17:58:50 UTC; frahik
Repository	CRAN
Date/Publication	2019-01-11 17:20:10 UTC

suggests	, covr , knitr , rmarkdown , testthat
imports	BGLR , doSNOW , dplyr , foreach , matrixcalc , mvtnorm , progress , snow , tidyr
depends	R (>= 3.0.0)
linkingto	Rcpp , RcppArmadillo
Contributors	Osval Antonio Montesinos-Lopez, Abelardo Montesinos-Lopez, Jose Crossa, Fernando H. Toledo