miga-base 0.4.3.0 → 0.5.0.0

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

@@ -1,34 +1,50 @@
-
+#' Enveomics: Color Alpha
+#' 
+#' Modify alpha in a color (or vector of colors).
+#'
+#' @param col Color or vector of colors. It can be any value supported by 
+#' \code{\link[grDevices]{col2rgb}}, such as \code{darkred} or \code{#009988}.
+#' @param alpha Alpha value to add to the color, from 0 to 1.
+#'
+#' @return Returns a color or a vector of colors in \emph{hex} notation, 
+#' including \code{alpha}.
+#'
+#' @author Luis M. Rodriguez-R [aut, cre]
+#'
+#' @export
 
 enve.col.alpha <- function
-  ### Modify alpha in a color (or vector of colors).
     (col,
-    ### Color or vector of colors. It can be any value supported by `col2rgb`, 
-    ### such as 'darkred' or '#009988'.
     alpha=1/2
-    ### Alpha value to add to the color, from 0 to 1.
     ){
   return(
     apply(col2rgb(col), 2,
       function(x) do.call(rgb, as.list(c(x[1:3]/256, alpha))) ) )
-  ### Returns a color or a vector of colors in hex notation including alpha.
 }
 
+#' Enveomics: Truncate
+#' 
+#' 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.
+#'
+#' @param x A vector of numbers.
+#' @param f The fraction of values to retain.
+#' @param FUN Summary function to apply to the vectors. To obtain the 
+#' truncated vector itself, use \code{c}.
+#' 
+#' @return Returns the summary \code{(FUN)} of the truncated vector.
+#' 
+#' @author Luis M. Rodriguez-R [aut, cre]
+#'
+#' @export
+
 enve.truncate <- function
-  ### 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.
     (x,
-    ### A vector of numbers.
     f=0.95,
-    ### The fraction of values to retain.
     FUN=mean
-    ### Summary function to apply to the vectors. To obtain the truncated
-    ### vector itself, use `c`.
     ){
   n <- round(length(x)*(1-f)/2)
   y <- sort(x)[ -c(seq(1, n), seq(length(x)+1-n, length(x))) ]
   return(FUN(y))
-  ### Returns the summary (`FUN`) of the truncated vector.
 }
-

data/utils/enveomics/enveomics.R/README.md

@@ -52,6 +52,13 @@ For additional information on recruitment plots, see the
 [Recruitment plots working document](https://github.com/lmrodriguezr/enveomics/blob/master/Docs/recplot2.md).
 
 ## Changelog
+* 1.7.0: Uniformized output for `enve.recplot2.extractWindows` and
+  `enve.recplot2.coordinates` to ease automation. Thanks to Tomeu Viver and
+  Roth Conrad for troubleshooting.
+* 1.6.0: Speed up in recplot2 with proper structure manipulation
+  (by: Kenji Gerhardt). Also, default value for `id.breaks` was changed from
+  300 to 60.
+* 1.5.0: Modernized documentation, now in ROxygen2 (by: Tatyana Kiryutina)
 * 1.4.4: Removes modeest library as requirement, and replaces mower peak-finder
   initialization to median (instead of mode).
 * 1.4.2: Solved bug #36.

data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/growthcurve.R
+\docType{methods}
+\name{$,enve.GrowthCurve-method}
+\alias{$,enve.GrowthCurve-method}
+\title{Attribute accessor}
+\usage{
+\S4method{$}{enve.GrowthCurve}(x, name)
+}
+\arguments{
+\item{x}{Object}
+
+\item{name}{Attribute name}
+}
+\description{
+Attribute accessor
+}

data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\docType{methods}
+\name{$,enve.RecPlot2-method}
+\alias{$,enve.RecPlot2-method}
+\title{Attribute accessor}
+\usage{
+\S4method{$}{enve.RecPlot2}(x, name)
+}
+\arguments{
+\item{x}{Object}
+
+\item{name}{Attribute name}
+}
+\description{
+Attribute accessor
+}

data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\docType{methods}
+\name{$,enve.RecPlot2.Peak-method}
+\alias{$,enve.RecPlot2.Peak-method}
+\title{Attribute accessor}
+\usage{
+\S4method{$}{enve.RecPlot2.Peak}(x, name)
+}
+\arguments{
+\item{x}{Object}
+
+\item{name}{Attribute name}
+}
+\description{
+Attribute accessor
+}

