TT.plot {soiltexture}R Documentation

Plot soil texture triangles / diagrams.

Description

Plot a soil texture triangle (also called soil texture diagrams, or soil texture ternary plots), with or without background soil texture classes boundaries, and with or without soil texture data points. The triangle geometry depends on the soil texture classification system chosen ('class.sys' argument) or on 'forcing' parameters (see below). Both the boundaries of the background texture classification system and the texture data points can be transformed from one particle size limits system to another (the particle size limits system of the plot). Default behaviour is no transformation (set 'css.transf' argument to TRUE to allow transformation). There are 3 different way to set the triangle geometry and characteristics (1) setting the 'class.sys' argument [lowest priority], (2) changing one or several values of the 'geo' list of arguments or (3) setting the corresponding arguments of TT.plot() [highest priority]. These arguments are "blr.clock", "tlr.an", "blr.tx", "text.sum", and "base.css.ps.lim". Different geometry arguments can be set at different levels (1, 2 or 3). Case (1) should be used when one wants to use the 'default' triangle geometry associated with a given texture classification system (chosen with the 'class.sys' argument). Case (2) should be used when TT.plot() has been called previously, with a call like geo <- TT.plot(), so the 'geo' object returned can be used for setting the geometry of a new texture triangle TT.plot( geo = geo ) identical to the previous one. Case (3) should be used whenever the user wants to set the geometry of a texture triangle plot different from default values of the texture classification system chosen, and without re-using the geometry from a previous plot. ON DEFAULT VALUES OF TT.plot() ARGUMENTS? As TT.plot() shares its arguments with many other functions, their default value is not defined in TT.plot() 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.plot(geo = NULL, tri.data = NULL, add = FALSE, css.names = NULL, 
    z.name = NULL, main = NULL, blr.tx = NULL, css.lab = 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, unit.ps = NULL, 
    unit.tx = NULL, blr.clock = NULL, tlr.an = NULL, font = NULL, 
    font.axis = NULL, font.lab = NULL, font.main = NULL, bg = NULL, 
    fg = NULL, col = NULL, col.axis = NULL, col.lab = NULL, col.main = NULL, 
    cex = NULL, cex.axis = NULL, cex.lab = NULL, cex.main = NULL, 
    lwd = NULL, lwd.axis = NULL, lwd.lab = NULL, family.op = NULL, 
    frame.bg.col = NULL, at = NULL, grid.show = NULL, grid.col = NULL, 
    grid.lty = NULL, class.sys = NULL, class.lab.show = NULL, 
    class.lab.col = NULL, class.line.col = NULL, class.p.bg.col = NULL, 
    class.p.bg.hue = NULL, arrows.show = NULL, arrows.lty = NULL, 
    points.type = NULL, pch = NULL, z.type = NULL, z.col.hue = NULL, 
    z.cex.range = NULL, z.pch = NULL, text.tol = NULL, tri.sum.tst = NULL, 
    tri.pos.tst = NULL, b.lim = NULL, l.lim = NULL, lang = NULL, 
    new.mar = NULL, new.centroid = TRUE)

Arguments

geo

List. 'geo' is one of the 3 way to set the texture triangle geometry. See there description and hierarchy in the function description. If geo != NULL, then geo must be a list containing 1 or several of the following items: "blr.clock", "tlr.an", "blr.tx", "text.sum", and "base.css.ps.lim". See the options with the same name for a description of the expected values and effects. The list can be created manually (like list( "text.sum" = 1000 ) ), or taken from the output of a previous call to TT.plot(), TT.baseplot() or TT.geo.get() (that return a 'geo' list).

tri.data

Data frame. Data frame containing the CLAY, SILT and SAND 'coordinates' of the texture data points to be plotted on top of the texture triangle and texture class boundaries. 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). If 'z.name' argument is not NULL, the data frame must also contain a column named after 'z.name' value. The sum of CLAY, SILT and SAND must be equal to 'text.sum' ('text.tol' determines the error tolerance).

add

Single logical. If FALSE, a new plot is created. If FALSE, the plot is added to the existing one.

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.

z.name

Single character string. Name of the column in 'tri.data' that contains the '4th quantitative variable' whose value must be used to define the points expansion factor and color (bubble plot). If NULL, a simple plot is drawn (no 'bubbles')

main

Single character string or expression. Main title of the plot.

