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IBCF.MTME Logo

Item Based Collaborative Filterign For Multi-Trait and Multi-Environment Data in R - Development version 1.6.0.

[Last README update: 2019-03-22]

Maturing Travis build status Appveyor build status Coverage Status LGPL, Version 3.0 Status of the Repo: Active Dowloads from the CRAN CRAN

Table Of Contents

News of this version (1.6.0)

  • Fixed important issue with the predictions output.
  • Fixed compatibility with dplyr 0.8.
  • Fixed barplot function.

See the last updates in NEWS.

Instructions for proper implementation

IBCF.MTME Logo

Installation

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('IBCF.MTME')

Load the package

library(IBCF.MTME)

Example of Cross-validation with IBCF.MTME

Load available data from other package

library(BGLR)
data(wheat)

Generate a new data set in tidy data form

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

Generate 10 partitions to do cross-validation

CrossV <- CV.RandomPart(pheno, NPartitions = 10, PTesting = 0.25, Set_seed = 123)

Fitting the predictive model

pm <- IBCF(CrossV)

Show some results

All the predictive model printed output:

pm
## Item Based Collaborative Filtering Model: 
##  Fitted with  10  random partitions
##  Runtime:  12.408  seconds 
## 
##  Some predicted values: 
##  [1]  -0.9554  -0.2731  -0.5007  -0.0909  -0.0501  -0.2599  -0.3494
##  [8]   0.0913  -0.0215  -0.4023  -0.8106   0.5702   0.4918  -1.5810
## [15]  -0.1540  -0.8060  -0.6665  -0.0671  -0.1934  -0.3210
## 
## Predictive capacity of the model: 
##    Environment  Trait  Pearson  SE_Pearson  MAAPE  SE_MAAPE
## 1         Env1          -0.131       0.024  0.931     0.011
## 2         Env2           0.686       0.010  0.674     0.012
## 3         Env3           0.612       0.017  0.682     0.007
## 4         Env4           0.307       0.027  0.762     0.011
## 
##  Use str() function to found more datailed information.

Predictions and observed data in tidy format

head(pm$predictions_Summary, 6)
##   Position Partition Environment Trait Observed Predicted
## 1        1         1        Env1         1.6716   -0.9554
## 2       14         1        Env1         0.3160   -0.2731
## 3       25         1        Env1        -1.1272   -0.5007
## 4       26         1        Env1        -0.4852   -0.0909
## 5       28         1        Env1         2.5940   -0.0501
## 6       30         1        Env1        -0.5190   -0.2599

Predictions and observed data in matrix format

head(pm$Data.Obs_Pred, 5)
##   ID      _Env1       _Env2      _Env3      _Env4 X_Env1.predicted
## 1  1  1.6716295 -1.72746986 -1.8902848  0.0509159       -0.9894943
## 2  2 -0.2527028  0.40952243  0.3093855 -1.7387588       -0.5478389
## 3  3  0.3418151 -0.64862633 -0.7995592 -1.0535691       -0.8596543
## 4  4  0.7854395  0.09394919  0.5704677  0.5517574        0.4040118
## 5  5  0.9983176 -0.28248062  1.6186819 -0.1142848        0.3243855
##   X_Env2.predicted X_Env3.predicted X_Env4.predicted
## 1       -0.8744692     -0.635018256       -0.5894103
## 2       -0.4165869     -0.370835578        0.1360170
## 3       -0.6766007              NaN       -0.3162934
## 4        0.5769577      0.347986885        0.5066996
## 5        1.0403187      0.001053535        0.7813698

Some plots

par(mai = c(2, 1, 1, 1))
plot(pm, select = 'Pearson')

plot(pm, select = 'MAAPE')

Example of Years prediction with IBCF.Years Function

Loading your data

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

Transforming the data from Tidy data to matrix form

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

Adjust the model

pm <- IBCF.Years(Data.Example, colYears = 1, Years.testing = c('2014', '2015', '2016'),
                 Traits.testing = c('Trait1', 'Trait2', 'Trait3', 'Trait4', "Trait5"))

Show some results

summary(pm)
##    Environment  Trait Pearson  MAAPE
## 1         2014 Trait1  0.7549 0.0409
## 2         2014 Trait2  0.1562 0.0473
## 3         2014 Trait3  0.6130 0.0353
## 4         2014 Trait4  0.5208 0.0447
## 5         2014 Trait5  0.7587 0.0240
## 6         2015 Trait1  0.8432 0.0277
## 7         2015 Trait2  0.6792 0.0371
## 8         2015 Trait3  0.7944 0.0327
## 9         2015 Trait4  0.7394 0.0384
## 10        2015 Trait5  0.7651 0.0298
## 11        2016 Trait1  0.7690 0.0343
## 12        2016 Trait2  0.7753 0.0286
## 13        2016 Trait3  0.6763 0.0369
## 14        2016 Trait4  0.8157 0.0325
## 15        2016 Trait5  0.8533 0.0250

par(mai = c(2, 1, 1, 1))
barplot(pm, las = 2)

barplot(pm, select = 'MAAPE', las = 2)

Load available data from the package

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

Citation

First option, by the article paper

@article{IBCF2018,
author = {Montesinos-L{\'{o}}pez, Osval A. and Luna-V{\'{a}}zquez, Francisco Javier and Montesinos-L{\'{o}}pez, Abelardo and Juliana, Philomin and Singh, Ravi and Crossa, Jos{\'{e}}},
doi = {10.3835/plantgenome2018.02.0013},
issn = {1940-3372},
journal = {The Plant Genome},
number = {3},
pages = {16},
title = {{An R Package for Multitrait and Multienvironment Data with the Item-Based Collaborative Filtering Algorithm}},
url = {https://dl.sciencesocieties.org/publications/tpg/abstracts/0/0/180013},
volume = {11},
year = {2018}
}

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 (2019). IBCF.MTME:
##   Item Based Collaborative Filtering for Multi-Trait and
##   Multi-Environment Data. R package version 1.6-0.
##   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 = {2019},
##     note = {R package version 1.6-0},
##     url = {https://github.com/frahik/IBCF.MTME},
##   }

Contributions

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.

Authors

  • Francisco Javier Luna-Vázquez (Author, Maintainer)
  • Osval Antonio Montesinos-López (Author)
  • Abelardo Montesinos-López (Author)
  • José Crossa (Author)