CONOP NOVICE GUIDE
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CONOP9 QUICKSTART GUIDE FOR NOVICES
A GUIDE FOR BIOSTRATIGRAPHY AND COMPUTER NEOPHYTES
CONOP9’s primary purpose is to correlate stratigraphic sections which contain fossils. It finds
the best sequence of first and last appearances of fossil taxa, can handle large amounts of data
from many section, s and be used to construct a composite range chart for the taxa. This guide
will take you quickly through the processes of 1. Installing the program, 2. selecting data, 3.
inputting the data, 4. running the program, and 5. examining the results. At the end is a section
on entering non-taxonomic data and an appendix on making a range chart in Excel.
INSTALLING CONOP
First, you need a copy of the CONOP9 program and some other files that go with it. It usually
comes with several example data sets and it is useful to copy some of these to use as templates
for your own data since they have to be in a particular format. Read the instructions provided
with the distribution disks or proceed as follows:
1. Copy all of the distribution files and their folder hierarchy onto your hard drive. Place
them in a folder named CONOP (they may already be organized this way on the distribution
CD). The folder will have various folders within it that contain manuals, documentation,
and sample data sets.
2. On some computers, the files retain their “read only” attributes from the CD. If you have
just copied the files onto your computer and no one has used them yet you might have to
change the ones you use from “read only” to “archive”. To do this in Microsoft Explorer
click the RIGHT mouse button on one of the files. A menu will come up, go to the bottom
and select “properties”. A dialog box appears and down near the bottom are check boxes
for “attributes”. If the “read only” box is checked, click it to remove the check mark. Now
click the “archive” box. The folders themselves shouldn’t have any of the boxes under
attributes checked.
SETTING UP YOUR OWN DATA FOLDER
In this section we set up a folder to contain your data set and the programs needed to run it. In
essence we will build a custom version of one of the sample data folders provided with the
distribution disks.
1. In order to carry out the following instructions it is necessary that you can see the threeletter extensions to file names. Windows uses these extensions to determine which
program will open or run the file. They also allow us to use the same name for several files
and differentiate them by their extensions; e.g. CONOP9.EXE is the executable program and
CONOP9.CFG is the configuration file that it always reads first in order to see what data set
you wish to run and how. Unfortunately, the Windows default is to hide the extensions
from the users’ view. If necessary, make them visible: In the Windows Explorer menu
bar, select Tools – Folder Options – View. Then click off the “Hide extensions for known
file types” box. This should make the extensions visible in any form of the view, whether
a detailed list or a set of thumbnails or icons. We recommend using a view that maximizes
the visible information, including the date and time at which a file is written.
2. You will need a copy of the CONOP9 program, some other files that go with it, and your
own data files. It is usually best to make a new folder within the CONOP folder for all the
files needed for each of your own projects. Open Windows Explorer, Click on the CONOP
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folder on your C drive (or whichever drive you copied it to) to open it. Click on the File
menu and then click on new, select ‘folder’ and a new folder will appear in the list of files
and folders in the CONOP folder. Type in an appropriate name to distinguish your new
project and hit enter.
3. Now you need to move some files into your new folder. We will start with just the
minimum. After you get used to CONOP you might add some auxiliary programs. Open the
one of the sample data folders; e.g. RILEY or MOHAWK. It will contain five files that we
can use. Make a copy of CONOP9.EXE, CONOP9.CFG, the .SCT file , the .EVT file, and
the .DAT file. To copy a file, click on it, go up to the edit menu and select “copy”,
double click on your new folder in explorer to open it and then click “paste” in the edit
menu. You can select more than one file to copy at once by holding down the control key
as you click on the files you want. Putting a copy of the CONOP program in each folder,
with each data set eliminates the need for long path names.
4. You will not be messing around inside the CONOP9.EXE file; that is the program file that
does all the work. You will be making a few changes in the CONOP.CFG file to match it to
your data. The other three files are for you to use as templates for your own input data.
SELECTING DATA
You need measured stratigraphic sections in which you know the levels at which you found the
fossils. You need to have the fossils identified. Sometimes, just the genus name can be
sufficient for useful correlations. For most clades the identification will need to be at the species
level and for some even the subspecies or morphotype level. For each section you will make a
list of the taxa found and, for each taxon, the lowest level at which it was found (FAD or First
Appearance Datum) and the highest level at which it was found (LAD or Last Appearance
Datum). That is three necessary pieces of information: taxon name, FAD, and LAD.
If you are collecting your own data it is also useful to know at what other levels in the section the
taxon was found and how many specimens were present at each level. That information is not
necessary for running CONOP9, but may be used to weight observed FADs and LADs according to
their relative reliability.
