designit: Blocking and Randomization for Experimental Design (original) (raw)
Intelligently assign samples to batches in order to reduce batch effects. Batch effects can have a significant impact on data analysis, especially when the assignment of samples to batches coincides with the contrast groups being studied. By defining a batch container and a scoring function that reflects the contrasts, this package allows users to assign samples in a way that minimizes the potential impact of batch effects on the comparison of interest. Among other functionality, we provide an implementation for OSAT score by Yan et al. (2012, <doi:10.1186/1471-2164-13-689>).
| Version: | 0.5.0 |
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| Depends: | R (≥ 4.1.0) |
| Imports: | rlang (≥ 0.4.0), dplyr (≥ 1.0.0), purrr, ggplot2, scales, tibble, tidyr, assertthat, stringr, R6, data.table, stats |
| Suggests: | testthat, roxygen2, pkgdown, knitr, markdown, rmarkdown, gt, bench, OSAT, tidyverse, printr, devtools (≥ 2.0.0), ggpattern, cowplot, bestNormalize, here |
| Published: | 2024-03-21 |
| DOI: | 10.32614/CRAN.package.designit |
| Author: | Iakov I. Davydov  [aut, cre, cph], Juliane Siebourg-Polster [aut, cph], Guido Steiner [aut, cph], Konrad Rudolph [ctb], Jitao David Zhang [aut, cph], Balazs Banfai [aut, cph], F. Hoffman-La Roche [cph, fnd] |
| Maintainer: | Iakov I. Davydov <iakov.davydov at roche.com> |
| BugReports: | https://github.com/BEDApub/designit/issues |
| License: | MIT + file |
| URL: | https://bedapub.github.io/designit/,https://github.com/BEDApub/designit/ |
| NeedsCompilation: | no |
| Materials: | README, NEWS |
| CRAN checks: | designit results |
Documentation:
| Reference manual: | designit.html , <designit.pdf> |
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| Vignettes: | Basic example (source, R code) Using custom shuffle schedule (source, R code) In-vivo study design (source, R code) designit: a flexible engine to generate experiment layouts (source, R code) Nested dimension example (source, R code) Optimizer examples (source, R code) OSAT and scoring functions (source, R code) Plate layouts (source, R code) Shuffling with constraints (source, R code) |
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