[Soiltexture-commits] r101 - in pkg/ternaryplot: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 28 16:15:38 CET 2014
Author: jmoeys
Date: 2014-03-28 16:15:38 +0100 (Fri, 28 Mar 2014)
New Revision: 101
Added:
pkg/ternaryplot/REVISION
pkg/ternaryplot/man/createTernarySystem.Rd
Modified:
pkg/ternaryplot/DESCRIPTION
pkg/ternaryplot/NAMESPACE
pkg/ternaryplot/R/aa00-ternaryplot-package.R
pkg/ternaryplot/R/aa01-ternaryplot-options.R
pkg/ternaryplot/R/aa02-ternaryplot-classes.R
pkg/ternaryplot/R/aa03-ternaryplot-classes-utility.R
pkg/ternaryplot/R/aa04-ternarysystems.R
pkg/ternaryplot/R/aa05-ternarydata.R
pkg/ternaryplot/R/aa06-ternary2xy.R
pkg/ternaryplot/R/ternaryplot.R
pkg/ternaryplot/man/blrLabels-methods.Rd
pkg/ternaryplot/man/blrNames-methods.Rd
pkg/ternaryplot/man/createTernaryGeometry.Rd
pkg/ternaryplot/man/createTernaryVariables.Rd
pkg/ternaryplot/man/getTernarySystem.Rd
pkg/ternaryplot/man/ternary2xy-methods.Rd
pkg/ternaryplot/man/ternaryData-methods.Rd
pkg/ternaryplot/man/ternaryLims-methods.Rd
pkg/ternaryplot/man/ternaryWindow-methods.Rd
pkg/ternaryplot/man/ternaryplot-package.Rd
pkg/ternaryplot/man/tpPar.Rd
Log:
bug fixes
Modified: pkg/ternaryplot/DESCRIPTION
===================================================================
--- pkg/ternaryplot/DESCRIPTION 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/DESCRIPTION 2014-03-28 15:15:38 UTC (rev 101)
@@ -7,5 +7,4 @@
Description: Ternary plots and ternary classifications.
License: AGPL-3
URL: http://www.slu.se/ckb
-Depends: R (>= 3.0.2), sp
-Imports: MASS
+Depends: R (>= 3.0.2), sp, MASS
Modified: pkg/ternaryplot/NAMESPACE
===================================================================
--- pkg/ternaryplot/NAMESPACE 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/NAMESPACE 2014-03-28 15:15:38 UTC (rev 101)
@@ -16,6 +16,7 @@
export(blrNames)
export(createTernaryGeometry)
export(createTernaryGrid)
+export(createTernarySystem)
export(createTernaryVariables)
export(deg2rad)
export(fracSum)
@@ -38,18 +39,6 @@
export(ternaryWindow)
export(tlrAngles)
export(tpPar)
-exportClasses(ternarySystem)
-importFrom(MASS,"data,")
-importFrom(MASS,"for")
-importFrom(MASS,and)
-importFrom(MASS,classes)
-importFrom(MASS,classification.)
-importFrom(MASS,classifications.)
-importFrom(MASS,kde2d)
-importFrom(MASS,plots)
-importFrom(MASS,S4)
-importFrom(MASS,ternary)
-importFrom(MASS,Ternary)
S3method("blrClock<-",ternaryGeometry)
S3method("blrClock<-",ternarySystem)
S3method("blrLabels<-",ternarySystem)
Modified: pkg/ternaryplot/R/aa00-ternaryplot-package.R
===================================================================
--- pkg/ternaryplot/R/aa00-ternaryplot-package.R 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/R/aa00-ternaryplot-package.R 2014-03-28 15:15:38 UTC (rev 101)
@@ -8,10 +8,6 @@
-#'@importFrom MASS kde2d
-
-
-
#' Ternary plots and ternary classifications.
#'
#' Ternary plots and ternary classifications. S4 classes for ternary
Modified: pkg/ternaryplot/R/aa01-ternaryplot-options.R
===================================================================
--- pkg/ternaryplot/R/aa01-ternaryplot-options.R 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/R/aa01-ternaryplot-options.R 2014-03-28 15:15:38 UTC (rev 101)
@@ -148,8 +148,9 @@
#'@param fracSumTol
#' Single numeric. Tolerance on the sum of the 3 ternary fractions. Overall
#' tolerance is \code{fracSum * fracSumTol}, where \code{fracSum} is the
-#' expected sum of the 3 ternary fractions, as given by a
-#' \code{\link[ternaryplot]{ternaryGeometry}} or a \code{\link[ternaryplot]{ternarySystem}}.
