The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, correlation lacks validity when
applied to relative data, including count data generated by next-generation
sequencing. This package implements several metrics for proportionality, including
phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and
rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>]. This package also
implements several metrics for differential proportionality. Unlike correlation,
these measures give the same result for both relative and absolute data.
ALDEx2, Biobase, cccrm, compositions, data.table, datasets,
grid, ggdendro, knitr, limma, plotly, reshape2, rgl, rmarkdown,
SDMTools, testthat

ALDEx2, Biobase, cccrm, compositions, data.table, datasets,
grid, ggdendro, knitr, limma, plotly, reshape2, rgl, rmarkdown,
SDMTools, testthat, vegan

c(
person("Thomas", "Quinn", email = "contacttomquinn@gmail.com", role = c("aut", "cre")),
person("David", "Lovell", email = "david.lovell@qut.edu.au", role = "aut"),
person("Ionas", "Erb", email = "ionas.erb@crg.eu", role = "aut"),
person("Anders", "Bilgrau", email = "anders.ellern.bilgrau@gmail.com", role = "ctb"),
person("Greg", "Gloor", email = "ggloor@uwo.ca", role = "ctb"),
person("Ryan", "Moore", email = "rmm1047@gmail.com", role = "ctb")
)
ALDEx2, Biobase, cccrm, compositions, data.table, datasets,
grid, ggdendro, knitr, limma, parallel, plotly, reshape2, rgl,
rmarkdown, SDMTools, testthat, vegan
Thomas Quinn [aut, cre],
David Lovell [aut],
Ionas Erb [aut],
Anders Bilgrau [ctb],
Greg Gloor [ctb],
Ryan Moore [ctb]

Tests of the Proportional Hazards Assumption
Tests of the proportional hazards assumption in the Cox
model: data-driven Neyman type smooth tests and score process based
tests for identifying nonproportional covariates.

Tests of the proportional hazards assumption in the Cox
model: data-driven Neyman type smooth tests and score process based
tests for identifying nonproportional covariates and for global
checks.