2.1  General Functions

The File, Options and Help menus contain functions that are common to every view in ArArCALC. These functions are amongst the most used in ArArCALC and range from opening files to printing to exiting to setting preferences and to getting help. However, depending whether you are in the Raw Data Reduction or Age Calculation view, there may be important differences in functionality, which will be explained in this section as well.

2.1.1  Open Datafile

There are three options when selecting the File # Open Datafile # Raw Intensity Data menu item. The first option allows you to open a text file containing your Raw Mass Spectrometry Data ready for data regression. The second option allows you to open an already prepared Age Calculation File, whereas the last option allows you to generate an Empty Age Calculation File (or template file) in which you can enter intensity and blank data manually. This latter option, in particular, is helpful if you want to (re)apply age calculations to old data from your laboratory or from the literature.

Raw Intensity Data

To open a raw intensities data file you should select the File # Open Datafile # Raw Intensity Data (Ctrl+D) menu item. This will give you the following Open DataFile dialogbox. Now browse, select and Open your data file. You can only select one file at a time.

When you have opened your data file, three dialogboxes will be shown to you in sequence. In the first dialogbox, you have to select an Input Filter. In this dialogbox select the input filter that is applicable for the data file you are trying to open. Like in this example, multiple input filters may sometimes be available for different sample types or, if over time, you needed to adjust your input filter(s) because the structure of your data files changed (see also: Setting the Preferences).

In the second dialogbox, you have to set the Sample Type and give an Experiment Name. You always have to make a selection in this dialogbox, but you can always change your settings later, when your data file has been opened successfully in the Raw Data Reduction view (see also: Sample Type and Experiment Name). When filling in the Experiment Name make sure to use unique names (see also: File Name Conventions). In the example below, the Experiment Name is based on the name of the first analysis in an incremental heating experiment. If you are processing data for a single incremental heating experiment, a set of single crystal analyses from one sample or a set of irradiation monitors from the same position in an irradiation package, leave the Experiment Name unchanged so that all your data can be collected and saved in one-and-the-same age calculation file.

In the final dialogbox, you have to set all Sample Parameters that are necessary to perform the age calculations (see also: Sample Parameters). The shown fields are always pre-filled with data from the previous calculation, even if these were performed a few days or weeks ago. Completing this dialogbox will be fast, because most entries will be similar and thus don't need changing. Most likely, only the GMT datum and Temperature need editing, unless you start to reduce a totally new experiment. If your raw data files already have header lines containing this information, ArArCALC will automatically transfer this header information into this dialogbox by using your Input Filter (see also: Setting the Preferences). You can always recall this dialogbox at a later stage in the Raw Data Reduction view via the Options # Sample Parameters menu in order to edit the sample parameters.

When you have entered all the Sample Parameters, you will be guided to the Raw Data Reduction view, where you can regress your argon isotope data by using different line fit methods (see also: Your First Calculation).

Age and Flux Monitor Calculation

To open an age calculation file you should select the File # Open Datafile # Age and Flux Monitor Calculation (Ctrl+A) menu item. This will give you the following Open DataFile dialogbox. Now browse, select and Open your data file. You can only select one file at a time. To open multiple files together, see the Import Additional Experiment help page for more details.

Empty Age Calculation File

To open an empty age calculation file to use as a template, you should select the File # Open Datafile # Empty Age Calculation File menu item. This is a helpful function that allows you to apply age calculations to old data from your laboratory or from the literature, even if you don't have the original raw data reduction files at hand. Instead you can fill in the regressed intensities of the analyses and, if these are not already blank corrected, you can fill in procedure blanks as well. You first will be asked to give a name for the Empty Age Calculation File.

