miga-base 1.2.17.1 → 1.2.17.3

data/utils/enveomics/enveomics.R/R/utils.R

@@ -11,15 +11,28 @@
 #'
 #' @author Luis M. Rodriguez-R [aut, cre]
 #'
+#' @examples
+#' # Hexcode for a color by hexcode
+#' enve.col.alpha("#009988", 3/4) # "#009988BF"
+#' 
+#' # Hexcode for a color by name
+#' enve.col.alpha("white", 1/4) # "#FFFFFF3F"
+#'
+#' # Hexcode for a color from other functions
+#' enve.col.alpha(rainbow(3)) # "#FF00007F" "#00FF007F" "#0000FF7F"
 #' @export
 
-enve.col.alpha <- function
-    (col,
-    alpha=1/2
-    ){
+enve.col.alpha <- function(col, alpha = 1/2) {
   return(
-    apply(col2rgb(col), 2,
-      function(x) do.call(rgb, as.list(c(x[1:3]/256, alpha))) ) )
+    apply(
+      col2rgb(col), 2,
+      function(x)
+        do.call(
+          rgb,
+          list(x[1], x[2], x[3], alpha * 255, maxColorValue = 255)
+        )
+    )
+  )
 }
 
 #' Enveomics: Truncate
@@ -39,13 +52,9 @@ enve.col.alpha <- function
 #'
 #' @export
 
-enve.truncate <- function
-    (x,
-    f=0.95,
-    FUN=mean
-    ){
-  n <- round(length(x)*(1-f)/2)
-  y <- sort(x)[ -c(seq(1, n), seq(length(x)+1-n, length(x))) ]
+enve.truncate <- function(x, f = 0.95, FUN = mean) {
+  n <- round(length(x) * (1 - f) / 2)
+  y <- sort(x)[-c(seq(1, n), seq(length(x) + 1 - n, length(x)))]
   return(FUN(y))
 }
 
@@ -65,16 +74,17 @@ enve.truncate <- function
 
 enve.selvector <- function(sel, dim.names) {
   if(is.logical(sel)) {
-    if(length(sel) != length(dim.names))
-      stop('sel is logical but differs in length from dim.names')
+    if (length(sel) != length(dim.names))
+      stop("sel is logical but differs in length from dim.names")
     sel
-  } else if(is.numeric(sel)) {
-    if(max(sel) > length(dim.names))
-      stop('sel includes numeric index beyond the length of dim.names')
+  } else if (is.numeric(sel)) {
+    if (max(sel) > length(dim.names))
+      stop("sel includes numeric index beyond the length of dim.names")
     1:length(dim.names) %in% sel
   } else {
-    if(any(!sel %in% dim.names))
-      stop('sel includes character index missing from dim.names')
+    if (any(!sel %in% dim.names))
+      stop("sel includes character index missing from dim.names")
     dim.names %in% sel
   }
 }
+

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

@@ -13,9 +13,10 @@ without selection is trivial, since both the distances space and the
 selection occur in the same transformed space. However, it's useful to
 compare randomly subsampled sets against a selected set of objects. This
 is intended to identify overdispersion or overclustering (see
-\code{\link{enve.TRIBStest}}) of a subset against the entire collection of objects
-with minimum impact of sampling biases. This object can be produced by
-\code{\link{enve.tribs}} and supports S4 methods \code{plot} and \code{summary}.
+\code{\link{enve.TRIBStest}}) of a subset against the entire collection of
+objects with minimum impact of sampling biases. This object can be produced
+by \code{\link{enve.tribs}} and supports S4 methods \code{plot} and
+\code{summary}.
 }
 \section{Slots}{
 

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

@@ -15,8 +15,8 @@ enve.TRIBS.merge(x, y)
 Returns an \code{\link{enve.TRIBS}} object.
 }
 \description{
-Merges two \code{\link{enve.TRIBS}} objects generated from the same objects at
-different subsampling levels.
+Merges two \code{\link{enve.TRIBS}} objects generated from the same objects
+at different subsampling levels.
 }
 \author{
 Luis M. Rodriguez-R [aut, cre]

