POLPAL

Application for plotting pollen diagrams, counting pollen grains, and performing numerical analysis (with data stored in text files, in MS Excel, Word, Notepad etc.)

Citation: Nalepka D. & Walanus A. 2003 Data processing in pollen analysis. Acta Palaeobotanica 43(1): 125-134

Manual

Adam Walanus, Department of Geoinformatics and Applied Computer Science, AGH University of Science and Technology, Al. Mickiewicza 30, 30-059 Krakow, Poland
walanus@geol.agh.edu.pl www.adamwalanus.pl

Dorota Nalepka, W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
D.Nalepka@botany.pl

POLPAL diagram in Encyclopedia of Quaternary Science

Introduction to POLPAL

Pollen data are stored in tables, with taxa in columns and samples (spectra) in rows. Such tables, typically are stored in spreadsheets (MS Excel), however it may have simple form of text, with values separated by tabulator (txt files) or by coma or semicolon (, ; csv files). For storing and printing of smaller tables (up to 30-50 taxa) also text editors (like MS Word) can be used.

In case of any of mentioned forms, and probably of some other, it is enough to copy the table to the Clipboard (Ctrl-C) and then, to click the menu option "Load table from Clipboard" in the described here application, to have data ready for diagram plotting. However, in POLPAL system, simple database may be constructed, with one, consistent list of taxa for all pollen tables. Advanced results can be obtained using such database.

Of course, not only pollen and spores data may be handled in POLPAL, also other remains counted in reasonable amount, like Cladocera, diatoms, molluscs, charcoal particles, fruits, seeds and other micro and macro objects.

Shown below are pollen tables in Notepad, Excel, and Word.

Application Diagram plots pollen diagrams, in many different forms. Also numerical (statistical) analysis of data (ConSlink, PCA, Rarefaction) may be added to the diagram, by two mouse clicks.

The final result, the diagram, is in the standard MS Windows format of bitmap (*.bmp file). It is very easy to add to the bitmap some additional descriptions, lines etc. Printing bitmap is easy as well, simply because it is standard format. Even the diagram of 300 taxa and 300 samples may be printed with perfect quality (see for example Ralska-Jasiewiczowa et al. 1998).

Bitmaps, however, are large files, even when saved as monochrome. It can be recommended to save bitmaps in GIF format, which is compressed one, with no lost of information. The JPG is also possible, however, not recommended since the compression rate is correlated with the lost of picture quality.

A few examples of diagrams are shown below (some figures are sized down).

Diagram in color:

Monochrome, large diagram (compressed):

Cyclogram (pie), see Layout options

Diagrams AP/NAP and special form of presentation of Pinus and Betula (see Miscellaneous information):

Different forms of pollen "curve" (the last one is obtained with help of MS Paint):

There is additional application PPTable that may be used instead of Excel. Counting pollen grains is supported in that application, with use of special coding of taxa.

1	t	ab	Abies alba
2	t	ac	Acer
44	h	acd	Aconitum

In order to keep many pollen tables in consistence, the list of taxa may optionally be used in POLPAL. Such a list consists of taxa names, taxa codes, taxa numbers, and life form code, which help in diagram construction.

Step by step - Starting Diagram

There is no installation of Diagram application, simply copy the file Diagram.exe into some folder (for example, where you already keep your pollen data). Then run the program. (The shortening to the application may be obtained by dragging it with the right mouse key).

Below is fragment of Windows screen with useful programs, and folder with pollen data (xls, csv, txt) and results (bmp).

Step by step - Data

It is assumed that pollen table is in MS Excel, or in other spreadsheet, or in text editor. Below is pollen table selected in MS Excel.

Taxa names are in the first row. Depths are in the first column. Other cells contain counts (empty cell = 0). Select table, copy it to the Clipboard (Ctrl-C), and then click the menu option Load table from Clipboard in Diagram.

How to select large table:

It operates in text editors also.

In case of difficulties in using Load table from Clipboard option, paste the content of clipboard into the Notepad (simply start Notepad from Windows/Programs/Accessories and press Ctrl-V). Because of long taxa names that form of table is not very convenient, anyway Excel may read it back. If the table is in Notepad; it is worth to save it, since ...

Pollen table may also be loaded to Diagram from the file. Click in the menu Load text table. In the Open dialog two types of file may be chosen: *.CSV or *.TXT. The first is produced by Excel ("save as csv"), the second may be obtained in Excel ("save as text") as well, and in Write, Word, Notepad and many other text editors. In case of CSV, data (numbers) are separated by coma (,) or semicolon (;), in case of TXT, the separator is TAB (tabulator).

Please note: .txt data files in POLPAL are ASCII files not Unicode files! Please, Save Unicode files As ANSI coded file.

Pollen table below may be copied (select it, and Ctrl-C) from here, and used by Diagram.

depth;Abies alba;Acer;Alnus undiff.;Betula undiff.

108;1;2;15;32

112;4;3;76;100

121;4;0;79;125

131;4;1;61;66

With taxon name additional information can be transferred to the program. The symbol '#' is used here. For example: Alnus#tg3 means, that taxon Alnus is a tree, the curve is to be of color "g" (defined in the program), and that taxon is to be the third in the diagram. Those three parameters are optional (if there is one only letter, it is treated as life form - used in pollen sum definition). However, if you have more than one table, it is recommended to use list of taxa.

Taxon name length is limited to 255 letters (Myriophyllum spicatum/verticillatum is much below that limit); taxa names can be edited in the program (as well as taxa color and position), during process of diagram adjusting.

Maximal number of taxa =400, Maximal number of samples =1000. Since MS Excel has only up to 256 columns, text file (txt or csv) is to be used in case of more taxa (see also application PPTable).

Step by step - Draw pollen diagram

Below is the result of loading to the application Diagram pollen table given on figure above, and clicking the button Diagram.

