CONOP9 EXCEL USERS’ GUIDE
1
CONOP9 QUICKSTART GUIDE FOR EXCEL USERS
WHAT CONOP WILL DO
CONOP9 is primarily used to correlate stratigraphic sections which contain fossils. The
correlation may be an end in itself, or one step in the construction of a diversity curve or a
calibrated time scale. CONOP9 makes a best estimate of the overall sequence of first and last
appearances of fossil taxa, based on the ranges of taxa preserved in each section. It can handle
large numbers of taxa from many sections. It constructs composite range charts, fence charts,
species richness curves, taxon longevity curves, etc.
This guide assumes you are familiar with Excel and will use it to enter your data. The important
steps in the process are
1) installing CONOP9
2) gathering the data
3) entering the data
4) adjusting settings in CONOP’s configuration file
5) running the program
6) looking at the results,
7) adding non-taxonomic data like marker beds and age dates.
INSTALLING CONOP
1. Copy the distribution files onto your hard drive. The following narrative assumes that all the
folders are stored within one named CONOP. In most distributed formats there will be a
‘DOCS’ folder that contains the complete user’s manual, (Manual9.doc/pdf may be split into
two files Guide.doc/pdf and Reference.doc/pdf), a NOVICE folder for inexperienced users,
and an EXCEL USERS folder with this manual. An example data set may be nested within the
Excel folder or must be sought in the general suite of data folders.
2. On some computers, the files copied from a CD source retain “read only” properties. Make
sure the files you will need to use are changed to ‘archive’. If you don’t know how to do
this, see INSTALLING CONOP in the NoviceGuide.doc file.
3. Make a new folder within the CONOP folder for your own project.
4. Move copies of the CONOP9.EXE and CONOP9.CFG files into your folder.
THE DATA YOU NEED
1. Two or more measured stratigraphic sections.
2. Taxon identifications with at least two taxa shared between sections.
3. The levels at which each taxon found in each section first appears (FAD = first appearance
datum) and last appears (LAD = last appearance datum).
ENTERING THE DATA
You next have to put your data into input files, within your folder, in a format that the CONOP
programs can read. The CONOP program will need these in text file format but you can build
them in Excel and then save them as “TEXT (tab delimited)” files (space delimited should also
work).
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CONOP9 EXCEL USERS’ GUIDE
1. The .SCT file labels your sections, assigns them numbers, and a place in the final fence
diagram. You can put in a header row while you are entering data if it helps you keep track of
which data goes into which column but it must be removed before you do a final save_as.
There are five columns (fields) of information and one row (record, line) for each section.
Inverted commas (single quotes) are necessary in the text file when there are blank spaces within
the entry meant to be in one column. Excel uses the leading inverted comma for something else
so you will have to enter a space before the inverted comma OR add them later, after converting
the file to .txt format.
.SCT file format
SECTION#
ABBREVIATION
consecutive
integers starting
with 1 in first
row
Nickname for each
section, three letter
maximum, in single
quotes.
A
1
2
1
2
FENCE
ORDER
consecutive integers 1
through number of
sections in any order
B
‘DL1’
‘KT2’
C
1
2
NAME
INCLUDE
Your identifier or name for each
section, in single quotes, 20 space
maximum.
Just put 1 for
all rows
D
‘Denmark section DL4’
‘Seymour Island KT2’
E
1
1
Column A on each line is the section number which you will be using when you enter your data
in the .DAT file so make a record of it in your notes for that section. Number the sections
consecutively, starting with 1, omit no numbers, and list them in the .SCT file in order, 1 first.
Column B is a three-letter abbreviation used to identify the column in output files. It must be
preceded and followed by single quote marks if it includes a blank space. It can be an
abbreviation of the name or any code that refers to other databases
Column C 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; i.e.
the same numbers as column A, but in custom order.
Column D 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 in Excel (space first!).
Don’t worry about the final column for now, just enter a 1 for each section.