+#' expected sum of the 3 ternary fractions. See
+#' \code{\link[ternaryplot]{createTernaryGeometry}} or
+#' \code{\link[ternaryplot]{createTernarySystem}}.
#'
#'@param ticksAt
#' Vector of numeric. Pre-defined position of the tick-marks for the 3 axis.
@@ -230,7 +231,7 @@
#'
#'@seealso \code{\link{getTpPar}}.
#'
-#'@export tpPar
+#'@export
#'
tpPar <- function(
par = NULL,
@@ -372,7 +373,7 @@
#' Return the value of the parameter \code{par}, without the list
#' container of \code{\link{tpPar}}.
#'
-#'@export getTpPar
+#'@export
#'
getTpPar <- function(
par
Modified: pkg/ternaryplot/R/aa02-ternaryplot-classes.R
===================================================================
--- pkg/ternaryplot/R/aa02-ternaryplot-classes.R 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/R/aa02-ternaryplot-classes.R 2014-03-28 15:15:38 UTC (rev 101)
@@ -373,9 +373,10 @@
#'@example inst/examples/createTernaryGeometry-example.R
#'
#'
-#'@name createTernaryGeometry
+#'@rdname createTernaryGeometry
+#'@aliases ternaryGeometry
#'
-#'@export createTernaryGeometry
+#'@export
#'
createTernaryGeometry <- function(
tlrAngles = c( 60, 60, 60 ),
@@ -433,9 +434,10 @@
#'@example inst/examples/createTernaryVariables-example.R
#'
#'
-#'@name createTernaryVariables
+#'@rdname createTernaryVariables
+#'@aliases ternaryVariables
#'
-#'@export createTernaryVariables
+#'@export
#'
createTernaryVariables <- function(
blrNames = paste0( "F", 1:3 ),
@@ -518,10 +520,10 @@
#'@example inst/examples/createTernarySystem-example.R
#'
#'
-#'@name ternarySystem-class
+#'@rdname createTernarySystem
+#'@aliases ternarySystem
+#'@export
#'
-#'@exportClass ternarySystem
-#'
createTernarySystem <- function(
ternaryGeometry = NULL,
ternaryVariables = NULL,
Modified: pkg/ternaryplot/R/aa03-ternaryplot-classes-utility.R
===================================================================
--- pkg/ternaryplot/R/aa03-ternaryplot-classes-utility.R 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/R/aa03-ternaryplot-classes-utility.R 2014-03-28 15:15:38 UTC (rev 101)
@@ -21,7 +21,7 @@
#' A \code{ternarySystem} object, as created with
#' \code{\link[ternaryplot]{createTernarySystem}}, or a
#' \code{ternaryVariables} object, as created with
-#' \code{\link[ternaryplot]{ternaryVariables}}.
+#' \code{\link[ternaryplot]{createTernaryVariables}}.
#'
#'@param \dots
#' Additional parameters passed to \code{\link[ternaryplot]{ternaryCheck}}.
@@ -136,7 +136,7 @@
#' A \code{ternarySystem} object, as created with
#' \code{\link[ternaryplot]{createTernarySystem}}, or a
#' \code{ternaryVariables} object, as created with
-#' \code{\link[ternaryplot]{ternaryVariables}}.
+#' \code{\link[ternaryplot]{createTernaryVariables}}.
#'
#'@param \dots
#' Additional parameters passed to \code{\link[ternaryplot]{ternaryCheck}}.
Modified: pkg/ternaryplot/R/aa04-ternarysystems.R
===================================================================
--- pkg/ternaryplot/R/aa04-ternarysystems.R 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/R/aa04-ternarysystems.R 2014-03-28 15:15:38 UTC (rev 101)
@@ -145,7 +145,7 @@
#'
#'
#'@return
-#' A \code{\link[ternaryplot]{ternarySystem}} object.
+#' A \code{ternarySystem} object.
#'
#'
#'@export
Modified: pkg/ternaryplot/R/aa05-ternarydata.R
===================================================================
--- pkg/ternaryplot/R/aa05-ternarydata.R 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/R/aa05-ternarydata.R 2014-03-28 15:15:38 UTC (rev 101)
@@ -34,7 +34,7 @@
#'
#'@param s
#' A \code{ternarySystem} object, as created with
-#' \code{\link[ternaryplot]{ternarySystem}}, or a single
+#' \code{\link[ternaryplot]{createTernarySystem}}, or a single
#' \code{character} string. Can be missing.