(If you prefer another picture at the left upper corner of the application window, prepare file Tree.jpg (64x64 pixels) and place it in the folder where is the Diagram.exe file.)

Button Taxa (see above) recalls the taxa of the table, with some parameters.

Five (editable) columns contain:

1. One letter of life form (decisive for pollen sum, AP/NAP diagram and so on). The letters are defined by the user, however, we use t-trees, h-herbs, s-shrubs, d-dwarf shrubs, l-local, n-non pollen, i-indicator, and x
2. Sequential number of taxon for diagram (see also Set of taxa)
3. One letter of color or pattern symbol for the curve
4. Taxon name to be printed above the curve (no limitations for that text, may be anything, of any length)
5. Miscellaneous information (letter b or p results in plotting Betula and Pinus pollen curves in form of circles, on the AP/NAP diagram; the text: %20 means that curve is to be exactly of 20% width)

The second column i.e. sequential number is of high importance. There are many mechanisms for manipulating them from the menu (Taxa arrangement). At start, numbers that correspond to the position of taxon in the table are used (if numbers are not given with taxa names - Alnus#50). However, 10, 20, ... not 1, 2, ... are used to make it possible to insert some taxa. One general rule is applied here: taxa with the same number will be summed up, and plotted under the name of the first taxon to be summed up. For example: 10 Abies, 10 Alnus, 10 Betula,....10 Ulmus will produce curve of trees (change Abies to trees). Taxa with no number (empty cell, or letter in the cell) will not be plotted.

Pollen concentration calculation

In order to plot the curves of absolute concentration of pollen the counts of the indicator are necessary. The program recognize the indicator taxon by the life form "i". In case of plotting diagram without use of the list of taxa, i.e. only with the pollen table, the life form of proper taxon (for example Lycopodium) is to be changed to i (see figure below).

Under the head Pollen sum the Concentration option is to be selected.

The program assumes the same the number of pollen grains added to samples, namely 10000. This value can be easily modified as any other parameter (see figure).

However, if different tablets are used for samples, the only way is to recalculate the indicator counted in MS Excel, or other spreadsheet. It is also the way to include into the calculation the sample volume, mass, etc.

The formula for calculation (=GP2/GQ2*10000) is visible. The constant number 10000 in the formula refer to the value of the parameter "Added indicator"(=10000). The artificial number of counted grains equal to 1000 is given here in order to present the operation of the formula.

It is easy to paste the pollen table (txt) into the spreadsheet as well as copy it after calculations back, see: Data.

On the diagram plotted, as a horizontal scale, thousends of pollen grains is used as a unit (50 means 50,000 grains per cubic centimeter, for example).

Description of menu, buttons, options

Buttons

Some buttons are visible only if available. For example Taxa is invisible when spreadsheet with taxa names is actually displayed.

Test one curve

The program is fast, however, memory demanding, so try at first one curve (indicated on the spreadsheet with taxa)

Diagram

Pressing that produces diagram for all taxa chosen in taxa spreadsheet

Best quality. Normal (1/2). Draft (1/5)

Try at fist to produce smaller diagram (2 or 5 times smaller). The final, Best quality diagram is large, in sense of file size (kB). In case of difficulties in producing Best quality diagram try: (1) Normal diagram (may be good enough), (2) use smaller vertical or horizontal scale, (3) use smaller font, (4) change in Windows settings color precision to 256 colors only, (5) plot diagram in a few separate parts (for example: trees, herbs, others) to be united later, in some graphical program or in Sum_d.exe.

Taxa

Recalls spreadsheet with taxa names and parameters

Multi diagram

When selected, next diagrams or single curves are added to previously plotted. New pollen table may be loaded, for comparison of, for example Quercus curves.

no grey

Enlargements of curves will by white, no grey (if no color is applied) what means that diagram would be b&w, and so much smaller in size

Project

At each state of the diagram construction the project can be saved to be reopened lately. It is enough to press the button Save in the Project group. Starting new session, it is enough to load table (in normal way, but not from the Clipboard). Pressing the Diagram button will produce the same diagram, which has been actual at the moment of project saving.

All settings of the program are saved in two text files. However, the user needs not to be interested in these files at all. Anyway, the files can be easily modified. Since the project is associated with the pollen table, the actual table name makes a part of the mentioned files names. The Par file simply contains All parameters. The Tax file saves settings of the taxa:

Many projects can be associated with the given pollen table. That is the reason for the white editable field, where numbers or letter can be placed to differentiate projects.

After starting the program, that field is already available, to be filled with the symbol of the project version to be loaded with the table. In case of one project, the field would be empty. If we have one project, saved with no additional symbols, it will be loaded with the table automatically. There are two ways to prevent project loading: (1) type any number/letter in the white field before table loading, (2) rename project files. However, the files to be still useful are to be renamed in a special way; one or more symbols are to be added just between the pollen table name and '_Par.txt'/'_Tax.txt' (zz_Site Abc_Tax.txt -> zz_Site Abc1_Tax.txt).

Project can be loaded (Load) at any moment, however, the program settings/parameters will be resetted according to the project loaded. In principle any project can be loaded with any pollen table, however, since taxa are identified by its position in the table, the loaded taxa names can be incorrectly assigned to the taxa. The Par files can be loaded separately, by clicking Load button at the All tab of the Parameters window (see above).

Menu

Load table

Shows Open dialog for two types of file: *.CSV or *.TXT

Paste from Clipboard

Loads from Clipboard table previously copied to the Clipboard.

Load taxa

Shows Open dialog for two types of file: *.CSV or *.TXT in order to load list of taxa. Note that the list of taxa contained in file taxa.txt, in the same folder where is the program Diagram.exe, is loaded automatically.

