[Soiltexture-commits] r85 - pkg/soiltexture/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jan 9 11:04:52 CET 2014
Author: jmoeys
Date: 2014-01-09 11:04:51 +0100 (Thu, 09 Jan 2014)
New Revision: 85
Modified:
pkg/soiltexture/man/TT.classes.Rd
pkg/soiltexture/man/TT.classes.tbl.Rd
pkg/soiltexture/man/TT.points.in.classes.Rd
pkg/soiltexture/man/soiltexture-package.Rd
Log:
Modified: pkg/soiltexture/man/TT.classes.Rd
===================================================================
--- pkg/soiltexture/man/TT.classes.Rd 2014-01-09 10:03:18 UTC (rev 84)
+++ pkg/soiltexture/man/TT.classes.Rd 2014-01-09 10:04:51 UTC (rev 85)
@@ -1,160 +1,80 @@
-\name{TT.classes}
+\name{TT.classes}
+\alias{TT.classes}
+\title{Plot the texture classes polygons in a texture triangle plot.}
+\description{Plot the texture classes ploygons in an existing texture
+triangle plot. Draw the polygons and the labels inside each
+polygons.}
+\usage{TT.classes(geo, class.sys, tri.css.ps.lim = NULL, css.transf = NULL,
+ text.transf.fun = NULL, trsf.add.opt1 = NULL, trsf.add.opt2 = NULL,
+ text.tol = NULL, text.sum = NULL, base.css.ps.lim = NULL,
+ blr.tx = NULL, blr.clock = NULL, tri.sum.tst = NULL, tri.pos.tst = NULL,
+ bg = NULL, class.lab.col = NULL, class.p.bg.col = NULL, class.p.bg.hue = NULL,
+ class.line.col = NULL, class.lty = NULL, class.lab.show = NULL,
+ cex.lab = NULL, font.lab = NULL, family.op = NULL, lwd.axis = NULL,
+ col.axis = NULL, new.centroid = TRUE)}
+\arguments{
+ \item{geo}{
+}
+ \item{class.sys}{
+}
+ \item{tri.css.ps.lim}{
+}
+ \item{css.transf}{
+}
+ \item{text.transf.fun}{
+}
+ \item{trsf.add.opt1}{
+}
+ \item{trsf.add.opt2}{
+}
+ \item{text.tol}{
+}
+ \item{text.sum}{
+}
+ \item{base.css.ps.lim}{
+}
+ \item{blr.tx}{
+}
+ \item{blr.clock}{
+}
+ \item{tri.sum.tst}{
+}
+ \item{tri.pos.tst}{
+}
+ \item{bg}{
+}
+ \item{class.lab.col}{
+}
+ \item{class.p.bg.col}{
+}
+ \item{class.p.bg.hue}{
+}
+ \item{class.line.col}{
+}
+ \item{class.lty}{
+}
+ \item{class.lab.show}{
+}
+ \item{cex.lab}{
+}
+ \item{font.lab}{
+}
+ \item{family.op}{
+}
+ \item{lwd.axis}{
+}
+ \item{col.axis}{
+}
+ \item{new.centroid}{Single logical. If TRUE (default) the new method (Paul Bourke)
+is used to calculate the centroid. If FALSE the centroid is
+taken as the mean x and y coordinates of the vertices.}
+}
-\alias{TT.classes}
-\title{Plot the texture classes polygons in a texture triangle plot.}
-\description{Plot the texture classes ploygons in an existing texture
+\author{Julien MOEYS <jules_m78-soiltexture at yahoo.fr>, contributions from Wei Shangguan.}
-triangle plot. Draw the polygons and the labels inside each
-polygons.}
-\usage{TT.classes(geo, class.sys, tri.css.ps.lim = NULL, css.transf = NULL,
- text.transf.fun = NULL, trsf.add.opt1 = NULL, trsf.add.opt2 = NULL,
- text.tol = NULL, text.sum = NULL, base.css.ps.lim = NULL,
-
- blr.tx = NULL, blr.clock = NULL, tri.sum.tst = NULL, tri.pos.tst = NULL,
-
- bg = NULL, class.lab.col = NULL, class.p.bg.col = NULL, class.p.bg.hue = NULL,
-
- class.line.col = NULL, class.lty = NULL, class.lab.show = NULL,
-
- cex.lab = NULL, font.lab = NULL, family.op = NULL, lwd.axis = NULL,
-
- col.axis = NULL, new.centroid = TRUE)}
-
-\arguments{
-
- \item{geo}{
-
-}
-
- \item{class.sys}{
-
-}
-
- \item{tri.css.ps.lim}{
-
-}
-
- \item{css.transf}{
-
-}
-
- \item{text.transf.fun}{
-
-}
-
- \item{trsf.add.opt1}{
-
-}
-
- \item{trsf.add.opt2}{
-
-}
-
- \item{text.tol}{
-
-}
-
- \item{text.sum}{
-
-}
-