If you are looking for data in the literature that you can use, seek the following.
1. More than one measured section in the same time interval. No use trying to correlate rocks
that aren’t even the same age (see 2 for one way to tell). More sections make for a better
composite range chart.
2. Measured sections that share many of the same taxa. No use trying to match apples with
oranges. Not all the taxa must be shared but the more the better.
3. The trick is finding papers that give the necessary information, i.e. stratigraphic level of FAD
and LAD. Look for figures of stratigraphic columns with collection levels marked and a
useable scale. Then see if there is a table listing taxa found at each level. A table with the
taxa and occurrence data which also lists the level for the collection would be suitable and
even easier than having to measure the level off the stratigraphic column. Some papers
include range charts from which you can also extract the necessary information by projecting
the range ends over to the stratigraphic column or scale. Beware, however, because many
people publish range charts with zones where they just mark every species which first
appears within the zone as appearing at the beginning of the zone and every species which
goes extinct within the zone as ranging all the way to the end of the zone. You can recognize
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these types of diagrams by the fact that the zones are marked on the diagram, there are no
collection levels shown, and taxon ranges all begin and end at zone boundaries.
4. Not all of the sections need to come from the same source. Try looking in the references at
the end of one suitable paper you find to try to find others that might cover the same interval
of time with the same group of fossils. The possible difficulty here is inconsistency in
identification. Some authors simply aren’t good taxonomists or the paper might have been
published before some of the species were split into two or more. For general purposes of
just learning how to use CONOP this is not a particular concern.
5. Good places to look are paleontology journals, theses, and papers on selecting global
boundary stratotypes. Electronic search strategies might include a fossil group name and a
boundary or the word “stratotype”. An example might be “conodont Devonian
Carboniferous boundary”.
ENTERING THE DATA
You must put the data into a format that the program can use so you will rebuild three of the
input files that we borrowed from the sample data set, replacing the file contents with your own
data while using the old content as a template for the correct format.
1. The .SCT file. First you need to work in the .SCT file. This file tells the program about the
sections you are using. Single click on the .SCT file in your project folder. After a moment or
two, single click it again and you will be able to type in a new name, like KTBOUNDARY.SCT or
some such name appropriate for your data. Press ‘Enter’ and the new name will be on your file.
Now open the .SCT for editing. This file is an ASCII text file that can be opened up in WordPad
-- a simple text editing program that comes with Microsoft Windows so anyone running
Windows probably has it in the “accessories” already on their computer. An ASCII text file is
used because it lacks the complicated formatting of something like a Microsoft Word or Excel
file that could have consequences when the CONOP9 program uses them.
There are three ways to open the .SCT file: 1) open WordPad first, then open the .SCT file from
within WordPad; 2) double click on the .SCT file from Explorer and follow the directions for
choosing WordPad as the file to read it; 3) set WordPad as the default program that
automatically opens whenever you click on a .sct file. If you don’t know how to do the third
option, it is better left undone.
You have to mimic the format you see in the data already in the file for the program to recognize
the information. So, pay attention to spaces and the single quote marks as they let the program
know where the columns separate.
Each line (row) in the file contains five entries. Depending upon the font and the use of tabs and
spaces, these five entries may line up one above the other as columns of information resembling
a table. This alignment looks good, but is not necessary; the program reads any space (outside
of quote marks or inverted commas) as signaling the end of one entry and the beginning of the
next. The columns are not labeled. You can refer back to the following table and example to see
what the labels might be. You can look over the sections already in the file to see how it works
but you will be erasing these and entering your own data. If it helps you see how to enter your
data, you can erase them after you have entered yours.
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CONOP NOVICE GUIDE
.SCT file format
SECTION#
ABBREVIATION
consecutive
integers
starting with 1
in first row
Nickname for each
section, three letter
maximum, in single
quotes.
1
2
‘DL4’
‘KT2’
FENCE
ORDER
consecutive integers 1
through number of
sections in any order
1
2
NAME
INCLUDE
Your identifier or name for each section, in single
quotes, 20 space maximum.
Just put 1 for
all rows
‘Denmark section DL4’
‘Seymour Island KT2’
1
1
Start a new line with the enter key (carriage return) for each section. The first column on each
line is the section number. You will be using this number when you enter your data in the .DAT
file so make a note of the section number in your notes for that section. Number the sections
consecutively, starting with 1, and list them in the .SCT file in order, 1 first. After the section
number enter a space or two before starting the next column.
The second column is for an abbreviation used to identify the section in some of the output files.
When there are many columns in a text file or crowded graphics on the screen, the full names
can take up too much room; these abbreviations are used instead. It can only be three symbols
long and must be preceded and followed by single quote marks. The single quote marks
(inverted commas) are used just in case you include a blank space in your abbreviation. The
computer would think it was a column break if it were not for the single quote marks. Use a
space or two to separate this column from the next one.