Save diagram

Shows Save dialog to save bitmap produced

Parameters

Shows small dialog with All parameters

Layout

That menu is described below

Taxa arrangement

That menu is described below

Numerical analysis

See Numerical analysis

View diagram

Shows window with the entire diagram visible. Note, that diagram shown is of poor quality, what has nothing in common with its real quality

Layout

Sum (define pollen sum)

Shows dialog where pollen sum may be defined (it is the sequence of letters, here is: tsdh (trees+shrubs+dwarf shrubs+herbs)). To obtain concentration diagram the indicator taxon with life form "i" is necessary. Amount of indicator added is defined in Parameters/Added indicator=10000. Option Numbers (1:1) means that row counts will be plotted.

Scales (of % and of cm)

Shows dialog where scales may be adjusted. There are two ways to define the vertical scale. Simply setting the number of pixels per depth unit (or age unit) used in the pollen table, or by defining the aspect ratio of the diagram. Which way is used is indicated by the white color of the field. The number in the field Proportion is the ratio of pollen curve height to the 100% curve width.

Fragment of profile

Shows dialog where you may decide to plot only some part of diagram.

AP/NAP

Switch on/off diagram of type AP/NAP (with all curves "added")

Histogram/macro

Switch on/off rectangular diagram. Below: the first diagram is obtained with: Histogram=20     the second: Histogram=50     the last: Histogram=

Cyclogram (pie)

Switch on/off cyclogram instead of typical diagram

Sample depths

Switch on/off printing depths

Lithology

Click these manu option to show Lithology tab of Parameters dialog (see Fig. below). Type or paste (Ctrl-V) description of lithology column to the large field at the left of the dialog. The format of the text is precisely defined. In each row there is: upper depth - space or tab - type of sediment - space or tab - lower depth. (The same unit of depth (or age) as used in the table.) The type of sediment is according to Troll-Smith; two letters (the first is capital) followed by the number 1, 2, or 3. Which types of sediment are available is given in the dialog. The width of the lithology column is defined automatically, however, it can be defined by parameter Lithol Width=. More than one type of sediment can be plotted at the same depths (see the small diagram below; 250-300 cm). Name of the column can be changed in the dialog shown below (default is 'Lithology').

Vertical axis

See the diagram above - the column "depth". The scale is plotted automatically, however, the amount of numbers can by adjusted by the parameter Vertical scale, how dense (0-1)=. The name for the axis is defined by the parameter Vertical axis name= (default is 'depth').

Print values of sums

Switch on/off printing sums (next to the last curve)

Font

Shows dialog where font size may be changed as well as proportion of font of taxa names size to that of depths. Also skewed taxa names may be chosen. Try to select the check box Test on one curve. Note that more font parameters are available after clicking Parameters (All).

Colors/Patterns

Shows dialog where the available colors are presented, with the letter symbols assigned to them. New colors may be created here and assigned to the letter symbols and/or to the taxa/sample font. Colors may be adjusted using scroll bars. When the proper color is obtained select the letter and press the button Assign to.

Exaggerations in color

Switch on/off gray color for enlarged curve. Switching it off may result in much smaller bitmap

Color to all taxa (F6)

Click it to assign color (defined in Parameters/Color for all=) to all taxa.

Smoothing

Switch on/off Gaussian smoothing (averaging) of pollen curves. Degree of smoothing is defined by Parameters/Smoothing=10 (below: curves on the left are obtained with Smoothing=10 on the right with Smoothing=30)

Taxa arrangement

10, 20, 30,...

Assigns to the sequence of taxa numbers like: 10, 20, 30, ...

Set of taxa (paste from Clipboard)

Pastes from Clipboard set of taxa (previously copied (Ctrl-C) to the Clipboard from Excel, Word, Notepad...). Taxa will get numbers according to the order of taxa in Set of taxa (taxa not included in the Set will not be plotted).

Set of taxa (load from file)

Shows dialog Open, where text file containing set of taxa may be chosen and loaded.

Exclude all

Clears all the column (no taxon will be plotted)

10 first

Good for trials

Search for summed up

Search for the first taxon from group of summed up taxa (in order to modify that taxon name)

Manually 10, 20, 30,...

Try it, after switching it on, click on the second column

Manually 10, 10, 10...

Try it, click on the second column

Manually remove

Try it, click on the second column

According to life form

assign numbers according to Parameters/ nr 10=... For example, in case of nr 10=ts, nr 20=dh all taxa with life form t or s (trees, shrubs) will get number 10, and will be summed up, while dwarf shrubs and herbs will get 20, and also will be summed up. It is the way to prepare taxa for AP/NAP diagram.

Stratigraphically

arranges taxa in stratigraphical order, only taxa which already posses numbers are taken into account

Exclude if too few grains

If the sum of pollen grains in the taxon is lower or equal to the number given in the All Parameters (Exclude if too few grains=...), the taxon position number for the diagram is cleared.

Change numbers to "X"

Exchanges numbers to "X", to mark taxa already plotted

Save chosen taxa as Set

Shows dialog Save as to save taxa currently selected for diagram plotting as set of taxa, for future use. Parameter Set of taxa save with=n (n-names, 1-numbers, c-codes) decides if set of taxa will be saved in text file using full taxa names (n), taxa numbers (1) or short taxa codes (c).

Text description of samples

At the left part of the Text tab of Parameters dialog, there are options for placing text instead of sample depths.

Zones

At the right part of the Text tab of Parameters dialog (see figure above), there are options for adding zones description at the end of the diagram. The text of zones definition has the following structure. In each row there is: depth - tabulator - letter s or d or nothing - tabulator - zone name. It is impossible to type tabulator into the proper field in the dialog, so the text is to be prepared in Excel, Word, or Notepad.

