Manual: Using Fitman, Estman and TGOF to obtain stopover estimates
from banding data using CMR models.
The Schematic of Stopover Estimation Using CMR models
Estimability
Can we estimate the parameters in
the model, for some reasonable
range of models?
No
Stop
Yes
GoodnessOf-Fit
Does the model describe the
variation present in the data
Yes
Model
Choice
Exactly what form of the model
should we use?
Model identified
Bootstrapping
What is the level of uncertainty in
the stopover estimate?
No
Stop
MarkMaker Manual:
In the first step, we convert our data files with dates of capture and banding numbers into
capture histories that indicate patterns of observation of birds.
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Open a new Excel file.
Choose a target species, year and location for the Markfile from your raw data file
containing initial captures.
Select (highlight) the band numbers for the given species. Copy (Ctrl C).
In your new Excel file, paste the copied cells into column A (Ctrl V).
Return to the raw data, and select the date for the corresponding band numbers.
Copy.
Paste the copied cells into column B in your new Excel file
Return to the raw data, and select the sex for the corresponding band numbers.
Copy.
Paste the copied cells into column C in the new Excel file.
Repeat the same process selecting the band numbers, dates, and sex for recaptured
individuals of the target species. Place the copied cells in the appropriate columns
already created. You should have a total of three columns.
Save as a text file.
Highlight column B containing the dates. Under the Format heading, select Cells,
highlight General, and click OK.
Highlight column C containing the sexes.
Sex descriptions: HY=hatch year, AHY=after hatch year, SY=second year,
ASY=after second year, L=local species.
Under the Edit heading, select Replace. Replace HY and L with 0, everything
else replace with a 1.
Save as a text tab delimited file.
Open MarkMaker Program
Click on Load Data and open your text tab delimited file for the target species
Click on Save Mark File, and save as an .inp file
You’re Done!!!!!
Making an F-list:
While it is possible to analyze capture histories one at a time (using the Fitman
program), we can automate the process and analyze 5 to 20 files at once. The F-list is a
set of instructions to the software telling it what files we want analyzed.
1. Open MS DOS (or command window)
2. Get to the directory you need:
 For floppy disk type A:
 Press enter
 Note-if you need to go back a directory, type CD:
 Type DIR to show you what is on the floppy disk. Enter
 Now you want to choose the file that your mark files are in. Type CD name_
of_directory Note the spacing!! The name of the directory should be the file
name that you have all the mark files in. If you have a folder that the files are
in, type the same thing with the name of the folder as the name of the
directory. Once in the folder you can then see your mark files. Only .inp files
should be in this directory!! If you have other files in there you can type
DIR *.inp to show just the inp files. Note-you need to type the asterisk after
the space. Enter
 Type DIR *.inp>flist.txt This will send all the inp files into a file called flist
Enter
3. Open Program Excel
 Open flist.txt Choose delimited, press next, select space and tab, click
finish
 Delete all cells with text in them except the ones with .inp file names, you are
essentially making a list of the file names, make sure the final list is in the top
left corner of the spreadsheet.
 Save as flist_year_.txt Example: flist95.txt
Note: all disks should contain files for just one location, season, and year. They should
have all appropriate markfiles and just one flist. This will eliminate confusion and make
for less errors when running stuff in the programs.
Estman Manual:
With our capture histories and F-list in hand, we are ready to determine if any models
may be fitted to the data.
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Open program Estman
Click on the blue Load File List button
Search through and load your flist file
Click on the green Go button, and make sure the minimum MDC on the right says
1, and the maximum is 7.
5. It will ask you to name the estimability output file. Type in
est_*location*season*year.txt For example: est_as1996.txt This is for
Appledore, spring, 1996
6. Next it will ask you to name the gof output file. Type in
est_*location*season*year_gof.txt For example: est_as1996_gof.txt
7. Once you click OK, the program will start running. YOU MUST LEAVE THE
FLOPPY DISK IN THE COMPUTER AS LONG AS THE PRGRAM IS
RUNNING. Also, do not touch or interrupt the computer while the program is
running, this will cause it to crash. It will run for at least 6 hours if you have 5-6
files, so it is best to load the computers and leave them overnight.
