miga-base 1.2.15.1 → 1.2.15.3

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

@@ -1,47 +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

@@ -1,75 +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.prefscore.Rd

@@ -1,50 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/prefscore.R
-\name{enve.prefscore}
-\alias{enve.prefscore}
-\title{Enveomics: Pref Score}
-\usage{
-enve.prefscore(
-  x,
-  set,
-  ignore = NULL,
-  signif.thr,
-  plot = TRUE,
-  col.above = rgb(148, 17, 0, maxColorValue = 255),
-  col.equal = rgb(189, 189, 189, maxColorValue = 255),
-  col.below = rgb(47, 84, 150, maxColorValue = 255),
-  ...
-)
-}
-\arguments{
-\item{x}{Occupancy matrix (logical or numeric binary) with species as rows and samples
-as columns}
-
-\item{set}{Vector indicating samples in the test set. It can be any selection vector:
-boolean (same length as the number of columns in \code{x}), or numeric or
-character vector with indexes of the \code{x} columns.}
-
-\item{ignore}{Vector indicating species to ignore. It can be any selection vector with
-respect to the rows in \code{x} (see \code{set}).}
-
-\item{signif.thr}{Absolute value of the significance threshold}
-
-\item{plot}{Indicates if a plot should be generated}
-
-\item{col.above}{Color for points significantly above zero}
-
-\item{col.equal}{Color for points not significantly different from zero}
-
-\item{col.below}{Color for points significantly below zero}
-
-\item{...}{Any additional parameters supported by \code{plot}}
-}
-\value{
-Returns a named vector of preference scores.
-}
-\description{
-Estimate preference score of species based on occupancy in biased sample sets
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,44 +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