#'
#'@param x
Modified: pkg/ternaryplot/R/aa06-ternary2xy.R
===================================================================
--- pkg/ternaryplot/R/aa06-ternary2xy.R 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/R/aa06-ternary2xy.R 2014-03-28 15:15:38 UTC (rev 101)
@@ -30,7 +30,7 @@
#'
#'Converts ternary point-data (bottom, left, right axis) into
#' x-y coordinates, according to the specification of a
-#' \code{\link[ternaryplot]{ternarySystem}}
+#' \code{ternarySystem}
#'
#'
#'@param s
Modified: pkg/ternaryplot/R/ternaryplot.R
===================================================================
--- pkg/ternaryplot/R/ternaryplot.R 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/R/ternaryplot.R 2014-03-28 15:15:38 UTC (rev 101)
@@ -21,7 +21,7 @@
#'
#'@param s
#' A \code{ternarySystem} object, as created with
-#' \code{\link[ternaryplot]{ternarySystem}}, or a single
+#' \code{\link[ternaryplot]{createTernarySystem}}, or a single
#' \code{character} string. Can be missing.
#'
#'@param x
@@ -1424,7 +1424,7 @@
#'@param s
#' Either a character string naming the ternary classification
#' system to be used (if pre-defined) or a
-#' \code{\link[ternaryplot]{ternarySystem}} x.
+#' \code{\link[ternaryplot]{ternarySystem}}, instead of \code{x}.
#'
#'@param x
#' A \code{\link[base]{data.frame}} or a \code{\link[base]{matrix}}
Added: pkg/ternaryplot/REVISION
===================================================================
--- pkg/ternaryplot/REVISION (rev 0)
+++ pkg/ternaryplot/REVISION 2014-03-28 15:15:38 UTC (rev 101)
@@ -0,0 +1 @@
+95:100M
Modified: pkg/ternaryplot/man/blrLabels-methods.Rd
===================================================================
--- pkg/ternaryplot/man/blrLabels-methods.Rd 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/man/blrLabels-methods.Rd 2014-03-28 15:15:38 UTC (rev 101)
@@ -26,7 +26,7 @@
\item{s}{A \code{ternarySystem} object, as created with
\code{\link[ternaryplot]{createTernarySystem}}, or a
\code{ternaryVariables} object, as created with
- \code{\link[ternaryplot]{ternaryVariables}}.}
+ \code{\link[ternaryplot]{createTernaryVariables}}.}
\item{\dots}{Additional parameters passed to
\code{\link[ternaryplot]{ternaryCheck}}.}
Modified: pkg/ternaryplot/man/blrNames-methods.Rd
===================================================================
--- pkg/ternaryplot/man/blrNames-methods.Rd 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/man/blrNames-methods.Rd 2014-03-28 15:15:38 UTC (rev 101)
@@ -25,7 +25,7 @@
\item{s}{A \code{ternarySystem} object, as created with
\code{\link[ternaryplot]{createTernarySystem}}, or a
\code{ternaryVariables} object, as created with
- \code{\link[ternaryplot]{ternaryVariables}}.}
+ \code{\link[ternaryplot]{createTernaryVariables}}.}
\item{\dots}{Additional parameters passed to
\code{\link[ternaryplot]{ternaryCheck}}.}
Modified: pkg/ternaryplot/man/createTernaryGeometry.Rd
===================================================================
--- pkg/ternaryplot/man/createTernaryGeometry.Rd 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/man/createTernaryGeometry.Rd 2014-03-28 15:15:38 UTC (rev 101)
@@ -1,5 +1,6 @@
\name{createTernaryGeometry}
\alias{createTernaryGeometry}
+\alias{ternaryGeometry}
\title{Creates a ternaryGeometry object: ternary plot geometry definition.}
\usage{
createTernaryGeometry(tlrAngles = c(60, 60, 60),
Added: pkg/ternaryplot/man/createTernarySystem.Rd
===================================================================
--- pkg/ternaryplot/man/createTernarySystem.Rd (rev 0)
+++ pkg/ternaryplot/man/createTernarySystem.Rd 2014-03-28 15:15:38 UTC (rev 101)
@@ -0,0 +1,87 @@
+\name{createTernarySystem}
+\alias{createTernarySystem}
+\alias{ternarySystem}
+\title{Creates a ternarySystem object: ternary plot system definition.}
+\usage{
+ createTernarySystem(ternaryGeometry = NULL,
+ ternaryVariables = NULL, main = character(0),
+ vertices = NULL, classes = NULL, scale = NULL, ...)
