Rewrite barplot method

DESCRIPTION

@@ -30,7 +30,7 @@ Imports:
     graphics,
     grDevices,
     isopleuros (>= 1.2.0),
-    khroma (>= 1.13.0),
+    khroma (>= 1.14.0),
     methods,
     MASS,
     stats,
@@ -56,6 +56,7 @@ Collate:
     'AllGenerics.R'
     'aggregate.R'
     'barplot.R'
+    'chemistry.R'
     'coerce.R'
     'condense.R'
     'covariance.R'

NAMESPACE

@@ -7,6 +7,8 @@ S3method(as.data.frame,OutlierIndex)
 S3method(barplot,CompositionMatrix)
 S3method(dist,CompositionMatrix)
 S3method(hist,CompositionMatrix)
+S3method(labels,CompositionMatrix)
+S3method(labels,LogRatio)
 S3method(mahalanobis,CompositionMatrix)
 S3method(mahalanobis,ILR)
 S3method(mean,CompositionMatrix)
@@ -47,10 +49,14 @@ exportMethods(condense)
 exportMethods(covariance)
 exportMethods(describe)
 exportMethods(dist)
+exportMethods(element_major)
+exportMethods(element_minor)
+exportMethods(element_trace)
 exportMethods(get_groups)
 exportMethods(get_totals)
 exportMethods(hist)
 exportMethods(is_assigned)
+exportMethods(labels)
 exportMethods(mahalanobis)
 exportMethods(margin)
 exportMethods(mean)
@@ -64,6 +70,7 @@ exportMethods(pip)
 exportMethods(plot)
 exportMethods(powering)
 exportMethods(quantile)
+exportMethods(rbind2)
 exportMethods(replace_NA)
 exportMethods(replace_zero)
 exportMethods(scalar)

NEWS.md

@@ -1,13 +1,15 @@
 # nexus 0.2.0.9000
 ## New classes and methods
+* Add transformation methods for `LogRatio` objects (clr <-> alr, clr -> ilr, alr -> ilr).
 * Add `condense()` to compute compositional mean of data subsets.
 * Add `pip()` to compute proportionality index of parts.
+* Add `rbind()` method for `CompositionMatrix` objects.
 * Add `show()` methods for `LogRatio` objects.
-* Add transformation methods for `LogRatio` objects (clr <-> alr, clr -> ilr, alr -> ilr).
+* Add `element_major()`, `element_minor()` and `element_trace()` methods for `CompositionMatrix` objects.
 
 ## Enhancements
 * Add example datasets.
-* Allow proportional sizing of faceted barplot.
+* Improve bar chart rendering.
 
 ## Breaking changes
 * `[` always returns a `CompositionMatrix` object by default, even if only one row/column is accessed.

R/AllClasses.R

@@ -82,7 +82,7 @@ setClassUnion("index", members = c("logical", "numeric", "character"))
 #' @slot totals A [`numeric`] vector to store the absolute row sums (before
 #'  the closure of the compositions).
 #' @slot groups A [`character`] vector to store the group names.
-#' @slot parts A [`character`] vector to store the part names.
+#' @slot parts A [`character`] vector to store the original part names.
 #' @slot ratio A [`character`] vector to store the ratio names.
 #' @slot order An [`integer`] vector to store the original ordering of the
 #'  columns.

R/AllGenerics.R

@@ -248,6 +248,59 @@ setGeneric(
   def = function(x, value) standardGeneric("set_groups<-")
 )
 