Next an adopted version of the Sample Parameters dialogbox appears, in which you can predefine the number of analyses (or steps) for the experiment. Adjust the spinner button to change the Step Number in the top right panel. In the example below, an Empty Age Calculation File with 10 incremental heating steps is being created. All other fields are similar to the normal Sample Parameters dialogbox and you should fill these out in a similar fashion (see also: Sample Parameters). However, be aware that in this case the dialogbox only appears ones for a single experiment. This means that you should select a Date in the GMT Datum panel that corresponds to the first analysis (or step) in your experiment. Later on you should edit the Sample Parameters table to enter the correct Time values for the incremental heating steps (see also: Editing the Sample Parameters Table). In some cases, you also should edit the Date values, if an experiment runs passed midnight on an experiment day or if a single experiment has be run on separate days. All other parameters always concern the entire experiment, so no extra editing is required.

When you have clicked the OK button, an Empty Age Calculation File is generated by ArArCALC. As you can see 10 place holders for Sample 001 to 010 have been created, but no calculation is possible since the key input data have not been entered yet (see further below).

Now select the Edit menu in order to start adding (or editing) your data (see also: Edit Menu). In the Intercepts Values table you should replace the 1.000000 and 0.010000 values for the Intensities and Uncertainties of all argon isotopes, respectively. Note that the Uncertainties in this table are always Standard Errors on the 1σ Level. The r2 values are optional.

If the Intercepts Values you entered above are not blank-corrected, you should replace the 0.000000 values for both the Blank Intensities and Uncertainties for all argon isotopes (see below). If the Intercepts Values are already corrected, you can leave the zero blank values in this table. However, in the latter case you should make certain that you have the Apply Procedure Blanks Corrections checkbox unchecked in your Preferences (see also: Preferences), which is the default ArArCALC setting when you generate these template files. Note that the Uncertainties in this table are again Standard Errors on the 1σ Level.

Finally, you should edit the Sample Parameters table. In this table you should (but it is not required) replace the Default Sample Names in the left-most column, the Temp values and you should edit the Date and Time values (not shown below).

When you are finished updating the tables in the Editing view, you should choose the File # Save, Close and Recalculate (Ctrl+S) menu item. Now ArArCALC will check if you have filled in your data correctly and warns you if it encounters problems with your data entries. Otherwise, it will switch back to the Age Calculation view and (re)calculate the ages and plots.

2.1.2  Print

Every data table and diagram is printable from ArArCALC. First select the data table you want to Print via the Table/Edit menu, or select a plateau or isochron diagram using Excel's Worksheet Tabs. Then choose the File # Print (Ctrl+P) menu option.

Check Current Page and select your Paper Size. Then click the Print button and your table or diagram is printed.

You can select another printer via the Chooser button (see above). This allows you to print in black & white, in color or on transparencies. Click the Setup button (see below) to adjust the settings for the selected printer. These settings will be remembered in between print sessions.

You can further customize your printouts by filling in the Laboratory Identifiers in the Preferences dialogbox (see also: Preferences). These identifiers will always be printed as header and footer, next to the date, time and ArArCALC version number on your printouts. Defining these identifiers is highly recommended, because it will make the archiving of your results more meaningful in the long term.

2.1.5  Irradiations and Projects

ArArCALC saves all age calculation data files in separate directories according to project name (see also: File Organization). This guarantees an automated and well-structured file organization. However, these project names are logged together with all irradiation parameters in the ArArCALC.log file (see also: Using the ArArCALC.log File). This log file can be accessed and updated through a set of easy-to-use dialogboxes. To activate the Changing Irradiations and Projects dialogbox, select the Options # Irradiation and Projects menu item.

The Changing Irradiations and Projects dialogbox lets you choose what via the option buttons Irradiations and Projects in the lower left Change panel. After making a selection, you can use the Add, Edit and Delete buttons to update either the list of project names or irradiations. To add a new list item, you first need to fill in the name of a new irradiation or project in the textbox in the upper right corner, followed by clicking the Add button. To edit or delete an existing irradiation or project, you first click on its name in the list box, followed by clicking either the Edit or Delete button.

