PaleoToolBox User Guide |
IntroductionFor computing paleoenvironmental parameters by means of the transfer function method, the program suite consisting of CABFAC, REGRESS and THREAD by Imbrie and Kipp (1971) is very popular. These three programs have been assembled in the program WinTransfer. Like the original programs, WinTransfer requires three data sets. To guarantee compatibility to other applications, the formats of these three files (*.CAB, *.REG and *.THR) have not been changed. The structure of these files is quite complicated and not easy to edit. The data (counting data and hydrographic parameters) are usually gathered and managed by means of a spreadsheet program (e.g. EXCEL). Therefore, the easiest way was to develop a program that converted spreadsheet files to the appropriate formats. The program PaleoToolBox that is described here does just that. Furthermore, it allows the creation of frequency tables and generation of ranking systems. Additionally, the counting process can be supported by PaleoToolBox.The program PaleoToolBox as a Windows program is very easy to handle. The difficulties lie in the complexity of the scientific context. Naturally this handbook can refer to these contexts only marginally. You can find further information in several papers. See especially Zielinski et al. (1998). |
Formats of data setsFor single raw data sets, tables that contain the station names (reference data set) or the sediment depth (core data sets) in the first line have proved useful. The names can contain a maximum of 63 characters.With the WinTransfer program they are shortened to eight characters. Therefore the first eight characters chosen should be unique. The first column contains a switch. The symbol "*" in this column switches the respective species off. In this way you can avoid rearranging data sets over and over. The second column contains the names of the species used. The eight- character-rule has to be followed again here. If there are more stations than there are columns provided by Excel (max. 255) a transformed table can be used. In this case you find the switches in the first line, the species names in the second line. If a ranking system has to be constructed or if you have to calculate relative frequencies, the individuals counted in the sample have to be positioned in the last line. The last line is separated from the rest of the data by a blank line. Note that the reference data set and the core data set are not allowed to contain this two lines if you create a project file (see passage New Transfer Function Project... or New RAM Project...). The hydrographical data set contains the hydrographical information of the individual reference stations. In the first column you find the names of the stations (eight characters). The following columns contain the hydrographical data of the corresponding stations. At most, ten different environmental parameters can be listed in the hydrographical data set. It is important to save all sets as text. See examples in the appendix. |
Menu structureThe menu structure of the PaleoToolBox program is separated into several groups. In the menu File you find the actual converting routines. The menu Edit has no real function in this program. It allows copying and pasting of texts in dialogs. The dialogs are contained in the menu Options. Here, for example, you can put in the number of factors calculated in the part of the program called CABFAC.The menu Ranking belongs to the second group of functionals. Here the routines that generate a simple ranking system from the reference data set can be called. Usually this ranking system still has to be worked on further by hand. Based on this ranking system, a data set can then be created. In the group Converter, several routines are summarized that allow reformatting of data sets. Under the menu Tools there are routines that can simplify the creation of data sets (e.g., Counting...). |
The Menu FileNew Transfer Function Project...The menu position "New Transfer Function Project..." is used to create a project file. The program WinTransfer loads this project file. When "New Transfer Function Project..." is called, the user is first asked for the name of the project file. Then possible options (number of factors, kind of regression, parts of program to use) are asked for. After that the file choosing dialog appears again. Here you are asked to specify the names of the reference data set, the hydrographic data set, and the core data set.
Note that the reference data set and the core data set are not allowed to
contain a sum line (see passage Formats of data sets).
Note that the reference data set and the core data set are not allowed to
contain a sum line (see passage Formats of data sets).
