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A set of tests for compositional pathologies. Tests for coherence of correlations with aIc.coherent() as suggested by (Erb et al. (2020) <doi:10.1016/j.acags.2020.100026>), compositional dominance of distance with aIc.dominant(), compositional perturbation invariance with aIc.perturb() as suggested by (Aitchison (1992) <doi:10.1007/BF00891269>) and singularity of the covariation matrix with aIc.singular(). Currently tests five data transformations: prop, clr, TMM, TMMwsp, and RLE from the R packages 'ALDEx2', 'edgeR' and 'DESeq2' (Fernandes et al (2014) <doi:10.1186/2049-2618-2-15>, Anders et al. (2013)<doi:10.1038/nprot.2013.099>).
| Version: | 1.0 |
| Depends: | R (≥ 3.5.0) |
| Imports: | matrixcalc, zCompositions, shiny, edgeR, ALDEx2, vegan |
| Suggests: | BiocStyle, knitr, rmarkdown |
| Published: | 2022-10-04 |
| Author: | Greg Gloor |
| Maintainer: | Greg Gloor <ggloor at uwo.ca> |
| BugReports: | https://github.com/ggloor/aIc/issues |
| License: | GPL (≥ 3) |
| URL: | https://github.com/ggloor/aIc |
| NeedsCompilation: | no |
| CRAN checks: | aIc results |
| Reference manual: | aIc.pdf |
| Vignettes: |
aIc: am I compositional? |
| Package source: | aIc_1.0.tar.gz |
| Windows binaries: | r-devel: aIc_1.0.zip, r-release: aIc_1.0.zip, r-oldrel: aIc_1.0.zip |
| macOS binaries: | r-release (arm64): aIc_1.0.tgz, r-oldrel (arm64): aIc_1.0.tgz, r-release (x86_64): aIc_1.0.tgz, r-oldrel (x86_64): aIc_1.0.tgz |
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