- \item{base.css.ps.lim}{
-
-}
-
- \item{blr.tx}{
-
-}
-
- \item{blr.clock}{
-
-}
-
- \item{tri.sum.tst}{
-
-}
-
- \item{tri.pos.tst}{
-
-}
-
- \item{bg}{
-
-}
-
- \item{class.lab.col}{
-
-}
-
- \item{class.p.bg.col}{
-
-}
-
- \item{class.p.bg.hue}{
-
-}
-
- \item{class.line.col}{
-
-}
-
- \item{class.lty}{
-
-}
-
- \item{class.lab.show}{
-
-}
-
- \item{cex.lab}{
-
-}
-
- \item{font.lab}{
-
-}
-
- \item{family.op}{
-
-}
-
- \item{lwd.axis}{
-
-}
-
- \item{col.axis}{
-
-}
-
- \item{new.centroid}{Single logical. If TRUE (default) the new method (Paul Bourke)
-
-is used to calculate the centroid. If FALSE the centroid is
-
-taken as the mean x and y coordinates of the vertices.}
-
-}
-
-
-
-
-
-
-
-\author{Julien MOEYS <jules_m78-soiltexture at yahoo.fr>, contributions from Wei Shangguan.}
-
-
-
-
-
-
-
-
-
-
-
Modified: pkg/soiltexture/man/TT.classes.tbl.Rd
===================================================================
--- pkg/soiltexture/man/TT.classes.tbl.Rd 2014-01-09 10:03:18 UTC (rev 84)
+++ pkg/soiltexture/man/TT.classes.tbl.Rd 2014-01-09 10:04:51 UTC (rev 85)
@@ -1,48 +1,24 @@
-\name{TT.classes.tbl}
+\name{TT.classes.tbl}
+\alias{TT.classes.tbl}
+\title{Returns the table of classes of a texture classification system.}
+\description{Returns the table of classes of a texture classification system.
+Returns the classes abbreviations, names and the vertices numbers
+that defines each class. Use TT.vertices.tbl() to retrieve the
+clay silt sand coordinates of the triangle classes vertices.
+See also TT.vertices.plot().}
+\usage{TT.classes.tbl(class.sys = "FAO50.TT", collapse = NULL)}
+\arguments{
+ \item{class.sys}{
+}
+ \item{collapse}{
+}
+}
-\alias{TT.classes.tbl}
-\title{Returns the table of classes of a texture classification system.}
-\description{Returns the table of classes of a texture classification system.
+\author{Julien MOEYS <jules_m78-soiltexture at yahoo.fr>, contributions from Wei Shangguan.}
-Returns the classes abbreviations, names and the vertices numbers
-that defines each class. Use TT.vertices.tbl() to retrieve the
-clay silt sand coordinates of the triangle classes vertices.
-See also TT.vertices.plot().}
-\usage{TT.classes.tbl(class.sys = "FAO50.TT", collapse = NULL)}
-
-\arguments{
-
- \item{class.sys}{
-
-}
-
- \item{collapse}{
-
-}
-
-}
-
-
-
-
-
-
-
-\author{Julien MOEYS <jules_m78-soiltexture at yahoo.fr>, contributions from Wei Shangguan.}
-
-
-
-
-
-
-
-
-
-
-
Modified: pkg/soiltexture/man/TT.points.in.classes.Rd
===================================================================
--- pkg/soiltexture/man/TT.points.in.classes.Rd 2014-01-09 10:03:18 UTC (rev 84)
+++ pkg/soiltexture/man/TT.points.in.classes.Rd 2014-01-09 10:04:51 UTC (rev 85)
@@ -1,468 +1,234 @@
-\name{TT.points.in.classes}
+\name{TT.points.in.classes}
+\alias{TT.points.in.classes}
+\title{Classify a table of soil texture data according to a soil texture triangle.}
+\description{The function calculate in which classe(s) of a texture triangle
+(classification system defined by 'class.sys') lies each soil
+sample (with texture data) in the table 'tri.data'. As a sample
+may lie inside a texture class, but also at the edge of 2 or
+more texture classes, the function does not only output
+one single texture class per sample. If 'PiC.type' is 'n' or
+'l', it rather output a table where each column is a texture
+class and each row a texture sample, and yes / no information
+about the belonging of the sample to each texture class.