The third column in each row is a number that tells the program what order to draw the sections
in for fence diagrams. They can be in any order but must be 1 through however many sections
you have. For now, just enter the same number as in the first column. Again, type in a space or
two before starting the next column. You can come back and change the order later if desired.
The fourth column is a longer description of the section for your own identification purposes. it
cannot be more than 20 letters. Set this entry off with single quote marks. Enter a space or more
before the final column.
Don’t worry about the final column for now, just enter a 1 for each section.
If you have not done so already, erase the lines with the section data that were already in the file
before you entered your sections.
Now save the file changes by clicking on File and then selecting ‘save’. Close the file.
2. The .EVT file. Now you need to define your events in the .EVT file. This essentially means
giving a number and a nickname to each taxon. Single click on the .EVT file twice, like you did
with the .SCT file, and rename it as you wish.
The .EVT file is another ASCII text file that will open in Word Pad. Open it in the same way that
you chose for the .SCT file. Again, you can look over the sample data that are already in order to
learn the format, but you will need to erase all the old lines in the file after entering your own.
There is one line for each named taxon and each line contains three entries. Again, the entries
need not align as columns. If they do, the format is as below.
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.EVT file format
TAXON#
NICKNAME
NAME
consecutive integers starting
with 1 in the first row
Shorthand code or
abbreviation for the name
Taxon name
1
2
3
‘Baa’
‘Ban’
‘Bco’
‘Bispathodus aculeatus aculeatus’
‘Bispathodus anteposicornis’
‘Bispathodus costatus’
The first entry is the event number and must be 1 in the first row, 2 in the second, and so on
consecutively. Enter a space or two before the next column.
The second column is for the taxon nickname. Start with a single quote (inverted comma) first,
‘, then a shorthand code for that taxon. It might just be a shortened version of the name, like
‘P.col’ for Polygnathus collinsoni, or a number. You may use up to eight characters. Want to
keep things very simple? You could make it the same number as the first column. Follow it
with another single quote and then a space or two before the next column.
Start the third column with another single quote and then the taxon name, followed by another
single quote, like ‘Polygnathus collinsoni’.
Enter a line like that for each taxon in your sections. Each taxon only needs one line, no matter
how many sections it is in. You might want to ignore questionable identifications and not enter
those taxa which were not identified positively in any of the sections. For the immediate purpose
of correlation there is no use for taxa that occur in only one section. If the ultimate purpose is to
construct a diversity history, however, then even these taxa should be included.
Save the file and then close it.
3. The .DAT file. The .DAT file contains all of the information on FAD and LAD levels for all
taxa in all sections. Rename the .DAT file appropriately as you did the other two files.
Think carefully about the program that you would like to use to edit the .DAT file. Sometimes
you just need to read it or edit a line or two; then WordPad is a good candidate. For building
and sorting the file, however, a spreadsheet program like Excel is much more powerful. It is
possible, but sometimes irritating, to set up all .DAT files so that double-clicking opens them in a
spreadsheet program. In a spreadsheet program it may be easier to enter the data and check for
errors and you may not need to enter spaces or single quotes to delineate the columns. You
must, however, save the file in its raw ASCII text format not the spreadsheet format. Experiment
with your spreadsheet’s export and “save as” formats to see which reproduces the correct format.
Pay particular attention to the inverted commas.
After looking over the example records erase them and enter your own. Some columns allow
decimals, some do not. If decimal numbers appear, or zeroes as in “1.00” for example, this
means that decimals are permitted. The zeroes are not necessary. Depending upon the samples
that you copied, and the behavior of your spreadsheet program, you may or may not see zeroes in
the decimal places (1.00 may be imported and displayed as 1). Therefore, the lack of decimal
places does not prove that the column disallows decimals! Pay attention to the example below;
it show the three columns that do allow decimals.
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CONOP NOVICE GUIDE
.DAT file format.
EVENT
TYPE
TAXON#
From the
.EVT file
1=FAD
2=LAD
A
1
2
3
4
1
1
2
2
SECTION#
From the
.SCT file
B
1
2
1
2
STRAT LEVEL
LEVEL #
in meters or
whatever from
your data (not 0)
see below
C
1
1
1
1
D
0.62
9.30
8.40
8.40
ALLOWED
MOVES
1 if FAD
2 if LAD
E
1
3
2
2
F
1
2
1
2
WEIGHT
UP
WEIGHT
DOWN
just put 1
just put 1
G
1.00
1.00
1.00
1.00
H
1.00
1.00
1.00
1.00
You can enter the data in any order and then do a “sort” to get it ready for CONOP to use. I have
found it most convenient and quick to enter one section at a time in the following method using
Excel. For each taxon in the first section, note the taxon number. You may reopen the .EVT file
to find the right numbers. In the column A on the spreadsheet enter each of those taxon numbers
twice, i.e. in two consecutive rows. You should have no rows for taxa that were not found in this
first section.
