miga-base 0.7.23.0 → 0.7.25.3

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

@@ -1,57 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/cliopts.R
-\name{enve.cliopts}
-\alias{enve.cliopts}
-\title{Enveomics: Cliopts}
-\usage{
-enve.cliopts(fx, rd_file, positional_arguments, usage, mandatory = c(),
-  vectorize = c(), ignore = c(), number = c(), defaults = list(),
-  o_desc = list(), p_desc = "")
-}
-\arguments{
-\item{fx}{Function for which the interface should be generated.}
-
-\item{rd_file}{(Optional) .Rd file with the standard documentation of 
-the function.}
-
-\item{positional_arguments}{(Optional) Number of \strong{positional} 
-arguments passed to \code{\link[optparse]{parse_args}} 
-(package: \pkg{optparse}).}
-
-\item{usage}{(Optional) Usage passed to \code{\link[optparse]{OptionParser}} 
-(package: \pkg{optparse}).}
-
-\item{mandatory}{Mandatory arguments.}
-
-\item{vectorize}{Arguments of the function to vectorize (comma-delimited).
-If numeric, use also \code{number}.}
-
-\item{ignore}{Arguments of the function to ignore.}
-
-\item{number}{Force these arguments as numerics. Useful for numeric
-vectors (see \code{vectorize}) or arguments with no defaults.}
-
-\item{defaults}{Defaults to use instead of the ones provided by the 
-formals.}
-
-\item{o_desc}{Descriptions of the options. Help from \code{rd} is ignored
-for arguments present in this list.}
-
-\item{p_desc}{Description Description of the function. Help from \code{rd} 
-is ignored for the function description unless this value is an empty string.}
-}
-\value{
-Returns a list with keys: 
-\itemize{
-   \item{\code{options}, a named list with the values for the function's 
-   arguments} 
-   \item{\code{args}, a vector with zero or more strings containing the
-   positional arguments}}
-}
-\description{
-Generates nicely formatted command-line interfaces for functions 
-(\strong{closures} only).
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd

@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{enve.col.alpha}
-\alias{enve.col.alpha}
-\title{Enveomics: Color Alpha}
-\usage{
-enve.col.alpha(col, alpha = 1/2)
-}
-\arguments{
-\item{col}{Color or vector of colors. It can be any value supported by 
-\code{\link[grDevices]{col2rgb}}, such as \code{darkred} or \code{#009988}.}
-
-\item{alpha}{Alpha value to add to the color, from 0 to 1.}
-}
-\value{
-Returns a color or a vector of colors in \emph{hex} notation, 
-including \code{alpha}.
-}
-\description{
-Modify alpha in a color (or vector of colors).
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd

@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/growthcurve.R
-\name{enve.col2alpha}
-\alias{enve.col2alpha}
-\title{Enveomics: Color to Alpha}
-\usage{
-enve.col2alpha(x, alpha)
-}
-\arguments{
-\item{x}{A vector of any value base colors.}
-
-\item{alpha}{Alpha level to set (in the 0-1 range).}
-}
-\description{
-Takes a vector of colors and sets the alpha.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd

@@ -1,39 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/df2dist.R
-\name{enve.df2dist}
-\alias{enve.df2dist}
-\title{Enveomics: Data Frame to Dist}
-\usage{
-enve.df2dist(x, obj1.index = 1, obj2.index = 2, dist.index = 3,
-  default.d = NA, max.sim = 0)
-}
-\arguments{
-\item{x}{A dataframe (or coercible object) with at least three columns:
-\enumerate{
-   \item ID of the object 1, 
-   \item ID of the object 2, and 
-   \item distance between the two objects.}}
-
-\item{obj1.index}{Index of the column containing the ID of the object 1.}
-
-\item{obj2.index}{Index of the column containing the ID of the object 2.}
-
-\item{dist.index}{Index of the column containing the distance.}
-
-\item{default.d}{Default value (for missing values).}
-
-\item{max.sim}{If not zero, assumes that the values are similarity
-(not distance) and this is the maximum similarity (corresponding to 
-distance 0). Applies transformation: 
-\eqn{distance = (max.sim - values)/max.sim.}}
-}
-\value{
-Returns a \strong{dist} object.
-}
-\description{
-Transform a dataframe (or coercible object, like a table) into a
-\strong{dist} object.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd

