README.md

In miceFast: Fast Imputations Using 'Rcpp' and 'Armadillo'

miceFast

Maciej Nasinski pkgdown: https://polkas.github.io/miceFast/index.html

Check the R CRAN for more details

Fast imputations under the object-oriented programming paradigm. Moreover there are offered a few functions built to work with popular R packages such as 'data.table' or 'dplyr'. The biggest improvement in time performance could be achieve for a calculation where a grouping variable have to be used. A single evaluation of a quantitative model for the multiple imputations is another major enhancement. A new major improvement is one of the fastest predictive mean matching in the R world because of presorting and binary search.

Performance benchmarks (check performance_validity.R file at extdata).

Advanced Usage - Vignette

Installation

install.packages('miceFast')

or

# install.packages("devtools")
devtools::install_github("polkas/miceFast")

Recommended to download boosted BLAS library, even x100 faster:

• Windows Users recommended to download MRO MKL: https://mran.microsoft.com/download
• Linux users recommended to download Optimized BLAS (linear algebra) library: sudo apt-get install libopenblas-dev
• Apple vecLib BLAS:

cd /Library/Frameworks/R.framework/Resources/lib
ln -sf /System/Library/Frameworks/Accelerate.framework/Frameworks/vecLib.framework/Versions/Current/libBLAS.dylib libRblas.dylib

Quick Implementation

library(miceFast)

set.seed(1234)
data(air_miss)

# plot NA structure
upset_NA(air_miss, 6)

naive_fill_NA(air_miss)

#Check vigniette for an advance usage
#there is required a thorough examination

#Other packages - popular simple solutions
#Hmisc
data.frame(Map(function(x) Hmisc::impute(x,'random'), air_miss))

#mice
mice::complete(mice::mice(air_miss, printFlag = F))

Quick Reference Table

| Function | Description | |----------------------|----------------------| | new(miceFast) | OOP instance with bunch of methods - check vigniette | | fill_NA() | imputation - lda,lm_pred,lm_bayes,lm_noise | | fill_NA_N() | multiple imputation - pmm,lm_bayes,lm_noise | | VIF() | Variance inflation factor | | naive_fill_NA() | auto imputations | | compare_imp() | comparing imputations | | upset_NA() | visualize NA structure - UpSetR::upset|

Summing up, miceFast offer a relevant reduction of a calculations time for:

• Linear Discriminant Analysis around (x5)
• where a grouping variable have to be used (around x10 depending on data dimensions and number of groups and even more than x100 although compared to data.table only a few k faster or even the same) because of pre-sorting by grouping variable
• multiple imputations is faster around x(a number of multiple imputations) because the core of a model is evaluated only ones.
• Variance inflation factors (VIF) (x5) because the unnecessary linear regression is not evaluated - we need only inverse of X'X
• Predictive mean matching (PMM) (x100) because of pre-sorting and binary search

If you are interested about the procedure of testing performance and validity check performance_validity.R file at the extdata folder.

miceFast documentation built on July 11, 2021, 1:06 a.m.