If you made a header row, save the .xls file then erase the header before saving the file as a TEXT
(tab delimited)(*.txt) file. Using .SCT as the extension might help you find it again more easily
than .txt. Close the file in Excel and then open it in a simple text editor like WordPad to make
sure the inverted commas are where they should be and the data are properly separated. It is not
necessary that the columns align vertically, or that the white spaces are of the same length in all
sections. For proof-reading it may be easier to align the columns. Achieve this with tabs and/or
a non-proportionally spaced font.
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CONOP9 EXCEL USERS’ GUIDE
2. The .EVT file labels your taxa (and other types of events) and assigns them a number and
nickname. Again, you may want to label a header row initially but it will have to be removed
before the final save.
.EVT file format
TAXON#
NICKNAME
NAME
consecutive integers starting
with 1 in the first row
Shorthand code or
abbreviation for the name
Taxon name
A
1
2
3
B
1
2
3
C
‘Bispathodus aculeatus aculeatus’
‘Bispathodus anteposicornis’
‘Bispathodus costatus’
‘Baa’
‘Ban’
‘Bco’
Column A is the event number and must be 1 in the first row, 2 in the second, etc.
Column B is for the taxon nickname. Start with a space and single quote 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 code that refers to another database. Follow it with another single quote.
Start Column C with another space and 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. Erase the header row if you made one and
save the file as TEXT (tab delimited)(*.txt) with your own file name and the extension .EVT.
3. The .DAT file will contain all of the information on FAD and LAD levels for all taxa in all
sections. There will be one row (line, record) You will be using the section numbers you
assigned in the .SCT file and Taxon numbers you assigned in the .EVT file.
.DAT file format.
TAXON#
From the
.EVT file
EVENT
TYPE
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
9.3
8.4
8.4
ALLOWED
MOVES
1 if FAD
2 if LAD
E
1
3
2
2
WEIGHT
UP
WEIGHT
DOWN
just put
1
just put
1
F
1
2
1
2
G
1
1
1
1
H
1
1
1
1
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 convenient and quick to enter one section at a time in the following manner. For each
taxon in the first section, note the taxon number from the .EVT file. In Column A 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. Now enter the section
CONOP9 EXCEL USERS’ GUIDE
4
number, the one you assigned in the .SCT file, in each row in Column C. Now you should have a
row for every first and every last appearance of every taxon found in the first section.
In 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. These numbers
may be entered with or without decimal places. It is safest to avoid using “0” in this column -early versions of CONOP used zero for taxa not seen and it is possible that some little-used
algorithms retain this feature. If one of your levels is 0, either change it to 0.01 or add an
arbitrary constant, like 100 or 1000.00, to all of the levels in the section. You can enter negative
numbers for well depth; this ensures that the values for both well depths and measured sections
will increase up-section from older to younger.
Filling in Column E is where Excel comes in handy. Highlight all rows of data for the section
you are working on. Do an ascending sort on column D. Your entries should now be in reverse
stratigraphic order with events that occur at the same level grouped together in column D. Now
number the levels in column E consecutively, use 1 for the lowest level. All events that occur at
the same level 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 and paste it into column F.
Enter a 1 or 1.00 in both column G and H for each row. Don’t worry about what they mean at
this point.
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. Each section has its own level numbers starting with one for the lowest.
Once you have entered all of your sections, go back and remove any blank rows you left between
sections and the header row if you made one.
You need to sort the data one last time for CONOP. Highlight the entire worksheet and do an
ascending sort on columns A, B, and C, in that order. 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.
You may prepare an unsorted file, with or without column E, and use CONSORT9.EXE to complete
and sort it. Nevertheless, it is more comforting to use the “hands-on,” and “what you do is what
you get” control offered by Excel.
Save the file now and be sure to do so in text file format with any name you choose but with the
extension .DAT. Close the file and Excel. 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.