@@ -1,38 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/df2dist.R
-\name{enve.df2dist.group}
-\alias{enve.df2dist.group}
-\title{Enveomics: Data Frame to Dist (Group)}
-\usage{
-enve.df2dist.group(x, obj1.index = 1, obj2.index = 2, dist.index = 3,
-  summary = median, empty.rm = TRUE)
-}
-\arguments{
-\item{x}{A dataframe (or coercible object) with at least three columns:
-\enumerate{
-   \item ID of the object 1, 
-   \item ID of the object 2, and 
-   \item distance between the two objects.}}
-
-\item{obj1.index}{Index of the column containing the ID of the object 1.}
-
-\item{obj2.index}{Index of the column containing the ID of the object 2.}
-
-\item{dist.index}{Index of the column containing the distance.}
-
-\item{summary}{Function summarizing the different distances between the 
-two objects.}
-
-\item{empty.rm}{Remove rows with empty or \code{NA} groups.}
-}
-\value{
-Returns a \strong{dist} object.
-}
-\description{
-Transform a dataframe (or coercible object, like a table) into a 
-\strong{dist} object, where there are 1 or more distances between each pair 
-of objects.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd

@@ -1,40 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/df2dist.R
-\name{enve.df2dist.list}
-\alias{enve.df2dist.list}
-\title{Enveomics: Data Frame to Dist (List)}
-\usage{
-enve.df2dist.list(x, groups, obj1.index = 1, obj2.index = 2,
-  dist.index = 3, empty.rm = TRUE, ...)
-}
-\arguments{
-\item{x}{A dataframe (or coercible object) with at least three columns:
-\enumerate{
-   \item ID of the object 1, 
-   \item ID of the object 2, and 
-   \item distance between the two objects.}}
-
-\item{groups}{Named array where the IDs correspond to the object IDs,
-and the values correspond to the group.}
-
-\item{obj1.index}{Index of the column containing the ID of the object 1.}
-
-\item{obj2.index}{Index of the column containing the ID of the object 2.}
-
-\item{dist.index}{Index of the column containing the distance.}
-
-\item{empty.rm}{Remove incomplete matrices.}
-
-\item{...}{Any other parameters supported by
-\code{\link{enve.df2dist.group}}.}
-}
-\value{
-Returns a \strong{list} of \strong{dist} objects.
-}
-\description{
-Transform a dataframe (or coercible object, like a table)
-into a \strong{dist} object.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,67 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/growthcurve.R
-\name{enve.growthcurve}
-\alias{enve.growthcurve}
-\title{Enveomics: Growth Curve}
-\usage{
-enve.growthcurve(x, times = 1:nrow(x), triplicates = FALSE, design,
-  new.times = seq(min(times), max(times), length.out = length(times) *
-  10), level = 0.95, interval = c("confidence", "prediction"),
-  plot = TRUE, FUN = function(t, K, r, P0) K * P0 * exp(r * t)/(K + P0
-  * (exp(r * t) - 1)), nls.opt = list(), ...)
-}
-\arguments{
-\item{x}{Data frame (or coercible) containing the observed growth data
-(e.g., O.D. values). Each column is an independent growth curve and each
-row is a time point. \code{NA}'s are allowed.}
-
-\item{times}{Vector with the times at which each row was taken. By default,
-all rows are assumed to be part of constantly periodic measurements.}
-
-\item{triplicates}{If \code{TRUE}, the columns are assumed to be sorted by
-sample with three replicates by sample. It requires a number of columns 
-multiple of 3.}
-
-\item{design}{Experimental design of the data. An \strong{array} of mode list
-with sample names as index and the list of column names in each sample as 
-the values. By default, each column is assumed to be an independent sample
-if \code{triplicates} is \code{FALSE}, or every three columns are assumed 
-to be a sample if \code{triplicates} is \code{TRUE}. In the latter case, 
-samples are simply numbered.}
-
-\item{new.times}{Values of time for the fitted curve.}
-
-\item{level}{Confidence (or prediction) interval in the fitted curve.}
-
-\item{interval}{Type of interval to be calculated for the fitted curve.}
-
-\item{plot}{Should the growth curve be plotted?}
-
-\item{FUN}{Function to fit. By default: logistic growth with paramenters
-\code{K}: carrying capacity, 
-\code{r}: intrinsic growth rate, and
-\code{P0}: Initial population.}
-
-\item{nls.opt}{Any additional options passed to \code{nls}.}
-
-\item{...}{Any additional parameters to be passed to 
-\code{plot.enve.GrowthCurve}.}
-}
-\value{
-Returns an \code{\link{enve.GrowthCurve}} object.
-}
-\description{
-Calculates growth curves using the logistic growth function.
-}
-\examples{
-# Load data
-data("growth.curves", package="enveomics.R", envir=environment())
-# Generate growth curves with different colors
-g <- enve.growthcurve(growth.curves[,-1], growth.curves[,1], triplicates=TRUE)
-# Generate black-and-white growth curves with different symbols
-plot(g, pch=15:17, col="black", band.density=45, band.angle=c(-45,45,0))
-
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd