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

@@ -7,9 +7,9 @@
 \title{Enveomics: TRIBS Test S4 Class}
 \description{
 Test of significance of overclustering or overdispersion in a selected
-set of objects with respect to the entire set (see \code{\link{enve.TRIBS}}). This
-object can be produced by \code{\link{enve.tribs.test}} and supports S4 methods
-\code{plot} and \code{summary}.
+set of objects with respect to the entire set (see \code{\link{enve.TRIBS}}).
+This object can be produced by \code{\link{enve.tribs.test}} and supports S4
+methods \code{plot} and \code{summary}.
 }
 \section{Slots}{
 

data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd

@@ -7,13 +7,16 @@
 enve.__prune.iter(t, dist, min_dist, quiet)
 }
 \arguments{
-\item{t}{A \strong{phylo} object}
+\item{t}{A \strong{phylo} object.}
 
-\item{dist}{Cophenetic distance matrix}
+\item{dist}{Cophenetic distance matrix.}
 
-\item{min_dist}{Minimum distance}
+\item{min_dist}{Minimum distance.}
 
-\item{quiet}{If running quietly}
+\item{quiet}{If running quietly.}
+}
+\value{
+Returns a \strong{phylo} object.
 }
 \description{
 Internal function for \code{\link{enve.prune.dist}}.

data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd

@@ -7,13 +7,16 @@
 enve.__prune.reduce(t, nodes, min_dist, quiet)
 }
 \arguments{
-\item{t}{A \strong{phylo} object}
+\item{t}{A \strong{phylo} object.}
 
-\item{nodes}{Vector of nodes}
+\item{nodes}{Vector of nodes.}
 
-\item{min_dist}{Minimum distance}
+\item{min_dist}{Minimum distance.}
 
-\item{quiet}{If running quietly}
+\item{quiet}{If running quietly.}
+}
+\value{
+A \strong{phylo} object.
 }
 \description{
 Internal function for \code{\link{enve.prune.dist}}.

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

@@ -32,6 +32,10 @@ enve.__tribs(
 
 \item{dist}{Distance}
 }
+\value{
+A numeric indicating the \code{summary.fx} value applied to the
+distance matrix subset
+}
 \description{
 Internal ancillary function (see \code{\link{enve.tribs}}).
 }

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

@@ -66,36 +66,44 @@ Any value above 100 indicates that no values are to be reported.}
 
 \item{order}{Controls how the rows should be ordered. 
 \itemize{
-   \item{If \code{NULL} 
-   (default), \code{sort.by} is applied per row and the results are 
-   sorted decreasingly.}
-   \item{If \code{NA}, no sorting is performed, i.e., the original
-   order is respected.}
-   \item{If a vector is provided, it is assumed to be the 
-   custom order to be used (either by numeric index or by row names).}
-   }}
+  \item{
+    If \code{NULL} (default), \code{sort.by} is applied per row and the
+    results are sorted decreasingly.
+  }
+  \item{
+    If \code{NA}, no sorting is performed, i.e., the original order is
+    respected.
+  }
+  \item{
+    If a vector is provided, it is assumed to be the custom order to be used
+    (either by numeric index or by row names).
+  }
+}}
 
 \item{col}{Colors to use. If provided, overrides the variables \code{top}
 and \code{colors.per.group}, but \code{other.col} is still used if the 
-vector is insufficient for all the rows. An additional palette is available with
-\code{col='coto'} (contributed by Luis (Coto) Orellana).}
+vector is insufficient for all the rows. An additional palette is available
+with \code{col='coto'} (contributed by Luis (Coto) Orellana).}
 
 \item{...}{Any additional parameters to be passed to barplot.}
 }
+\value{
+No return value
+}
 \description{
 Creates nice barplots from tab-delimited tables.
 }
 \examples{
 # Load data
-data("phyla.counts", package="enveomics.R", envir=environment())
+data("phyla.counts", package = "enveomics.R", envir = environment())
 # Create a barplot sorted by variance with organic trends
 enve.barplot(
-    phyla.counts, # Counts of phyla in four sites
-    sizes=c(250,100,75,200), # Total sizes of the datasets of each site
-    bars.width=2, # Decrease from default, so the names are fully displayed
-    organic.trend=TRUE, # Nice curvy background
-    sort.by=var # Sort by variance across sites
-    )
+  phyla.counts, # Counts of phyla in four sites
+  sizes = c(250,100,75,200), # Total sizes of the datasets of each site
+  bars.width = 2, # Decrease from default, so the names are fully displayed
+  organic.trend = TRUE, # Nice curvy background
+  sort.by = var # Sort by variance across sites
+)
 