@@ -1,139 +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]
-}

data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd

@@ -1,45 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\docType{class}
-\name{enve.RecPlot2-class}
-\alias{enve.RecPlot2-class}
-\alias{enve.RecPlot2}
-\title{Enveomics: Recruitment Plot (2) - S4 Class}
-\description{
-Enve-omics representation of Recruitment plots. This object can
-be produced by \code{\link{enve.recplot2}} and supports S4 method plot.
-}
-\section{Slots}{
-
-\describe{
-\item{\code{counts}}{\code{(matrix)} Counts as a two-dimensional histogram.}
-
-\item{\code{pos.counts.in}}{\code{(numeric)} Counts of in-group hits per position bin.}
-
-\item{\code{pos.counts.out}}{\code{(numeric)} Counts of out-group hits per position bin.}
-
-\item{\code{id.counts}}{\code{(numeric)} Counts per ID bin.}
-
-\item{\code{id.breaks}}{\code{(numeric)} Breaks of identity bins.}
-
-\item{\code{pos.breaks}}{\code{(numeric)} Breaks of position bins.}
-
-\item{\code{pos.names}}{\code{(character)} Names of the position bins.}
-
-\item{\code{seq.breaks}}{\code{(numeric)} Breaks of input sequences.}
-
-\item{\code{peaks}}{\code{(list)} Peaks identified in the recplot.
-Limits of the subject sequences after concatenation.}
-
-\item{\code{seq.names}}{\code{(character}) Names of the subject sequences.}
-
-\item{\code{id.metric}}{\code{(character}) Metric used as 'identity'.}
-
-\item{\code{id.ingroup}}{\code{(logical}) Identity bins considered in-group.}
-
-\item{\code{call}}{\code{(call)} Call producing this object.}
-}}
-
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2.ANIr}
-\alias{enve.recplot2.ANIr}
-\title{Enveomics: Recruitment Plot (2) ANI Estimate}
-\usage{
-enve.recplot2.ANIr(x, range = c(0, Inf))
-}
-\arguments{
-\item{x}{\code{\link{enve.RecPlot2}} object.}
-
-\item{range}{Range of identities to be considered. By default, the full range
-is used (note that the upper boundary is \code{Inf} and not 100 because
-recruitment plots can also be built with bit-scores). To use only
-intra-population matches (with identities), use c(95,100). To use only
-inter-population values, use c(0,95).}
-}
-\description{
-Estimate the Average Nucleotide Identity from reads (ANIr) from a
-recruitment plot.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,77 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2}
-\alias{enve.recplot2}
-\title{Enveomics: Recruitment Plot (2)}
-\usage{
-enve.recplot2(
-  prefix,
-  plot = TRUE,
-  pos.breaks = 1000,
-  pos.breaks.tsv = NA,
-  id.breaks = 60,
-  id.free.range = FALSE,
-  id.metric = c("identity", "corrected identity", "bit score"),
-  id.summary = sum,
-  id.cutoff = 95,
-  threads = 2,
-  verbose = TRUE,
-  ...
-)
-}
-\arguments{
-\item{prefix}{Path to the prefix of the \code{BlastTab.catsbj.pl} output files. At
-least the files .rec and .lim must exist with this prefix.}
-
-\item{plot}{Should the object be plotted?}
-
-\item{pos.breaks}{Breaks in the positions histogram. It can also be a vector of break
-points, and values outside the range are ignored. If zero (0), it
-uses the sequence breaks as defined in the .lim file, which means
-one bin per contig (or gene, if the mapping is agains genes). Ignored
-if `pos.breaks.tsv` is passed.}
-
-\item{pos.breaks.tsv}{Path to a list of (absolute) coordinates to use as position breaks.
-This tab-delimited file can be produced by \code{GFF.catsbj.pl}, and it
-must contain at least one column: coordinates of the break positions of
-each position bin. If it has a second column, this is used as the name
-of the position bin that ends at the given coordinate (the first row is
-ignored). Any additional columns are currently ignored. If \code{NA},
-position bins are determined by \code{pos.breaks}.}
-
-\item{id.breaks}{Breaks in the identity histogram. It can also be a vector of break
-points, and values outside the range are ignored.}
-
-\item{id.free.range}{Indicates that the range should be freely set from the observed
-values. Otherwise, 70-100\% is included in the identity histogram
-(default).}
-
-\item{id.metric}{Metric of identity to be used (Y-axis). Corrected identity is only
-supported if the original BLAST file included sequence lengths.}
-
-\item{id.summary}{Function summarizing the identity bins. Other recommended options
-include: \code{median} to estimate the median instead of total bins, and
-\code{function(x) mlv(x,method='parzen')$M} to estimate the mode.}
-
-\item{id.cutoff}{Cutoff of identity metric above which the hits are considered
-\code{in-group}. The 95\% identity corresponds to the expectation of
-ANI<95\% within species.}
-
-\item{threads}{Number of threads to use.}
-
-\item{verbose}{Indicates if the function should report the advance.}
-
-\item{...}{Any additional parameters supported by \code{\link{plot.enve.RecPlot2}}.}
-}
-\value{
-Returns an object of class \code{\link{enve.RecPlot2}}.
-}
-\description{
-Produces recruitment plots provided that \code{BlastTab.catsbj.pl} has
-been previously executed.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-
-Kenji Gerhardt [aut]
-}

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

@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2.__counts}
-\alias{enve.recplot2.__counts}
-\title{Enveomics: Recruitment Plot (2) Internal Ancillary Function}
-\usage{
-enve.recplot2.__counts(x, pos.breaks, id.breaks, rec.idcol)
-}
-\arguments{
-\item{x}{\code{\link{enve.RecPlot2}} object}
-
-\item{pos.breaks}{Position breaks}
-
-\item{id.breaks}{Identity breaks}
-
-\item{rec.idcol}{Identity column to use}
-}
-\description{
-Internal ancillary function (see \code{\link{enve.recplot2}}).
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-
-Kenji Gerhardt [aut]
-}