The first row for each taxon is for the FAD and the second row for the LAD so go down column B
entering 1,2,1,2,1,2 and so on. In Excel, you can fill those first two cells with 1 and 2, select both
cells with the mouse, and then copy it to the clipboard up on the menu bar. Then highlight the
rest of the cells in the column with the mouse and click on the clipboard on the task bar to paste
them into the highlighted cells. They should all fill with alternating 1 and 2 unless you made a
mistake and highlighted an odd number of rows.
Enter the section number, the one assigned in the .SCT file, in each row in column C. In Excel
you can enter it in the first cell of the column, select that cell with the mouse, move the mouse
arrow to the lower right corner of the cell until it becomes a cross, and then drag the mouse down
the column to fill the cells in that column for all rows of that section. Now you should have a
row for every first and every last appearance of every taxon found in the first section.
In the column D enter the stratigraphic level at which the event occurred, either the lowest level
at which it was found for the FAD or the highest level for the LAD. If the taxon was found at only
one level, enter the same number in both the FAD and LAD rows of column D. Because the early
versions of CONOP could not handle it, some users prefer not to using “0” for any level. If one of
your levels is 0, then arbitrarily make it 0.01, say, or add a constant, like 100 or 1000, to all of
the levels in the section. The number itself is not important, the spacing is. Conop follows the
normal stratigraphic procedure for measured sections, starting at the bottom and measuring
upwards. Some data are published in the opposite order. Well data in particular are usually
measured downward, as depths. Notice that you can retain the published well depths -- enter
them as negative numbers and the conop convention remains intact (the values increase
upward). It is possible, but not necessary, to completely rescale a well upwards from some
arbitrary base level set to zero.
Filling in the column E is where Excel comes in handy. Highlight all rows of data for the section
you are working on with the mouse by clicking the mouse arrow on the row number and
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dragging the mouse over all of the row numbers for that section. Go up to the menu bar and
click on “DATA”. From the pull-down menu select “Sort”. A sort dialog box appears. In the
first box select “Column D”, ascending sort. The next two sort options can be left blank. At the
bottom select “no header row” and then click on “OK”. Your entries should now be in reverse
stratigraphic order with all events that occur at the same level grouped together. Now you can
easily number the levels in column E, use 1 for the lowest level and number them consecutively .
All events that occur at the same level in column D should have the same number in column E.
In column F, enter a 1 if column B is 1 or a 2 if column B is 2. You can also just highlight
column B and copy it, then paste into column F.
Don’t worry about columns G and H, simply enter 1 (or better 1.00) in both columns for all
events. In Excel, you can fill them all quickly as you did with the section number. Type ‘1’s
into columns G and H in the first row, select both of those cells, move the mouse arrow over the
lower right corner, hold down the left mouse button and drag down to the last row for that
section. Let go the button.
Now you are ready to enter the next section. If you keep it separate from the first section you
entered you can highlight just that section when you sort and assign level numbers for that
section in column E. Once you have entered all of your sections, go back and remove any blank
rows you left between sections. To do that in Excel, highlight the rows to be removed by
clicking the left mouse button on the row number along the left margin. That highlights the
entire row, all across the spreadsheet. Now go up to the task bar and click on Edit. On the Edit
pull-down menu select ‘delete’. You can select and delete several rows at once my holding
down the mouse button as you move the arrow over several row numbers to highlight them.
With blank rows removed you need to sort the data one last time for CONOP. Highlight the entire
worksheet by clicking the mouse with the arrow up in the top left corner of the worksheet. Click
on DATA on the top menu bar and select “Sort”. This time, in the first dialog box enter “column
A”, ascending. In the second box select ‘Column B’, ascending and in the third box “column C”,
ascending. Then click on OK. Now the first rows of the spreadsheet should group together all of
the first occurrences of the first taxon in order by section. Next will be the last appearances for
that same taxon, in the same order by section.
Save the file now and be sure to do so in the old text format, not converted to an Excel
worksheet. Close the file and Excel. You are now ready to see if the data will run. There are
usually some errors in data entry and you can find some of those by trying to run the data and
reading the error messages in CONOP.
RUNNING CONOP
SETTING UP THE CONOP9.CFG FILE
You have to tell CONOP a few things about your particular data before you run the program.