Tgof Manual:
Once we know that one or more models can be fitted to the data, we need to determine if
the models adequately describe the data, will they pass a Goodness-of-Fit (GOF) test.
1. Open Program TGOF
2. Click on the seagreen button Go, TGOF, Go!
3. It will ask you to select an input file. Search through and select your gof output
file from estman. The file should look like est_as1996_gof.txt
4. It will then ask you to name your output file. Type in
est_*location*season*year_gof_out.txt For example: est_as1996_gof_out.txt
5. As soon as you hit OK, the program starts. Once again the disk must remain in
the computer the entire time it is running, and don’t touch the computer once it’s
running!!!!
6. Tgof takes a LONG time to run; sometimes it can take 12+ hours for 5-6 files to
run. The weekends are usually the best time to run these guys.
7. Lastly, once the program is done, you will see that it created an extra file for you.
For example it will be named est_as1996_gof_out_short.txt This is a short, and
more useful data sheet.
MDC Manual:
If the model can be fitted to the data (is estimable), and adequately describes the data
(GOF) we know need to carry out a model choice procedure, and select the appropriate
Multi-Day Constancy interval (MDC) to use.
1. Open Program TGOF.
2. Click on the purple button MDC Sweep Model Choice
3. It will ask you to specify an input file, search through and select your gof output
file from Estman. It will look something like est_as1996_gof.txt
4. It will then ask you to name the output file. Type in
est_*location*season*year_mdc.txt For example: est_as1996_mdc.txt
5. As soon as you hit OK, the program will start running. MDC can be funny,
sometimes is takes just a couple hours or less to run, or it can take 6+ hours to
run. Once again, the disk MUST stay in the computer the whole time and do not
touch the computer while the program is running.
6. When the program is done, you will notice that it created another output file for
you. It will look something like est_as1996_mdc_short.txt.
The Tricky Part (Of Model Choice):
In the regular MDC output file, the weight for each individual file must add up to .95 or
higher. However, the program only takes the highest weight and lists that model choice
in the short output file. To fix this:
1. Copy and paste the short MDC list into Excel
2. Keep everything in list fashion, don’t change the format of anything!
3. Copy the file name exactly, and by looking at the long MDC output, write
in the appropriate model choice. For example, if the model you need is
P.Phi(7) Gamma. You would write is like this in excel: 0707
Basically, periods = 0 and numbers=numbers. The last number represents
the day and it always be a number of 1-7.
Ex. Original List
Edited List
GCKIsd97.inp
0606
GCKIsd97.inp
0606
MGWAsd97.inp 0077
GCKIsd97.inp
0066
MGWAsd97.inp 0077
MGWAsd97.inp 0066
MGWAsd97.inp 0707
You will notice that MGWA has 3 models chosen. This is because it took
three models to equal the .95 weight limit.
4. Save the new list as est_*location*season*year_mdc_shortc.txt
However, do not lose the old short file, we still want this.
BOOT manual:
Now that we know which model is the optimal one to use, we want to estimate the
stopover, and how variable the estimate of stopover is, given our data. This process is
achieved through a bootstrapping procedure.
1. Open Program TGOF
2. Click on the orange button labeled Bootstrap SO from file
3. It will ask you to specify an input file. Search through and select the shortc file:
est_as1996_mdc_shortc.txt
4. It will ask you to name the output file. Type in boot_*location*season*year.txt
For example: boot_as1996.txt
5. As soon as you click OK, the program starts running. It will only take around an
hour for the program to run. Once again, the disk MUST stay in the computer for
the entire duration and do not touch the computer while the program is running.
6. When the program is finished running, you will notice that it created another short
file for you, this is useful for data processing.