Package: SFSI 1.4.1

Marco Lopez-Cruz

SFSI: Sparse Family and Selection Index

Here we provide tools for the estimation of coefficients in penalized regressions when the (co)variance matrix of predictors and the covariance vector between predictors and response, are provided. These methods are extended to the context of a Selection Index (commonly used for breeding value prediction). The approaches offer opportunities such as the integration of high-throughput traits in genetic evaluations ('Lopez-Cruz et al., 2020') <doi:10.1038/s41598-020-65011-2> and solutions for training set optimization in Genomic Prediction ('Lopez-Cruz & de los Campos, 2021') <doi:10.1093/genetics/iyab030>.

Authors:Marco Lopez-Cruz [aut, cre], Gustavo de los Campos [aut], Paulino Perez-Rodriguez [ctb]

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SFSI.pdf |SFSI.html✨
SFSI/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/marcoolopez/sfsi/issues

Uses libs:
  • openblas– Optimized BLAS
Datasets:

On CRAN:

17 exports 1.16 score 38 dependencies 20 scripts 921 downloads

Last updated 25 days agofrom:39406ddc1c. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 23 2024
R-4.5-win-x86_64OKAug 23 2024
R-4.5-linux-x86_64OKAug 23 2024
R-4.4-win-x86_64OKAug 23 2024
R-4.4-mac-x86_64OKAug 23 2024
R-4.4-mac-aarch64OKAug 23 2024
R-4.3-win-x86_64OKAug 23 2024
R-4.3-mac-x86_64OKAug 23 2024
R-4.3-mac-aarch64OKAug 23 2024

Exports:cov2cor2cov2distfitBLUPget_foldsgetGenCovLARSmultitrait.plotnetpath.plotPruneread_SGPread_summaryreadBinarysaveBinarySGPSGP.CVsolveEN

Dependencies:clicolorspacecpp11fansifarverggplot2gluegridExtragtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtensorEVDtibbleutf8vctrsviridisviridisLitewithr

Documentation: Optimal breeding value prediction using a Sparse Selection Index

Marco Lopez-Cruz^1^, and Gustavo de los Campos^2,3,4,$\star$^

Rendered fromSGP-documentation.Rmdusingknitr::rmarkdownon Aug 23 2024.

Last update: 2024-06-25
Started: 2024-06-25

Documentation: Regularized selection indices for breeding value prediction using hyper-spectral image data

Marco Lopez-Cruz^1^, Eric Olson^1^, Gabriel Rovere^2,3,4^, Jose Crossa^6^, Susanne Dreisigacker^6^, Suchismita Mondal^6^, Ravi Singh^6^, and Gustavo de los Campos^3,4,5,$\star$^

Rendered fromSSI-documentation.Rmdusingknitr::rmarkdownon Aug 23 2024.

Last update: 2024-06-25
Started: 2022-08-13