Description: By using 'RAINBOWR' (Reliable Association INference By Optimizing Weights with R), users can test multiple SNPs (Single Nucleotide Polymorphisms) simultaneously by kernel-based (SNP-set) methods. This package can also be applied to haplotype-based GWAS (Genome-Wide Association Study). Users can test not only additive effects but also dominance and epistatic effects. In detail, please check our paper on PLOS Computational Biology: Kosuke Hamazaki and Hiroyoshi Iwata (2020) <doi:10.1371/journal.pcbi.1007663>.

Imports: Rcpp, rgl, tcltk, Matrix, cluster, MASS, pbmcapply, optimx,
methods, ape, stringr, pegas, ggplot2, ggtree, scatterpie,
phylobase, haplotypes, ggimage, rrBLUP, expm, parallel, pbapply

Imports: Rcpp, Matrix, cluster, MASS, pbmcapply, optimx, methods, ape,
stringr, pegas, ggplot2, ggtree, scatterpie, phylobase,
haplotypes, rrBLUP, expm, here, htmlwidgets, Rfast

stringr, pegas, rrBLUP, expm, here, htmlwidgets, Rfast, gaston,
Suggests: knitr, rmarkdown, plotly, haplotypes, adegenet, ggplot2,
ggtree, scatterpie, phylobase, furrr, future, progressr,

Title: R Analyzer for Large-Scale Assessments
Authors@R: c(person(given = "Plamen V.",
Author: Plamen V. Mirazchiyski [aut, cre],
Maintainer: Plamen V. Mirazchiyski <plamen.mirazchiyski@ineri.org>
Prepare and analyze data from large-scale assessments and surveys with
complex sampling and assessment design (see 'Rutkowski', 2010
international assessments like 'TIMSS', 'PIRLS' and 'PISA'. A graphical
interface is available for the non-technical user.The package includes
functions to covert the original data from 'SPSS' into 'R' data sets
keeping the user-defined missing values, merge data from different
respondents and/or countries, generate variable dictionaries, modify
data, produce descriptive statistics (percentages, means, percentiles,
benchmarks) and multivariate statistics (correlations, linear
regression, binary logistic regression). The number of supported
studies and analysis types will increase in future.
Imports: data.table, openxlsx, Hmisc, stringr, foreign, gdata, readr,
stringi, shiny, shinydashboard, DT, shinyjs, shinyFiles