Description of (almost) All parameters

There are many parameters used in plotting diagram. They are stored in the text field. Most of them are accessible from menu; however, some more advanced parameters are to be customized in the editable taxt field. Click menu Parameters to get it, or press F10. The values (numbers or texts) after the "=" mark can be modified. The text field of All parameters can be saved and loaded back. File Param.txt, if exists, is loaded automatically. Note that the parameters may be rearranged. User can move the frequently used parameters to the front.

Scale %=1

Horizontal scale, in [pixels per 1%] (accessible from Options/Scales menu)

Scale depth=2

Vertical scale, in [pixels per 1cm], in fact in [pixels per unit of the first column in data file], if empty, proportion is used (see below) (accessible from Options/Scales menu)

Depth/100% proportion=5

Proportion (aspect ratio) of diagram is defined here, ignored if Scale depth= has some value (accessible from Options/Scales menu)

Top=10

Bottom=170

Samples depths; top and bottom to be plotted (accessible from Options/Fragment menu)

Color for all=c

That color will be assigned to all taxa after clicking Options/Assign color to all

Sample numbers=y

The sample numbers (depths) to be printed (y) or not (n) (accessible from Options menu)

Sum, numbers=n

Pollen sums to be printed (y) or not (n) (accessible from Options/Sum (numbers..) menu)

Site name=y

Site name (name of the data file) to be plotted in upper-left corner or not

Italic for no ..eae=y

If =y then taxa names, which does not contain eae will be printed in italic. (If an non eae taxon is to be printed regularly, among other italics, than add to it's name eae, and remove this suffix on the resulting bitmap.) The angle of italic font slope is defined by the parameter Font ital angle (default =5.0).

Round %=

If the width of curves is to be equal to 5% or 10% or 15% or..., type here 5, or other value

AP/NAP=y

If the AP/NAP diagram is to be plotted (accessible from Options menu)

Macro=n

If the macrofossils-type diagram is to be plotted (accessible from Options/HistogramMacro menu)

Histogram=10

The thickness of histogram bars, for macro-diagram, no value after "=" (Histogram=)

Exaggerated curve=y

If 10x enlarged curves are to be added

Exaggerated curve in color=y

Exag col fraction=0.2

See above; the frst curve is obtained for the default value =0.2, next are for 0.1 and 0.5, respectively

Horiz.lines in AP/NAP=y

If horizontal lines in AP/NAP diagram are to be plotted

Horiz.lines while no enl.=n

If horizontal lines are to be plotted while no exaggerated curve is plotted

Additional space=5

Additional space between curves [in pixels]

Max width=1000

Maximal width (horizontal) of curves [in pixels]

Sum up close samples=n

If the depth difference between neighbouring samples is 0 the samples could be summed up

Smoothing=n

Curves may be smoothed (Gaussian smoothing), type here range of smoothing [in pixels], for example: =50 (accessible from Options menu)

Smoothing assym=1

If this parameter is not 1, other smoothing constant will be used for older and younger samples, taking into account that plant can be faster in coming than in extinction (Smoothing assym >1), or opposite (Smoothing assym <1).

CirclesPB=6

Diameter of circles [pixels] for p or b curves (see description of the fifth column of taxa list)

Cyklogram=400

Diameter of the cyclogram [pixels]

Space in front of taxa name=10

%scale=y

Cross + 4001=n (n or fraction of sample width ex. 0.2)

If the number is given (for example 0.2) the number of count larger than 4000 (for example 4001, 4002) will be plotted as cross (one or more). The dimension of the crosses is defind by the given here number.

Save as color=n

If color is not used in diagram (no grey, no colored letters) diagram will be saved as monochrome bitmap, much smaller. However, it results in deterioration of letters shape after saving bitmap as monochrome. This option may help in such a case (see below; left case =y, right case =n).

Smaller diagram 1/=2

Parameter of diminishing diagram (accessible from the main dialog) (any number >1 may be used)

Exclude if too few grains=0

If the sum of pollen grains in the taxon is lower or equal to the given number (here 0), the taxon is excluded from the diagram.

If no count in taxon=a

(a-ask, n-do not plot, y-do plot)

Horizontal=

Width of the resulting diagram (bitmap) [pixels], read only value!

Vertical=

Height of the resulting diagram [pixels], read only value!

y0=

Space [in pixels] from the top of the bitmap to the top of the curves (read only parameter). The value depends on taxa font and length of the longest taxa name.

y0 external=n

See above; type here the value [pixels] you need (for example, the value "y0=" from other diagram), makes it easy to attach parts of diagram plotted separately (see Sum_d.exe)

Max plotting time=60

Program will ask user after that time [s] if to continue plotting

Numbers 1:1=y

If row data are to be plotted (numbers from the table, no %, no conc.) (accessible from Options/Sum (define ..) menu)

Concentration=y

If concentration instead of % is to be plotted (accessible from Options/Sum (define ..) menu)

Added indicator=10000

Number of indicator grains added (used for concentration calculation)

Sum=tsdh

Definition of pollen sum for % calculation (accessible from Options/Sum (define ..) menu)

Over 100% possible=y

If 'y', then, for taxa which are not included into the sum (for example, life forms x, n, ...), the formula for the calculation of percentages is: %=100%*taxon/sum. In opposite case: %=100%*taxon/(sum+taxon).

Hiatus on >10000=n

If 'y', then the diagram between the depth which is >10000, and the next depth will not be plotted (hiatus). The width of the hiatus will be equal to depth-10000. For example, in the sequence of sample depths: 120; 125; 10130; 135; 140, the hiatus is between 130 and 135 cm.