+}
+\arguments{
+ \item{ternaryGeometry}{A ternary geometry (as defined by
+ \code{\link[ternaryplot]{createTernaryGeometry}}). If
+ \code{NULL}, use the default output of
+ \code{\link[ternaryplot]{createTernaryGeometry}}.}
+
+ \item{ternaryVariables}{A set of ternary variables (as
+ defined by
+ \code{\link[ternaryplot]{createTernaryVariables}}. If
+ \code{NULL}, use the default output of
+ \code{\link[ternaryplot]{createTernaryVariables}}.}
+
+ \item{main}{Single character string. Title of the
+ triangle plot.}
+
+ \item{vertices}{See \code{\link[ternaryplot]{tpPar}}. If
+ non-null, \code{\link[base]{data.frame}} with 4 columns:
+ \code{id}, and 3 other columns corresponding to
+ \code{blrNames} in \code{ternaryVariables}. If
+ \code{NULL}, default values will be used
+ \code{getTpPar("vertices")}, and the columns names
+ changed to those of \code{ternaryVariables}.}
+
+ \item{classes}{See \code{\link[ternaryplot]{tpPar}}.}
+
+ \item{scale}{See \code{\link[ternaryplot]{tpPar}}. If
+ non-null, \code{\link[base]{data.frame}} with 3 columns,
+ corresponding to \code{blrNames} in
+ \code{ternaryVariables}. If \code{NULL}, default values
+ will be used \code{getTpPar("scale")}, and the columns
+ names changed to those of \code{ternaryVariables}. NOT
+ USED YET.}
+
+ \item{\dots}{Additional parameters passed to
+ \code{\link[ternaryplot]{ternaryCheck}}}
+}
+\description{
+ Creates a ternarySystem object: ternary plot system
+ definition.
+}
+\details{
+ Ternary systems are a combination of (a) a ternary
+ geometry (as defined by
+ \code{\link[ternaryplot]{createTernaryGeometry}}), (b) a
+ set of ternary variables (as defined by
+ \code{\link[ternaryplot]{createTernaryVariables}} and an
+ optional classification system, that is polygons drawn on
+ top of ternary plots, that define different zones in the
+ fractions.
+
+ The classification is defined by a collection of polygons
+ (in \code{classes}) with different \code{vertices}.
+}
+\examples{
+library( "ternaryplot" )
+
+
+## Default variables
+tsy <- createTernarySystem()
+tsy
+
+## Custom variables
+tsy2 <- createTernarySystem(
+ "ternaryVariables" = createTernaryVariables(
+ "blrNames" = c( "CLAY", "SILT", "SAND" ),
+ "blrLabels" = c( "Clay [\%]", "Silt [\%]", "Sand [\%]" )
+ ),
+ "ternaryGeometry" = createTernaryGeometry(
+ "ternaryGeometry",
+ "fracSum" = 100,
+ "tlrAngles" = c( 45, 45, 90 ) # top, left, right angles
+ ),
+ "main" = "My ternary plot" )
+
+tsy2
+
+}
+
Modified: pkg/ternaryplot/man/createTernaryVariables.Rd
===================================================================
--- pkg/ternaryplot/man/createTernaryVariables.Rd 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/man/createTernaryVariables.Rd 2014-03-28 15:15:38 UTC (rev 101)
@@ -1,5 +1,6 @@
\name{createTernaryVariables}
\alias{createTernaryVariables}
+\alias{ternaryVariables}
\title{Creates a ternaryVariables object: ternary plot variables definitions.}
\usage{
createTernaryVariables(blrNames = paste0("F", 1:3),
Modified: pkg/ternaryplot/man/getTernarySystem.Rd
===================================================================
--- pkg/ternaryplot/man/getTernarySystem.Rd 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/man/getTernarySystem.Rd 2014-03-28 15:15:38 UTC (rev 101)
@@ -9,7 +9,7 @@
classification to be fetched.}
}
\value{
- A \code{\link[ternaryplot]{ternarySystem}} object.
+ A \code{ternarySystem} object.
