 |
|||
|
|
Need help using these programs? Maybe we can help.
Tilia© and Tiliagraph© programs are written by Eric Grimm at the Illinois State Museum, Research and Collection Center, 1920 South 10th Street, Springfield, IL 62703.
This unofficial manual, though posted with Eric Grimm's permission, is intended solely as a supplement for users of these programs. Unfortunately, we are not able to offer support beyond what is explained on this page. If you have questions about what we post, email us and we will try to help. If you would like to add to or suggest changes, let us know.
Contents:
Excel file formatting for Tilia (Read before entering Tilia)
* Use "esc" when done with each screen, to get to previous screen.
* Tilia and Tiliagraph want you to have a floppy disk in the a: drive whenever you are running them.
Pacify Tilia by letting it have what it wants. Even if you copy
your file to the hard drive and use this, Tilia often will not
function for you unless you let it have a disk in the
a: drive.
* If any step did not seem to work, make sure you hit "enter" before "esc" on that step. (This saves your changes)
* Tilia and Tiliagraph both work off hierarchical directories. It is similar to the format of an old-fashioned outline. If in doubt, esc. up level by level until you know where you are. You can always go back. As long as you have not hit ENTER before you hit esc., you have not damaged anything.
Every time you hit enter and then escape from a menu level, Tiliagraph automatically saves/updates your open working file. Tilia does not.
You will want to select CTRL S while you are IN THE TILIA SPREADSHEET and save your file as you go. If something goes wrong, this way you will not have to start over.
* WRITE EVERYTHING DOWN!
This includes your file names and the parameters you choose both
in Tilia and Tiliagraph. In Tiliagraph, especially, write down
the settings you have chosen so that you can compare and more
easily know which menus to return to for editing. This way you
will not have to start over every time if you accidentally make
a mistake (calculate sums one too many times, delete the wrong
row, .etc....) or Tilia/Tiliagraph decides to lock up on you.
* When working with complex Tiliagraphs, periodically exit the Tiliagraph shell and copy a backup of your file at the c:/ DOS prompt. ("_" equals a space).
EX. c:/ copy a:lm2a.tgf_lm2abkup.tgf
If you cannot save on the hard drive for some reason, just save on your disk:
EX. c:/a:
a:/copy lm2a.tgf_lm2abkup.tgf
To start Tilia from the DOS c:/prompt, just type Tilia and hit enter. Tilia will automatically start itself up for you.
c:/tilia [enter]
To enter Tiliagraph from the DOS prompt without going through Tilia, simply type "tg" (lower case, no quotation marks) and hit enter.
c:/tg [enter]
If you need to see a listing of your files, just type a: to change to the floppy disk drive, then at the prompt, type "dir[enter]". You will see a listing of all files by name, date, and size. Copy to the appropriate drive if necessary.
All Tilia files (those produced by you in Tilia and suitable for export to Tiliagraph will be *******.til files.
All Tiliagraph files (those edited inside Tiliagraph to design
a graph) will
be ********.tgf files.
If you are ever in doubt of your file name, when you are asked
by either program the name of the file you wish to load, just
hit [enter] and you will Tilia/Tiliagraph will display a directory
window for your floppy disk (a:drive) with all of the (in Tilia)
*******.wks files OR (in Tiliagaph) all of the ********.til or
********.tgf files.
To open Tilia, go to the DOS c:/prompt and type "tilia" [enter]
Tilia will open to the main menu.
1. Select: [C] Load data file.
A. Choose [H] WKS or WK1 format. (Hit [enter] twice to get dir listing of a:) Once file is selected and loaded, [escape] and select
B. Column label into [A] variable name
C. [C] Default range
- If some of the data is missing use [B] specifiy
Use range from Excel file, with A1 the first value in range and
whatever code will be the last cell address for your last
(bottom right) value in your range. Example: "A1..AN15" (You
can easily read these ranges from your Excel file)
2. [A] Spreadsheet
A. To Edit, CTRL E.
a. Number - these are your data #'s. Number from 1 to N, with N=the number of samples.