+Alternatively, If 'PiC.type' is 't'it will output a text
+string (per sample) containing all the texture classes
+to which that point belong.
+The texture data in 'tri.data' can be transformed into
+another particle size system prior to their classification
+if needed. See the options base.css.ps.lim, tri.css.ps.lim,
+dat.css.ps.lim, css.transf and text.transf.fun.
+ON DEFAULT VALUES OF TT.points.in.classes() ARGUMENTS? As
+TT.points.in.classes() shares
+its arguments with many other functions, their default value
+is not defined in TT.points.in.classes() source code, but rather in
+a dedicated list object called 'TT.par' and stored in the
+environment TT.env. The function TT.get() is used to retrieve
+the default value of the arguments defined in TT.par (see
+?TT.get). For instance, to know the default value of 'class.sys',
+you can type TT.get("class.sys"). To set a different default
+value for a given argument in R, use TT.set() (see ?TT.set).
+For instance to change the default value of 'class.sys', type
+TT.set( "class.sys" = "USDA.TT" ).}
+\usage{TT.points.in.classes(tri.data, class.sys = NULL, PiC.type = NULL,
+ css.names = NULL, text.sum = NULL, base.css.ps.lim = NULL,
+ tri.css.ps.lim = NULL, dat.css.ps.lim = NULL, css.transf = NULL,
+ text.transf.fun = NULL, trsf.add.opt1 = NULL, trsf.add.opt2 = NULL,
+ text.tol = NULL, tri.sum.tst = NULL, tri.pos.tst = NULL,
+ collapse = NULL, texture2xy = FALSE, blr.tx = NULL, blr.clock = NULL)}
+\arguments{
+ \item{tri.data}{Data frame. Data frame containing the CLAY, SILT and SAND
+'coordinates' of the texture data points to be classified The data
+frame can contain more column than needed (ignored). The data
+frame must have column named CLAY, SILT and SAND (uppercase,
+the order has no importance) or named after the 'css.names'
+argument (alternative names). The sum of CLAY, SILT and SAND
+must be equal to 'text.sum'
+('text.tol' determines the error tolerance).}
+ \item{class.sys}{Single text string. Text code of the texture classification
+system to be used for the classification of 'tri.data'.
+Possible values are "none" (no classification plotted), "USDA.TT"
+(USDA texture triangle), "FAO50.TT" (FAO texture triangle with a 50
+microns silt-sand limit. DEFAULT VALUE), "FR.AISNE.TT" (French
+texture triangle of the Aisne region soil survey), "FR.GEPPA.TT" (French GEPPA
+texture triangle), "DE.BK94.TT" (German texture triangle),
+"UK.SSEW.TT" (Soil Survey of England and Wales), "AU.TT"
+(Australian texture triangle), "BE.TT" (Belgium texture triangle),
+"CA.EN.TT" (Canadian texture triangle, with English class abbreviations) and
+"CA.FR.TT" (Canadian texture triangle, with French class abbreviations)
+(see the package vignette for a complete list).}
+ \item{PiC.type}{Single character string. If equal to 'n', then a table of 0,
+1, 2 or 3 is outputed (0 if the sample does not belong to a class,
+1 if it does, 2 if it lies on an edge and 3 if it lies on a
+vertex). Notice that the accuracy of the classification is
+not garanteed for samples lying very close to an edge, or right
+on it. See <http://www.mail-archive.com/r-help@r-project.org/msg96180.html>}
+ \item{css.names}{Vector of 3 character strings. Name of the columns in 'tri.data'
+that contains the CLAY SILT and SAND values, respectively.
+If NULL, default c("CLAY","SILT","SAND") value is assumed. Not
+to be confused with 'css.lab' that defines the labels of the
+CLAY SILT and SAND axes in the plot.}
+ \item{text.sum}{Single numerical. Sum of the 3 particle size classes for each texture
+value (fixed). The real sum of the 3 particle size classes in 'tri.data'
+should be >= text.sum * (1-text.tol) OR <= text.sum * (1+text.tol),
+where 'text.tol' is an argument that can be changed. If some
+of the texture values don't match this requirement, an error
+occur (function fails) and TT.points.in.classes returns a of bad values with
+their actual particle size classes sum. You can 'normalise' you data
+table () prior to the use of TT.points.in.classes, by using the function
+TT.normalise.sum(), so all values match the 'text.sum' criteria.
+See also 'tri.sum.tst' that can be set to FALSE to avoid
+sum of particle size classes tests.}
+ \item{base.css.ps.lim}{Vector of 4 numericals. Particle size boundaries (upper and lower)
+of the 3 particle size classes (CLAY, SILT and SAND, starting from
+the lower size of CLAY particles, 0, to the upper size of the
+SAND particles, 2000), in micrometers, FOR THE BASE SYSTEM. These
+particles size class limits are the references and all other
+texture values with different limits will be converted into
+that reference if (and only if) css.transf == TRUE (not default).
