Package: bigstatsr 1.6.3

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_1.6.3.tar.gz
bigstatsr_1.6.3.zip(r-4.7)bigstatsr_1.6.3.zip(r-4.6)bigstatsr_1.6.3.zip(r-4.5)
bigstatsr_1.6.3.tgz(r-4.6-x86_64)bigstatsr_1.6.3.tgz(r-4.6-arm64)bigstatsr_1.6.3.tgz(r-4.5-x86_64)bigstatsr_1.6.3.tgz(r-4.5-arm64)
bigstatsr_1.6.3.tar.gz(r-4.7-arm64)bigstatsr_1.6.3.tar.gz(r-4.7-x86_64)bigstatsr_1.6.3.tar.gz(r-4.6-arm64)bigstatsr_1.6.3.tar.gz(r-4.6-x86_64)
bigstatsr_1.6.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
bigstatsr/json (API)
NEWS

# Install 'bigstatsr' in R:

install.packages('bigstatsr', repos = c('https://privefl.r-universe.dev', 'https://cloud.r-project.org'))

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

Pkgdown/docs site:https://privefl.github.io

Uses libs:

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

On CRAN:

big-data large-matrices memory-mapped-file parallel-computing statistical-methods openblas cpp openmp

11.57 score 180 stars 43 packages 499 scripts 7.6k downloads 7 mentions 48 exports 42 dependencies

Last updated from:99fb318025. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	323
linux-devel-x86_64	OK	312
source / vignettes	OK	322
linux-release-arm64	OK	296
linux-release-x86_64	OK	302
macos-release-arm64	OK	247
macos-release-x86_64	OK	434
macos-oldrel-arm64	OK	189
macos-oldrel-x86_64	OK	474
windows-devel	OK	356
windows-release	OK	343
windows-oldrel	OK	331
wasm-release	OK	176

Exports:add_code256 as_FBM as_scaling_fun asPlotlyText AUC AUCBoot big_apply big_attach big_attachExtdata big_colstats big_copy big_cor big_counts big_cprodMat big_cprodVec big_crossprodSelf big_increment big_parallelize big_prodMat big_prodVec big_randomSVD big_read big_scale big_spLinReg big_spLogReg big_SVD big_tcrossprodSelf big_transpose big_univLinReg big_univLogReg big_write block_size cols_along covar_from_df diag FBM FBM.code256 get_beta nb_cores pasteLoc pcor plot_grid plus rows_along sub_bk theme_bigstatsr typeof without_downcast_warning

Dependencies:bigassertr bigparallelr bit cli codetools cowplot cpp11 doParallel farver ff flock foreach ggplot2 glue gtable isoband iterators labeling lattice lifecycle magrittr Matrix parallelly pillar pkgconfig ps R6 RColorBrewer Rcpp RcppArmadillo RcppEigen RhpcBLASctl rlang rmio RSpectra S7 scales tibble utf8 vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Scaling function creator	as_scaling_fun
Plotly text	asPlotlyText
AUC	AUC AUCBoot
Split-Apply-Combine	big_apply
Standard univariate statistics	big_colstats
Copy as a Filebacked Big Matrix	big_copy
Correlation	big_cor
Counts for class FBM.code256	big_counts
Cross-product with a matrix	big_cprodMat crossprod,FBM,matrix-method crossprod,matrix,FBM-method tcrossprod,FBM,matrix-method tcrossprod,matrix,FBM-method
Cross-product with a vector	big_cprodVec
Crossprod	big_crossprodSelf crossprod,FBM,missing-method
Increment an FBM	big_increment
Split-parApply-Combine	big_parallelize
Product with a matrix	%%,FBM,matrix-method %%,matrix,FBM-method big_prodMat
Product with a vector	big_prodVec
Randomized partial SVD	big_randomSVD
Read a file as FBM	big_read
Some scaling functions	big_scale
Sparse linear regression	big_spLinReg
Sparse logistic regression	big_spLogReg
Partial SVD	big_SVD
Tcrossprod	big_tcrossprodSelf tcrossprod,FBM,missing-method
Transpose an FBM	big_transpose
Column-wise linear regression	big_univLinReg
Column-wise logistic regression	big_univLogReg
Write an FBM to a file	big_write
Determine a correct value for the block.size parameter	block_size
Numeric matrix from data frame	covar_from_df
Class FBM	as_FBM FBM FBM-class FBM_RC
Methods for the FBM class	diag,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.code256	add_code256 FBM.code256 FBM.code256-class FBM.code256_RC
Combine sets of coefficients	get_beta
Get coordinates on plot	pasteLoc
Partial correlation	pcor
Plot method	plot.big_sp_list
Plot method	plot.big_SVD
Plot method	plot.mhtest
Predict method	predict.big_sp
Predict method	predict.big_sp_list
Scores of PCA	predict.big_SVD
Predict method	predict.mhtest
Replace extension '.bk'	sub_bk
Summary method	summary.big_sp_list
Theme ggplot2	theme_bigstatsr
Temporarily disable downcast warning	without_downcast_warning