You do that in the configuration file, CONOP9.CFG. Double click on the CONOP9.CFG file in
Windows Explorer to open it in WordPad. Scroll down to 1.1 Input Data. Replace the words or
numbers in the following lines with your own, in single quotes where shown. You don’t need to
use italics, they are just used here to show what parts you enter.
PROJECT = ‘your own title’
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SECTIONS = the number of sections in your .SCT file
TAXA = the number of taxa in your .EVT file
EVENTS = 0
MAX_LEVELS=100
MAX_LABELS=30
LOADFILE = the name of your .DAT file
PREPFILE = ‘OFF.dis’
SECTFILE = ‘the name of your .SCT file’
LABELFILE = ‘OFF.lbl’
EVENTFILE = ‘the name of your .EVT file’
BESTKNOWN=0.0
In the next section, 1.2 you may not have to make any changes. The settings should be:
PENALTY='LEVEL'
LETCONTRACT='OFF'
WEIGHTING='on'
USENEGATIVE='OFF'
NEARENOUGH=5.00
EXCLUSIVES='yes'
FORCECOEX='ss'
HOMERANGE='sl'
SMOOTHER=0.00
SQUEEZER=0.00
SHRINKER=0.00
TEASER=1.0
STACKER='COEX'
Section 1.3 will look something like this. You will be coming back later to change the STEPS,
TRIALS, and STARTEMP settings. Leave the other settings as they are except for the last two.
You can either enter ‘OFF’ in front of the file name there or replace the file name with your own,
‘KT3x15.grd’ for example.
SOLVER='anneal'
STEPS=500
TRIALS=100
STARTEMP=200
RATIO=0.98
HOODSIZE='big'
STARTYPE='rand'
STARTSECT=1
STARTEVENT=0
SHOWMOVIES='CHT'
TRAJECTORY='ALL'
VIDEOMODE='SVGA'
PAUSES='ON'
CURVFILE='OFFyourfilename.grd'
CRV2FILE='OFFyourfilename.gr2'
Section 1.4 should look something like this and you probably won’t have to make any changes.
COLUMNS=7
UNLOADMAIN='outmain.txt'
FITS_OUT='ON'
CNFG_OUT='ON'
SEQN_OUT='ON'
INCR_OUT='ON'
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LOC_OUT='ON'
OBS_OUT='ON'
COMP_OUT='ON'
UNLOADSECT='outsect.txt'
SECT_OUT='OFF'
UNLOADEVNT='outevnt.txt'
EVNT_OUT='ON'
COEX_OUT='COUNT'
RUNLOGFILE='runlog.txt'
CULLFILE='cull.txt'
SOLNLIST='OFFyourfilename.sln'
STARTFILE='soln.dat'
STEPFILE='OFFstepsoln.dat'
BESTARTFILE='bestsoln.dat'
COMPOSFILE='cmpst.dat'
COMPOSNMBR=1
COMPOSTYPE='ZST'
OBSDFILE='ab.dat'
PLCDFILE='albet.dat'
EXTNFILE='delta.dat'
COEXISTFILE='coex.dat'
ORDERFILE='ordr.dat'
ERROR MESSAGES AND CORRECTIONS
Now save the file and close it. You are now ready to try a run of CONOP9. In Microsoft Explorer
double click on CONOP9.EXE in your folder. You will probably get some errors in the data and
some error messages. Errors in the .DAT file are usually identified well enough in the error
message to find and correct them. Omitting a single quote mark in the .SCT or .EVT files will also
bring up error messages. Correct the errors, save the corrected file, close the CONOP program,
and try again by double clicking on the .EXE file.
RUN THE PROGRAM
Repeat trying to run the program and making necessary error corrections until the program
accepts the data and builds an array to use, then press Enter when prompted to start the program.
You should see and automated range chart building on the screen. Ranges will extend and
contract through numerous trials until the program reaches a solution.
The “answer” you are looking for is the “lowest penalty” It is shown in green in small numbers
off to the left, near the bottom of the range chart diagram. As the program is running, it adds a
little green box whenever it finds a solution with a lower penalty. Initially there are lots of these
but they become fewer near the end of the run. The lowest penalty is the solution that extends
the ranges as little as possible to fit the data in the sections. There may be more than one
sequence of first and last occurrence events that gives the lowest penalty. Especially when there
are few sections, several events may fall at the same level in the “answer” although they can
appear in any order amongst themselves and not change the penalty any. Not every run will
necessarily come up with the lowest penalty.