+If NULL, 'base.css.ps.lim' will be set to the default value of the
+texture classification system chosen ('class.sys'). The
+transformation function is set by 'text.transf.fun' and is
+a log-linear interpolation by default.}
+ \item{tri.css.ps.lim}{Vector of 4 numericals. Particle size boundaries (upper and lower)
+of the 3 particle size classes (CLAY, SILT and SAND, starting from
+the lower size of CLAY particles, 0, to the upper size of the
+SAND particles, 2000), in micrometers, FOR THE TEXTURE TRIANGLE.
+If not NULL, different from 'base.css.ps.lim', and
+css.transf == TRUE (not default), then the CLAY SILT and SAND
+coordinates of the texture triangle will be converted into
+the 'base.css.ps.lim' reference. If NULL, 'tri.css.ps.lim' will
+be set to the default value of the texture classification system
+chosen ('class.sys'). The transformation function is set by
+'text.transf.fun' and is a log-linear interpolation by default.}
+ \item{dat.css.ps.lim}{Vector of 4 numericals. Particle size boundaries (upper and lower)
+of the 3 particle size classes (CLAY, SILT and SAND, starting from
+the lower size of CLAY particles, 0, to the upper size of the
+SAND particles, 2000), in micrometers, FOR THE TEXTURE DATA TABLE
+('tri.data'). If not NULL, different from 'base.css.ps.lim', and
+css.transf == TRUE (not default), then the CLAY SILT and SAND
+coordinates of the texture data in tri.data will be converted into
+the 'base.css.ps.lim' reference. If NULL, 'tri.css.ps.lim' will
+be set to the default value of the texture classification system
+chosen ('class.sys'). The transformation function is set by
+'text.transf.fun' and is a log-linear interpolation by default.}
+ \item{css.transf}{Single logical. Set to TRUE to transform the texture coordinates
+of the texture triangle ('class.sys') or the texture data
+('tri.data') into the base particle size class limits.
+See 'base.css.ps.lim' for the base plot particle size class limits,
+'tri.css.ps.lim' for the triangle particle size class limits
+and 'dat.css.ps.lim' for the data table particle size class limits.
+The transformation function is set by 'text.transf.fun' and
+is a log-linear interpolation by default. The default value is
+FALSE, so no transformation is made.}
+ \item{text.transf.fun}{R function with the same argument names and same output as
+the function TT.text.transf(). 'text.transf.fun' is the function
+that transform the texture values from one system of particle
+class size limits to another. Only used if css.transf == TRUE.
+Default value is text.transf.fun=TT.text.transf. See also
+'base.css.ps.lim', 'tri.css.ps.lim' and 'dat.css.ps.lim'.}
+ \item{trsf.add.opt1}{Non pre-defined format. If the user specifies its own texture
+transformation function in 'text.transf.fun' (not TT.text.transf()),
+then he can use 'trsf.add.opt1' and 'trsf.add.opt1' as
+new, additional, argument for his function. So the format of
+'trsf.add.opt1' depends on the function defined by the user
+in 'text.transf.fun'.}
+ \item{trsf.add.opt2}{Non pre-defined format. If the user specifies its own texture
+transformation function in 'text.transf.fun' (not TT.text.transf()),
+then he can use 'trsf.add.opt1' and 'trsf.add.opt1' as
+new, additional, argument for his function. So the format of
+'trsf.add.opt1' depends on the function defined by the user
+in 'text.transf.fun'.}
+ \item{text.tol}{Single numerical. Tolerance on the sum of the 3 particle size classes.
+The real sum of the 3 particle size classes in
+'tri.data' should be >= text.sum * (1-text.tol) OR
+<= text.sum * (1+text.tol). See 'text.sum' for more details, as
+well as 'tri.sum.tst' (to prevent texture sum tests).}
+ \item{tri.sum.tst}{Single logical. If TRUE (the default), the sum of the 3 texture
+classes of each texture value in 'tri.data' will be checked
+in regard to 'text.sum' and 'text.tol'. If FALSE, no test
+is done.}
+ \item{tri.pos.tst}{Single logical. If TRUE (the default), the position of texture
+values in 'tri.data' are tested to check that they are not
+OUTSIDE the texture triangle (i.e. that some texture values may
+be negative).}
+ \item{collapse}{Single character string. If PiC.type = "t" and a sample lie
+on the edge of 2 texture classes, then both will be outputed
+in a single character string, separated by 'collapse'. Example of
+output: [1] "C" "VF, F" "C" "C" "M"}
+ \item{texture2xy}{Single logical. Set to FALSE to avoid any transformation of the
+texture data (trigonometric) prior to testure data classification.