}
\description{
Fetch a pre-defined ternary classification system
Modified: pkg/ternaryplot/man/ternary2xy-methods.Rd
===================================================================
--- pkg/ternaryplot/man/ternary2xy-methods.Rd 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/man/ternary2xy-methods.Rd 2014-03-28 15:15:38 UTC (rev 101)
@@ -36,6 +36,6 @@
\description{
Converts ternary point-data (bottom, left, right axis)
into x-y coordinates, according to the specification of a
- \code{\link[ternaryplot]{ternarySystem}}
+ \code{ternarySystem}
}
Modified: pkg/ternaryplot/man/ternaryData-methods.Rd
===================================================================
--- pkg/ternaryplot/man/ternaryData-methods.Rd 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/man/ternaryData-methods.Rd 2014-03-28 15:15:38 UTC (rev 101)
@@ -14,8 +14,8 @@
}
\arguments{
\item{s}{A \code{ternarySystem} object, as created with
- \code{\link[ternaryplot]{ternarySystem}}, or a single
- \code{character} string. Can be missing.}
+ \code{\link[ternaryplot]{createTernarySystem}}, or a
+ single \code{character} string. Can be missing.}
\item{x}{A \code{\link[base]{data.frame}} or a
\code{\link[base]{matrix}} containing point ternary data
Modified: pkg/ternaryplot/man/ternaryLims-methods.Rd
===================================================================
--- pkg/ternaryplot/man/ternaryLims-methods.Rd 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/man/ternaryLims-methods.Rd 2014-03-28 15:15:38 UTC (rev 101)
@@ -13,7 +13,8 @@
\arguments{
\item{s}{Either a character string naming the ternary
classification system to be used (if pre-defined) or a
- \code{\link[ternaryplot]{ternarySystem}} x.}
+ \code{\link[ternaryplot]{ternarySystem}}, instead of
+ \code{x}.}
\item{x}{A \code{\link[base]{data.frame}} or a
\code{\link[base]{matrix}} containing point ternary data
Modified: pkg/ternaryplot/man/ternaryWindow-methods.Rd
===================================================================
--- pkg/ternaryplot/man/ternaryWindow-methods.Rd 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/man/ternaryWindow-methods.Rd 2014-03-28 15:15:38 UTC (rev 101)
@@ -14,8 +14,8 @@
}
\arguments{
\item{s}{A \code{ternarySystem} object, as created with
- \code{\link[ternaryplot]{ternarySystem}}, or a single
- \code{character} string. Can be missing.}
+ \code{\link[ternaryplot]{createTernarySystem}}, or a
+ single \code{character} string. Can be missing.}
\item{x}{A \code{\link[base]{data.frame}} or a
\code{\link[base]{matrix}} containing point ternary data
Modified: pkg/ternaryplot/man/ternaryplot-package.Rd
===================================================================
--- pkg/ternaryplot/man/ternaryplot-package.Rd 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/man/ternaryplot-package.Rd 2014-03-28 15:15:38 UTC (rev 101)
@@ -3,8 +3,12 @@
\alias{ternaryplot-package}
\title{Ternary plots and ternary classifications}
\description{
- Ternary plots and ternary classifications
+ Ternary plots and ternary classifications.
}
+\details{
+ Ternary plots and ternary classifications. S4 classes for
+ ternary data, ternary plots and ternary classification.
+}
\examples{
# Examples coming later
}
Modified: pkg/ternaryplot/man/tpPar.Rd
===================================================================
--- pkg/ternaryplot/man/tpPar.Rd 2014-03-28 14:58:55 UTC (rev 100)
+++ pkg/ternaryplot/man/tpPar.Rd 2014-03-28 15:15:38 UTC (rev 101)
@@ -37,9 +37,9 @@
\item{fracSumTol}{Single numeric. Tolerance on the sum of
the 3 ternary fractions. Overall tolerance is
\code{fracSum * fracSumTol}, where \code{fracSum} is the
- expected sum of the 3 ternary fractions, as given by a
- \code{\link[ternaryplot]{ternaryGeometry}} or a
- \code{\link[ternaryplot]{ternarySystem}}.}
+ expected sum of the 3 ternary fractions. See
+ \code{\link[ternaryplot]{createTernaryGeometry}} or
+ \code{\link[ternaryplot]{createTernarySystem}}.}
\item{ticksAt}{Vector of numeric. Pre-defined position of
the tick-marks for the 3 axis. Between 0 and 'fracSum'
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