all: A list of most parameters.
In propr: Calculating Proportionality Between Vectors of Compositional Data

A list of most parameters.

`counts`	A data.frame or matrix. A "count matrix" with subjects as rows and features as columns. Note that this matrix does not necessarily have to contain counts.
`metric`	A character string. The proportionality metric to calculate. Choose from "rho", "phi", or "phs".
`ivar`	A numeric scalar. Specifies reference feature(s) for additive log-ratio transformation. The argument will also accept feature name(s) instead of the index position(s). Set to "iqlr" to use inter-quartile log-ratio transformation. Ignore to use centered log-ratio transformation.
`select`	Optional. Use this to subset the final proportionality matrix without altering the result. Use this argument to rearrange feature order.
`symmetrize`	A logical. If `TRUE`, forces symmetry by reflecting the "lower left triangle".
`alpha`	A double. See vignette for details. Leave missing to skip Box-Cox transformation.
`p`	An integer. The number of permutation cycles.
`...`	Arguments passed to the wrapped method.
`object, x, rho, propr, propd`	A `propr` or `propd` object.
`subset`	Subsets via `object@counts[subset, ]`. Use this argument to rearrange subject order. For backwards compatibility.
`i`	Operation used for the subset indexing. Select from "==", "=", ">", ">=", "<", "<=", "!=", or "all". For backwards compatibility.
`j`	Provide a numeric value to which to compare the proportionality measures in the `@matrix` slot. For backwards compatibility.
`tiny`	A logical scalar. Toggles whether to pass the indexed result through `simplify`. For backwards compatibility.
`group`	A character vector. Group or sub-group memberships, ordered according to the row names in `counts`.
`weighted`	A boolean. Toggles whether to calculate theta using `limma::voom` weights.
`cutoff`	For `updateCutoffs`, a numeric vector. this argument provides the FDR cutoffs to test. For graph functions, a numeric scalar. This argument indicates the maximum theta to include in the figure. For graph functions, a large integer will instead retrieve the top N pairs as ranked by theta.
`what`	A character string. The theta type to set active.
`moderated`	For `updateF`, a boolean. Toggles whether to calculate a moderated F-statistic.
`ncores`	An integer. The number of parallel cores to use.
`y`	Missing. Ignore. Leftover from the generic method definition.
`prompt`	A logical scalar. Set to `FALSE` to disable the courtesy prompt when working with big data.
`plotly`	A logical scalar. Set to `TRUE` to produce a dynamic plot using the `plotly` package.
`k`	An integer. For `propr` methods, the number of co-clusters (where all pairs receive a specified color if and only if both members belong to same the cluster). For `propd` methods, the maximum number of PALs to index when calculating `pals` in the network.
`col1, col2`	A character vector. Specifies which nodes to color `red` or `blue`, respectively.
`d3`	A boolean. Use `rgl` to plot 3D network.
`include`	This argument indicates which features by name should belong to a pair for that pair to get included in the results. Subset performed by `Partner %in% subset \| Pair %in% subset`.
`or`	A boolean. If `FALSE`, `include` subsets by `Partner %in% subset & Pair %in% subset`.
`clean`	A boolean. Toggles whether to remove pairs with "Bridged" or "Missing" PALs. Used by `geyser`, `bowtie`, and `gemini`.
`plotSkip`	A boolean. Toggles whether to build the network graph without plotting it. Used by `pals`.