+Setting to FALSE avoid some numerical accuracy problems when
+a point is on the border of a texture class.}
+ \item{blr.tx}{Vector of 3 character strings. The 1st, 2nd and 3rd values must
+be either CLAY, SILT or SAND, and determines the particle size classes
+associated with the BOTTOM, LEFT and RIGHT axis, respectively.
+CLAY, SILT and SAND order in the vector is free, but they should
+all be used one time. The CLAY, SILT and SAND names must appear
+whatever the corresponding columns names in 'tri.data' (eventually
+set by 'css.names') and whatever the labels of the axis in the
+plot (eventually set by 'css.lab') }
+ \item{blr.clock}{Vector of logicals, eventually with NA values. Direction of
+increasing texture values on the BOTTOM, LEFT and RIGHT axis,
+respectively. A value of TRUE means that the axis direction is
+clockwise. A value of FALSE means that the axis direction is
+counterclockwise. A value of NA means that the axis direction
+is centripetal. Possible combinations are c(T,T,T); c(F,F,F);
+c(F,T,NA) and c(T,NA,F), for fully clockwise, fully counterclockwise,
+right centripetal and left centripetal orientations, respectively.}
+}
-\alias{TT.points.in.classes}
-\title{Classify a table of soil texture data according to a soil texture triangle.}
-\description{The function calculate in which classe(s) of a texture triangle
+\author{Julien MOEYS <jules_m78-soiltexture at yahoo.fr>, contributions from Wei Shangguan.}
-(classification system defined by 'class.sys') lies each soil
-sample (with texture data) in the table 'tri.data'. As a sample
-may lie inside a texture class, but also at the edge of 2 or
-more texture classes, the function does not only output
+\examples{require( "soiltexture" )
-one single texture class per sample. If 'PiC.type' is 'n' or
+# Create a dummy data frame of soil textures:
+my.text <- data.frame(
+ "CLAY" = c(05,60,15,05,25,05,25,45,65,75,13,47),
+ "SILT" = c(05,08,15,25,55,85,65,45,15,15,17,43),
+ "SAND" = c(90,32,70,70,20,10,10,10,20,10,70,10),
+ "OC" = c(20,14,15,05,12,15,07,21,25,30,05,28)
+) #
-'l', it rather output a table where each column is a texture
+# Display the table:
+my.text
-class and each row a texture sample, and yes / no information
+# Classify according to the FAO classification
+TT.points.in.classes(
+ tri.data = my.text[1:5,],
+ class.sys = "FAO50.TT"
+) #
-about the belonging of the sample to each texture class.
+# Classify according to the USDA classification
+TT.points.in.classes(
+ tri.data = my.text[1:5,],
+ class.sys = "USDA.TT"
+) #
-Alternatively, If 'PiC.type' is 't'it will output a text
+# Classify according to the FAO classification, returns logicals
+TT.points.in.classes(
+ tri.data = my.text[1:5,],
+ class.sys = "FAO50.TT",
+ PiC.type = "l"
+) #
-string (per sample) containing all the texture classes
+# Classify according to the FAO classification, returns text
+TT.points.in.classes(
+ tri.data = my.text[1:5,],
+ class.sys = "FAO50.TT",
+ PiC.type = "t"
+) #
-to which that point belong.
-
-The texture data in 'tri.data' can be transformed into
-
-another particle size system prior to their classification
-
-if needed. See the options base.css.ps.lim, tri.css.ps.lim,
-
-dat.css.ps.lim, css.transf and text.transf.fun.
-
-ON DEFAULT VALUES OF TT.points.in.classes() ARGUMENTS? As
-
-TT.points.in.classes() shares
-
-its arguments with many other functions, their default value
-
-is not defined in TT.points.in.classes() source code, but rather in
-
-a dedicated list object called 'TT.par' and stored in the
-
-environment TT.env. The function TT.get() is used to retrieve
-
-the default value of the arguments defined in TT.par (see
-
-?TT.get). For instance, to know the default value of 'class.sys',
-
-you can type TT.get("class.sys"). To set a different default
-
-value for a given argument in R, use TT.set() (see ?TT.set).