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

@@ -1,30 +1,25 @@
-\name{enve.GrowthCurve-class}
-\Rdversion{1.1}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/growthcurve.R
 \docType{class}
+\name{enve.GrowthCurve-class}
 \alias{enve.GrowthCurve-class}
 \alias{enve.GrowthCurve}
-%% \alias{$}
-
-\title{enve.GrowthCurve S4 class}
-\description{Enve-omics representation of fitted growth curves.}
-\section{Objects from the Class}{Objects can be created by calls of the form \code{new(enve.GrowthCurve ...)}}
-\section{Slots}{
-  \describe{
-    \item{\code{design}:}{(\code{array}) Experimental design of the experiment.}
-    \item{\code{models}:}{(\code{list}) Fitted growth curve models.}
-    \item{\code{predict}:}{(\code{list}) Fitted growth curve values.}
-    \item{\code{call}:}{(\code{call}) Call producing this object.}
-  }
+\title{Enveomics: Growth Curve S4 Class}
+\description{
+Enve-omics representation of fitted growth curves.
 }
-\section{Methods}{
-  \describe{
-    \item{$}{\code{signature(x = "enve.GrowthCurve")}: ... }
-	 }
-}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
+\section{Slots}{
 
+\describe{
+\item{\code{design}}{\code{(array)} Experimental design of the experiment.}
 
+\item{\code{models}}{\code{(list)} Fitted growth curve models.}
 
+\item{\code{predict}}{\code{(list)} Fitted growth curve values.}
 
+\item{\code{call}}{\code{(call)} Call producing this object.}
+}}
 
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

@@ -1,43 +1,46 @@
-\name{enve.TRIBS-class}
-\Rdversion{1.1}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
 \docType{class}
+\name{enve.TRIBS-class}
 \alias{enve.TRIBS-class}
 \alias{enve.TRIBS}
-
-\title{enve.TRIBS S4 class}
-\description{Enve-omics representation of "Transformed-space Resampling In Biased Sets
-(TRIBS)".  This object represents sets of distances between objects,
-sampled nearly-uniformly at random in "distance space".  Subsampling
+\title{Enveomics: TRIBS S4 Class}
+\description{
+Enve-omics representation of "Transformed-space Resampling In Biased Sets
+(TRIBS)". This object represents sets of distances between objects,
+sampled nearly-uniformly at random in "distance space". Subsampling
 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
-`enve.TRIBStest`) of a subset against the entire collection of objects
+\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
-`enve.tribs` and supports S4 methods `plot` and `summary`.}
-\section{Objects from the Class}{Objects can be created by calls of the form \code{new(enve.TRIBS ...)}}
-\section{Slots}{
-  \describe{
-    \item{\code{distance}:}{(\code{numeric}) Centrality measurement of the distances between the
-<< selected objects (without subsampling).}
-    \item{\code{points}:}{(\code{matrix}) Position of the different objects in distance
-<< space.}
-    \item{\code{distances}:}{(\code{matrix}) Subsampled distances, where the rows are replicates
-<< and the columns are subsampling levels.}
-    \item{\code{spaceSize}:}{(\code{numeric}) Number of objects.}
-    \item{\code{selSize}:}{(\code{numeric}) Number of selected objects.}
-    \item{\code{dimensions}:}{(\code{numeric}) Number of dimensions in the distance space.}
-    \item{\code{subsamples}:}{(\code{numeric}) Subsampling levels (as fractions, from 0 to 1).}
-    \item{\code{call}:}{(\code{call}) Call producing this object.}
-  }
-}
-\section{Methods}{
-No methods defined with class "enve.TRIBS" in the signature.
+\code{\link{enve.tribs}} and supports S4 methods \code{plot} and \code{summary}.
 }
+\section{Slots}{
+
+\describe{
+\item{\code{distance}}{\code{(numeric)} Centrality measurement of the distances 
+between the selected objects (without subsampling).}
+
+\item{\code{points}}{\code{(matrix)}    Position of the different objects in distance
+space.}
 
-\author{Luis M. Rodriguez-R [aut, cre]}
+\item{\code{distances}}{\code{(matrix)} Subsampled distances, where the rows are 
+replicates and the columns are subsampling levels.}
 
+\item{\code{spaceSize}}{\code{(numeric)} Number of objects.}
 
+\item{\code{selSize}}{\code{(numeric)} Number of selected objects.}
 
+\item{\code{dimensions}}{\code{(numeric)} Number of dimensions in the distance space.}
 
+\item{\code{subsamples}}{\code{(numeric)} Subsampling levels (as fractions, from 
+0 to 1).}
 
+\item{\code{call}}{\code{(call)} Call producing this object.}
+}}
+
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

@@ -1,19 +1,23 @@
-\name{enve.TRIBS.merge}
-\alias{enve.TRIBS.merge}
-\title{enve TRIBS merge}
-\description{Merges two `enve.TRIBS` objects generated from the same objects at
-different subsampling levels.}
-\usage{enve.TRIBS.merge(x, y)}
-\arguments{
-  \item{x}{First `enve.TRIBS` object.}
-  \item{y}{Second `enve.TRIBS` object.}
-}
-
-\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.merge}
+\alias{enve.TRIBS.merge}
+\title{Enveomics: TRIBS Merge}
+\usage{
+enve.TRIBS.merge(x, y)
+}
+\arguments{
+\item{x}{First \code{\link{enve.TRIBS}} object.}
+
+\item{y}{Second \code{\link{enve.TRIBS}} object.}
+}
+\value{
+Returns an \code{\link{enve.TRIBS}} object.
+}
+\description{
+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