When the program stops click Enter to see the final range chart it came up with and then Enter
again for a screen with a menu bar that includes pull-down menus for various graphical and text
outputs. Close this window and run the program again. Repeat several runs to see if you
consistently get the lowest penalty. If not, you can monkey with the settings in the configuration
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file to try to improve the penalty and consistency. This is called “adjusting the cooling schedule”
and involves telling the program just how it should conduct its search for a better solution (lower
penalty).
ADJUSTING THE COOLING SCHEDULE
This is basically a matter of trial and error but with practice you get a feel for what changes
might be needed. Reopen the CONOP9.CFG file, scroll down to section 1.3 and find the lines
STEPS, TRIALS, and STARTEMP. Experiment changing the values, saving the file, and then doing
more runs to try to get the lowest penalty more consistently and faster. The larger the data set the
less likely it is you will get the same low penalty each time. Length of time it takes to do a run
will be a factor in larger data sets.
Some Example Settings:
PROBLEM SIZE
STEPS
TRIALS
STARTEMP
7 sections, 62 taxa
27 sections, 131 taxa
198 sections, 1170 taxa
500
500
50
100
500
10000
200
100
100
The number of steps is the number of times that the algorithm reduces the temperature and
launches another set of trials. If the green boxes were still appearing near the end of the run then
add steps by increasing the STEPS = number. Try increasing it by intervals of 50. Decrease steps
if the latter part of the run showed no improvement (green boxes). For larger data sets the length
of time it takes to test a single trial solution is longer. Depending upon hardware, small data sets
of 5 sections and maybe 40 taxa can run in less than a minute. Moderate data sets of 20 sections
and 150 taxa might take 5 to 10 minutes. Very large data sets of more than 100 sections and
1000 taxa can take 4 days or more on a 1 GHz computer.
The number of trials are the number of different possible solutions that the program tests at each
cooling step. Well behaved data sets, where there is generally good agreement in the order of
events from section to section, can reach a good solution with fewer trials. You might need just
1 trial or you might need 10,000. You might be able to lower the number of steps if you increase
the trials. In general, increase trials rather than steps. That will lengthen the run but not lower
the final temperature.
The STARTEMP is too high if the program runs for awhile with no green boxes appearing. If it is
too low and the data is poorly constrained you risk getting stuck in a hole. Poor data? Use
higher startemp and more trials. See also “RATIO” in the large Manual9.doc. In general larger
data sets need a higher startemp.
THE RESULTS
Once you have gotten the parameters set for running the data through CONOP you will want to
look more carefully at the results. You may have noticed already that once you got the program
to run, more files appeared in the folder. Which files these are depends on the ‘ON’ ‘OFF’
settings in the .CFG file. You can also choose to create some others once you have a good run
with the lowest penalty. Perform another run and when it stops, push ‘enter’ once. This is your
range chart, with the ranges shown from top to bottom in order of the taxon number assigned in
the .EVT file. One of the ranges is light blue instead of white. The name of the taxon for that
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range appears in blue at the bottom of the left side of the screen. You can examine each range in
turn and identify the taxon by moving through the ranges using the “+” and “-“ keys. When you
have exhausted your interest in this amusement, click on the ‘enter’ key once more. This is a
blank page but at the top, on the menu bar, are some output options to examine. Click ‘TEXTFILE OUTPUT’ and a pull down menu will appear. Under ‘RANGE CHARTS’ click on ‘In FAD order’
and then click ‘enter’ when prompted. This will create an output file for you that will list the
taxon ranges in order of FADs for each section. Now create one for the composite ranges by
clicking on the TEXT-FILE OUTPUT again and selecting ‘best sequence’ under the COMPOSITE
RANGES heading. Create the cpcht.txt file by pressing ‘enter’ when prompted. Alternatively,
select ‘best sequence’ under ‘RANGE SEQUENCE’.) Those two files should have the output data
you need. The file outmain.txt, which is automatically created by CONOP, also has this
information but it is organized differently.
Correlation of sections.
To find the levels at which CONOP has placed events in each section you will want to look in the
FADCHART.TXT file. This is a text file that will open in WordPad or you can open it in Word.
The file lists, for each section in order, the projected levels for each taxon’s FAD and LAD. This
includes FADs that might be projected to occur lower and LADs higher in the section than they
were actually observed as well as the levels at which taxa not observed (‘not seen’) in the section
but which are believed to be contemporaneous would appear or disappear if they did occur there.
The taxa whose ranges do not overlap with that section will not be listed. Note that there will be
a plethora of FADs listed at the bottom and LADs at the top which represent taxa which
originated before the lowest collection level or disappeared after the highest collection level
respectively. Drawing a line from any one of these events placed in the section to the level the
same event is placed in another section would be a line of correlation.