@@ -1,37 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/autoprune.R
-\name{enve.prune.dist}
-\alias{enve.prune.dist}
-\title{Enveomics: Prune Dist}
-\usage{
-enve.prune.dist(t, dist.quantile = 0.25, min_dist, quiet = FALSE,
-  max_iters = 100, min_nodes_random = 40000, random_nodes_frx = 1)
-}
-\arguments{
-\item{t}{A \strong{phylo} object or a path to the Newick file.}
-
-\item{dist.quantile}{The quantile of edge lengths.}
-
-\item{min_dist}{The minimum distance to allow between two tips.
-If not set, \code{dist.quantile} is used instead to calculate it.}
-
-\item{quiet}{Boolean indicating if the function must run without output.}
-
-\item{max_iters}{Maximum number of iterations.}
-
-\item{min_nodes_random}{Minimum number of nodes to trigger \emph{tip-pairs} nodes sampling. 
-This sampling is less reproducible and more computationally expensive,
-but it's the only solution if the cophenetic matrix exceeds \code{2^31-1} 
-entries; above that, it cannot be represented in R.}
-
-\item{random_nodes_frx}{Fraction of the nodes to be sampled if more than \code{min_nodes_random}.}
-}
-\value{
-Returns a pruned \strong{phylo} object.
-}
-\description{
-Automatically prunes a tree, to keep representatives of each clade.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,122 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot.R
-\name{enve.recplot}
-\alias{enve.recplot}
-\title{Enveomics: Recruitment Plots}
-\usage{
-enve.recplot(prefix, id.min = NULL, id.max = NULL, id.binsize = NULL,
-  id.splines = 0, id.metric = "id", id.summary = "sum",
-  pos.min = 1, pos.max = NULL, pos.binsize = 1000, pos.splines = 0,
-  rec.col1 = "white", rec.col2 = "black", main = NULL,
-  contig.col = grey(0.85), ret.recplot = FALSE, ret.hist = FALSE,
-  ret.mode = FALSE, id.cutoff = NULL, verbose = TRUE, ...)
-}
-\arguments{
-\item{prefix}{Path to the prefix of the BlastTab.catsbj.pl output files. At
-least the files \strong{.rec} and \strong{.lim} must exist with this prefix.}
-
-\item{id.min}{Minimum identity to be considered. By default, the minimum detected
-identity. This value is a percentage.}
-
-\item{id.max}{Maximum identity to be considered. By default, 100\%.}
-
-\item{id.binsize}{Size of the identity bins (vertical histograms). By default, 0.1 for
-identity metrics and 5 for bit score.}
-
-\item{id.splines}{Smoothing parameter for the splines in the identity histogram. Zero (0) for no
-splines. A generally good value is 1/2. If non-zero, requires the \pkg{stats} package.}
-
-\item{id.metric}{Metric of identity to be used (Y-axis). 
-It can be any unambiguous prefix of:
-\itemize{
-\item "identity"
-\item "corrected identity" 
-\item "bit score"}}
-
-\item{id.summary}{Method used to build the identity histogram (Horizontal axis of the right panel).
-It can be any unambiguous prefix of: 
-\itemize{
-\item "sum"
-\item "average" 
-\item "median"
-\item "90\% lower bound"
-\item "90\% upper bound"
-\item "95\% lower bound"
-\item "95\% upper bound" }
-The last four options
-correspond to the upper and lower boundaries of the 90\% and 95\% empirical confidence
-intervals.}
-
-\item{pos.min}{Minimum (leftmost) position in the reference (concatenated) genome (in bp).}
-
