miga-base 1.2.15.1 → 1.2.15.3

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

@@ -1,81 +0,0 @@
-# enveomics.R
-
-## Installing `enveomics.R`
-To install the latest version of `enveomics.R` uploaded to CRAN, execute in R:
-
-```R
-install.packages('enveomics.R')
-```
-
-To install the current developer version of `enveomics.R`, execute in R:
-
-```R
-install.packages('devtools')
-library('devtools')
-install_github('lmrodriguezr/enveomics', subdir='enveomics.R')
-```
-
-## Using `enveomics.R`
-To load enveomics.R, simply execute:
-
-```R
-library(enveomics.R);
-```
-
-And open help messages using any of the following commands:
-
-```R
-?enveomics.R
-?enve.barplot
-?enve.recplot2
-?enve.recplot2.compareIdentities
-?enve.recplot2.changeCutoff
-?enve.recplot2.findPeaks
-?enve.recplot2.corePeak
-?enve.recplot2.windowDepthThreshold
-?enve.recplot2.extractWindows
-?enve.recplot2.coordinates
-?enve.recplot2.seqdepth
-?enve.recplot2.ANIr
-?enve.prune.dist
-?enve.tribs
-?enve.tribs.test
-?enve.growthcurve
-?enve.col.alpha
-?enve.truncate
-```
-
-You can run some examples using these libraries in the
-[enveomics-GUI](https://github.com/lmrodriguezr/enveomics-gui).
-
-For additional information on recruitment plots, see the
-[Recruitment plots working document](https://github.com/lmrodriguezr/enveomics/blob/master/Docs/recplot2.md).
-
-## Changelog
-* 1.8.0: New functions `enve.selvector` and `enve.prefscore`.
-* 1.7.1: Improved efficiency of `enve.df2dist` about five-fold.
-* 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.
-* 1.4.0: New option `pos.breaks.tsv` for `enve.recplot2`.
-* 1.3.4: Gracefully handles and plots recruitment plots with insufficient data
-  to find peaks.
-* 1.3.3: New function `enve.recplot2.windowDepthThreshold`.
-* 1.3.2: New option `panel.fun` for `plot.enve.RecPlot2`.
-* 1.3.1: New function enve.truncate.
-* 1.3: Several bug fixes and new utilities for recruitment plots (recplot2).
-* 1.1.0: New function enve.growthcurve and related class enve.GrowthCurve
-  with S3 methods plot and summary.
-* 1.0.2: Fine-tuned default parameters in enve.recplot2.findPeaks and
-  solved a minor bug in enve.recplot2 that caused failures in low-coverage
-  datasets when using too many threads.
-* 1.0.1: enve.recplot2 now supports pos.breaks=0 to define a
-  bin per subject sequence.
-

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

@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/growthcurve.R
-\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

@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\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

@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\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

@@ -1,25 +0,0 @@
-% 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}
-\title{Enveomics: Growth Curve S4 Class}
-\description{
-Enve-omics representation of fitted growth curves.
-}
-\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

@@ -1,46 +0,0 @@
-% 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{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
-\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}{
-
-\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.}
-}}
-
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,23 +0,0 @@
-% 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

@@ -1,47 +0,0 @@
-% 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{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
-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 \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

@@ -1,23 +0,0 @@
-% 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

@@ -1,23 +0,0 @@
-% 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]
-}

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

@@ -1,40 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/tribs.R
-\name{enve.__tribs}
-\alias{enve.__tribs}
-\title{Enveomics: TRIBS - Internal Ancillary Function}
-\usage{
-enve.__tribs(
-  rep,
-  frx,
-  selection,
-  dimensions,
-  dots,
-  dist.method,
-  summary.fx,
-  dist
-)
-}
-\arguments{
-\item{rep}{Replicates}
-
-\item{frx}{Fraction}
-
-\item{selection}{Selection}
-
-\item{dimensions}{Dimensions}
-
-\item{dots}{Sampling points}
-
-\item{dist.method}{Distance method}
-
-\item{summary.fx}{Summary function}
-
-\item{dist}{Distance}
-}
-\description{
-Internal ancillary function (see \code{\link{enve.tribs}}).
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,103 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/barplot.R
-\name{enve.barplot}
-\alias{enve.barplot}
-\title{Enveomics: Barplot}
-\usage{
-enve.barplot(
-  x,
-  sizes,
-  top = 25,
-  colors.per.group = 9,
-  bars.width = 4,
-  legend.ncol = 1,
-  other.col = "#000000",
-  add.trend = FALSE,
-  organic.trend = FALSE,
-  sort.by = median,
-  min.report = 101,
-  order = NULL,
-  col,
-  ...
-)
-}
-\arguments{
-\item{x}{Can be either the input data or the path to the file containing 
-the table. 
-\itemize{
-   \item{If it contains the data, it must be a data frame or an
-   object coercible to a data frame.} 
-   \item{If it is a path, it must point to a
-   tab-delimited file containing a header (first row) and row names 
-   (first column).}
-   }}
-
-\item{sizes}{A numeric vector containing the real size of the samples
-(columns) in the same order of the input table. If set, the values are
-assumed to be 100\%. Otherwise, the sum of the columns is used.}
-
-\item{top}{Maximum number of categories to display. Any additional
-categories will be listed as "Others".}
-
-\item{colors.per.group}{Number of categories in the first two saturation 
-groups of colors. The third group contains the remaining categories if 
-needed.}
-
-\item{bars.width}{Width of the barplot with respect to the legend.}
-
-\item{legend.ncol}{Number of columns in the legend.}
-
-\item{other.col}{Color of the "Others" category.}
-
-\item{add.trend}{Controls if semi-transparent areas are to be plotted
-between the bars to connect the regions (trend regions).}
-
-\item{organic.trend}{Controls if the trend regions are to be smoothed 
-(curves). By default, trend regions have straight edges. If \code{TRUE}, 
-forces \code{add.trend=TRUE}.}
-
-\item{sort.by}{Any function that takes a numeric vector and returns a
-numeric scalar. This function is applied to each row, and the resulting
-values are used to sort the rows (decreasingly). Good options include: 
-\code{sd, min, max, mean, median}.}
-
-\item{min.report}{Minimum percentage to report the value in the plot.
-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{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).}
-
-\item{...}{Any additional parameters to be passed to barplot.}
-}
-\description{
-Creates nice barplots from tab-delimited tables.
-}
-\examples{
-# Load data
-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
-    )
-
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,67 +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

@@ -1,45 +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

@@ -1,44 +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]
-}