Composite Range Chart
If you are, instead, interested in building a range chart for the taxa, establishing a record of the
order of their appearances and disappearances, you then can look in the cpcht.txt file. The FAD
and LAD levels are listed for each taxon in a calculated “master section” where the spacing of the
levels is based on the correlation of individual sections you entered. 1000 was added to the
levels along the way in the program so you could subtract 1000 if you wanted. The sqcht.txt
option is similar but the levels are numbered sequentially and not spaced to any scale.
GRAPHICAL OUTPUT
You can create your own range charts from data in the output files using Excel or a drafting
program. Some are available in simple form in the “GRAPHICAL OUTPUT” pull-down menu after
you have done a CONOP run. Most of these require more explanation than we can go into here
but try the “TAXON RANGE CHARTS”, “FENCE DIAGRAM” and “SECTION RANGE CHARTS”. Note
that the section range charts give each FAD and LAD a separate line even though several might
actually occur at the same level. You navigate through a variety of styles with simultaneous ‘x’
plus ‘+’ or ‘-‘ keys and through events with the + and – keys. this may take some
experimentation to master. Return to the CONOP program by clicking the mouse and then the
escape key. More details on each output style and navigation within it is in the full CONOP
Manual.
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Directions for making a range chart in Excel are included in an appendix at the end of this
manual and in the files ExcelVRangeChart.xls and ExcelHRangeChart in the Making Charts
subfolder within the Excel Users folder.
For fence diagrams, you are better off printing out one of the graphics from the pull-down menu
in CONOP or drafting one up in your own style in a drawing program. Select the ‘Fence Charts’
line, not the smoothing ones, for a standard fence diagram in which events that occur at the same
level are plotted together. Note that with the ‘+’ and ‘-‘ keys you can change to a version of the
fence diagram centered on different events (‘base line’ levels). Choose one that best illustrated
what you want to show. To save a fence diagram (or other graphic) to Corel Draw select it from
the pull-down Graphical Output menu in CONOP. Press Esc or click on the graphic so that you
can see the menu bar. Open the File menu and select save. In the save dialog box choose a
location for the file and a file name, then click ‘Save’. Open a new file in Corel Draw, from the
file menu select ‘Import’ and in the import dialog box at the bottom, in the Files of Type box
select either ‘All types’ or ‘BMP Windows Bitmap’. Then find your file and double click on it
in the box with the file names. You can now resize the fence and add your own annotations, etc.
OTHER TYPES OF EVENTS: MARKER BEDS AND HORIZONS
There may be additional types of information with measured stratigraphic sections that can be
used by CONOP in conjunction with the taxon ranges. Unique beds or horizons can force
correlations and absolute ages can add absolute time to the scale. The .SCT input file should not
be affected by including these types of events unless you are adding a section which is only tied
to the others by marker beds and dated horizons.
“Acme Horizons” = type 3 events
An acme horizon is a layer in which a taxon, for which you also have FAD and LAD
information, is unusually abundant. Such layers might have local significance time-wise. The
taxon involved should already be defined in the .EVT file. You would, however add a row to the
.DAT file for each section in which the layer appears. The first column contains the same taxon
number as you assigned to the FAD and LAD, the second column should be ‘3’. The ‘allowed
moves’, column F, should also be ‘3’. There must also be an FAD and LAD for the same taxon
in the same section. In the .CFG file you must count this as an event so go to section 1.1 and set
EVENTS = (number of type 3, 4, and/or 5 events). This event type has only had limited testing
so examine results carefully.
Unique Chronostratigraphical Marker Horizon = type 4 events
A distinctive ash bed would be an example of this type of event. You do have to be careful that
the bed seen in several sections is truly the same one. You will have to add an entry in the .EVT
file to define each marker bed and assign it a number. In the .DAT file you will have to add one
row for each section in which it appears. The event type in column B is ‘4’ and the allowed
moves in column F is ‘0’. In the .CFG file you must go to section 1.1 and set EVENTS =
(number of type 3,4, and/or 5 events).
Age Dates = type 5 events
Age dates must also be given their own event numbers in the .EVT file. In the .DAT file they
are entered as event type ‘5’ in column B and allowed moves in column F should be ‘0’. Since
the last two columns in the .DAT file have no meaning with regard to weight in this instance
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they are used to record the age range on the date (+ or – 2 sigma). In the .CFG file you must go
to section 1.1 and set EVENTS = (number of type 3,4, and/or 5 events).
THERE’S MORE
There are numerous options in the graphical output that we didn’t discuss. Most of these take
some getting used to but do help understand how the data is behaving during the run and
between runs. For a more detailed treatment of all options and aspects of CONOP9 see the file
MANUAL9.DOC in the Docs folder within the CONOP folder. You can also find more information
in text at the end of the CONOP.CFG file.