CONOP9 EXCEL USERS’ GUIDE
5
SETTING UP THE CONOP9.CFG FILE
You have to tell the CONOP algorithms 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’
SECTIONS = the number of sections in your .SCT file
TAXA = the number of taxa in your .EVT file
EVENTS = 0
MAX_LEVELS=100 (change only if you have more than 100 levels in a single section)
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='OFFfilename.grd'
CRV2FILE='OFFfilename.gr2'
CONOP9 EXCEL USERS’ GUIDE
Section 1.4 should
look something like
this and you
probably won’t
have to make any
changes here.
6
COLUMNS=7
UNLOADMAIN='outmain.txt'
FITS_OUT='ON'
CNFG_OUT='ON'
SEQN_OUT='ON'
INCR_OUT='ON'
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='OFFfilename.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 -- these will result from incompatible or inconsistent values entered into
the excel spreadsheet. 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, usually in a blue box. Correct the errors, save the corrected file, and
close the CONOP program, and try again by double clicking on the .EXE file.
CONOP9 EXCEL USERS’ GUIDE
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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 run. You
should see and animated range chart twinkling 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,” or smallest misfit between the model
sequence of events and all the local stratigraphic sections. The misfit penalty is shown in green
in small numbers to the left, near the bottom of the animated range chart diagram. As the
program runs, it adds a green box whenever it finds a model sequence (trial solution) with a
lower misfit penalty. The lowest penalty is the solution that extends the ranges as little as
possible to fit the data in all the sections to a single sequence. There may be more than one
sequence of 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. Not every run will necessarily yield the lowest penalty –
see remarks about the “cooling schedule.”
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 adjust the settings in the .CFG file to try to
improve the penalty and consistency. This is called “adjusting the cooling schedule”.
ADJUSTING THE COOLING SCHEDULE
This is basically a matter of trial and error but with practice gained from watching the animation
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 how many times the program lowers the temperature and moves on to
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).
The number of trials is the number of trial sequences the program examines at each temperature
step, trying to find a better solution. 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
CONOP9 EXCEL USERS’ GUIDE
8
trials. You might need just 1 trial or you might need 10000. You might be able to lower the
number of steps if you increase the trials. But beware, in combination with the cooling ratio, the
number of steps ensures that the final temperature is suitably low to freeze-in a good solution. In
general, increase trials rather than steps.
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 bad solution -- during the
animation, the line of green boxes dives rapidly down the screen and stops abruptly without the
characteristic negative exponential curve of diminishing returns. If the starting temperature is
raised substantially, it may be necessary to increase the number of steps in order to achieve a low
enough final temperature.
THE RESULTS
Once you have found the parameters that run the data through CONOP to a consistent result, 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 more once you have a good
run through with the lowest penalty. Perform another run and when it stops, click ‘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 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
‘TEXT-FILE 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.
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. 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 base of the section or disappeared after the top collection level
respectively.
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
CONOP9 EXCEL USERS’ GUIDE
9
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 and fence diagrams 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 but also see the full Manual9.doc for more detailed explanations
and navigation directions for each type. Return to the CONOP program by clicking the mouse and
then pressing the escape key.
ADDING 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. The taxon involved should already be defined in the .EVT file. 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 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
they are used to record the age range on the date (+ or – 2 sigma), youngest in column G. In the
.CFG file you must go to section 1.1 and set EVENTS = (number of type 3,4, and/or 5 events).
CONOP9 EXCEL USERS’ GUIDE
10
THERE’S MORE
For a more detailed treatment of all options, input, output and aspects of CONOP9 see the file
MANUAL9.DOC or MANUAL9.PDF in the ‘Docs’ folder within the CONOP folder. In some versions,
MANUAL9 has been split into two parts: GUIDE9.PDF and REFERENCE9.PDF. You can also find
more information in text at the end of the CONOP.CFG file. There are directions on and examples
of a couple of ways of making range charts in Excel in the .xls files. ExcelHRangeCht.xls
illustrates a chart with horizontal ranges. ExcelVRangeCht.xls illustrates a chart with vertical
ranges.
Marilyn Ann Kooser
Geology Museum
University of California, Riverside
Summer 2002 – Winter 2003