Item Based Collaborative Filterign For Multi-Trait and Multi-Environment Data in R - Development version 1.3.2.
- NEWS
- Instructions
- How to cite this package
- Contributions
- Authors
IBCF.Years()now hascolIDparameter to select the identifiers of the observations.- Fixed a bug caused by the sequence in a for cycle.
See the last updates in NEWS.
To complete installation of dev version of the package IBCF.MTME from
GitHub, you must have previously installed the devtools package.
install.packages('devtools')
devtools::install_github('frahik/IBCF.MTME')If you want to use the stable version of IBCF.MTME package, install it
from CRAN.
install.packages('BGGE')library(IBCF.MTME)library(BGLR)
data(wheat)pheno <- data.frame(ID = gl(n = 599, k = 1, length = 599*4),
Response = as.vector(wheat.Y),
Env = paste0('Env', gl(n = 4, k = 599)))
head(pheno)## ID Response Env
## 1 1 1.6716295 Env1
## 2 2 -0.2527028 Env1
## 3 3 0.3418151 Env1
## 4 4 0.7854395 Env1
## 5 5 0.9983176 Env1
## 6 6 2.3360969 Env1
CrossV <- CV.RandomPart(pheno, NPartitions = 10, PTesting = 0.25, Set_seed = 123)pm <- IBCF(CrossV)summary(pm)## Trait_Env Pearson SE_Cor MSEP SE_MSEP
## 1 _Env1 -0.1307 0.0230 1.9010 0.0452
## 2 _Env2 0.6859 0.0092 0.5454 0.0118
## 3 _Env3 0.6116 0.0164 0.6284 0.0234
## 4 _Env4 0.3068 0.0257 1.0640 0.0495
par(mai = c(2, 1, 1, 1))
plot(pm, select = 'Pearson')plot(pm, select = 'MSEP')load('DataExample.RData')
head(Data.Example)## Years Gids Trait Response
## 1 2014 1 Trait1 15.14401
## 2 2014 2 Trait1 15.67879
## 3 2014 3 Trait1 14.85489
## 4 2014 4 Trait1 13.57002
## 5 2014 5 Trait1 15.01838
## 6 2014 6 Trait1 13.19616
Data.Example <- getMatrixForm(Data.Example, onlyTrait = TRUE)
head(Data.Example)## Years Gids Trait1 Trait10 Trait11 Trait12 Trait2 Trait3
## 1 2014 1 15.14401 18.51428 17.08970 19.16776 16.21435 17.53858
## 2 2014 2 15.67879 18.21569 17.89645 19.94429 15.80614 17.89946
## 3 2014 3 14.85489 17.72576 15.78198 17.53058 14.06164 16.11997
## 4 2014 4 13.57002 18.57009 15.73343 17.49995 14.58312 15.22495
## 5 2014 5 15.01838 18.57348 16.97414 19.03081 14.98192 15.65125
## 6 2014 6 13.19616 16.83588 15.12312 17.39867 15.81264 14.80517
## Trait4 Trait5 Trait6 Trait7 Trait8 Trait9
## 1 15.51840 17.59132 17.14852 17.04474 17.48970 18.36118
## 2 15.13337 18.36446 17.32734 17.46764 18.08501 18.67266
## 3 15.04329 17.28942 16.50978 16.26685 17.02774 17.05612
## 4 14.93028 16.33687 15.11493 15.06632 17.56798 16.48810
## 5 16.70963 16.81113 17.24170 15.53379 16.07600 16.54047
## 6 14.82150 16.49238 15.37325 14.07796 15.98419 15.84705
pm <- IBCF.Years(Data.Example, colYears = 1, Years.testing = c('2014', '2015', '2016'),
Traits.testing = c('Trait1', 'Trait2', 'Trait3', 'Trait4', "Trait5"))summary(pm)## Year_Trait Pearson MSEP
## 2014_Trait1 2014_Trait1 0.7549 0.4836
## 2014_Trait2 2014_Trait2 0.1562 0.7769
## 2014_Trait3 2014_Trait3 0.6130 0.4164
## 2014_Trait4 2014_Trait4 0.5208 0.6821
## 2014_Trait5 2014_Trait5 0.7587 0.2408
## 2015_Trait1 2015_Trait1 0.8432 0.2987
## 2015_Trait2 2015_Trait2 0.6792 0.5828
## 2015_Trait3 2015_Trait3 0.7944 0.4416
## 2015_Trait4 2015_Trait4 0.7394 0.5425
## 2015_Trait5 2015_Trait5 0.7650 0.4739
## 2016_Trait1 2016_Trait1 0.7690 0.3517
## 2016_Trait2 2016_Trait2 0.7753 0.3818
## 2016_Trait3 2016_Trait3 0.6763 0.5527
## 2016_Trait4 2016_Trait4 0.8157 0.4076
## 2016_Trait5 2016_Trait5 0.8533 0.2779
par(mai = c(3, 1, 1, 1))
barplot(pm, las = 2)barplot(pm, select = 'MSEP', las = 2)You can use the data sets in the package to test the functions
library(IBCF.MTME)
data('Wheat_IBCF')
head(Wheat_IBCF)## GID Trait Env Response
## 1 6569128 DH Bed2IR -17.565895
## 2 6688880 DH Bed2IR -4.565895
## 3 6688916 DH Bed2IR -3.565895
## 4 6688933 DH Bed2IR -4.565895
## 5 6688934 DH Bed2IR -7.565895
## 6 6688949 DH Bed2IR -7.565895
data('Year_IBCF')
head(Year_IBCF)## Years Gids Trait Response
## 1 2014 1 T1 5.144009
## 2 2014 2 T1 5.678792
## 3 2014 3 T1 4.854895
## 4 2014 4 T1 3.570019
## 5 2014 5 T1 5.018380
## 6 2014 6 T1 3.196160
First option, by the article paper
(Comming soon)
Second option, by the manual package
citation('IBCF.MTME')##
## To cite package 'IBCF.MTME' in publications use:
##
## Francisco Javier Luna-Vazquez, Osval Antonio Montesinos-Lopez,
## Abelardo Montesinos-Lopez and Jose Crossa (2018). IBCF.MTME:
## Item Based Collaborative Filtering for Multi-Trait and
## Multi-Environment Data. R package version 1.3-2.
## https://github.com/frahik/IBCF.MTME
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {IBCF.MTME: Item Based Collaborative Filtering for Multi-Trait and Multi-Environment Data},
## author = {Francisco Javier Luna-Vazquez and Osval Antonio Montesinos-Lopez and Abelardo Montesinos-Lopez and Jose Crossa},
## year = {2018},
## note = {R package version 1.3-2},
## url = {https://github.com/frahik/IBCF.MTME},
## }
If you have any suggestions or feedback, I would love to hear about it. Feel free to report new issues in this link, also if you want to request a feature/report a bug, or make a pull request if you can contribute.
- Francisco Javier Luna-Vázquez (Author, Maintainer)
- Osval Antonio Montesinos-López (Author)
- Abelardo Montesinos-López (Author)
- José Crossa (Author)