If you want to save your edits, please hit the Save button first, because the Close button will close the Changing Irradiations and Projects dialogbox without saving. If you want to ignore or undo any of your changes, hit the Close button without hitting the Save button first.

When adding or editing irradiation definitions, ArArCALC will show you the Change Irradiation dialogbox to allow you to define the irradiation parameters, including up to 999 irradiation segments or cycli (see further below).

information
In this tab you can find summary info and notes for a particular irradiation. In here only the Notes can be edited and it is highly recommended that you provide a short description of the irradiation in this field. This description may include which reactor was used, whether the samples were shielded or not, the purpose of the irradiation, the related project(s) and what time zone was used in the definition of the Irradiation Cycli or Segments (see below). The Date and Total Duration of the irradiation are automatically calculated from the Irradiation Cycli data, where the Date represents the first segment listed in the irradiation list and the Total Duration the summed durations as listed in the first column.

Interference Correction
In this tab you should define the Interference Correction factors and their uncertainties. These constants differ per reactor and whether the samples were shielded or not.

Irradiation segments
In the final tab you can define the Duration, Date, End Time and MW (reactor power) of all Irradiation Cycli or Segments. It is highly recommended that you use either GMT or your Local Time Zone, as long as you consistently apply it throughout ArArCALC. For example, you should make certain that you apply the same Time Zone when you define your irradiations and when you supply dates and times in the Sample Parameters (see also: Sample Parameters). Use the spin button to increase or decrease the Number of Irradiation Segments. Click on a line in the list box to adjust your settings, which will appear for editing in the text boxes at the bottom of this dialogbox. To speed up data entry you can also check the Auto Fill option.

2.1.6  Preferences

The program ArArCALC does not contain any constant in its computer code. Every constant, parameter and setting can be set by the user. This is done to give you 100% control over what you calculate in ArArCALC. Below follows a list of adjustable settings in the Preferences dialogbox.

Calculation Preferences

Isochron Settings
These options let you influence the precision of the YORK2 Isochron calculations (see reference: York, 1969). The Convergence determines how small the difference in slope of the isochron should be for two consecutive iterations to result in a successful least-squared fit. The Convergence is here expressed as a percentage of the slope itself (see also: Isochron Calculations). The number of Iterations determines after how many iterations the isochron calculation should be terminated, in case the calculation is not converging. If you set the Convergence to a higher precision (a lower percentage), you also should adjust the number of Iterations accordingly (to a higher number). Clicking the option button Weighted YORK-2 forces ArArCALC to calculate a least-squared linear fit with correlated errors that is weighted by the inverse of the variance (see reference: York, 1969). You can overrule this setting when performing isochron calculations by selecting Normal Isochron # Weighted YORK-2 or Normal Isochron # Unweighted YORK-2 in the menu bar. You can do the same for the Inverse Isochron independently.

Data Reduction Settings
The data reduction settings determine the precision when you apply the Exponential Fit to your mass spectrometry data. The Convergence is expressed as a percentage of the curvature coefficient that is iteratively derived in this least-squared fit (see also: Line Fitting).

Error Propagation
By checking Irradiation Constants in the Error Propagation box, the errors on the irradiation correction factors will be propagated in the reported analytical error (see also: Analytical, Internal and External Errors). You can set these errors in the Change Irradiation dialogbox (see also: Managing Irradiations and Projects). If the Multiply Errors by Sqr(MSWD) is checked, then the errors on the ages and some isotope ratios (e.g. ⁴⁰Ar/³⁶Ar and ⁴⁰Ar/³⁹Ar) will be multiplied by the sqr(MSWD) in case the MSWD becomes larger than 1 (see also: Analytical, Internal and External Errors). Both options are activated by default in ArArCALC.