Set of taxa save with=n

(n-names, 1-numbers, c-codes). It is a parameter for option Taxa arrangement/Save chosen taxa as Set; decides if set of taxa will be saved in text file using full taxa names (n), taxa numbers (1) or short taxa codes (c)

Font size= 1.00

It is relative font size

Font nr/tax, size= 0.75

Proportion of sample depths font size to taxa font size

Font tax, name=Arial

Font nr, name=Arial

Font tax, angle=90

Degrees

Font tax, height=80

Font tax, width=30

Below different Font tax, width= has been applied, as well as Font tax, angle=

Font tax, thickness=100

Font tax, color=$000000

Font nr, angle=0

Font nr, height=40

Font nr, width=40

Font nr, thickness=100

Font nr, color=$000000

font parameters for taxa names and sample numbers (accessible, to some extent from Options/Font menu)

Font ital angle=5.0

The angle of italic font slope.

nr 10=ts

nr 20=dh

nr 30=

nr 40= nr 50= nr 60= nr 70= nr 80=

After clicking Taxa arrangement/according to life forms (or F8) that numbers will be attached as sequential numbers to given life form (here: 10 to trees and shrubs, and 20 to dwarf shrubs and herbs). Parameters used for AP/NAP type diagram

pt 10=l

pt 20=3

pt 30=l

pt 40=c

pt 50=A

pt 60=c

pt 70=A

pt 80=c

If Color for all= is empty; that colors or patterns will be used after clicking Options/Assign color to all (used for AP/NAP type diagram)

Draw line=

(Right, Left, Up, Down, Vertical, Horizontal) type a letter here if to draw lines on the diagram, by clicking on diagram (try it)

Clear taxa name after equation mark=y

Taxa names sometimes looks like: Asteroideae=Asteroideae undiff.=Asteraceae undiff.

Color w=$FFFFFF

Color c=$000000

Color s=$808080

Color r=$0000FF

Color g=$00FF00

Color a=$FF8080

Color b=$800000

Color y=$00FFFF

Color o=$008080

Color m=$000080

Color e=$008000

here colors are assigned to letters; red: $0000FF, green: $00FF00, blue: $FF0000, dark blue: $880000, grey: $aaaaaa, and so on

Color PCA & Raref=$808080

color for curves obtained from the numerical analysis (rarefaction, and PCA)

Use of the right mouse key on the diagram.

Click on the diagram with the right mouse key to show popup menu. There are four options: Start here - X, Start here - Y, Start here - X and Y, and Up to the program. It may be decided to start plotting of the next curve (in Multi diagram mode) at the horizontal (X) or vertical (Y) position defined by the right mouse click. The last option make free the decision about the Y position (see y0 external=n).

MS Paint

The final result, the diagram in form of bitmap can be enhanced, for example using the simplest graphical program - MS Paint, part of Windows Accessories.

List of taxa

For many reasons it is good to have one list of taxa names. Such a list may be easily maintained, errors in names has to be corrected once only, not in each table. In the POLPAL list of taxa, in addition to taxa names the life form is added (one letter code: t-tree, s-shrub, d-dwarf shrub, h-herb, n-non-pollen, l-local, p-spore, i-indicator, x-other, ...).

As identifier of taxon, its number or its code may be used. Code is composed of two, three or four letters. The code, as well as number is to be unique in the list (application PPTable checks it). Codes are used mainly for counting pollen.

Below is Notepad with list of taxa. Tabulator separates columns. It is possible to create list of taxa from scratch in Notepad, however better is Excel. From Excel the list of taxa is to be exported as text (txt) file. List of taxa saved in file named taxa.txt, in the same folder where is application Diagram.exe, will be loaded automatically by Diagram.exe (as well as by PPTable) after running it.

Other form of list of taxa:

1;t;ab;Abies alba

2;t;ac;Acer

555;h;acd;Aconitum

104;h;ad;Adoxa moschatellina

281;h;agc;Agrimonia

349;h;aga;Agropyron t.

350;h;agb;Agrostemma githago

...

Below is the example (rather artificial one) of pollen table when list of taxa is in use.

Used are numbers of taxa (4, 24, 370, 29), codes (bn, abi), and simply names (Boraginaceae, Artemisia, Grass). In any of that 3 cases there are two possibilities: (1) program will find the number, the code or name in the list of taxa or (2) will not. In the first case, the name of taxon from the list of taxa will be taken to diagram, in the second, the "name" from the table will by taken (probably "Grass" does not exists in the list of taxa). In the first case, also the life form of the recognized taxon will be taken to diagram from the list of taxa. Note, that while using full taxon name in the table, it must be precisely the same taxt as in the list of taxa. For example "Allium vineale t.", "Allium vineale t", and "Allium vineale" are three different names.

Taxon name length is limited to 255 letters (Myriophyllum spicatum/verticillatum is much below that limit).

In the list of taxa, please start taxa names with capital letters (Betula not betula).

Set of taxa

Set of taxa is a structure as simple as useful. It is a set of taxa names (or taxa codes or numbers - if list of taxa exists), in separate rows. Below are three sets of taxa in Excel and one in Notepad. The order of taxa in set of taxa will be used in plotting diagram.

Taxa can be summed up. Character "&" in front of taxon name or code will result in summing the taxon up to the previous one. Here, in the first set Tilia platyphyllos will be added to Tilia cordata-type. (In application Diagram taxa will get numbers 10 Pinus, 20 Betula, 30 Abies alba, 40 Quercus, 50 Artemisia, 60 Tilia cordata-type, 60Tilia platyphyllos.) In the second set Betula nana-type cf. will be added to &Betula nana-type; Tilia platyphyllos and Tilia cordata-type will be added to Tilia. In the third set taxon number 478 will be added to taxon bb.

Sets of taxa from Excel can be sent to application Diagram using Clipboard (Crtl-C in Excel, click menu Taxa arrangement/Set of taxa (paste from Clipboard) in Diagram). Sets of taxa stored in separate text files (for example: Set of taxa Trees.txt) can be leaded to Diagram by menu option Set of taxa (load from file). Having adjusted sequence of taxa in the program Diagram, the sequence can be saved as set of taxa (in text file) - see menu option Taxa arrangement - Save chosen taxa as Set.