-
-For instance to change the default value of 'class.sys', type
-
-TT.set( "class.sys" = "USDA.TT" ).}
-
-\usage{TT.points.in.classes(tri.data, class.sys = NULL, PiC.type = NULL,
-
- css.names = NULL, text.sum = NULL, base.css.ps.lim = NULL,
-
- tri.css.ps.lim = NULL, dat.css.ps.lim = NULL, css.transf = NULL,
-
- text.transf.fun = NULL, trsf.add.opt1 = NULL, trsf.add.opt2 = NULL,
-
- text.tol = NULL, tri.sum.tst = NULL, tri.pos.tst = NULL,
-
- collapse = NULL, texture2xy = FALSE, blr.tx = NULL, blr.clock = NULL)}
-
-\arguments{
-
- \item{tri.data}{Data frame. Data frame containing the CLAY, SILT and SAND
-
-'coordinates' of the texture data points to be classified The data
-
-frame can contain more column than needed (ignored). The data
-
-frame must have column named CLAY, SILT and SAND (uppercase,
-
-the order has no importance) or named after the 'css.names'
-
-argument (alternative names). The sum of CLAY, SILT and SAND
-
-must be equal to 'text.sum'
-
-('text.tol' determines the error tolerance).}
-
- \item{class.sys}{Single text string. Text code of the texture classification
-
-system to be used for the classification of 'tri.data'.
-
-Possible values are "none" (no classification plotted), "USDA.TT"
-
-(USDA texture triangle), "FAO50.TT" (FAO texture triangle with a 50
-
-microns silt-sand limit. DEFAULT VALUE), "FR.AISNE.TT" (French
-
-texture triangle of the Aisne region soil survey), "FR.GEPPA.TT" (French GEPPA
-
-texture triangle), "DE.BK94.TT" (German texture triangle),
-
-"UK.SSEW.TT" (Soil Survey of England and Wales), "AU.TT"
-
-(Australian texture triangle), "BE.TT" (Belgium texture triangle),
-
-"CA.EN.TT" (Canadian texture triangle, with English class abbreviations) and
-
-"CA.FR.TT" (Canadian texture triangle, with French class abbreviations)
-
-(see the package vignette for a complete list).}
-
- \item{PiC.type}{Single character string. If equal to 'n', then a table of 0,
-
-1, 2 or 3 is outputed (0 if the sample does not belong to a class,
-
-1 if it does, 2 if it lies on an edge and 3 if it lies on a
-
-vertex). Notice that the accuracy of the classification is
-
-not garanteed for samples lying very close to an edge, or right
-
-on it. See <http://www.mail-archive.com/r-help@r-project.org/msg96180.html>}
-
- \item{css.names}{Vector of 3 character strings. Name of the columns in 'tri.data'
-
-that contains the CLAY SILT and SAND values, respectively.
-
-If NULL, default c("CLAY","SILT","SAND") value is assumed. Not
-
-to be confused with 'css.lab' that defines the labels of the
-
-CLAY SILT and SAND axes in the plot.}
-
- \item{text.sum}{Single numerical. Sum of the 3 particle size classes for each texture
-
-value (fixed). The real sum of the 3 particle size classes in 'tri.data'
-
-should be >= text.sum * (1-text.tol) OR <= text.sum * (1+text.tol),
-
-where 'text.tol' is an argument that can be changed. If some
-
-of the texture values don't match this requirement, an error
-
-occur (function fails) and TT.points.in.classes returns a of bad values with
-
-their actual particle size classes sum. You can 'normalise' you data
-
-table () prior to the use of TT.points.in.classes, by using the function
-
-TT.normalise.sum(), so all values match the 'text.sum' criteria.
-
-See also 'tri.sum.tst' that can be set to FALSE to avoid
-
-sum of particle size classes tests.}
-
- \item{base.css.ps.lim}{Vector of 4 numericals. Particle size boundaries (upper and lower)
-
-of the 3 particle size classes (CLAY, SILT and SAND, starting from
-
-the lower size of CLAY particles, 0, to the upper size of the
-
-SAND particles, 2000), in micrometers, FOR THE BASE SYSTEM. These
-
-particles size class limits are the references and all other
-
-texture values with different limits will be converted into
-
-that reference if (and only if) css.transf == TRUE (not default).
-
-If NULL, 'base.css.ps.lim' will be set to the default value of the
-
-texture classification system chosen ('class.sys'). The
-
-transformation function is set by 'text.transf.fun' and is
-
-a log-linear interpolation by default.}
-
- \item{tri.css.ps.lim}{Vector of 4 numericals. Particle size boundaries (upper and lower)
-
-of the 3 particle size classes (CLAY, SILT and SAND, starting from
-
-the lower size of CLAY particles, 0, to the upper size of the
-
-SAND particles, 2000), in micrometers, FOR THE TEXTURE TRIANGLE.
