miga-base 0.4.3.0 → 0.5.0.0

data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd

@@ -1,26 +1,32 @@
-\name{enve.recplot2.windowDepthThreshold}
-\alias{enve.recplot2.windowDepthThreshold}
-\title{enve recplot2 windowDepthThreshold}
-\description{Identifies the threshold below which windows should be identified as
-variable or absent.}
-\usage{enve.recplot2.windowDepthThreshold(rp, peak, lower.tail = TRUE, 
-    significance = 0.05)}
-\arguments{
-  \item{rp}{Recruitment plot, an `enve.RecPlot2` object.}
-  \item{peak}{Peak, an `enve.RecPlot2.Peak` object. If list, it is assumed to be a
-list of `enve.RecPlot2.Peak` objects, in which case the core peak is
-used (see `enve.recplot2.corePeak`).}
-  \item{lower.tail}{If FALSE, it returns windows significantly above the peak in
-sequencing depth.}
-  \item{significance}{Significance threshold (alpha) to select windows.}
-}
-
-\value{Returns a float. The units are depth if the peaks were estimated in
-linear scale, or log-depth otherwise (`peak$log`).}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.windowDepthThreshold}
+\alias{enve.recplot2.windowDepthThreshold}
+\title{Enveomics: Recruitment Plot (2) Window Depth Threshold}
+\usage{
+enve.recplot2.windowDepthThreshold(rp, peak, lower.tail = TRUE,
+  significance = 0.05)
+}
+\arguments{
+\item{rp}{Recruitment plot, an \code{\link{enve.RecPlot2}} object.}
+
+\item{peak}{Peak, an \code{\link{enve.RecPlot2.Peak}} object. If list, it is assumed to be a
+list of \code{\link{enve.RecPlot2.Peak}} objects, in which case the core peak is
+used (see \code{\link{enve.recplot2.corePeak}}).}
+
+\item{lower.tail}{If \code{FALSE}, it returns windows significantly above the peak in
+sequencing depth.}
+
+\item{significance}{Significance threshold (alpha) to select windows.}
+}
+\value{
+Returns a float. The units are depth if the peaks were estimated in
+linear scale, or log-depth otherwise (\code{peak$log}).
+}
+\description{
+Identifies the threshold below which windows should be identified as
+variable or absent.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.tribs.Rd

@@ -1,44 +1,59 @@
-\name{enve.tribs}
-\alias{enve.tribs}
-\title{enve tribs}
-\description{Subsample any objects in "distance space" to reduce the effect of
-sample-clustering.  This function was originally designed to subsample
-genomes in "phylogenetic distance space", a clear case of strong
-clustering bias in sampling, by Luis M. Rodriguez-R and Michael R
-Weigand.}
-\usage{enve.tribs(dist, selection = labels(dist), replicates = 1000, 
-    summary.fx = median, dist.method = "euclidean", subsamples = seq(0, 
-        1, by = 0.01), dimensions = ceiling(length(selection) * 
-        0.05), metaMDS.opts = list(), threads = 2, verbosity = 1, 
-    points, pre.tribs)}
-\arguments{
-  \item{dist}{Distances as a `dist` object.}
-  \item{selection}{Objects to include in the subsample. By default, all objects are
-selected.}
-  \item{replicates}{Number of replications per point}
-  \item{summary.fx}{Function to summarize the distance distributions in a given replicate. By
-default, the median distance is estimated.}
-  \item{dist.method}{Distance method between random points and samples in the transformed
-space. See `dist`.}
-  \item{subsamples}{Subsampling fractions}
-  \item{dimensions}{Dimensions to use in the NMDS. By default, 5\% of the selection length.}
-  \item{metaMDS.opts}{Any additional options to pass to metaMDS, as `list`.}
-  \item{threads}{Number of threads to use.}
-  \item{verbosity}{Verbosity. Use 0 to run quietly, increase for additional information.}
-  \item{points}{Optional. If passed, the MDS step is skipped and this object is used
-instead.  It can be the `$points` slot of class `metaMDS` (from `vegan`).
-It must be a matrix or matrix-coercible object, with samples as rows and
-dimensions as columns.}
-  \item{pre.tribs}{Optional. If passed, the points are recovered from this object (except if
-`points` is also passed. This should be an `enve.TRIBS` object estimated
-on the same objects (the selection is unimportant).}
-}
-
-\value{Returns an `enve.TRIBS` object.}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{enve.tribs}
+\alias{enve.tribs}
+\title{Enveomics: TRIBS}
+\usage{
+enve.tribs(dist, selection = labels(dist), replicates = 1000,
+  summary.fx = median, dist.method = "euclidean", subsamples = seq(0,
+  1, by = 0.01), dimensions = ceiling(length(selection) * 0.05),
+  metaMDS.opts = list(), threads = 2, verbosity = 1, points,
+  pre.tribs)
+}
+\arguments{
+\item{dist}{Distances as a \code{dist} object.}
+
+\item{selection}{Objects to include in the subsample. By default, all objects are
+selected.}
+
+\item{replicates}{Number of replications per point.}
+
+\item{summary.fx}{Function to summarize the distance distributions in a given replicate. By
+default, the median distance is estimated.}
+
+\item{dist.method}{Distance method between random points and samples in the transformed
+space. See \code{dist}.}
+
+\item{subsamples}{Subsampling fractions.}
+
+\item{dimensions}{Dimensions to use in the NMDS. By default, 5\% of the selection length.}
+
+\item{metaMDS.opts}{Any additional options to pass to metaMDS, as \code{list}.}
+
+\item{threads}{Number of threads to use.}
+
+\item{verbosity}{Verbosity. Use 0 to run quietly, increase for additional information.}
+
+\item{points}{Optional. If passed, the MDS step is skipped and this object is used
+instead.  It can be the \code{$points} slot of class \code{metaMDS} 
+(from \code{vegan}).
+It must be a matrix or matrix-coercible object, with samples as rows and
+dimensions as columns.}
+
+\item{pre.tribs}{Optional. If passed, the points are recovered from this object (except if
+\code{points} is also passed. This should be an \code{\link{enve.TRIBS}} object 
+estimated on the same objects (the selection is unimportant).}
+}
+\value{
+Returns an \code{\link{enve.TRIBS}} object.
+}
+\description{
+Subsample any objects in "distance space" to reduce the effect of
+sample-clustering. This function was originally designed to subsample
+genomes in "phylogenetic distance space", a clear case of strong
+clustering bias in sampling, by Luis M. Rodriguez-R and Michael R
+Weigand.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd