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APPENDIX A: HOW TO MAKE A RANGE CHART IN
EXCEL FROM THE CPCHT.TXT FILE
At the end of a good CONOP run select TEXT FILE OUTPUT on the menu bar.
Select ‘best sequence to cpcht.txt’ under COMPOSITE RANGES on the pull-down menu and
press enter when prompted. Close CONOP
Open cpcht.txt in WordPad or other text editor and delete any titles and text that is not in
column format. Save and close the file.
Open Excel and from the Excel tool bar select the ‘Open’ folder.
In the ‘Open’ dialog box, at the bottom, in the ‘Files of type’ box, select ‘All files (*.*)’.
Find your folder in the CONOP folder on the C: drive and select the cpcht.txt file.
Click on ‘Open’ and a dialog box will appear to translate the file into a spreadsheet format.
In the dialog box select ‘fixed width’ at the top and then click on the ‘Next’ button.
In the next dialog box check the placement of the column lines to make sure they don’t bisect
any numbers. Move them with the mouse if necessary. Then click on the ‘Next’ button.
In this dialog box you select just the columns you need. The first column is highlighted first.
In the ‘Column data format’ box at upper right select ‘General’. Mouse click on the second
column to highlight it and select ‘do not import column (skip)’ Click on the third column
and select ‘do not import ’. Click on the fourth column and select ‘General’. Click on the
fifth column and select ‘do not import’. Click on the sixth column and select ‘do not
import’. Click on the last column and select ‘General’.
Mouse click on the ‘Finish’ button at the bottom right of the dialog box.
You should now have three columns of data in a spreadsheet, FAD, LAD, and Name.
Delete any blank rows above or within the data and adjust the column width if desired.
You may want to delete any type 3, 4, or 5 events by deleting their rows.
You will need to add two columns for the range chart plotting. You will need to subtract the
1000 that CONOP added to the section measurements from column A. Otherwise, the Excel
chart will be way off scale. In the first cell of Column D enter the formula =A1-1000 and
move the cursor over the lower right corner of the box so that it becomes a black cross. Hold
down the left mouse button and drag the mouse down the column to the last row of data and
release. This will fill all of the cells with the formula for calculating the FAD for that row.
This will be the value Excel uses to plot the bottom of the range.
Now fill column E with the length of the range, i.e. the LAD-FAD. To do this type =B1-A1 in
the first cell and then drag it down to fill the rest of the cells in the column as you did in
column D. Excel will use column E to calculate the ends of the ranges in the chart.
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Highlight columns D and E with the mouse by clicking on the ‘D’, holding down the mouse
button, and drag it over to ‘E’.
You are now ready to have Excel plot the chart. With those two columns still highlighted,
click on the ‘Chart Wizard’ up on the task bar. The Chart Wizard symbol looks like a little
three-dimensional bar chart with blue, yellow and red vertical bars.
Click on the ‘Custom types’ tab in the Chart Wizard dialog box that appears.
Select ‘Floating Bars’ in the ‘chart type’ box. You should see a thumbnail of the chart in the
dialog box now. Click the ‘Next’ button.
Select the 'Series' tab in the step 2 dialog box. To get taxon names onto the chart, at the
bottom, where it says 'category x axis labels', click on the table symbol on the right side of
the empty dialog entry box. That takes you to your data table. Highlight the column with the
taxon names. That will make the ‘address’ for those names appear in the little dialog box.
You can close that box and select OK and you return to your Chart Wizard step 2 dialog box.
Click on the 'Next' button to go to step 3.
In the next ‘Chart options’ box you can experiment with various options for labeling your
chart. You can experiment with these and see how they look in the thumbnail and remove
them or change them as you wish. You can change these same aspects or remove or change
the background color and type color later. When you are satisfied, click the ‘Next’ button.
The last step is deciding whether you wish to save the chart to a separate sheet in the cpcht
file or on the same page with the data. If you choose a separate sheet, it will add a tab at the
bottom of the page called Chart1 and your data will be on a sheet with a tab marked cpcht.
Click on either tab to look at it.
If you select the chart area you can change various aspects and formatting by then clicking
on the 'Chart Options' in the Chart Menu or 'Selected Plot Area' in the Format Menu.
You can also rotate or move titles and some other labels. To rotate the chart title, click on it
so that a select box appears around it. Open the Format menu on the menu bar and select
‘Selected Chart Title’. Click on the Alignment tab and use the mouse to rotate the red
diamond in the orientation box.
See also the two Excel files ExcelVRangeChart.xls and ExcelHRangeChart.xls in the Making
Charts folder inside the Excel Users folder for instructions and examples.
Marilyn Kooser
Geology Museum
University of California, Riverside
Summer 2002