Starts the program WinTransfer. Starts the program WinRAM. |
The menu OptionsHere different options for the processing of data can be adjusted.Format of species...Depending on the volume of data, it may be useful to arrange names of species either in columns or lines. Note that Excel can only process 255 columns. If you have to process 400 species, you have to write the species name in the second column (the first column is a switch column) (see passage Formats of data sets). Through the dialog that appears with this option, the format (name of species in columns or rows) can be adjusted. For accurate results it is important to avoid mistakes at this point.Format of data...Sometimes the data at hand are in percent format, but the program expects counting data. If you choose the percent data format here, every entry will be multiplied by 1000 for further processing.CABFAC options...Here the number of factors (PCs) can be changed.Regress options...The regression can be carried out as a linear or square regression.Thread options...Thread has no options. Therefore this menu item cannot be chosen.Program...Here you can adjust the parts of the program that WinTransfer uses to calculate with later on. |
The menu RankingThe ranking of a data set is necessary if the frequency of species is to large or to small. With the help of a ranking system, the counting data can be transferred to frequency classes.Create ranking system...After choosing this menu option, the PaleoToolBox program asks for the name of the reference data set. This set is loaded and a ranking system is created. Afterwards the program offers to store this ranking system. The user usually will have to employ the automatically created ranking system.Create data set...A ranked data set is created from the raw counting data set by using the ranking system. First the program asks for the name of the data set that is to be ranked (reference data set or core data set), then the name for the ranking system must be chosen. The choice of the name for the ranked data set completes this option. |
The menu ConverterThis menu contains a collection of routines that convert existing data sets.Raw data --> HMatrix...Here a frequency data set can be created from a raw data set. It is important that the last line of the raw data set includes the number of individuals counted in each sample (see passage Formats of data sets).Raw data --> data set...If a data set is present in the form described in the passage Counting..., and includes a total sum line, it is possible to remove this line (+ blank line) from the data set by this option.%data set --> HMatrix...This is equivalent to the option raw data --> HMatrix..., but the line containing the number of individuals counted in each sample is not necessary. The program adds up the individuals that were found and equates the sum to 100 percent.HMatrix --> data set...The frequency matrix contains not only the frequency of species, but also, in the third column (or third line), the respective maximum frequencies. This column (or line) is removed from the table by using this option. |
The menu ToolsThis menu is a collection of routines that can change the existing data sets or create new ones.Turn matrix...The PaleoToolBox program can process two different formats of data sets (see passage Formats of data sets). The menu option "turn matrix" transfers the data set from one format to the other. Note that before this you have to adjust to the correct format under the menu option species format.Split fileWith this option, large matrices with more than 255 columns can be divided into several small ones.Connect files...Using this routine, two data matrices of can be connected. The entries are added.Counting...This menu point can be used for computer-aided counting. Upon selecting this option a window appears for choosing a file. Here a raw data set is chosen. The file is loaded and the next step asks for the name of the new file. After input of the filename the counting dialog appears.This dialog is intentionally not Windows conformable, so the cursor is not positioned in the first, but in the second editable field. Here the desired species is chosen. If a value between one and the number of species present in the file is input, and the enter button is pressed, you move to the appropriate panel, which is then editable. The increment is added to the corresponding species in the corresponding sample. Then the dialog starts again. The data set can be changed and extended arbitrarily by this dialog. For example the name of a species can be modified or a new species can be added. If the maximum possible number of species is exceeded, a corresponding notice appears and the routine is terminated. |
The menu WOA(under construction)
Access to the data CDs of WOA is made easier by this menu. The data for
individual stations can be acquired as well as complete lists of stations.
At the same time, the program not only looks for the data for the requested
position, but also for the neighboring points in the WOA grid. The results are
saved as depth profiles in a form readable by
PanPlot.
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The program WinTransferThe WinTransfer program (download PaleoTools) is a simple combination of the three well known programs (Imbrie and Kipp, 1971) CABFAC, REGRESS and THREAD. WinTransfer assumes that the reference data set, the hydrographic data set, and the core data set are all available in their respective correct formats. After starting the WinTransfer program and opening the program window, a file-select dialog appears. Here the name of the project file has to be input (see passage New Transfer Function Project...). WinTransfer then loads one after the other of the three program files and calculates. The program then presents a window with some notes regarding the calculation. If the user needs a printout of the text shown in this window, he must make it before the program ends. The program is terminated by pressing the return button. In addition, this step erases all temporary files. If such an interim file is required (only for experienced users) it must be saved before closing.The output files of the WinTransfer program can be processed directly by Excel,Word or PanPlot. The PanPlot program allows the quick graphical display of the calculated climate data. |
ReferenceImbrie, J., and N.G. Kipp (1971): A new micropaleontological method for Quantitative Paleoclimatology: Application to a late Pleistocene Caribbean Core, in The Late Cenozoic Glacial Ages. edited by K.K. Turekian, pp. 71-181, Yale Univ. Press, New Haven, CT Levitus, S. and T. Boyer (1994): World Ocean Atlas 1994 Volume 4: Temperature. NOAA Atlas NESDIS 4, U.S. Dep. of Commerce, Washington, D.C. Zielinski, U, Gersonde, R, Sieger, R and D. Fütterer (1998): Quaternary surface water temperature estimations: Calibration of a diatom transfer function for the Southern Ocean. Paleoceanography, 13 (4), 365 - 383. |
Appendix | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Example for a reference dataset | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Example for an environment dataset | ||||||||||||||||||||||||||||||||||||||||||||||||
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Example for a WOA dataset | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Filenames | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Levitus levels | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Parameters | ||||||||||||||||||||
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rsieger@pangaea.de |