@@ -1,21 +1,28 @@
-\name{enve.tribs.test}
-\alias{enve.tribs.test}
-\title{enve tribs test}
-\description{Estimates the empirical difference between all the distances in a set of
-objects and a subset, together with its statistical significance.}
-\usage{enve.tribs.test(dist, selection, bins = 50, ...)}
-\arguments{
-  \item{dist}{Distances as `dist` object.}
-  \item{selection}{Selection defining the subset.}
-  \item{bins}{Number of bins to evaluate in the range of distances.}
-  \item{\dots}{Any other parameters supported by `enve.tribs`, except `subsamples`.}
-}
-
-\value{Returns an `enve.TRIBStest` object.}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{enve.tribs.test}
+\alias{enve.tribs.test}
+\title{Enveomics: TRIBS Test}
+\usage{
+enve.tribs.test(dist, selection, bins = 50, ...)
+}
+\arguments{
+\item{dist}{Distances as \code{dist} object.}
+
+\item{selection}{Selection defining the subset.}
+
+\item{bins}{Number of bins to evaluate in the range of distances.}
+
+\item{...}{Any other parameters supported by \code{\link{enve.tribs}}, 
+except \code{subsamples}.}
+}
+\value{
+Returns an \code{\link{enve.TRIBStest}} object.
+}
+\description{
+Estimates the empirical difference between all the distances in a set of
+objects and a subset, together with its statistical significance.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.truncate.Rd

@@ -1,22 +1,27 @@
-\name{enve.truncate}
-\alias{enve.truncate}
-\title{enve truncate}
-\description{Removes the `n` highest and lowest values from a vector, and applies a
-summary function. The value of `n` is determined such that the central
-range is used, corresponding to the `f` fraction of values.}
-\usage{enve.truncate(x, f = 0.95, FUN = mean)}
-\arguments{
-  \item{x}{A vector of numbers.}
-  \item{f}{The fraction of values to retain.}
-  \item{FUN}{Summary function to apply to the vectors. To obtain the truncated
-vector itself, use `c`.}
-}
-
-\value{Returns the summary (`FUN`) of the truncated vector.}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{enve.truncate}
+\alias{enve.truncate}
+\title{Enveomics: Truncate}
+\usage{
+enve.truncate(x, f = 0.95, FUN = mean)
+}
+\arguments{
+\item{x}{A vector of numbers.}
+
+\item{f}{The fraction of values to retain.}
+
+\item{FUN}{Summary function to apply to the vectors. To obtain the 
+truncated vector itself, use \code{c}.}
+}
+\value{
+Returns the summary \code{(FUN)} of the truncated vector.
+}
+\description{
+Removes the \code{n} highest and lowest values from a vector, and applies
+summary function. The value of \code{n} is determined such that the central
+range is used, corresponding to the \code{f} fraction of values.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd

