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-López, et al. (2016) also in Montesinos-López et al. (2018) and Montesinos-López et al. (2018) .


News

BMTME v1.0.6

Changes:

  • [Fix bug] Fixed eigen values in BME and BMTME functions.

BMTME v1.0.5

Changes:

  • [Update] Fixed package to keep it compatible with new version of dplyr.
  • [Update] New parameter tolerance in cholesky function.

BMTME v1.0.4 [First CRAN release]

Changes:

  • [Update] Examples provided to BMORS, BME, BMTME and BMORS_Env functions.
  • [Update] Description of the package.

BMTME v1.0.3

Changes:

  • [Update] New tests was added.
  • [refactoring code] Update validation of cores to use only the 50% of the available cores.
  • [refactoring code] Change to snow and doSNOW packages to parallel work.
  • [refactoring code] Bug fixed.

BMTME v1.0.2

Changes:

  • [Update] New tests was added.
  • [refactoring code] Now the progress bar with parallel work it is with pbapply package
  • [refactoring code] Change snow and doSNOW packages to parallel package
  • [refactoring code] New function to crossvalidation, easier to maintain.
  • [Update] Add a good description.

BMTME v1.0.1

Changes:

  • [Fixed] Makevars.win to compile C++ code.
  • [refactoring code] cholesky function.

BMTME v1.0.0

Changes:

  • Fixed typo
  • Include vignettes
  • Removed unused code

BMTME v0.0.26

Changes:

  • Improvements in tests
  • Minor fixes

BMTME v0.0.25

Changes:

  • Include coverage test
  • Typo fixed
  • Fixed bug in BMTME() function with a vector as testingSet parameter.
  • Fixed bug in RandomPartition() function.
  • Implemented predictions with not crossvalidation in BMORS() function.
  • Include print() function to BMORS object with not crossvalidation.

BMTME v0.0.24

Changes:

  • Removed stratified random partitions.
  • Fixed barplot for BMORS_Env.
  • Good practice with <-
  • complete F or T, logical arguments.
  • Bug fixed: changed 1:length to seq_len to avoid bugs.
  • Include ORCID.

BMTME v0.0.23

Changes:

  • Include more tests.
  • Fixed print message of BMORS() and BMORS_Env() functions.
  • Fixed parallel work of BMORS() function.

BMTME v0.0.22

Changes:

  • Important updates to the documentation.
  • Fixed MAC-OS 10.11 El Capitan, installation (issue #1).

BMTME v0.0.21

Changes:

  • BMTERS() function now is BMORS() function.
  • BMTERS_Env() function now is BMORS_Env() function.

BMTME v0.0.20

Changes:

  • Update Windows c++ support.
  • Fixed issues #1 (Installation in Windows) and #2 (Typos). Thanks to @volpatoo and @j450h1 by reporting it.

BMTME v0.0.19

Changes:

  • Update plot and boxplot functions

BMTME v0.0.18

Changes:

  • New predictor_Sec_complete parameter in BMTMERS_Env() function.

BMTME v0.0.17

Changes:

  • New predictor_Sec_complete parameter in BMTMERS() function.

BMTME v0.0.16

Changes:

  • The MSEP was changed to MAAPE for the error estimations of the predictions.
  • Minor fixes in the documentation.
  • Now the boxplots can be ordered by the MAAPE.
  • fixed the predicted output.

BMTME v0.0.15

Changes:

  • Implement parallel mode in the BMTMERS function
  • Implement validation to parallelCores parameter in the functions that could use it.
  • export n_cores used to fit the models that could use parallelCores parameter.
  • fixed class of BME function.

BMTME v0.0.14

Changes:

  • Update Unix support

BMTME v0.0.13

Changes:

  • Initial development is in progress, but there has not yet been a stable, usable release suitable for the public; this is a pre-release, be careful.

BMTME v0.0.1

Changes:

  • Initial commit

Reference manual

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install.packages("BMTME")

1.0.6 by Francisco Javier Luna-Vazquez, 4 months ago


https://github.com/frahik/BMTME


Report a bug at https://github.com/frahik/BMTME/issues/new


Browse source code at https://github.com/cran/BMTME


Authors: Francisco Javier Luna-Vazquez [aut, cre] , Fernando H. Toledo [aut] , Osval Antonio Montesinos-Lopez [aut] , Abelardo Montesinos-Lopez [aut] , Jose Crossa [aut]


Documentation:   PDF Manual  


LGPL-3 license


Imports BGLR, doSNOW, dplyr, foreach, matrixcalc, mvtnorm, progress, snow, tidyr

Suggests covr, knitr, rmarkdown, testthat

Linking to Rcpp, RcppArmadillo

System requirements: C++11


See at CRAN