How to create list of taxa from the pollen table

Using Excel: (1) select row with taxa, (2) copy it (Ctrl-C) to the Clipboard, (3) go to some free spreadsheet, (4) select cell D1 (5) use menu option Edition/Paste special, and check option Transpose, then (5) click OK. (6) Fill columns A, B, and C:

(7) Save spreadsheet as text file taxa.txt.

Using Notepad or Word: (1) remove all data but taxa names, (2) in Notepad manually, or in Word automatically, change tabulators (or ;) to new lines, (3) add in front of each taxon its number, life form and code (separated by tab or ;), and (4) save result as text file taxa.txt.

Application PPTable

Application PPTable is a spreadsheet for manipulating pollen table. It may be used instead of Excel. Some operations, typical for palynology is simpler here. However, the option of counting pollen grains may be of special interest.

PPTable is able only to read pollen table stored as text files (txt or csv). Anyway, using PPTable one need no to be familiar with text files. It is enough to write numbers to the spreadsheet or use Counting option, to fill the table, and then to Save it.

PPTable uses list of taxa and checkes any loaded table if it is compatible with the list of taxa. Any unrecognized taxon is to be identified with some from the list of taxa (see below). Note that the list of taxa contained in file taxa.txt, in the same folder where is the program is loaded automatically.

Both mentioned features of PPTable enforce mutual consistence of pollen tables, what is necessary for performing comparisons of profiles, and integration of data.

To find taxon in long list of taxa click the list of taxa and type on the keybord the first letters of taxon name, starting with capital letter, of course: P or Po or Pop or Popu, and so on.

Note, that columns can be dragged form one position to the other. To do that press left mouse key on the header of a column and move cursor left or right.

Description of menu options

Load table

Shows Open dialog for files *.txt or *.csv

Load taxa

However, the list of taxa taxa.txt (located in the same folder in which programs are) is automatically loaded, any other list of taxa (for example Tax 1.txt) can be loaded. New list of taxa must be loaded before loading table.

Save with ...

Shows Save as dialog to save pollen table (not list of taxa). Table may be stored with full taxa names or with taxa numbers (numerical identifiers). The second option is preferred in order to achieve database-type flexibility of data. If taxa in tables are coded with numbers, the names of taxa can be changed (corrected) in the list of taxa only. For example changing Betula undiff. to Betula, in the list of taxa, will result in shorter description of that taxon on diagrams, for all pollen tables.

Insert, Remove

Adds new column or row or removes existing column or row indicated by the position of cursor. Column may be filled with given number. Row may be interpolated from two neighbouring rows, using depths. Row and column can be removed, but with counts stored in it previously added to the neighbouring one. That option is useful if, for an unknown reason, counts for a taxon are stored in two separate columns.

Taxon

Click it to change taxon for column indicated by cursor to taxon indicated by cursor in the list of taxa.

Taxa alphabetically

Will arrange taxa in alphabetic order, within life form. The order of life forms is decided in the edit field in bottom-right corner; in line ABC..=tsdhlpnx (Trees first, then Shrubs, Dwarf shrubs ...).

%

Calculates % according to pollen sum decided in the edit field in bottom-right corner; in line Sum=tsdh (Trees + Shrubs + Dwarf shrubs + Herbs). Please do not overwrite original table with table of % (save it with other name if necessary). Note that % cannot be edited. If indicator has been counted (taxon with life form i) concentration can be calculated. You will be asked for number of indicator grains added:

Note that; if the amount of indicator added differs from sample to sample, the indicator counted is to be recalculated. Choose an amount of indicator added as standard (for example 13500) and use it for that window. However, indicator counted must be recalculated as follow: ic_recalculated=ic_original*13500/ia, where ia is for indicator added (to given sample), and instead of exemplar 13500 some other value may be used. Round the obtained value off to the integer.

Counting

See below.

Column width

Moves around from narrow to medium and to wide columns. Note that individual column width may be adjusted by placing cursor in between column headers and moving it left or right.

Counting pollen grains

In the upper part of the dialog for counting (see below) there is green text field. Here letters and other keys should be typed in. If program does recognize a code, the taxon name will be displayed (program also may tell you the taxon name, using wav files, see below). One count will be added to the taxon in the sample selected in the main dialog. If taxon is absent in the table, it will be added at the end of the table. During counting, two sums are displayed. To define the sums (also its names) use proper lines in Parameters field. Sums are defined by life form.

The codes dictionary is obtained by pressing capital letter, and, if necessary, next letters of the taxon name (in lower case). After making use of dictionary (by reading and remembering taxon code), press Esc. Double click on taxon in the dictionary field adds one count. Single click only selects taxon, then one of the function keys (F1, F2, ..., F9, F11, F12) may be assigned to the taxon by keystroke.

Menu options shows: field of some parameters, record of the process of counting, and picture with simple help. Clicking menu option switches these items on and off.

Parameters may be saved and loaded. The blue field of Parameters may be edited as text file, however, only the text on the right side of the „=” mark may be changed. Most of lines are of obvious meaning, other are commented below.

F1=al

F2=bb

and so on F3=coh F4=qq F5=pp F6=ar F7=ska F8=cya F9=gg F11=ii F12=st

Here codes may be assigned to function keys (see also the description of codes dictionary above).

Dictionary Font=Arial

Dictionary Font Size=12

Green Font=Arial

Sample warning=y

If the warning dialog about actual sample is not necessary, type here n instead of y.

Voice=

If =y then sound will be used, if wav files are prepared

Sum1=ts

There are definitions of two sums calculated during counting process.

Sum1 name=AP

Sum1 limit=600

If that limit is exceeded the color of the text field changes from green to yellow.