@@ -1,43 +1,63 @@
-\name{plot.enve.GrowthCurve}
-\alias{plot.enve.GrowthCurve}
-\title{plot enve GrowthCurve}
-\description{Plots an `enve.GrowthCurve` object.}
-\usage{\method{plot}{enve.GrowthCurve}(x, col, pt.alpha = 0.9, ln.alpha = 1, ln.lwd = 1, 
-    ln.lty = 1, band.alpha = 0.4, band.density = NULL, band.angle = 45, 
-    xp.alpha = 0.5, xp.lwd = 1, xp.lty = 1, pch = 19, new = TRUE, 
-    legend = new, add.params = FALSE, ...)}
-\arguments{
-  \item{x}{`enve.GrowthCurve` object to plot.}
-  \item{col}{Base colors to use for the different samples. Can be recycled. By
-default, grey for one sample or rainbow colors for more than one.}
-  \item{pt.alpha}{Color alpha for the observed data points, using `col` as a base.}
-  \item{ln.alpha}{Color alpha for the fitted growth curve, using `col` as a base.}
-  \item{ln.lwd}{Line width for the fitted curve.}
-  \item{ln.lty}{Line type for the fitted curve.}
-  \item{band.alpha}{Color alpha for the confidence interval band of the fitted growth curve,
-using `col` as a base.}
-  \item{band.density}{Density of the filling pattern in the interval band. If NULL, a solid
-color is used.}
-  \item{band.angle}{Angle of the density filling pattern in the interval band. Ignored if
-`band.density` is NULL.}
-  \item{xp.alpha}{Color alpha for the line connecting individual experiments, using `col`
-as a base.}
-  \item{xp.lwd}{Width of line for the experiments.}
-  \item{xp.lty}{Type of line for the experiments.}
-  \item{pch}{Point character for observed data points.}
-  \item{new}{Should a new plot be generated? If FALSE, the existing canvas is used.}
-  \item{legend}{Should the plot include a legend? If FALSE, no legend is added. If TRUE,
-a legend is added in the bottom-right corner. Otherwise, a legend is
-added in the position specified as `xy.coords`. }
-  \item{add.params}{Should the legend include the parameters of the fitted model?}
-  \item{\dots}{Any other graphic parameters.}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/growthcurve.R
+\name{plot.enve.GrowthCurve}
+\alias{plot.enve.GrowthCurve}
+\title{Enveomics: Plot of Growth Curve}
+\usage{
+\method{plot}{enve.GrowthCurve}(x, col, pt.alpha = 0.9, ln.alpha = 1,
+  ln.lwd = 1, ln.lty = 1, band.alpha = 0.4, band.density = NULL,
+  band.angle = 45, xp.alpha = 0.5, xp.lwd = 1, xp.lty = 1,
+  pch = 19, new = TRUE, legend = new, add.params = FALSE, ...)
+}
+\arguments{
+\item{x}{An \code{\link{enve.GrowthCurve}} object to plot.}
+
+\item{col}{Base colors to use for the different samples. Can be recycled.
+By default, grey for one sample or rainbow colors for more than one.}
+
+\item{pt.alpha}{Color alpha for the observed data points, using \code{col}
+as a base.}
+
+\item{ln.alpha}{Color alpha for the fitted growth curve, using \code{col}
+as a base.}
+
+\item{ln.lwd}{Line width for the fitted curve.}
+
+\item{ln.lty}{Line type for the fitted curve.}
+
+\item{band.alpha}{Color alpha for the confidence interval band of the 
+fitted growth curve, using \code{col} as a base.}
+
+\item{band.density}{Density of the filling pattern in the interval band.
+If \code{NULL}, a solid color is used.}
+
+\item{band.angle}{Angle of the density filling pattern in the interval 
+band. Ignored if \code{band.density} is \code{NULL}.}
+
+\item{xp.alpha}{Color alpha for the line connecting individual experiments,
+using \code{col} as a base.}
+
+\item{xp.lwd}{Width of line for the experiments.}
+
+\item{xp.lty}{Type of line for the experiments.}
+
+\item{pch}{Point character for observed data points.}
+
+\item{new}{Should a new plot be generated? If \code{FALSE}, the existing
+canvas is used.}
+
+\item{legend}{Should the plot include a legend? If \code{FALSE}, no legend
+is added. If \code{TRUE}, a legend is added in the bottom-right corner.
+Otherwise, a legend is added in the position specified as \code{xy.coords}.}
+
+\item{add.params}{Should the legend include the parameters of the fitted 
+model?}
+
+\item{...}{Any other graphic parameters.}
+}
+\description{
+Plots an \code{\link{enve.GrowthCurve}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd