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')

css.lab

Vector of 3 character strings or 3 expressions. The 1st, 2nd and 3rd values must be text strings or expressions, and determines the axes plot labels for the CLAY, SILT and SAND particle size classes, respectively. 'css.lab' values are independent from columns names in 'tri.data' (eventually set by 'css.names') and from whatever the placement of particle size classes on each axis (eventually set by 'blr.tx')

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.plot returns a of bad values with their actual particle size classes sum. You can 'normalise' you data table () prior to the use of TT.plot, 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.

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 PLOT. 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.

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.

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.

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.

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'.

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'.

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'.

unit.ps

Single text string or expression. Unit of particle size class limits displayed on the plot (= part of the axis labels). Does not affect the other calculations. Default micrometers.

unit.tx

Single text string or expression. Unit of particle texture values displayed on the plot (= part of the axis labels). Does not affect the other calculations. Default is percentage.

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.

tlr.an

Vector of numericals. Value - in degrees - of the TOP, LEFT and RIGHT angles of the triangle. Any value between 0 and 90 is possible, but values belonging to 0 or 45 or 60 or 90 give a better graphical rendering.

font

Single integer. Not used yet.

font.axis

Single integer. Same definition as par("font.axis"). Font of the triangle axis's numbering.

font.lab

Single integer. Same definition as par("font.lab"). Font of the triangle axis's labels.

font.main

Single integer. Same definition as par("font.main"). Font of the triangle main title.

bg

Text string containing an R color code. Background color of the plot (= outside the triangle). See 'frame.bg.col' for the background color inside the triangle frame.

fg

Text string containing an R color code. DEPRECATED. foreground color of the plot (= point fill color).

col

Text string containing an R color code. Same definition as par("col"). Color of the points plotted in the triangle.

col.axis

Text string containing an R color code. Color of the triangle's axis (line and tics) The color of the texture classes boundaries is set by 'class.line.col'.

col.lab

Text string containing an R color code. Color of the triangle's labels (text) and arrows. The color of the texture classes labels is set by 'class.lab.col'.

col.main

Text string containing an R color code. Color of the main title.

cex

Vector of numerical or single numerical. Same definition as par("cex"). Expansion factor for the points plotted on the triangle.

cex.axis

Single numerical. Same definition as par("cex.axis"). Expansion factor for the axis tics labels (numbering).

cex.lab

Single numerical. Same definition as par("cex.lab"). Expansion factor for the axis labels AND the texture classes labels.

cex.main

Single numerical. Same definition as par("cex.main"). Expansion factor for the main title.

lwd

Single numerical. Same definition as par("lwd"). Line width for the graphical elements inside the triangle (points plotted).

lwd.axis

Single numerical. Same definition as par("lwd.axis"). Line width for the axis lines, tics and the grid lines inside the triangle.

lwd.lab

Single numerical. Same definition as par("lwd"). Line width for the direction arrows.

family.op

Single text string. Same definition as par("family"). Font type to be used in the plot text elements (title, labels)

frame.bg.col

Text string containing an R color code. Background color of the triangle plot (= inside the triangle). See 'bg' for the background color outside the triangle frame.

at

Vector of numericals. Location of the grid line start points on all 3 triangles axis. At the moment values are identical for all 3 axis, and changes to that parameter have not been tested.

grid.show

Single logical. If set to TRUE (the default) a grid is drawn on the background of the texture triangle. Set to FALSE to remove the grid.

grid.col

Text string containing an R color code. Color of the grid lines. If equal to NULL, then an appropriate color is used. Appropriate means (i) if 'class.p.bg.col' is FALSE (no color gradient in texture class polygons), then grid.col is equal to 'bg' (without transparency) unless a color is specified for the triangle frame background ('frame.bg.col'), in which case grid.col is a mix of 'frame.bg.col' and 'col.axis'. (ii) if 'class.p.bg.col' is TRUE, then grid.col is a light or dark color based on 'class.p.bg.hue' (light if 'bg' is dark and dark if 'bg' is light).

grid.lty

Single numerical. Line type of the grid lines (same types as par("lty")).

class.sys

Single text string. Text code of the texture classification system to be plotted on the background of the texture triangle. That texture classification system will determines the triangle geometry and particle class size system of the plot, unless higher level options are chosen (see the function definition). Possible values are "none" (no classification plotted), "USDA.TT" (USDA texture triangle), "HYPRES.TT" (texture triangle of the European Sil Map), "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).