Sum2=tsdh

Sum2 name=total

Sum1 limit=1000

Confirmation of counts by voice

To use sound, prepare wave files: V_bb.wav (listen here), V_cya.wav ( ), ... with the taxa codes in its names (between V_ and .wav). Additionally, it is good to prepare two more files: V_error.wav ( ) for unrecognized code and V_.wav ( ) for taxon with no its own .wav file. The wav files are to be stored it in the same folder where the program is.
Then click Parameters and set: Voice=y. Close the counting window, and start it again. (Here is a 2.7MB zip file with more wav'es, with typical taxa codes. It is possible, however, to rename the typical Windows wav'es, like C:\WINDOWS\Media\chimes.wav, chord.wav, ding.wav, recycle.wav etc.)

One image of help summarizes all options:

F1...F4...

The most frequent taxa may be coded by function keys

bn, ac

Two letter codes

sp. cya

Before three letter code, space must be pressed

, mfvt

Before four letter code coma (,) must be pressed

Pin

Capital letter call dictionary, Esc closes it

/pp

Half of Pinus (pp) grain

-

Minus subtracts one count

pp++

"+" adds the next count to the same taxon

pp123 Enter

Number (for example 123) will be added

pp15+20+8 Enter

Sum (15+20+8=43) will be added

Coding taxa: ab ac al bb cr ff fx pc pp po qq tx uu tt my lx cohx fr hi jj rha ss bn cv em ach ca cal cea ch cra cya faa .........

INQUA Working Group on Data-Handling Methods Newsletter 11: January 1994 OPTIMIZING TAXON CODES IN POLLEN COUNTING, Adam Walanus

There seems to be a rule that whenever a computer keyboard gets too close to the microscope a new program for counting pollen arises. However, many programs "emulate" mechanical counters only, whereas even the oldest XT can do much more (Davis, 1993). In my POLPAL (Walanus, 1991) a kind of optimization of the taxa codes is applied. In the process of counting, two things should be minimized: the number of keystrokes and the amount of human memory occupied by the codes. That is possible under the obvious assumption that some taxa are frequent, some are rare and the rest are very rare. Up to the ten most frequent taxa are coded by the function keys F1..F10. The next group (in principle up to 26 x 26 = 676 taxa) is coded by the sequence of two letter keys. The remaining "very rare" taxa are coded by the three-letter codes, which are four keystrokes in fact, because the space bar must be pressed before the letters. How many taxa should be coded with one-, two- or three-keys codes is a matter of which kind of effort is preferred: to search for the key on the keyboard or to remember codes. It must be mentioned that a codes dictionary is available in POLPAL any time by pressing Enter and the first letter of the taxon's name. However, searching for the code on the screen is the most time-consuming task during counting. It is really a personal decision whether it is worth to remember: F5 = Alnus, and use one keystroke per Alnus grain, or to use: al = Alnus, easy to remember but with the 100% additional wear to the finger. Only the most frequent taxa should be coded by Fn keys. The less frequent taxa are coded by the two-letter codes. However, like the Fn's, not all possible pairs of letters must be used. There is no reason to code Corylus avellana by, say, iy because co, ca and comparable options are already occupied. Certainly, the three-letter cor is a pretty combination for remembrance. The rareness of a taxon can be estimated automatically. Having to use the dictionary frequently to look up a taxon's code will soon fix the combination in your long-term memory!

Bitmaps joining and cutting

There are two small, additional applications used in manipulating large bitmaps produced by Diagram:

Program Sum_d.exe makes it easy to combine two diagrams. By mouse click you mark the point on the "1" and on the "2" diagram. Pressing Merge button adds diagrams in such a way that marked points coincide. New diagram is as large as necessary to comprise both summed up.

Program Cut_d.exe makes it easy to combine some curves from diagram, which is already in the form of bitmap. By two mouse clicks you mark the vertical fragments of "source" diagram. Pressing Extract and add button adds the fragment to the new "resulting" diagram. Note, that in order to merge curves from different diagrams, both diagrams have to have the same vertical position of the first sample; use option y0 external with some numerical parameter (for example y0 external=500) to ensure that.

Numerical analysis

The next step in pollen analysis may be numerical analysis of pollen table. Below three types of numerical analysis are added to piece of pollen diagram.

Click on the menu option Numerical analysis shows dialog:

Description of buttons

Use taxa

ConSLink and PCA (in opposition to Rarefaction analysis) are performed, as a rule, not for all taxa from the table. For example, rare taxa are not useful in analysis; so the percentage limit may be used (default value is 1%). In analysis used are only taxa that are, at least in one sample, more abundant than given % limit. Instead of defining taxa by % limit, they may be chosen explicitly, as for diagram, in spreadsheet obtained by button Taxa. The set of taxa may be used here.

ConSLink

Constrained Single Link of samples. It is dendrogram constrained by stratigraphical order. Single link means that the most similar samples from two groups of previously aggregated samples give a measure of similarity of groups.

PCA

Principal Components Analysis. Gives three plots; of I, II, and III PCA. In the text field of comments (below) loadings of taxa to PCA's are given.

Rarefaction

Rarefacted number of taxa is obtained here. Number of taxa in each sample is scaled down to be comparable with that of the sample with the lowest pollen sum. It is obvious, that in sample of 1000 pollen grains more taxa is present than in sample of 100 grains. Rarefaction makes samples comparable in sense of taxa abundance, independently of the sum.

Minimal sum

Samples with pollen sum lower than given here value will be removed from the analysis (thay are interpolated on the plot of rarefaction analysis). It is useful in case when a few samples (one, two) have much smaller sum than typical sample.

Life forms excluded

A letters given here define life forms that are to be excluded from analysis. Default is "ixnlp" - Indicator, X, Nonpollen, Local, sPoromorph.