 }
 \author{

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

@@ -19,6 +19,16 @@ including \code{alpha}.
 \description{
 Modify alpha in a color (or vector of colors).
 }
+\examples{
+# Hexcode for a color by hexcode
+enve.col.alpha("#009988", 3/4) # "#009988BF"
+
+# Hexcode for a color by name
+enve.col.alpha("white", 1/4) # "#FFFFFF3F"
+
+# Hexcode for a color from other functions
+enve.col.alpha(rainbow(3)) # "#FF00007F" "#00FF007F" "#0000FF7F"
+}
 \author{
 Luis M. Rodriguez-R [aut, cre]
 }

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

@@ -2,18 +2,24 @@
 % Please edit documentation in R/growthcurve.R
 \name{enve.col2alpha}
 \alias{enve.col2alpha}
-\title{Enveomics: Color to Alpha}
+\title{Enveomics: Color to Alpha (deprecated)}
 \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).}
+\item{alpha}{Alpha level to set, in the [0, 1] range.}
+}
+\value{
+A vector of colors with alpha set.
 }
 \description{
 Takes a vector of colors and sets the alpha.
 }
+\details{
+DEPRECATED: Use instead \code{\link{enve.col.alpha}}.
+}
 \author{
 Luis M. Rodriguez-R [aut, cre]
 }

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

@@ -39,6 +39,20 @@ Returns a \strong{dist} object.
 \description{
 Transform a dataframe (or coercible object, like a table) into a
 \strong{dist} object.
+}
+\examples{
+# A sparse matrix representation of similarities as data frame.
+# The column "extra_data" is meaningless, only included to illustrate
+# the use of the obj*.index parameters
+sim <- data.frame(
+  extra_data = c(0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.5),
+  query      = c("A", "A", "A", "B", "C", "C", "D"),
+  subject    = c("A", "B", "C", "B", "C", "B", "A"),
+  similarity = c(100,  90,  60, 100, 100,  70,  10)
+)
+dist <- enve.df2dist(sim, "query", "subject", "similarity", max.sim = 100)
+print(dist)
+
 }
 \author{
 Luis M. Rodriguez-R [aut, cre]

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

@@ -18,7 +18,8 @@ enve.df2dist.group(
 \enumerate{
    \item ID of the object 1, 
    \item ID of the object 2, and 
-   \item distance between the two objects.}}
+   \item distance between the two objects.
+}}
 
 \item{obj1.index}{Index of the column containing the ID of the object 1.}
 
@@ -38,6 +39,24 @@ Returns a \strong{dist} object.
 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.
+}
+\examples{
+# A sparse matrix representation of distances as data frame.
+# Note that some pairs are repeated.
+dist.df <- data.frame(
+  query    = c("A", "A", "A", "B", "C", "C", "B", "B", "B"),
+  subject  = c("A", "B", "C", "B", "C", "B", "A", "C", "C"),
+  distance = c(  0, 0.1, 0.4,   0,   0, 0.4, 0.2, 0.2, 0.1)
+)
+dist <- enve.df2dist.group(dist.df)
+print(dist)
+
+# Use the mean of all repeated occurrences instead of the median.
+dist <- enve.df2dist.group(dist.df, summary = mean)
+
+# Simply use the first occurrence for any given pair.
+dist <- enve.df2dist.group(dist.df, summary = function(x) head(x, n = 1))
+
 }
 \author{
 Luis M. Rodriguez-R [aut, cre]

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

@@ -32,15 +32,14 @@ and the values correspond to the group.}
 
 \item{empty.rm}{Remove incomplete matrices.}
 
-\item{...}{Any other parameters supported by
-\code{\link{enve.df2dist.group}}.}
+\item{...}{Any other parameters supported by \code{\link{enve.df2dist}}.}
 }
 \value{
 Returns a \strong{list} of \strong{dist} objects.
 }
 \description{
 Transform a dataframe (or coercible object, like a table)
-into a \strong{dist} object.
+into a \strong{list} of \strong{dist} objects, one per group.
 }
 \author{
 Luis M. Rodriguez-R [aut, cre]

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

@@ -63,9 +63,12 @@ Calculates growth curves using the logistic growth function.
 }
 \examples{
 # Load data
-data("growth.curves", package="enveomics.R", envir=environment())
+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)
+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))
 

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

@@ -40,29 +40,31 @@ identity. This value is a percentage.}
 \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.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:
+\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 "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: 
+\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" }
+  \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.}
+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).}
 