Ar40, Ar39, Ar38, Ar37 and Ar36
You can chance the option buttons to the right of the Preferences dialogbox in order to set your Default Calculation Type for the raw data reductions (see also: Line Fitting). You can do this independently for each isotope by choosing from four calculation types: exponentional (Exp), parabolic or second order polynomial (Par), linear (Lin) and averaging (Ave). You can always overrule these default settings in ArArCALC when performing the actual line fits.

Other Calculation Settings
With these checkboxes you can determine which Additional Corrections to apply (or not apply) during the age calculations (see also: Other Calculation Settings). However, it is always recommended that you apply the corrections for ³⁷Ar and ³⁹Ar Decay following sample irradiation, for ³⁶Ar Ingrowth in chlorine-rich samples, and for Procedure Blanks. However, for samples younger than 1 Ma it is recommended that you uncheck the Force Negative Intensities to be Zero ... option. This will allow for more accurate age calculations, because negative ages (or error bars) are statistically expected and valid for these kind of samples. ArArCALC will generate a warning when you select a non-default setting.

Configuring the Input Filter

Defining your own Input Filter is most critical while using ArArCALC. Although it may look complicated, it gives you the flexibility to read-in different types of mass spectrometry data files. ArArCALC does not read-in binary files and expects that the measurements were saved in sequentional text files. Furthermore, the actual intensity measurements should be given per line, including the intensity (in volts, amps or counts) and the time (in hours, minutes or seconds) after inlet of the argon gas in the mass spectrometer. By clicking on the Settings button you can define the internal structure of both the header and data sections in a separate dialogbox (see explanation below). By checking the Choose Input Filter when ... checkbox, ArArCALC allows for the selection of an input filter every time you open a new data file. Otherwise the input filter selected in the list box shown below will be used by default.

General Settings
The File Structure is determined by the Number of Header Rows and the Number of Peak Measurements for each measurement cycle, and whether the text file is Space, Comma or Tab delimited. The Number of Peaks should be at least five to cover all five argon peaks between Ar36 and Ar40. In the Peak Cycle Structure the user defines which lines represent peak measurements for the argon isotopes and which lines represent baseline measurements. These lines can be assigned in random order as long as the Number of Peaks is not exceeded. If you provide two baseline measurements, ArArCALC calculates an average baseline (see Ar36 through Ar39 below). If you provide one baseline measurement, the baseline value will be subtracted as is (see Ar40 below). You can also fill in "0" when your data already have been baseline corrected (by your data acquisition software, for example). Two positions for the masses Ar41 and Ar35 have already been reserved for future importing and monitoring of this data.

Record Settings
In the Record Settings tab you can define which records in the peak lines represent the Peak Measurement, the Error on Peak Measurement and the Time Measurement. Here you can also define in which units the Time and Intensity Measurements are given and you can define settings such as the File Extension, the Maximum Number of Records and Header Lines, and how the Date and Time parameters and the Errors are represented in the data files. By default ArArCALC assumes absolute errors.

Header Structure
Your raw data files may contain more than 1 header line. In the Header Structure tab you can define on which header line (H#) and on which record position (R#) the Sample Name or J-Value was stored. This of course requires that these headers were originally saved in the data file. In the rather simple example below, only one parameter is stored, namely the Number of Cycli, which is stored in the first record of the first header line. Further below a more complicated example is shown and explained as well.

Example Input Filters

This is one of the most simple text files possible (see settings in the dialogboxes displayed above). Its space delimited and it has the minimum amount of headers. The Number of Headers should be set to 1 and consequently the Cycle # should be set to [1,1] as well. Since there is only one header line with only one parameter in it, all other possible header positions should be set to zeros (which is the default value). In this example, each measurement cycle produces 10 individual peak measurements (5 isotopic peaks and 5 baselines) and thus the Number of Peaks should be set at 10. The net peak of Ar40 is calculated based on peak 1 minus the average baseline calculated from peak 2 and peak 2, the net peak of Ar39 is calculated based on peak 3 minus the average baseline calculated from peak 2 and peak 4, etc. etc.

