OxCal > Viewing output
The GUI is designed to allow the output from OxCal analysis to be presented in a number of different ways and also to allow output to other programs.
The file handling should normally be fairly straight forward. When running OxCal on a server the output data is automatically loaded either by performing a simple calibration (which generates an quick.js file) or by performing a more complex analysis using the input window. If you wish to open the output of a specific application which was performed on the server previously this can be done by selecting [File > Open] or [File > Manage].
The [File] menu in the output utility allows for other file operations, depending on the details of the OxCal configuration and the type of browser you are using. The available functions are:
The most complete set of file handling options are available using Firefox or other Mozilla browsers with native SVG support. See installation instructions and section below on dealing with SVG plots.
There are a range of different types available for the analysis. These are:
The default view is a table which summarises the ranges of the output and (in the case of Bayesian analysis) some of the diagnostics. This table view also allows you to link directly to the individual plots (by clicking on the name of the item) or to the raw output for the item (by clicking on the ≡ symbol).
There are various options of what is shown, these are found under the [Format > Show] menu item. In particular you may wish to display results in cal BP rather than cal BC/AD and you may wish to reverse the order of the table.
A number of different plots are available. The single plots are most conveniently accessed through the table view. The other plots show what is currently selected in the table. The multi-plots are arranged by type (dates, intervals and parameters) to ensure that similar types of distribution are shown together. The [View > Plot selected] option allows you to plot specific distributions in the order in which you select them. Plots can also be made against the calibration curve (radiocarbon dated events only) and against depth where the z parameter is set for the items.
In most plot views an additional control is shown which allows you to navigate multiple plots. The buttons perform the following operations:
| Move back one whole page (or 10 individual items) | |
| Move back one item | |
| Move forward one item | |
| Move on one whole page (or 10 individual items) | |
| Return to table view |
In addition to normal plots which have a time axis, it is also possible to plot data on a map. To do this each item which you wish to have plotted on the map must be tagged with location information using the longitude and latitude tags.
The following is a simple example:
Sequence()
{
Boundary();
Phase("Group 1")
{
R_Date("A1",4376,39){longitude=2.084;latitude=48.232;country="France";};
R_Date("A2",4366,37){longitude=3.536;latitude=48.646;country="France";};
R_Date("A3",4469,36){longitude=2.483;latitude=48.165;country="France";};
R_Date("A4",4420,31){longitude=4.625;latitude=48.901;country="France";};
R_Date("A5",4463,37){longitude=3.23;latitude=48.211;country="France";};
R_Date("A6",4537,38){longitude=3.254;latitude=48.435;country="France";};
R_Date("A7",4537,37){longitude=2.558;latitude=48.211;country="France";};
R_Date("A8",4517,32){longitude=4.178;latitude=49.075;country="France";};
};
Boundary();
};
Sequence()
{
Boundary();
Phase("Group 2")
{
R_Date("B1",4719,33){longitude=-1.778;latitude=52.116;country="UK";};
R_Date("B2",4693,32){longitude=-1.712;latitude=53.573;country="UK";};
R_Date("B3",4546,30){longitude=-1.268;latitude=52.936;country="UK";};
R_Date("B4",4561,40){longitude=-1.699;latitude=52.261;country="UK";};
R_Date("B5",4718,32){longitude=-1.085;latitude=53.272;country="UK";};
R_Date("B6",4832,34){longitude=-1.485;latitude=52.904;country="UK";};
R_Date("B7",4512,38){longitude=-0.857;latitude=52.79;country="UK";};
R_Date("B8",4712,30){longitude=-1.182;latitude=53.567;country="UK";};
};
Boundary();
};
In this case the dates have also been tagged by country. When you do [View > Plot on map] you can choose to split the datasets by country.
In addition to the plot outputs there are a number of other summary reports available. These are:
Finally the status view shows the status of an analysis in progress. This shows the proportion of the analysis that has been completed, the current status of the convergence, and the proportion of MCMC passes that have given results in accordance with the model.
Run status
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If you press the [Cancel] button you can abandon the particular analysis and output all of the results so far calculated. If the MCMC analysis has difficulty starting any temporary error messages will appear in red at the bottom of this box.
Once the analysis is complete the program will show the table window.
You can return to the input view and, if you like, change the model by selecting the input window.
There are a few options which can be included into the analysis code which affect the output views. The relevant commands are:
The following example shows all of these in action and how they are used:
Plot()
{
Label("Site I");
Axis(BC(600), BC(100));
R_Date("A", 2250, 20)
{
color="Red";
};
R_Date("B", 2200, 20)
{
color="Green";
};
Page( );
Label("Site II");
Axis(BC(1800), BC(1300));
R_Date("C", 3200, 20)
{
color="Blue";
};
R_Date("D", 3300, 20)
{
color="Magenta";
};
};
Note that the color command will work with any of the color definitions compatable with html or svg and the color can be used to label radiocarbon calibration data-sets as well as individual distributions.
Most of the different display views allow changes to be made to exactly what is shown. All of these changes are accessed through the [Edit] menu. Depending on the window the following submenus are available:
When you make any changes they are immediately shown in the output. If you then press [Ok] they will be retained. If you press [Cancel] the settings will return to their previous values.
Some of the options set are remembered between sessions.
Dynamic plot manipulation: The most convenient way to alter axes and the size of the plot is by using the mouse directly on the plot. This allows you to dynamically drag, stretch and zoom the plot. To do this just click and drag anywhere in a plot and you can move the axes. Using the curve plot, this enables you to explore the calibration curve. If you press [Shift] at the same time as you drag the mouse you can change the overall scale of the plot instead (covering a wider or narrower range). Pressing [Alt] at the same time as dragging allows you to change the overall size of the plot (zoom in and out).
Rather than using the [Format > Adjust ] menu or direct manipulation of the plots with the mouse, you can also use the adjustment tools which are shown just above the plot using the keyboard arrow keys. The options are:
| Zoom: | the left or down keys reduces the size of the plot, the right or up keys increases it; holding down shift makes it behave like 'Span' | Center: | arrow keys recenter the plot; holding down shift makes it behave like 'Span' | Span: | re-scales the plot in either direction |
In all cases holding down the [alt] key makes smaller changes. The adjustments made result in an immediate.
All of the output plots and the Model schematic view are generated as SVG (scalable vector graphics) plots dynamically by your web browser. They are not generated on the serverand this should mean that changes to the plot do not rely on a fast access to the server.
SVG is a scalar vector graphics format. See:
In any modern browsers you can use the [File > Save as] function of the OxCal plot window to save the plot in SVG format, or on the server version to convert this to PDF or PNG format. You can use Inkscape or Adobe Illustrator to edit the SVG plots. You can also use utilities such as the Batik-rasterizer to convert them to other formats (PDF, PNG etc) which is what is used on the server version.
Inkscape is an open source SVG editor, viewer and converter and is available from:
You can also convert svg files to raster formats using the utility at:
http://www.fileformat.info/convert/image/svg2raster.htm
The full range of options is available for single calibration. These options can be set under the [View > Options] menu item at the top of the OxCal page. The details of of these options are given in the section on input of information. The same options are also available from the single calibration dialog box by pressing the [Options] button.