@@ -1,29 +1,38 @@
-\name{plot.enve.TRIBS}
-\alias{plot.enve.TRIBS}
-\title{plot enve TRIBS}
-\description{Plot an `enve.TRIBS` object.}
-\usage{\method{plot}{enve.TRIBS}(x, new = TRUE, type = c("boxplot", "points"), 
-    col = "#00000044", pt.cex = 1/2, pt.pch = 19, pt.col = col, 
-    ln.col = col, ...)}
-\arguments{
-  \item{x}{`enve.TRIBS` object to plot.}
-  \item{new}{Should a new canvas be drawn?}
-  \item{type}{Type of plot. The 'points' plot shows all the replicates, the 'boxplot'
-plot represents the values found by `boxplot.stats` as areas, and plots
-the outliers as points.}
-  \item{col}{Color of the areas and/or the points.}
-  \item{pt.cex}{Size of the points.}
-  \item{pt.pch}{Points character.}
-  \item{pt.col}{Color of the points.}
-  \item{ln.col}{Color of the lines.}
-  \item{\dots}{Any additional parameters supported by `plot`.}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{plot.enve.TRIBS}
+\alias{plot.enve.TRIBS}
+\title{Enveomics: TRIBS Plot}
+\usage{
+\method{plot}{enve.TRIBS}(x, new = TRUE, type = c("boxplot", "points"),
+  col = "#00000044", pt.cex = 1/2, pt.pch = 19, pt.col = col,
+  ln.col = col, ...)
+}
+\arguments{
+\item{x}{\code{\link{enve.TRIBS}} object to plot.}
+
+\item{new}{Should a new canvas be drawn?}
+
+\item{type}{Type of plot. The \strong{points} plot shows all the replicates, the 
+\strong{boxplot} plot represents the values found by
+\code{\link[grDevices]{boxplot.stats}}.
+as areas, and plots the outliers as points.}
+
+\item{col}{Color of the areas and/or the points.}
+
+\item{pt.cex}{Size of the points.}
+
+\item{pt.pch}{Points character.}
+
+\item{pt.col}{Color of the points.}
+
+\item{ln.col}{Color of the lines.}
+
+\item{...}{Any additional parameters supported by \code{plot}.}
+}
+\description{
+Plot an \code{\link{enve.TRIBS}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd

@@ -1,30 +1,38 @@
-\name{plot.enve.TRIBStest}
-\alias{plot.enve.TRIBStest}
-\title{plot enve TRIBStest}
-\description{Plots an `enve.TRIBStest` object.}
-\usage{\method{plot}{enve.TRIBStest}(x, type = c("overlap", "difference"), col = "#00000044", 
-    col1 = col, col2 = "#44001144", ylab = "Probability", xlim = range(attr(x, 
-        "dist.mids")), ylim = c(0, max(c(attr(x, "all.dist"), 
-        attr(x, "sel.dist")))), ...)}
-\arguments{
-  \item{x}{`enve.TRIBStest` object to plot.}
-  \item{type}{What to plot. 'overlap' generates a plot of the two contrasting empirical
-PDFs (to compare against each other), 'difference' produces a plot of the
-differences between the empirical PDFs (to compare against zero).}
-  \item{col}{Main color of the plot if type='difference'.}
-  \item{col1}{First color of the plot if type='overlap'.}
-  \item{col2}{Second color of the plot if type='overlap'.}
-  \item{ylab}{Y-axis label.}
-  \item{xlim}{X-axis limits.}
-  \item{ylim}{Y-axis limits.}
-  \item{\dots}{Any other graphical arguments.}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{plot.enve.TRIBStest}
+\alias{plot.enve.TRIBStest}
+\title{Enveomics: TRIBS Plot Test}
+\usage{
+\method{plot}{enve.TRIBStest}(x, type = c("overlap", "difference"),
+  col = "#00000044", col1 = col, col2 = "#44001144",
+  ylab = "Probability", xlim = range(attr(x, "dist.mids")),
+  ylim = c(0, max(c(attr(x, "all.dist"), attr(x, "sel.dist")))), ...)
+}
+\arguments{
+\item{x}{\code{\link{enve.TRIBStest}} object to plot.}
+
+\item{type}{What to plot. \code{overlap} generates a plot of the two contrasting empirical
+PDFs (to compare against each other), \code{difference} produces a plot of the
+differences between the empirical PDFs (to compare against zero).}
+
+\item{col}{Main color of the plot if type=\code{difference}.}
+
+\item{col1}{First color of the plot if type=\code{overlap}.}
+
+\item{col2}{Second color of the plot if type=\code{overlap}.}
+
+\item{ylab}{Y-axis label.}
+
+\item{xlim}{X-axis limits.}
+
+\item{ylim}{Y-axis limits.}
+
+\item{...}{Any other graphical arguments.}
+}
+\description{
+Plots an \code{\link{enve.TRIBStest}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}