@@ -1,37 +1,47 @@
-\name{enve.TRIBStest-class}
-\Rdversion{1.1}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
 \docType{class}
+\name{enve.TRIBStest-class}
 \alias{enve.TRIBStest-class}
 \alias{enve.TRIBStest}
-
-\title{enve.TRIBStest S4 class}
-\description{Test of significance of overclustering or overdispersion in a selected
-set of objects with respect to the entire set (see `enve.TRIBS`). This
-object can be produced by `enve.tribs.test` and supports S4 methods
-`plot` and `summary`.}
-\section{Objects from the Class}{Objects can be created by calls of the form \code{new(enve.TRIBStest ...)}}
+\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}.
+}
 \section{Slots}{
-  \describe{
-    \item{\code{pval.gt}:}{(\code{numeric}) P-value for the overdispersion test.}
-    \item{\code{pval.lt}:}{(\code{numeric}) P-value for the overclustering test.}
-    \item{\code{all.dist}:}{(\code{numeric}) Empiric PDF of distances for the entire dataset (subsampled at selection
+
+\describe{
+\item{\code{pval.gt}}{\code{(numeric)}
+P-value for the overdispersion test.}
+
+\item{\code{pval.lt}}{\code{(numeric)}
+P-value for the overclustering test.}
+
+\item{\code{all.dist}}{\code{(numeric)}
+Empiric PDF of distances for the entire dataset (subsampled at selection
 size).}
-    \item{\code{sel.dist}:}{(\code{numeric}) Empiric PDF of distances for the selected objects (without subsampling).}
-    \item{\code{diff.dist}:}{(\code{numeric}) Empiric PDF of the difference between `all.dist` and `sel.dist`. The
-p-values are estimating by comparing areas in this PDF greater than and
-lesser than zero.}
-    \item{\code{dist.mids}:}{(\code{numeric}) Midpoints of the empiric PDFs of distances.}
-    \item{\code{diff.mids}:}{(\code{numeric}) Midpoints of the empiric PDF of difference of distances.}
-    \item{\code{call}:}{(\code{call}) Call producing this object.}
-  }
-}
-\section{Methods}{
-No methods defined with class "enve.TRIBStest" in the signature.
-}
 
-\author{Luis M. Rodriguez-R [aut, cre]}
+\item{\code{sel.dist}}{\code{(numeric)}
+Empiric PDF of distances for the selected objects (without subsampling).}
 
+\item{\code{diff.dist}}{\code{(numeric)}
+Empiric PDF of the difference between \code{all.dist} and \code{sel.dist}. 
+The p-values are estimating by comparing areas in this PDF greater than and
+lesser than zero.}
 
+\item{\code{dist.mids}}{\code{(numeric)}
+Midpoints of the empiric PDFs of distances.}
 
+\item{\code{diff.mids}}{\code{(numeric)}
+Midpoints of the empiric PDF of difference of distances.}
 
+\item{\code{call}}{\code{(call)}
+Call producing this object.}
+}}
 
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

@@ -1,24 +1,23 @@
-\name{enve.__prune.iter}
-\alias{enve.__prune.iter}
-\title{enve   prune iter}
-\description{Internal function for enve.prune.dist}
-\usage{enve.__prune.iter(t, dist, min_dist, quiet)}
-\arguments{
-  \item{t}{
-}
-  \item{dist}{
-}
-  \item{min_dist}{
-}
-  \item{quiet}{
-}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/autoprune.R
+\name{enve.__prune.iter}
+\alias{enve.__prune.iter}
+\title{Enveomics: Prune Iter (Internal Function)}
+\usage{
+enve.__prune.iter(t, dist, min_dist, quiet)
+}
+\arguments{
+\item{t}{A \strong{phylo} object}
+
+\item{dist}{Cophenetic distance matrix}
+
+\item{min_dist}{Minimum distance}
+
+\item{quiet}{If running quietly}
+}
+\description{
+Internal function for \code{\link{enve.prune.dist}}.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

@@ -1,24 +1,23 @@
-\name{enve.__prune.reduce}
-\alias{enve.__prune.reduce}
-\title{enve   prune reduce}
-\description{Internal function for enve.prune.dist}
-\usage{enve.__prune.reduce(t, nodes, min_dist, quiet)}
-\arguments{
-  \item{t}{
-}
-  \item{nodes}{
-}
-  \item{min_dist}{
-}
-  \item{quiet}{
-}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/autoprune.R
+\name{enve.__prune.reduce}
+\alias{enve.__prune.reduce}
+\title{Enveomics: Prune Reduce (Internal Function)}
+\usage{
+enve.__prune.reduce(t, nodes, min_dist, quiet)
+}
+\arguments{
+\item{t}{A \strong{phylo} object}
+
+\item{nodes}{Vector of nodes}
+
+\item{min_dist}{Minimum distance}
+
+\item{quiet}{If running quietly}
+}
+\description{
+Internal function for \code{\link{enve.prune.dist}}.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}