+#' Chemical Elements and Compounds
+#'
+#' Identify major, minor and traces elements in a compositional data matrix.
+#' @param object A [`CompositionMatrix-class`] object.
+#' @param min A length-one [`numeric`] vector specifying the lower bound for
+#'  element identification.
+#' @param max A length-one [`numeric`] vector specifying the upper bound for
+#'  element identification.
+#' @param ... Currently not used.
+#' @details
+#'  There is no definite classification of what are the major, minor and trace
+#'  elements are. By default, the following rule of thumb is used:
+#'  \describe{
+#'   \item{major elements}{The major elements are those that define the material
+#'   under study. Major elements usually have concentrations of above 1%.}
+#'   \item{minor elements}{Minor elements usually have concentrations between
+#'   1% and 0.1%}
+#'   \item{trace elements}{Trace elements usually have concentrations of less
+#'   than 0.1%.}
+#'  }
+#' @return A [`logical`] vector.
+#' @example inst/examples/ex-barplot.R
+#' @author N. Frerebeau
+#' @docType methods
+#' @family tools
+#' @name element
+#' @rdname element
+NULL
+
+#' @rdname element
+#' @aliases element_major-method
+setGeneric(
+  name = "element_major",
+  def = function(object, ...) standardGeneric("element_major"),
+  valueClass = "logical"
+)
+
+#' @rdname element
+#' @aliases element_minor-method
+setGeneric(
+  name = "element_minor",
+  def = function(object, ...) standardGeneric("element_minor"),
+  valueClass = "logical"
+)
+
+#' @rdname element
+#' @aliases element_trace-method
+setGeneric(
+  name = "element_trace",
+  def = function(object, ...) standardGeneric("element_trace"),
+  valueClass = "logical"
+)
+
 #' Row Sums
 #'
 #' Retrieves or defines the row sums (before closure).
@@ -305,7 +358,7 @@ setGeneric(
 #' @example inst/examples/ex-subset.R
 #' @author N. Frerebeau
 #' @docType methods
-#' @family mutators
+#' @family subsetting methods
 #' @name subset
 #' @rdname subset
 NULL
@@ -324,11 +377,26 @@ NULL
 #' @example inst/examples/ex-split.R
 #' @author N. Frerebeau
 #' @docType methods
-#' @family mutators
+#' @family subsetting methods
 #' @name split
 #' @rdname split
 NULL
 
+#' Combine Two Composition Matrices
+#'
+#' @param x,y A [`CompositionMatrix-class`] object.
+#' @details
+#'  `rbind2()` combine by rows.
+#' @return
+#'  A [`CompositionMatrix-class`] objects.
+#' @example inst/examples/ex-split.R
+#' @author N. Frerebeau
+#' @docType methods
+#' @family subsetting methods
+#' @name bind
+#' @rdname bind
+NULL
+
 #' Matrix Transpose
 #'
 #' @param x A [`CompositionMatrix-class`] object.
@@ -906,25 +974,26 @@ NULL
 #'
 #' Displays a compositional bar chart.
 #' @param height A [`CompositionMatrix-class`] object.
+#' @param subset A vector of column indices.
 #' @param groups A `vector` of grouping elements, as long as the variables in
-#'  `height`. If set, a matrix of panels defined by `groups` will be drawn.
-#' @param order An [`integer`] vector giving the index of the column to be used
-#'  for the ordering of the data.
-#' @param decreasing A [`logical`] scalar: should the sort order be increasing
-#'  or decreasing?
-#' @param horiz A [`logical`] scalar. If `FALSE`, the bars are drawn vertically
-#'  with the first bar to the left. If `TRUE` (the default), the bars are drawn
-#'  horizontally with the first at the bottom.
-#' @param xlab,ylab A [`character`] vector giving the x and y axis labels.
-#' @param main A [`character`] string giving a main title for the plot.
-#' @param sub A [`character`] string giving a subtitle for the plot.
-#' @param ann A [`logical`] scalar: should the default annotation (title and x
-#'  and y axis labels) appear on the plot?
+#'  `height`.
+#' @param order_columns A [`logical`] scalar: should should columns be reorderd?
+#' @param order_rows An [`integer`] vector giving the index of the column to be
+#'  used for the ordering of the data.
+#' @param decreasing A [`logical`] scalar: should the sort order of rows be
+#'  increasing or decreasing?
+#' @param space A length-one [`numeric`] vector giving the the amount of space
+#'  (as a fraction of the width of a bar) left between each bar
+#'  (defaults to \eqn{0.2}).
+#' @param offset A length-one [`numeric`] vector giving the the amount of space
+#'  (as a fraction) left between groups (defaults to \eqn{0.025}). Only used if
+#'  `groups` is not `NULL`.
+#' @param colors A vector of colors or a `function` that when called with a
+#'  single argument (an integer specifying the number of colors) returns a
+#'  vector of colors. Will be mapped to the part names.
+#' @param border The color to draw the borders.
 #' @param axes A [`logical`] scalar: should axes be drawn on the plot?
-#' @param col A vector of colors for the bar components.
-#' @param legend A [`list`] of additional arguments to be passed to
-#'  [graphics::legend()]; names of the list are used as argument names.
-#'  If `NULL`, no legend is displayed.
+#' @param legend A [`logical`] scalar: should the legend be displayed?
 #' @param ... Further parameters to be passed to [graphics::barplot()].
 #' @return
 #'  `barplot()` is called for its side-effects: is results in a graphic being