Example: you have 10 samples. Number from 1 to 10.
b. Name - put provenance info corresponding to each sample. Usually this will be depth and code of number for each feature.
EX. Number Name
1 35-40
2 40-45
....
10 65-70
_______________
CTRL S is save. Do this after each step.
B. Edit with CTRL D
a. Edit out any rows which contain only zeros. To do this go down
name list and hit "Ctrl Y" to delete unwanted rows.
It is best to do this in Excel before you ever save it as
a WKS file and import into Tilia.
escape
b. CTRL D *Calculate percentages:
- under SUM type 'A' for each type
- leave Total Sum blank.
C. 'F3' [A] Define sums. Fill in table as follows: (enter italicized values exactly as shown here. Caps must be capitalized)
Sum Name % Subsum
A Phytolith W ******
W
A
___________________________________________
* Make sure to hit 'enter' before you hit 'escape'. Put nothing
in line W under "Name" and "%".
D. Calculate percentages: 'F4'
(you should see two rows entitled sigma A and SigmaW at the
bottom two rows of your spreadsheet.)
CTRL S to save spreadsheet at this stage. This is your *******.til file
You are now ready to enter Tiliagraph.
Select [K] Tiliagraph
BE SURE TO:
* write down the name you saved your tilia file under. (on the disk label AND in your lab notebook.)
* make sure your file also has a backup copy.
Example: LM2.til and LM2bkup.til
(I know this seems like overkill, but files can easily be overwritten
by tilia.)
To enter Tiliagraph from Tilia, select [K] Tiliagraph from main menu.
To enter Tiliagraph from the DOS prompt, simply type "tg" and hit Enter.
1. LOAD YOUR FILE. Select the file from Tilia you wish to graph.
Say yes 'y' to bring ******.TIL from Tiliagraph in as your *****.TGF file if you want to continue with a file you've been editing in Tilia.
OR Type in the name of another preferred ******.TIL file.
OR If entering from the dos prompt, main menu of Tiliagraph will appear.
Select [ ] Load .TIL file or [ ] Load .TGF file
A ***.TIL file will be one edited in Tilia. A ****.TGF
file is one you have manipulated in Tiliagraph. Once you manipulate
your
file in Tiliagraph, a .tgf version will be saved.
Your .til file will still remain as it was when you began.
2. EDIT YOUR FILE
A. [D] Edit
- Skip Sigma A and Sigma W by cursoring down to them and entering 'F4' to skip them.
B. [E] Graph Style. Select in the following order:
1. [A] All graphs
2. [B] Histogram
3. [A] Bar thickness - factor. Set at '10'
C. Text.
- [B] Diagram heading.
Enter the name of the project. This will be the title of your figure and will appear in the upper left hand corner. All caps looks nice.
D. [G] Axes.
[A] X-axes
[B] Select graphs - mark all graphs except for total by hitting 'enter' on that line.
escape
- [A] Tic marks, then
- [A] Step size, then
- [A] Set - try setting values as Minor '5'
Major '10'
Label '10'
These settings will vary in graphs with variable amounts among
taxa. You will probably have to
repeat this stage numerous times. Once for very large taxa (50,100,100),
again for moderate sized taxa (10,50,50), and again with very
small values (1,5,5).
repeat until all size groups of taxa are set.
E. [B] Y-axes
[F] Axis style
- [C] Sample names
[B] Primary scale
- [D] Scale label
- [A] Enter label- enter "Depth in cm."
F. [I] Groups
- [A] Define groups. Select groups according to the Association Chart. Hit 'enter'
to get list of groups.
First code- First in the list that belongs to that group.
* Hit ENTER to mark it.
* Hit ENTER again to return to table.
Last code- Last in list that belongs to that group.
Type in the name of the group. Ex. "Poaceae" or "Arboreal & Forest Indicators."
Height - try something in the range of .15
to .20. Smaller groups need to have smaller Heights. You may have
to change these settings
after viewing graph.