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

@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2.__peakHist}
-\alias{enve.recplot2.__peakHist}
-\title{Enveomics: Recruitment Plot (2) Peak S4 Class - Internal Ancillary Function}
-\usage{
-enve.recplot2.__peakHist(x, mids, counts = TRUE)
-}
-\arguments{
-\item{x}{\code{\link{enve.RecPlot2.Peak}} object}
-
-\item{mids}{Midpoints}
-
-\item{counts}{Counts}
-}
-\description{
-Internal ancillary function (see \code{\link{enve.RecPlot2.Peak}}).
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2.__whichClosestPeak}
-\alias{enve.recplot2.__whichClosestPeak}
-\title{Enveomics: Recruitment Plot (2) Peak Finder - Internal Ancillary Function}
-\usage{
-enve.recplot2.__whichClosestPeak(peak, peaks)
-}
-\arguments{
-\item{peak}{Query \code{\link{enve.RecPlot2.Peak}} object}
-
-\item{peaks}{list of \code{\link{enve.RecPlot2.Peak}} objects}
-}
-\description{
-Internal ancillary function (see \code{\link{enve.recplot2.findPeaks}}).
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2.changeCutoff}
-\alias{enve.recplot2.changeCutoff}
-\title{Enveomics: Recruitment Plot (2) Change Cutoff}
-\usage{
-enve.recplot2.changeCutoff(rp, new.cutoff = 98)
-}
-\arguments{
-\item{rp}{\code{\link{enve.RecPlot2}} object.}
-
-\item{new.cutoff}{New cutoff to use.}
-}
-\description{
-Change the intra-species cutoff of an existing recruitment plot.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,47 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2.compareIdentities}
-\alias{enve.recplot2.compareIdentities}
-\title{Enveomics: Recruitment Plot (2) Compare Identities}
-\usage{
-enve.recplot2.compareIdentities(
-  x,
-  y,
-  method = "hellinger",
-  smooth.par = NULL,
-  pseudocounts = 0,
-  max.deviation = 0.75
-)
-}
-\arguments{
-\item{x}{First \code{\link{enve.RecPlot2}} object.}
-
-\item{y}{Second \code{\link{enve.RecPlot2}} object.}
-
-\item{method}{Distance method to use. This should be (an unambiguous abbreviation of)
-one of:
-\itemize{
-   \item{"hellinger" (\emph{Hellinger, 1090, doi:10.1515/crll.1909.136.210}),}
-   \item{"bhattacharyya" (\emph{Bhattacharyya, 1943, Bull. Calcutta Math. Soc. 35}),}
-   \item{"kl" or "kullback-leibler" (\emph{Kullback & Leibler, 1951,
-   doi:10.1214/aoms/1177729694}), or}
-   \item{"euclidean"}
-}}
-
-\item{smooth.par}{Smoothing parameter for cubic spline smoothing. Use 0 for no smoothing.
-Use \code{NULL} to automatically determine this value using leave-one-out
-cross-validation (see \code{smooth.spline} parameter \code{spar}).}
-
-\item{pseudocounts}{Smoothing parameter for Laplace smoothing. Use 0 for no smoothing, or
-1 for add-one smoothing.}
-
-\item{max.deviation}{Maximum mean deviation between identity breaks tolerated (as percent
-identity). Difference in number of \code{id.breaks} is never tolerated.}
-}
-\description{
-Compare the distribution of identities between two
-\code{\link{enve.RecPlot2}} objects.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,29 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2.coordinates}
-\alias{enve.recplot2.coordinates}
-\title{Enveomics: Recruitment Plot (2) Coordinates}
-\usage{
-enve.recplot2.coordinates(x, bins)
-}
-\arguments{
-\item{x}{\code{\link{enve.RecPlot2}} object.}
-
-\item{bins}{Vector of selected bins to return. It can be a vector of logical values
-with the same length as \code{x$pos.breaks-1} or a vector of integers. If
-missing, returns the coordinates of all windows.}
-}
-\value{
-Returns a data.frame with five columns: \code{name.from} (character),
-\code{pos.from} (numeric), \code{name.to} (character), \code{pos.to}
-(numeric), and \code{seq.name} (character).
-The first two correspond to sequence and position of the start point of the
-bin. The next two correspond to the sequence and position of the end point of
-the bin. The last one indicates the name of the sequence (if defined).
-}
-\description{
-Returns the sequence name and coordinates of the requested position bins.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2.corePeak}
-\alias{enve.recplot2.corePeak}
-\title{Enveomics: Recruitment Plot (2) Core Peak Finder}
-\usage{
-enve.recplot2.corePeak(x)
-}
-\arguments{
-\item{x}{\code{list} of \code{\link{enve.RecPlot2.Peak}} objects.}
-}
-\description{
-Finds the peak in a list of peaks that is most likely to represent the
-"core genome" of a population.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}