class.lab.show

Single text string. If equal to "abr" (default) or "full", labels are drawn inside texture class polygons with their full name ("full") or abbreviated name ("abr"). If equal to "none", no label is drawn.

class.lab.col

Text string containing an R color code. Color of the text label drawn inside texture class polygons.

class.line.col

Text string containing an R color code. Color of the texture class polygon boundary lines.

class.p.bg.col

Single logical OR vector of R colors (character strings). If FALSE (the default), no color gradient is used inside the texture class polygons. If TRUE, a color gradient is drawn, with the color hue specified in 'class.p.bg.hue' and with saturation and values that vary with texture. If 'class.p.bg.col' is a vector of R colors of the same length as the number of classes in the triangle, these colors will be used as background color for each texture classe plygons.

class.p.bg.hue

Single numerical. Only used if class.p.bg.col == TRUE (no default). Color hue (between 0 and 1) used to create a color gradient between the different texture class polygons.

arrows.show

Single logical. If TRUE (default), 3 arrows are drawn outside the triangle, along each axis, that show the direction of increasing values (arrow base) and of isovalue (arrow tip) of the texture class. If FALSE no arrows are drawn.

arrows.lty

Single numerical. Line type of the arrows drawn outside the triangle, along each axis. Same possible types as par("lty").

points.type

Single text letter. Point type. Either "p" (points only), "l" (lines only) or "b" (both points and lines), as for plot() or points(). Point refer here to soil texture values plotted on the triangle.

pch

Single numerical or vector of numericals, or single text string or vector of text string. Point shape number(s) or point character(s) to be plotted. Point refer here to soil texture values plotted on the triangle.

z.type

Single character string. Type of plot to be used for displaying a 4th variable on the texture triangle (in addition to Clay, Silt and Sand). Only used if 'z.name' is not NULL. Currently only one value is supported, "bubble", for displaying a bubble plot with bubble sizes and color saturation and values proportional to the value of tri.data[,z.name]. The value 'map' is deprecated and replaced by TT.iwd(), TT.image() or TT.contour().

z.col.hue

Single numerical. Hue of the bubble color ([0-1]) to be used if 'z.name' is not NULL. A gradient of saturation and value is automatically created for the bubbles (with this hue).

z.cex.range

Vector of 2 numericals. Minimum and maximum 'cex' of the bubbles plotted on the triangle if 'z.name' is not NULL.

z.pch

Single numerical or vector of numericals. Point symbol number(s) to be used for the bubbles if 'z.name' is not NULL.

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).

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.

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).

b.lim

Vector of 2 numerical values. This is an equivalent to plot() xlim argument. Minimum and maximum x / bottom value of the texture triangle area, in FRACTION OF THE MAXIMAL EXTENSION. Default is c(0,1). The real span is then b.lim * text.sum. This is a minimal 'zoom' implementation (results are not always perfect). 'b.lim' and 'l.lim' should be equal for better rendering.

l.lim

Vector of 2 numerical values. This is an equivalent to plot() ylim argument. Minimum and maximum y / left value of the texture triangle area, in FRACTION OF THE MAXIMAL EXTENSION. Default is c(0,1). The real span is then l.lim * text.sum. This is a minimal 'zoom' implementation (results are not always perfect). 'b.lim' and 'l.lim' should be equal for better rendering.

lang

Single text string. Determines the language used for the plot main title and axis labels. Possible values are 'en' (English, the default), "fr" (French), "it" (Italian), "es" (Spanish), "de" (German), "nl" (Dutch), "se" (Swedish) and "fl" (Flemish).

new.mar

Vector of 4 numericals. Margin sizes of the plot. Default is the same as par("mar"). See par("mar") for more details. Use this at your own risks!