This is a more complicated text file that can be read-in by ArArCALC (see settings in the dialogboxes displayed below). Its comma delimited. It has 10 header lines as is set for the Number of Headers. Each measurement cycle produces 6 individual peak measurements (5 isotopic peaks and 1 baseline at mass 35.5), explaining why the Number of Peaks is only set to 6. The net peak of Ar40 is calculated based on peak 1 minus the average baseline calculated from peak 6 and peak 6 (which is the actual baseline value as measured on mass 35.5), the net peak of Ar39 is calculated based on peak 3 minus the average baseline calculated from peak 6 and peak 6, etc. etc.

The number of cycles can be found on the first record of the 9th header line in this text file and the Cycle # is thus set to [9,1]. The Sample Name, Material, Location and Analyst are all located on the first record of header lines 1 through 4. The Temperature for the measurement is located on header line 5, the J-value and Fractionation Correction Factors and their errors are located on header lines 6 and 7 at records 1 and 2, respectively. The Irradiation Name is located on the first record of header line 8. Finally, the Date and Time are located on header line 10 at records 1 and 2 as well. Since the One String for the Data and Time checkboxes have been selected (see above) only one option is available to you for the Date and Time. If you have them unchecked, you can point to individual values for the Day, Month, Year, Hours and Minutes in the header structure.

Constants

The Decay Constants and their percentual standard deviations can be set and changed in the Preferences dialogbox below. Here you can also define the data for Decay Activities and Other Physical Constants that are needed for the primary age calculations and recalibrations based on the formulations of Karner & Renne (1998), Renne et al. (1998) and Min et al. (2000). For more details read the Primary Age Recalibration Toolbox help page. The expected units are given in the brackets, unless the numbers are dimensionless.

Laboratory Preferences

The information you fill out in the Laboratory Identifiers panel will always be printed as headers and footers, next to the date, time and the ArArCALC version number, when you are making a printout from within ArArCALC. You can also set the File Location of the mass spectrometry data files on your hard disk to ensure that ArArCALC swiftly finds your data files. Finally, you may want to set a Password to protect your settings in the Preferences and Irradiation and Project dialogboxes. Setting passwords is, in particular, advised for the person who is managing the Master ArArCALC.log file, in order to circumvent accidental deletion of these important parameters (see also: Using the ArArCALC.log File).

2.1.8  ArArCALC Online Help

This ArArCALC package comes with help files written in HTML that are accessible through your web browser. These help files can be reached when running ArArCALC through the Help menu by selecting the ArArCALC Online Help (Ctrl+H) menu item. Note that these help files are not locally stored on your hard drive. This setup allows you to retrieve the most up-to-date help files without downloading the updated help files to your own computer. The ArArCALC Help Library will be launched in your default browser with the Table of Contents as the first page.

Most dialogboxes used in ArArCALC also have Online Help buttons. Click on these buttons to retrieve "context sensitive help" information from the help files stored in this online ArArCALC Help Library.

2.1.9  ArArCALC on the Web

The ArArCALC Website is continuously maintained at http://earthref.org/tools/ararcalc.htm. You can reach this website by placing a bookmark in your web browser, but you can also select the ArArCALC on the Web (Ctrl+W) menu item from within the ArArCALC software itself. On the ArArCALC Home Page you will find links to the latest downloads and news on the ArArCALC program. The website will be launched in your default browser.

2.1.10  About ArArCALC

If you want to verify what version of ArArCALC you are currently using, select the Help # About ArArCALC menu item. A window will appear (and disappear after a few seconds) that is the same as the splash window shown during the startup of ArArCALC. This window contains the basic information about the ArArCALC software and its developer.

See also ...

Contents	ArArCALC
Chapter 2	Function by Function
Section 2.2	Raw Data Reduction
Section 2.3	Age Calculations
Section 2.5	Editing Mode

	First  |  Previous  |  Next  |  Last