Package: bigstatsr 1.6.1

Florian Privé

bigstatsr: Statistical Tools for Filebacked Big Matrices

Easy-to-use, efficient, flexible and scalable statistical tools. Package bigstatsr provides and uses Filebacked Big Matrices via memory-mapping. It provides for instance matrix operations, Principal Component Analysis, sparse linear supervised models, utility functions and more <doi:10.1093/bioinformatics/bty185>.

Authors:Florian Privé [aut, cre], Michael Blum [ths], Hugues Aschard [ths]

bigstatsr_1.6.1.tar.gz
bigstatsr_1.6.1.tar.gz(r-4.5-noble)bigstatsr_1.6.1.tar.gz(r-4.4-noble)
bigstatsr_1.6.1.tgz(r-4.4-emscripten)bigstatsr_1.6.1.tgz(r-4.3-emscripten)
bigstatsr.pdf |bigstatsr.html
bigstatsr/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/privefl/bigstatsr/issues

Pkgdown:https://privefl.github.io

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

openblascppopenmp

4.67 score 16 packages 2.8k downloads 7 mentions 48 exports 46 dependencies

Last updated 3 months agofrom:ad9b1584e4. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 09 2024
R-4.5-linux-x86_64OKDec 09 2024

Exports:add_code256as_FBMas_scaling_funasPlotlyTextAUCAUCBootbig_applybig_attachbig_attachExtdatabig_colstatsbig_copybig_corbig_countsbig_cprodMatbig_cprodVecbig_crossprodSelfbig_incrementbig_parallelizebig_prodMatbig_prodVecbig_randomSVDbig_readbig_scalebig_spLinRegbig_spLogRegbig_SVDbig_tcrossprodSelfbig_transposebig_univLinRegbig_univLogRegbig_writeblock_sizecols_alongcovar_from_dfdiagFBMFBM.code256get_betanb_corespasteLocpcorplot_gridplusrows_alongsub_bktheme_bigstatsrtypeofwithout_downcast_warning

Dependencies:bigassertrbigparallelrbitclicodetoolscolorspacecowplotdoParallelfansifarverffflockforeachggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmeparallellypillarpkgconfigpsR6RColorBrewerRcppRcppArmadilloRcppEigenRhpcBLASctlrlangrmioRSpectrascalestibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Scaling function creatoras_scaling_fun
Plotly textasPlotlyText
AUCAUC AUCBoot
Split-Apply-Combinebig_apply
Standard univariate statisticsbig_colstats
Copy as a Filebacked Big Matrixbig_copy
Correlationbig_cor
Counts for class FBM.code256big_counts
Cross-product with a matrixbig_cprodMat crossprod,FBM,matrix-method crossprod,matrix,FBM-method tcrossprod,FBM,matrix-method tcrossprod,matrix,FBM-method
Cross-product with a vectorbig_cprodVec
Crossprodbig_crossprodSelf crossprod,FBM,missing-method
Increment an FBMbig_increment
Split-parApply-Combinebig_parallelize
Product with a matrix%*%,FBM,matrix-method %*%,matrix,FBM-method big_prodMat
Product with a vectorbig_prodVec
Randomized partial SVDbig_randomSVD
Read a file as FBMbig_read
Some scaling functionsbig_scale
Sparse linear regressionbig_spLinReg
Sparse logistic regressionbig_spLogReg
Partial SVDbig_SVD
Tcrossprodbig_tcrossprodSelf tcrossprod,FBM,missing-method
Transpose an FBMbig_transpose
Column-wise linear regressionbig_univLinReg
Column-wise logistic regressionbig_univLogReg
Write an FBM to a filebig_write
Determine a correct value for the block.size parameterblock_size
Numeric matrix from data framecovar_from_df
Class FBMas_FBM FBM FBM-class FBM_RC
Methods for the FBM classdiag,FBM-method dim,FBM-method FBM-methods length,FBM-method typeof,FBM-method [,FBM,ANY,ANY,ANY-method [<-,FBM,ANY,ANY,ANY-method
Class FBM.code256add_code256 FBM.code256 FBM.code256-class FBM.code256_RC
Combine sets of coefficientsget_beta
Get coordinates on plotpasteLoc
Partial correlationpcor
Plot methodplot.big_sp_list
Plot methodplot.big_SVD
Plot methodplot.mhtest
Predict methodpredict.big_sp
Predict methodpredict.big_sp_list
Scores of PCApredict.big_SVD
Predict methodpredict.mhtest
Replace extension '.bk'sub_bk
Summary methodsummary.big_sp_list
Theme ggplot2theme_bigstatsr
Temporarily disable downcast warningwithout_downcast_warning