-
-If not NULL, different from 'base.css.ps.lim', and
-
-css.transf == TRUE (not default), then the CLAY SILT and SAND
-
-coordinates of the texture triangle will be converted into
-
-the 'base.css.ps.lim' reference. If NULL, 'tri.css.ps.lim' will
-
-be set to the default value of the texture classification system
-
-chosen ('class.sys'). The transformation function is set by
-
-'text.transf.fun' and is a log-linear interpolation by default.}
-
- \item{dat.css.ps.lim}{Vector of 4 numericals. Particle size boundaries (upper and lower)
-
-of the 3 particle size classes (CLAY, SILT and SAND, starting from
-
-the lower size of CLAY particles, 0, to the upper size of the
-
-SAND particles, 2000), in micrometers, FOR THE TEXTURE DATA TABLE
-
-('tri.data'). If not NULL, different from 'base.css.ps.lim', and
-
-css.transf == TRUE (not default), then the CLAY SILT and SAND
-
-coordinates of the texture data in tri.data will be converted into
-
-the 'base.css.ps.lim' reference. If NULL, 'tri.css.ps.lim' will
-
-be set to the default value of the texture classification system
-
-chosen ('class.sys'). The transformation function is set by
-
-'text.transf.fun' and is a log-linear interpolation by default.}
-
- \item{css.transf}{Single logical. Set to TRUE to transform the texture coordinates
-
-of the texture triangle ('class.sys') or the texture data
-
-('tri.data') into the base particle size class limits.
-
-See 'base.css.ps.lim' for the base plot particle size class limits,
-
-'tri.css.ps.lim' for the triangle particle size class limits
-
-and 'dat.css.ps.lim' for the data table particle size class limits.
-
-The transformation function is set by 'text.transf.fun' and
-
-is a log-linear interpolation by default. The default value is
-
-FALSE, so no transformation is made.}
-
- \item{text.transf.fun}{R function with the same argument names and same output as
-
-the function TT.text.transf(). 'text.transf.fun' is the function
-
-that transform the texture values from one system of particle
-
-class size limits to another. Only used if css.transf == TRUE.
-
-Default value is text.transf.fun=TT.text.transf. See also
-
-'base.css.ps.lim', 'tri.css.ps.lim' and 'dat.css.ps.lim'.}
-
- \item{trsf.add.opt1}{Non pre-defined format. If the user specifies its own texture
-
-transformation function in 'text.transf.fun' (not TT.text.transf()),
-
-then he can use 'trsf.add.opt1' and 'trsf.add.opt1' as
-
-new, additional, argument for his function. So the format of
-
-'trsf.add.opt1' depends on the function defined by the user
-
-in 'text.transf.fun'.}
-
- \item{trsf.add.opt2}{Non pre-defined format. If the user specifies its own texture
-
-transformation function in 'text.transf.fun' (not TT.text.transf()),
-
-then he can use 'trsf.add.opt1' and 'trsf.add.opt1' as
-
-new, additional, argument for his function. So the format of
-
-'trsf.add.opt1' depends on the function defined by the user
-
-in 'text.transf.fun'.}
-
- \item{text.tol}{Single numerical. Tolerance on the sum of the 3 particle size classes.
-
-The real sum of the 3 particle size classes in
-
-'tri.data' should be >= text.sum * (1-text.tol) OR
-
-<= text.sum * (1+text.tol). See 'text.sum' for more details, as
-
-well as 'tri.sum.tst' (to prevent texture sum tests).}
-
- \item{tri.sum.tst}{Single logical. If TRUE (the default), the sum of the 3 texture
-
-classes of each texture value in 'tri.data' will be checked
-
-in regard to 'text.sum' and 'text.tol'. If FALSE, no test
-
-is done.}
-
- \item{tri.pos.tst}{Single logical. If TRUE (the default), the position of texture
-
-values in 'tri.data' are tested to check that they are not
-
-OUTSIDE the texture triangle (i.e. that some texture values may
-
-be negative).}
-
- \item{collapse}{Single character string. If PiC.type = "t" and a sample lie
-
-on the edge of 2 texture classes, then both will be outputed
-
-in a single character string, separated by 'collapse'. Example of
-
-output: [1] "C" "VF, F" "C" "C" "M"}
-
- \item{texture2xy}{Single logical. Set to FALSE to avoid any transformation of the
-
-texture data (trigonometric) prior to testure data classification.
-
-Setting to FALSE avoid some numerical accuracy problems when
-
-a point is on the border of a texture class.}
-
- \item{blr.tx}{Vector of 3 character strings. The 1st, 2nd and 3rd values must
-
-be either CLAY, SILT or SAND, and determines the particle size classes
-
-associated with the BOTTOM, LEFT and RIGHT axis, respectively.