@@ -71,8 +73,8 @@ 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{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.}
 
@@ -89,13 +91,14 @@ If non-zero, requires the stats package.}
 \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{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).}
+\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:
@@ -104,31 +107,36 @@ Returns a list with the following elements:
 \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}).}
+      (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.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.}
+      \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.}
+      This is returned because \code{id.cutoff=NULL} may vary.}
 \item{\code{seqdepth.mean.top}}{Average sequencing depth with identity above 
-     \code{id.cutoff}.}
+      \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.}
+      \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.}}
+\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

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

@@ -12,8 +12,11 @@ enve.recplot2.ANIr(x, range = c(0, Inf))
 \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).}
+intra-population matches (with identities), use \code{c(95, 100)}. To use
+only inter-population values, use \code{c(0, 95)}.}
+}
+\value{
+A numeric value indicating the ANIr (as percentage).
 }
 \description{
 Estimate the Average Nucleotide Identity from reads (ANIr) from a

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

@@ -15,6 +15,9 @@ enve.recplot2.__counts(x, pos.breaks, id.breaks, rec.idcol)
 
 \item{rec.idcol}{Identity column to use}
 }
+\value{
+2-dimensional matrix of counts per identity and position bins.
+}
 \description{
 Internal ancillary function (see \code{\link{enve.recplot2}}).
 }

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

@@ -13,6 +13,9 @@ enve.recplot2.__peakHist(x, mids, counts = TRUE)
 
 \item{counts}{Counts}
 }
+\value{
+A numeric vector of counts (histogram)
+}
 \description{
 Internal ancillary function (see \code{\link{enve.RecPlot2.Peak}}).
 }

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

@@ -11,6 +11,9 @@ enve.recplot2.__whichClosestPeak(peak, peaks)
 
 \item{peaks}{list of \code{\link{enve.RecPlot2.Peak}} objects}
 }
+\value{
+A numeric index out of \code{peaks}.
+}
 \description{
 Internal ancillary function (see \code{\link{enve.recplot2.findPeaks}}).
 }

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

@@ -11,6 +11,9 @@ enve.recplot2.changeCutoff(rp, new.cutoff = 98)
 
 \item{new.cutoff}{New cutoff to use.}
 }
+\value{
+The modified \code{\link{enve.RecPlot2}} object.
+}
 \description{
 Change the intra-species cutoff of an existing recruitment plot.
 }

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

@@ -21,10 +21,12 @@ enve.recplot2.compareIdentities(
 \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{"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"}
 }}
 
@@ -38,6 +40,9 @@ cross-validation (see \code{smooth.spline} parameter \code{spar}).}
 \item{max.deviation}{Maximum mean deviation between identity breaks tolerated (as percent
 identity). Difference in number of \code{id.breaks} is never tolerated.}
 }
+\value{
+A \strong{numeric} indicating the distance between the objects.
+}
 \description{
 Compare the distribution of identities between two
 \code{\link{enve.RecPlot2}} objects.

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

@@ -9,6 +9,9 @@ enve.recplot2.corePeak(x)
 \arguments{
 \item{x}{\code{list} of \code{\link{enve.RecPlot2.Peak}} objects.}
 }
+\value{
+A \code{\link{enve.RecPlot2.Peak}} object.
+}
 \description{
 Finds the peak in a list of peaks that is most likely to represent the
 "core genome" of a population.

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

@@ -15,9 +15,9 @@ enve.recplot2.extractWindows(
 \arguments{
 \item{rp}{Recruitment plot, a \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{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.}

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

@@ -31,6 +31,4 @@ sub-population mixtures.
 }
 \author{
 Luis M. Rodriguez-R [aut, cre]
-
-export
 }

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

@@ -11,6 +11,10 @@ enve.recplot2.findPeaks.__em_e(x, theta)
 
 \item{theta}{Parameters list}
 }
+\value{
+A list with components \code{ll} (numeric) the log-likelihood, and
+\code{posterior} (numeric) the posterior probability.
+}
 \description{
 Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.em}}).
 }

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

@@ -11,6 +11,11 @@ enve.recplot2.findPeaks.__em_m(x, posterior)
 
 \item{posterior}{Posterior probability}
 }
+\value{
+A list with components \code{mu} (numeric) the estimated mean,
+\code{sd} (numeric) the estimated standard deviation, and \code{alpha}
+(numeric) the estimated alpha parameter.
+}
 \description{
 Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.em}}).
 }