% horizontal size

Makes possible to obtain narrower (50) or wider (200) plots.

To Clipboard

Copying text of comments to Clipboard (go to Word, Notepad, Excel and Ctrl-V).

Field of text comments

Some comments as well as results of analysis are given here.

The color of curves resulted from rarefaction, and PCA analysis is defined by the parameter Color PCA & Raref (see All paramaters)

Numerical analysis - comparing two tables - SSM - Samples Similarity Matrix

The next stepe in Numerical data analysis may by attempt to compare two pollen tables. Eeach sample from one table is to be compared with each sample from the second.

Application PP_SSM.exe has six tabs: List of Taxa, Table 1, Table 2, Set of Taxa, SMM, and Options. The sequence of tabs is equivalent to the typical sequence of steps in producing Similarity Matrix.

The List of taxa is visible at the first tab. List of taxa is necessary here, since two pollen tables are to be compared. Taxa from one table are to be identified with the proper taxa from the second table. If some list of taxa is in the file Taxa.txt (in the same folder where is the program), that list is loaded automatically at the start of the program. However, any other list of taxa can be loaded.

Two tables are to be loaded (using tabs Table 1, Table 2), to be compared. Taxa from tables, which program has been unable to identified with any taxon from the list of taxa, are listed in special field. If there are taxa not to be used in the analysis, there is no problem.

For numerical analysis, as a rule, only taxa more frequent than one grain in one sample, are used. The Set of taxa can be loaded to define taxa to be used in SSM analysis.

List of taxa may be pasted from Excel (Ctrl-V) to the upper white field. List of taxa can be edited in that field. It is enough to change one letter to remove taxon. List of recognized taxa is given below the editable field. Taxa form the first or the second table can be used as set of taxa (use buttons Table 1, Table 2).

Tab SSM is very simple. Click button Draw to obtain the resulting figure. Deselect Draft option to produce final, printing quality plot. The button Save shows typical dialog; use it to save bitmap obtained.

Options tab.

Default options ore OK for the most of typical cases. However, depth scale of final plot sometimes should be adjusted. Especially, in order to combine typical pollen diagrams with SSM matrix (see Sum_d.exe) it is necessary to use the same scale. The Vertical scale from Diagram is to be used here. It is possible, of course, to calculate scale for already obtained diagram:

In MS Paint read (in pixels) the vertical position of two samples. Here sample 210 is at 35 pixels, sample 250 is at 316 pixels, so vertical scale=(315-35)/(250-210)=7 [pixels per depth unit].

SSM - technical details

Let us denote by p_1,i,k and p_2,j,k the transformed (or not) values for k-th taxon from the i-th sample from the first table, and from the j-th sample from the second table. Attenuated Euclidian difference of these numbers is calculated:

d_i,j,k=abs(p_1,i,k-p_2,j,k)/sqrt(p_1,i,k+p_2,j,k)

where abs is a function abslolute value, and sqrt is a square root. Attenuation (achieved by division by sqrt of sum of %) is for diminishing influence of the most abundant taxa. It has little or no influence for present/absent data, as well as for data transformed to Equal Taxa Weight.

The values d_i,j,k are summed over all taxa used for analysis, to give the final value d_i,j of dissimilarity between sample i and j. Since it is more interesting to see which samples are similar, rather then dissimilar, squares plotted on the matrix are rare while d_i,j,k is small. The value of d_i,j,k is normalize so, that the largest d_i,j,k is equal to 1, and the value of 1-d_i,j,k is used in plotting black squares. However, the additional transformation may be used for 1-d_i,j,k (see Options tab).

Extended functionality of POLPAL system

A number of pollen tables with taxa names (or codes or numbers) consistent with one list of taxa make a database. Data acquired from such a database can be used, for example, for creation of iso-pollen maps. Below example is presented, obtained using data base of about 200 pollen tables (sites). Hundreds of such maps are created automatically, for different time horizons and different taxa. More

References

Main

Description of methods used in POLPAL

Some examples of POLPAL diagrams

More examples of POLPAL diagrams

Acta Palaeobotanica: 1995 35(1) 15-45; 1995 35 (2) 253-274; 1996 36 (2) 159-206; 1998 38 (1) 175-192; 1998 38 (1) 193-216; 1999 39(1) 89-135; 1999 39 (2) 183-271; 2001 41(1) 3-13; 2001 41 (1) 69-81; 2003 43(1) 101-112

Other Journals:

Index

Additional parameters with the taxon name (#)

All parameters (for diagram drawing)

Arrangement of taxa (for diagram drawing)

ASCII files

Axis vertical

Betula, pinus by circles (on diagram)

Codes of taxa

Colors (on diagram)

Concentration calculation (indicator)

Counting pollen grains

CSV, TXT - types of data files

Cut_d.exe - application for bitmap manipulation

Cyclogram (pie) instead of typical pollen diagram

Depth - name for the depth scale

Hiatus (horizontal break in the diagram)

Histogram

GIF graphic format

Indicator (concentration)

Isopollen map (extended options of POLPAL)

Life form of taxon

List of taxa

Lithology column

Macrofossil-type diagram

Miscellaneous information to taxa (for diagram drawing)

Paint Windows Accesories

Param.txt file

Pinus, betula by circles

Project

Right mouse key on the diagram

Scale calculation from the bitmap

Set of taxa

Skewed taxa names (on diagram)

SSM Samples Similarity Matrix; application PP_SSM.exe

SSM technical details

Sum_d.exe - application for bitmap manipulation

Taxa.txt file

Taxa codes

Taxa in Diagram

Text description of samples

Tree.jpg tree or flower photo at the upper-left corner

Troll-Smith

Unicode

Voice .wav files use in counting

wav files

y0 external (for diagram drawing)

Zones

Contents