-
-CLAY, SILT and SAND order in the vector is free, but they should
-
-all be used one time. The CLAY, SILT and SAND names must appear
-
-whatever the corresponding columns names in 'tri.data' (eventually
-
-set by 'css.names') and whatever the labels of the axis in the
-
-plot (eventually set by 'css.lab') }
-
- \item{blr.clock}{Vector of logicals, eventually with NA values. Direction of
-
-increasing texture values on the BOTTOM, LEFT and RIGHT axis,
-
-respectively. A value of TRUE means that the axis direction is
-
-clockwise. A value of FALSE means that the axis direction is
-
-counterclockwise. A value of NA means that the axis direction
-
-is centripetal. Possible combinations are c(T,T,T); c(F,F,F);
-
-c(F,T,NA) and c(T,NA,F), for fully clockwise, fully counterclockwise,
-
-right centripetal and left centripetal orientations, respectively.}
-
-}
-
-
-
-
-
-
-
-\author{Julien MOEYS <jules_m78-soiltexture at yahoo.fr>, contributions from Wei Shangguan.}
-
-
-
-
-
-
-
-
-
-\examples{require( "soiltexture" )
-
-
-
-# Create a dummy data frame of soil textures:
-
-my.text <- data.frame(
-
- "CLAY" = c(05,60,15,05,25,05,25,45,65,75,13,47),
-
- "SILT" = c(05,08,15,25,55,85,65,45,15,15,17,43),
-
- "SAND" = c(90,32,70,70,20,10,10,10,20,10,70,10),
-
- "OC" = c(20,14,15,05,12,15,07,21,25,30,05,28)
-
-) #
-
-
-
-# Display the table:
-
-my.text
-
-
-
-# Classify according to the FAO classification
-
-TT.points.in.classes(
-
- tri.data = my.text[1:5,],
-
- class.sys = "FAO50.TT"
-
-) #
-
-
-
-# Classify according to the USDA classification
-
-TT.points.in.classes(
-
- tri.data = my.text[1:5,],
-
- class.sys = "USDA.TT"
-
-) #
-
-
-
-# Classify according to the FAO classification, returns logicals
-
-TT.points.in.classes(
-
- tri.data = my.text[1:5,],
-
- class.sys = "FAO50.TT",
-
- PiC.type = "l"
-
-) #
-
-
-
-# Classify according to the FAO classification, returns text
-
-TT.points.in.classes(
-
- tri.data = my.text[1:5,],
-
- class.sys = "FAO50.TT",
-
- PiC.type = "t"
-
-) #
-
-
-
-# Classify according to the FAO classification, returns text,
-
-# custom class separator in case of points belonging to
-
-# several classes.
-
-TT.points.in.classes(
-
- tri.data = my.text[1:5,],
-
- class.sys = "FAO50.TT",
-
- PiC.type = "t",
-
- collapse = ";"
-
-) #}
-
+# Classify according to the FAO classification, returns text,
+# custom class separator in case of points belonging to
+# several classes.
+TT.points.in.classes(
+ tri.data = my.text[1:5,],
+ class.sys = "FAO50.TT",
+ PiC.type = "t",
+ collapse = ";"
+) #}
Modified: pkg/soiltexture/man/soiltexture-package.Rd
===================================================================
--- pkg/soiltexture/man/soiltexture-package.Rd 2014-01-09 10:03:18 UTC (rev 84)
+++ pkg/soiltexture/man/soiltexture-package.Rd 2014-01-09 10:04:51 UTC (rev 85)
@@ -2,6 +2,8 @@
\alias{soiltexture-package}
+\alias{soiltexture}
+
\docType{package}
\title{Functions for soil texture plot, classification and transformation}
@@ -32,9 +34,9 @@
\tabular{ll}{Package: \tab soiltexture\cr
-Version: \tab 1.2.10\cr
+Version: \tab 1.2.11\cr
-Date: \tab 2012-09-12\cr
+Date: \tab 2014-01-08\cr
Title: \tab Functions for soil texture plot, classification and transformation\cr
@@ -42,9 +44,9 @@
Maintainer: \tab Julien MOEYS <jules_m78-soiltexture at yahoo.fr>\cr
-Depends: \tab R (>= 2.4.1), sp, MASS\cr
+Depends: \tab R (>= 3.0.2), sp, MASS\cr
-Suggests: \tab drc, plotrix, xtable\cr
+Suggests: \tab xtable\cr
License: \tab AGPL (>=3)\cr
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