3. MAKE DIAGRAMS
-[A] Make Diagram - wait until it is done
-[B] View Diagram - inspect graph. If any changes need to be made, be sure to go
back to the appropriate section and make those changes.
Write down the changes in your lab notebook so that
you can remember ( and later replicate ) the settings you used.
To Enlarge diagram for better viewing, hit the + sign.
Hit "escape" to leave view diagram and return to menu to edit or plot.
- Repeat Part 2. steps until all editing changes are
made, repeat part 3 to re-make and view diagram until it is satisfactory.
4. PRINTING graphs
-[C] Plot diagram
- If graph is < 1 page, don't scale. Go straight to
-[A] Plot diagram - and select printer.
OR - If graph is about 1 page, select [B] scale diagram,
then, [A] fit to page. Then 'escape' and back to
-[C] Plot diagram and
-[A] Plot diagram.
Select printer.
OR - If graph is very large, select
-[C] Plot diagram
-[B] Scale diagram
-[B] Maximum height
escape
-[A] Plot diagram
Select printer.
---------------------------------------------------------------------------------------------
To PRINT a previously saved ****.TGF file:
1. enter Tiliagraph,
2. load ________.tgf file
3. [A] Make diagram
4. [B] View diagram
5. If anything needs to be edited. Follow Tiliagraph instructions above. Repeat until all is satisfactory.
6. [C] Plot diagram. Follow detailed steps as above to PRINT DIAGRAM.
To transfer Tiliagraph files over the internet: Send completed tiliagraphs to someone else for them to print on their program and computer.
1. attach your *****.tgf file to email.
2. transfer to ****.tgf file to a floppy disk or the appropriate DOS directory (your tilia directory).
3. enter Tiliagraph as above.
4. LOAD .tgf file
5. [A] Make diagram
[B] View diagram
6. take a look, see if you want to make changes. If so, follow
directions above. If not, print as above.
STYLE AND EDITING, TILIAGRAPHS:
Setting Margins:
To set margins, use TG main menu.
1. Go to ENHANCEMENTS
2. Select WHITESPACE
3. Set margins. For best results, set bottom margin at 2.00" Be
sure to set side margins at 1.00"
To create page breaks. (PRINTING MULTIPAGE TGs)
1. Create a master .til file. Take this into TG and print. DO
NOT PUT IN GROUPS YET! (It will then be a .tgf file, ex. lm2.tgf)
2. Use this to decide where you want your page breaks.
3. Save as many copies of your .til file as you will have pages.
For ex. lm2pg1.tgf and lm2pg2.tgf
Do this by going to the DOS prompt and copying your master
file to first one working file, then another.
For ex. c:\copy lm2.tgf (space)lm2pg1.tgf
You will get the message that one file has been copied.
4. Enter TG. Load [N] your page 1 file.
5. Edit your file, putting in groups, proper axes, title, etc... (You can label pg. 2, etc..
6. Under PLOT [C] select SCALE DIAGRAM and SET Y-AXIS HEIGHT.
7. Set y-axis height. Be sure to remember this height. You must use the exact same height for your second page so that all of your pages will fit together.
8. Print page 1.
9. LOAD [N] your page two file and edit it in the same way. Print it with the same height as page 1. The two graphs should be scaled to the same height.
10. Continue until you have printed all of your pages. Be sure to check and make sure that the scale truly is the same for all pages.
EXCEL FILE FORMATTING for TILIA
FIRST :
Be aware of the desired Tiliagrah format before you format your Excel file. This will make things much easier down the line. Sketch your desired sequence, labels, title, etc..... For instance, where do you want your total phytolith/sample count? Where (or do) you want your sums of ecological categories to appear? at the front or at the end?. Do you want to use percentages or absolute counts? Write down all of these goals before you begin to format your spreadsheet.
The graph will order the taxa in the same order in which they
are in the spreadsheet. If you wish your summary data to be at
the end, move all of the summary categories to the end in the
order desired (Arboreal & Forest Indicators, Wet Habitat Indicators,
etc..)
