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]

SFSI_1.4.1.tar.gz
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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:

4.78 score 20 scripts 579 downloads 17 exports 38 dependencies

Last updated 3 months agofrom:39406ddc1c. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-win-x86_64OKNov 21 2024
R-4.5-linux-x86_64OKNov 21 2024
R-4.4-win-x86_64OKNov 21 2024
R-4.4-mac-x86_64OKNov 21 2024
R-4.4-mac-aarch64OKNov 21 2024
R-4.3-win-x86_64OKNov 21 2024
R-4.3-mac-x86_64OKNov 21 2024
R-4.3-mac-aarch64OKNov 21 2024

Exports:cov2cor2cov2distfitBLUPget_foldsgetGenCovLARSmultitrait.plotnetpath.plotPruneread_SGPread_summaryreadBinarysaveBinarySGPSGP.CVsolveEN

Dependencies:clicolorspacecpp11fansifarverggplot2gluegridExtragtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtensorEVDtibbleutf8vctrsviridisviridisLitewithr

Documentation: Optimal breeding value prediction using a Sparse Selection Index

Rendered fromSGP-documentation.Rmdusingknitr::rmarkdownon Nov 21 2024.

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

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

Rendered fromSSI-documentation.Rmdusingknitr::rmarkdownon Nov 21 2024.

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