PaleoToolBox User Guide

PaleoToolBox User Guide


Introduction

For 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 sets

For 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 structure

The 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 File

New 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).

New RAM Project...

The menu position "New RAM Project..." is used to create a project file. The program WinRAM (WinRAM is an adapted version of the program RAM98. RAM98 was developed by Claire Waelbroeck) loads this project file. When "New RAM Project..." is called, the user is first asked for the name of the project file. Then possible options are asked for. After that the file choosing dialog appears again. Here you are asked to specify the names of the location file of the reference data set, the reference data set, the hydrographic data set, location file of the core 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).

Execute WinTransfer

Starts the program WinTransfer.

Execute WinRAM

Starts the program WinRAM.

Quit

Closes PaleoToolBox.

The menu Options

Here 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 Ranking

The 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 Converter

This 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 Tools

This 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 file

With 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.

Options...

For access to individual geographical positions, the program first needs the exact path and name of the relevant file on the CD. With the menu point "options", the file is chosen by means of a dialog clicking the desired time period and parameters. Moreover, the data directory has to be chosen. The name of the data directory is recorded in a "preferences" file. Therefore the directory normally has to be chosen only once.

Station ...

This option initiates the searching procedure. A dialog box appears asking for the exact position of the station. The position information is put into the data grid later. If the file "world.dat" is present in the program file a mercator world map will be drawn. As the search continues, the requested positions are displayed in this map.

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.

List...

For a large number of requested stations, you can create a control file in advance. This control file contains the positions and the names of the stations and the requested depths, the time periods, and the parameters. The appendix contains information regarding the precise format of the control file.

Close window

If a map has been drawn, the corresponding window can be closed using this option.

The program WinTransfer

The 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.


Reference

Imbrie, 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.

PanPlot


Appendix

Example for a reference dataset
FlagTaxaPS1195-1PS1200-4PS1208-1PS1209-1PS1214-1PS1222-1

A.actino2100
0

A.curvat






A.hooker1





A.parvul






A.noduli






A.tabula

00
0

Ch.spore359422313756159
*E.antarc824581727

H.cuneif

00
0

Nav.dire






N.angula7
02
1

N.bicapi

00
0

N.cu.gro281110131152146141

N.kergue210010

N.marina






N.obliqu594311292811

N.ritsch132241

N.separa

00
0

N.sublin282020221620









Diat. sum426296392354268360

Example for an environment dataset
Event labelTemp.10mTemp.20m
PS1195-1-1.79-1.795
PS1200-4-1.77-1.794
PS1208-1-1.67-1.689
PS1209-1-1.643-1.651
PS1214-1-1.764-1.761
PS1222-1-1.143-1.132
PS1223-1-1.132-1.156
PS1273-1-0.12-0.308
PS1277-1-1.632-1.607
PS1278-1-1.669-1.594
PS1366-2-0.663-0.759
PS1372-2-0.623-0.849
PS1374-2-0.623-0.849
PS1384-1-0.68-0.766
PS1388-10.5110.336

Example for a WOA dataset
Label stationLatitudeLongitudeTimeLevelParameter
PS2487-35.82618.106011
PS2488-38.55615.801 421
PS2489-42.886 8.9811031
PS2490-43.276 7.9381341
PS2491-44.955 5.97 551
PS2492-43.175-4.0511261
PS2493-42.883-6.02 1401
PS2494-41.69 -12.341601

Filenames
TimeIDFilenameTimeIDFilename
January1xxxx01.OBJSeptember9xxxx09.OBJ
February2xxxx02.OBJOctober10xxxx10.OBJ
March3xxxx03.OBJNovember11xxxx11.OBJ
April4xxxx04.OBJDecember12xxxx12.OBJ
May5xxxx05.OBJJanuary-March13xxxx13.OBJ
June6xxxx06.OBJApril-June14xxxx14.OBJ
July7xxxx07.OBJJuly-September15xxxx15.OBJ
August8xxxx08.OBJOctober-December16xxxx16.OBJ



annual0xxxx00.OBJ

Levitus levels
LevelDepth (m)LevelDepth (m)LevelDepth (m)
1 012 300231400
2 1013 400241500
3 2014 500251750
4 3015 600262000
5 5016 700272500
6 7517 800283000
710018 900293500
8125191000304000
9150201100314500
10200211200325000
11250221300335500

Parameters
ParameterIDParameterID
Temperature1AOU5
Salinity2Oxygen (sat.)6
Phosphate3Silicate7
Oxygen4Nitrate8

rsieger@pangaea.de