On the same note, if you wish your phytolith total to be at the
end, place it there in the spreadsheet, if you wish it to be at
the beginning, place it in the first data row.
A. FORMAT:
1. A. Begin with an Excel file containing your phytolith scanning data in a matrix with
rows = taxa
columns = samples
B. Check your excel file for accuracy. Print a hard copy
for your reference. Be sure that it (and a backup) are saved.
2. OPEN NEW SHEET:
A. You will need to SELECT the spreadsheet you are using and open
a NEW SHEET within your Excel file.
Along the bottom of your Excel screen, you will see several sheets
listed. You will probably be in sheet 1.
Click on any empty sheet (2, 3, ....) and you will move to that
sheet.
B. TRANSPOSING YOUR SPREADSHEET:
1. Under EDIT, select PASTE SPECIAL.
2. A small window will come up. At the bottom ofthat window is
a box called TRANSPOSE. Click on the box to the left of TRANSPOSE
so that Excel will transpose your rows and columns.
3. Then, click to the top left corner cell and PASTE
(either with the mouse or by hitting CTRL V).
At this point, your spreadsheet will be in a sample by taxa
format.
Rows = sample
Columns = taxa
4. PRINT your spreadsheet to serve as a reference during editing in both Excel and Tilia.
C. REMOVE information unacceptable to Tilia
A. Delete the depth range column, this data has -'s in it and
cannot be
read by Tilia. Keep note of this information, however, as you
will need to enter this information during the editing stage inside
Tilia as your row labels for the Tiliagraph y axis.
B. Delete any empty rows or columns (those containing nothing)
C. Delete any zero presence columns (TAXA)(those containing all 0's as values.)
4. ORGANIZE your data to suit your desired Tiliagraph design.
A. Move columns into the order you wish them to be presented
on your tiliagraph. (Put category sums at the end, but make sure
you know where your
categories begin and end so that you can mark and title
them in Tiliagraph.)
B. Edit Column headings
1. * If certain taxa vary in quality, make sure this is
in the column headings.
For example, "Total # of phytoliths per slide"
should be fully written and spelled out as you wish it to appear
on your column
heading in the Tiliagraph.
2. * Only use abbreviations if you wish them to appear that way on the graph.
3. * If you wish scientific names to be italicized or underlined, do this now.
5. SAVE YOUR FILE to WKS format.
A. SAVE AS
When everything is to your satisfaction, save the entire
file
(SAVE AS). Be sure to include the date in your file name.
B. RECORD FILE NAMES: Record this file name and be sure that it is in excel format with the .xls tag.
C. Then, while you are in the sheet with your spreadsheet completely formatted for Tilia, select SAVE AS again.
Enter your name for this file. It must be 8 characters or less, and it must have the .wks tag.
Example: lm2core.wks
DO NOT SAVE YET. At the bottom of the SAVE AS window, there will be an open box containing .xls Excel file.
Click on this box's arrow and drag down to fine WKS 1,2, or 3.
Select this option. Save your file, once to hard drive, and once to the floppy disk in the a: drive.
You will receive a warning from the computer letting you know that WKS will save only the active sheet. You want this. Your new file will contain ONLY the currently active spreadsheet containing your Tilia formatted spreadsheet.
DO NOT save over your main Excel spreadsheet.
DO NOT use the exact same file name as your main Excel spreadsheet
or you will overwrite it.
Keep track IN WRITING, IN YOUR NOTEBOOK, of all files saved. You
may think that you will easily remember each of the files, but
any variation whatsoever will cause trouble down the road, not
to mention numerous files you can't easily tell apart at a later
date.
ALWAYS back up your files. For main Excel spreadsheets of phytolith data, make a copy on the zip drive as well as a permanent file on the hard drive. This may seem overly cautious, but the files need to be archived for use years down the road.
6. Close your excel file. Remove your disk and proceed to Tilia.