-\item{pos.max}{Maximum (rightmost) position in the reference (concatenated) genome (in bp).
-By default: Length of the genome.}
-
-\item{pos.binsize}{Size of the position bins (horizontal histograms) in bp.}
-
-\item{pos.splines}{Smoothing parameter for the splines in the position histogram. Zero (0) for no splines.
-If non-zero, requires the stats package.}
-
-\item{rec.col1}{Lightest color in the recruitment plot.}
-
-\item{rec.col2}{Darkest color in the recruitment plot.}
-
-\item{main}{Title of the plot.}
-
-\item{contig.col}{Color of the Contig boundaries. Set to \code{NA} to ignore Contig boundaries.}
-
-\item{ret.recplot}{Indicates if the matrix of the recruitment plot is to be returned.}
-
-\item{ret.hist}{Ignored, for backwards compatibility.}
-
-\item{ret.mode}{Indicates if the mode of the identity is to be computed. It requires the 
-\pkg{modeest} package.}
-
-\item{id.cutoff}{Minimum identity to consider an alignment as "top". By default, it is 0.95 for the
-identity metrics and 95\% of the best scoring alignment for bit score.}
-
-\item{verbose}{Indicates if the function should report the advance.}
-
-\item{...}{Any additional graphic parameters to be passed to plot for all panels except the
-recruitment plot (lower-left).}
-}
-\value{
-Returns a list with the following elements:
-
-\describe{
-\item{\code{pos.marks}}{Midpoints of the position histogram.}
-\item{\code{id.matrix}}{Midpoints of the identity histogram.}
-\item{\code{recplot}}{Matrix containing the recruitment plot values 
-     (if \code{ret.recplot=TRUE}).}
-\item{\code{id.mean}}{Mean identity.}
-\item{\code{id.median}}{Median identity.}
-\item{\code{id.mode}}{Mode of the identity (if \code{ret.mode=TRUE}). Deprecated.}
-\item{\code{id.hist}}{Values of the identity histogram (if \code{ret.hist=TRUE}).}
-\item{\code{pos.hist.low}}{Values of the position histogram (depth) with "low"
-     identity (i.e., below id.cutoff) (if \code{ret.hist=TRUE}).}
-\item{\code{pos.hist.top}}{Values of the position histogram (depth) with "top"
-     identity (i.e., above id.cutoff) (if \code{ret.hist=TRUE}).}
-\item{\code{id.max}}{Value of \code{id.max}. This is returned because 
-     \code{id.max=NULL} may vary.}
-\item{\code{id.cutoff}}{Value of \code{id.cutoff}. 
-     This is returned because \code{id.cutoff=NULL} may vary.}
-\item{\code{seqdepth.mean.top}}{Average sequencing depth with identity above 
-     \code{id.cutoff}.}
-\item{\code{seqdepth.mean.low}}{Average sequencing depth with identity below 
-     \code{id.cutoff}.} 
-\item{\code{seqdepth.mean.all}}{Average sequencing depth without identity filtering.}
-\item{\code{seqdepth.median.top}}{Median sequencing depth with identity above 
-     \code{id.cutoff}.}
-\item{\code{seqdepth.median.low}}{Median sequencing depth with identity below 
-     \code{id.cutoff}.}
-\item{\code{seqdepth.median.all}}{Median sequencing depth without identity filtering.}
-\item{\code{id.metric}}{Full name of the used identity metric.}
-\item{\code{id.summary}}{Full name of the summary method used to build the identity plot.}}
-}
-\description{
-Produces recruitment plots provided that BlastTab.catsbj.pl has
-been previously executed. Requires the \pkg{gplots} library.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}