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(s)

Julien Moeys [aut, cre], Wei Shangguan [ctb], Rainer Petzold [ctb], Budiman Minasny [ctb], Bogdan Rosca [ctb], Nic Jelinski [ctb], Wiktor Zelazny [ctb], Rodolfo Marcondes Silva Souza [ctb], Jose Lucas Safanelli [ctb], Alexandre ten Caten [ctb]

Examples

require( soiltexture ) 

# ::: Texture triangles without data

# :: Base plot (HYPRES / European Soil Map triangle) 
TT.plot() 

# same as
TT.plot( class.sys = "HYPRES.TT" ) 

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# :: Same plot, but with USDA texture triangle 
TT.plot( class.sys = "USDA.TT" ) 

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# :: Same plot, but with a color gradient 
TT.plot( 
    class.sys       = "USDA.TT", 
    class.p.bg.col  = TRUE
)   #

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# :: No texture classification system
TT.plot( class.sys = "none" ) 

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# ::: Texture triangles with texture data 

# :: 1st create a dummy texture dataset 
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)  
)   #

# :: And plot it on a French Aisne texture triangle
#    with a title
TT.plot( 
    class.sys   = "FR.AISNE.TT", 
    tri.data    = my.text, 
    main        = "Soil texture data" 
)   #

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# ::: Bubble plots (4th variable) 

# :: 1st generate a dummy texture dataset with a 4th variable 
#    with TT.dataset() 
rand.text   <- TT.dataset( n = 100, seed.val = 1980042401 ) 

# :: Plot the dummy dataset as a bubble plot
TT.plot( 
    class.sys   = "none", 
    tri.data    = rand.text, 
    z.name      = "Z", 
    main        = "Soil texture triangle and Z bubble plot" 
)   #

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# ::: Test all the texture triangles
TT.plot( class.sys = "none" )           # no classification 

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TT.plot( class.sys = "HYPRES.TT" )      # HYPRES / European Soil Map 

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TT.plot( class.sys = "USDA.TT" )        # USDA 

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TT.plot( class.sys = "FR.AISNE.TT" )    # French Aisne 

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TT.plot( class.sys = "FR.GEPPA.TT" )    # French GEPPA 

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TT.plot( class.sys = "DE.BK94.TT" )     # Germany 

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TT.plot( class.sys = "DE.SEA74.TT" )    # German SEA 1974 

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TT.plot( class.sys = "DE.TGL85.TT" )    # German TGL 1985 

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TT.plot( class.sys = "UK.SSEW.TT" )     # UK 

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TT.plot( class.sys = "BE.TT" )          # Belgium 

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TT.plot( class.sys = "CA.FR.TT" )       # Canada (fr) 

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TT.plot( class.sys = "CA.EN.TT" )       # Canada (en) 

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TT.plot( class.sys = "AU2.TT" )         # Australian 

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TT.plot( class.sys = "ISSS.TT" )        # ISSS 

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TT.plot( class.sys = "ROM.TT" )         # Romanian 

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TT.plot( class.sys = "USDA1911" )       # USDA 1911 (M. Whitney, 1911)

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TT.plot( class.sys = "BRASIL.TT" )      # Brasil (Lemos & Santos 1996)

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TT.plot( class.sys = "SiBCS13.TT" )     # Brasil (Lemos & Santos 1996)

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#   Triangles with special characters
#   (may not work on all platforms + some accents can be missing)
try( TT.plot( class.sys = "PL.TT" ) )   # Polish 

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# ::: Test all the languages:
TT.plot( class.sys = "USDA.TT", lang = "en" )  # English, default 

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TT.plot( class.sys = "USDA.TT", lang = "fr" )  # French 

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TT.plot( class.sys = "USDA.TT", lang = "de" )  # German 

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TT.plot( class.sys = "USDA.TT", lang = "es" )  # Spanish 

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TT.plot( class.sys = "USDA.TT", lang = "it" )  # Italian 

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TT.plot( class.sys = "USDA.TT", lang = "nl" )  # Dutch 

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TT.plot( class.sys = "USDA.TT", lang = "fl" )  # Dutch (Belgium) / Flemish 

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TT.plot( class.sys = "USDA.TT", lang = "se" )  # Swedish 

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TT.plot( class.sys = "USDA.TT", lang = "ro" )  # Romanian 

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#   Languages with special characters
#   (may not work on all platforms + some accents can be missing)
try( TT.plot( class.sys = "USDA.TT", lang = "pl"  ) ) # Polish 

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try( TT.plot( class.sys = "USDA.TT", lang = "pt"  ) ) # Portuguese 

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try( TT.plot( class.sys = "USDA.TT", lang = "es2" ) ) # Spanish

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try( TT.plot( class.sys = "USDA.TT", lang = "ro2" ) ) # Romanian

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[Package soiltexture version 1.3.1 Index]