gcdOptions {GCDkit}R Documentation

GCDkit options

Description

A graphical user interface (GUI, programmed in Tcl/Tk) for setting the main options controlling the behaviour of the GCDkit.

Usage

    gcdOptions(permanent.only=FALSE)

Arguments

permanent.only

logical; should be shown exclusively the option that can be set permanently?

Details

The settings are stored permanently in the file 'gcdkit.xxx' residing in the main GCDkit directory. They are loaded upon start up. If is missing or damaged, this file is created anew based on the default values.

The panel connected to the function 'gcdOptions' serves to change several parameters. Most of them are passed to a list accessible in a way similar to the standard R options. See the corresponding manual page for details and Examples for their implementation. Only a few are stored in dedicated variables (see below).

Firstly, the default working directory can be set (and stored in the global variable data.dir).

Secondly, the default Graphical User Interface (GUI) including the menu system can be specified using the option gcd.menus. It can attain one of the three values: "", "win", "tcltk".

If GCDkit is run under Windows OS using RGui (standard behaviour), a default value of the gcd.menus parameter is set to "win" automatically.

Otherwise (any other operating system, Windows in batch mode using the RTerm window), the default value is "" unless it has been modified previously in the configuration file. In these cases, "tcltk" would be the correct setting.

From within GCDkit under any operating system, Tcl/Tk interface can be (re)started anytime using the menuet command.

The parameter 'Minimize output on screen?' is linked to the option gcd.shut.up. It controls excessive output to the Console window. Its default value is FALSE, meaning that detailed information is to be printed. This, however, may become not viable on slower systems and/or for extensive data sets.

The preferred precision of the numeric values that need to be rounded off are controlled by the parameter 'Precision of results' (option gcd.digits).

Using the parameter 'Plotting symbols magnification', linked to the option gcd.cex, one can define a factor, by which are multiplied the plotting sizes defined for individual analyses upon startup and stored in the variable 'labels[,"Size"]'. Please note that this is effective for the next plot if the GUI frontend is used to set this parameter, otherwise it will work for data files loaded from now on.

In this way, the magnification is maintained proportional to the original sizes. If uniform plotting symbols sizes are desired, one should use the function setCex invoked from the menu

Plot settings|Set uniform symbol size.

The parameter 'Annotate fields in discrimination plots?' toggles the labeling of the fields on and off, typically for classification or geotectonic diagrams. It is stored in a logical variable gcd.plot.text, whose default is TRUE. The language for the field annotations can be selected using the list box connected to the option gcd.language.

The next possibility is to alter the colours used, e.g, for texts or field boundaries on diagrams. There are in total three colours stored in the list plt.col. Alternatively, all the plots can be set to black and white (check box 'Set to BW?' linked to the option 'gcd.plot.bw'), excluding the data points. The default is FALSE (i.e. colour plotting).

The parameter 'Identify points?' toggles on and off the identification/labelling of individual data points on plots. In general, the identification can be either interactive (option
gcd.ident.each = TRUE) or all the points can be labeled automatically as soon as the plotting is finished (option
gcd.ident.each = FALSE). In the former case, the user may click the left mouse button near the points to be identified, pressing the right mouse button when finished.

The option gcd.ident determines whether identification should take place at all (the default value is zero, which means no identification). If the identification is on, the option gcd.ident attains either 1 (identification by sample name), or the sequential number of the column in the data frame 'labels' increased by one (identification by a label).

The identification by sample name for a current plot can be invoked also from the menu
'Plot editing|Identify points'. There can be also chosen alternative means of points identification ('Plot editing|Highlight multiple points').

Value

Sets the following options:

gcd.plot.text

logical; should be fields on classification diagrams labeled by their names?

gcd.language

language for these labels.

gcd.plot.bw

logical; if TRUE, plots are produced as black and white.

gcd.shut.up

logical; determines whether extensive textual output is to be printed.

gcd.ident

numeric; if zero, no identification takes place after plotting each diagram. If greater than zero, indicates the variable used to identify individual data points. See Details.

gcd.ident.each

logical; are the data points to be identified individually?

gcd.digits

preferred number of digits for rounding off the numeric values.

gcd.cex

a factor by which are multiplied all symbol sizes previously defined.

gcdOptions.png

Remaining options changed by GCDkit which cannot be altered via the GUI, though:

prompt

"GCDkit-> "

windowsBuffered

FALSE

locatorBell

FALSE

scipen

20

max.print

99999999

If necessary they can be set directly in the file 'gcdkit.xxx'.

Apart from that the GUI panel sets the variables data.dir (default data directory) and plt.col (colours for Figaro-compatible plots).

Author(s)

Vojtěch Janoušek, vojtech.janousek@geology.cz

See Also

options identify ID figaro setCex menuet

Examples

    bak <- options()                # backup the current options
    options("gcd.ident"=1)          # identify by sample names
    options("gcd.ident.each"=FALSE) # to label by sample names automatically, 
                                    # i.e. without the user interference
                            
    plotDiagram("TAS",FALSE,FALSE)
    options("gcd.ident"=0)          # to turn off the identification completely
    options("gcd.plot.bw"=TRUE)     # to set the diagram to black and white
    plotDiagram("TAS",FALSE,FALSE)
     
    options("gcd.cex"=2)            # make the plotting symbols double as big 
                                    # (effective for the data files loaded from now on;
                                    # for immediate result use the GUI front end)
    
    getOption("gcd.plot.bw")        # printing the current value of the given option
    options(bak)                    # restore the previous options

[Package GCDkit version 6.1 Index]