potential .inp file formating/input issues

[Kamerus88]

Hello everyone,

I'm a first time MARK software user. I've been reading up and following instructions for data input and analysis directly out of an exercise book ("Problem-solving in conservation biology and wildlife management"). Chapter 14 of the book discusses ways to use MARK for population estimation size. It gives some sample data in the form of Tiger photo encounters over a several day period, etc. I've run this given file with success multiple times. However now that i'm attempting to run my own data through MARK it is not working for me. I've been pretty meticulous in the data input to keep the format identical to that of the sample file so I do not think thats the reason i'm seeing a lack of function. My data set currently has 38 encounter days with 12 individuals in one analysis, is this too many encounter days for MARK to handle? I'm not sure of the capacity that the program can reach. Every time I upload the data file I get a message of something along the lines of "Only 12 Semicolons present, are you sure this is a proper MARK histories file?" and then upon selecting OK it goes to another message which has a bunch of Line error read out and such. I'm using closed capture data type specifications when I begin input. Any ideas on what I can do to get some analysis going?


**Here is an example of what I have written in the Notepad .inp file:

/* P.n W MARK data 2010-2011 */

/* 1 */ 00000000000000100000000000000000000000 1;
/* 2 */ 00000000000100000000000010000000000000 1;
/* 3 */ 00000000000000000001000000000000000000 1;
/* 4 */ 00000000000101001100000000000000000000 1;
/* 5 */ 00000000010000001000001000000000000000 1;
/* 6 */ 00000000000000100000000000000001000000 1;
/* 7 */ 00000000000000001000000000000000000000 1;
/* 8 */ 00000000000000000000000000000000100000 1;
/* 9 */ 00000000000000000000000000000001000000 1;
/* a */ 00000000000000000000000000000001000000 1;
/* b */ 00000000000000000000000000000000000010 1;
/* c */ 00000000000000000000000000000000100000 1;


Thanks for any suggestions,

K88

[bacollier]

K88
Your data set is not too big, so your fine there. The semicolon warning is not a problem, its just ensuring you check your numbers to be sure you have the right numbers.

What 'model' are you specifying when you set it too close captures? Are you sure you are defining the number of occasions correctly? Can you post the dataset and the steps you took and the error you are getting? I am betting it is something simple with your setup that is causing the error to occur.

Bret

[bacollier]

K88
Sorry, on laptop did not see the data you posted before my first response. I just loaded your data fine using 38 encounter occasions, 1 group, and selecting "Closed Captures" then selecting the first Closed Capture Option. Your data is really sparse for a abundance model as you rarely have more than a couple of captures, so you will probably not get very sensible estimates of either capture, recapture, or N once you get it loaded though...

Bret

[Kamerus88]

Bret,

Thank you for the quick reply!

I followed the same procedure you went through, Closed Captures, then closed again. Can you elaborate what you mean by Model specification here? I'm using what the book chapter describes as an M0 model, where the samples are assumed to not respond differently after the initial capture. After that I'm going to run several different models, adding the assumption of behavioral changes due to capture attempts etc ( what the book labels as Mb, Mh models etc). However Once I get into the specifications screen and upload the file, I get that semicolon number message, and then the next message that I get only allows for "Abort" to be selected thus I cannot even get to my PIM displays.

[bacollier]

Bret,

Thank you for the quick reply!

I followed the same procedure you went through, Closed Captures, then closed again. Can you elaborate what you mean by Model specification here? I'm using what the book chapter describes as an M0 model, where the samples are assumed to not respond differently after the initial capture. After that I'm going to run several different models, adding the assumption of behavioral changes due to capture attempts etc ( what the book labels as Mb, Mh models etc). However Once I get into the specifications screen and upload the file, I get that semicolon number message, and then the next message that I get only allows for "Abort" to be selected thus I cannot even get to my PIM displays.

No worries, happened to be sitting at computer.

Here are the steps I used:

Save the file as filename.inp on your desktop (make sure it is not filename.inp.txt which sometimes Notepad will do-get gsnote by the way, its better)
In the "enter specifications for mark analysis window" set it to closed captures
When the next window opens up, click the top row "closed captures"
type in a name (test) for your analysis
load your data file
put 38 for encounter occasions
put 1 for group labels
hit ok

you should get the 12 semicolons statement and then it should work. If not, you have a MARK problem, try uninstalling and reinstalling the program.

But, pay attention to my earlier statement, you don't hardly have the data to be testing for behavioral responses to capture or temporal responses, etc., its just too sparse of a data set (or at least the example data you provided was, maybe you have more).

Bret

[Kamerus88]

Thanks again Bret!

Ok so i went through the steps as you laid them out and still no dice, I uninstalled and reinstalled MARK as well to no avail. Perhaps there is some sort of settings issue in my computer that could remedy this? I just don't understand why I'm continuing to get this abort error message.

this is what my Research mentor has recommended for analysis so he and I will be going over the results to see how viable they are and what not, I was wondering myself how the data would stack up considering the sheer amount of re-captures and capture days.

Also, are you using the latest edition of MARK for your analysis? I'm wondering if that might have something to do with it.

K88

[cooch]

Hello everyone,

I'm a first time MARK software user. I've been reading up and following instructions for data input and analysis directly out of an exercise book ("Problem-solving in conservation biology and wildlife management"). Chapter 14 of the book discusses ways to use MARK for population estimation size. It gives some sample data in the form of Tiger photo encounters over a several day period, etc. I've run this given file with success multiple times. However now that i'm attempting to run my own data through MARK it is not working for me. I've been pretty meticulous in the data input to keep the format identical to that of the sample file so I do not think thats the reason i'm seeing a lack of function. My data set currently has 38 encounter days with 12 individuals in one analysis, is this too many encounter days for MARK to handle? I'm not sure of the capacity that the program can reach. Every time I upload the data file I get a message of something along the lines of "Only 12 Semicolons present, are you sure this is a proper MARK histories file?" and then upon selecting OK it goes to another message which has a bunch of Line error read out and such. I'm using closed capture data type specifications when I begin input. Any ideas on what I can do to get some analysis going?


**Here is an example of what I have written in the Notepad .inp file:

/* P.n W MARK data 2010-2011 */

/* 1 */ 00000000000000100000000000000000000000 1;
/* 2 */ 00000000000100000000000010000000000000 1;
/* 3 */ 00000000000000000001000000000000000000 1;
/* 4 */ 00000000000101001100000000000000000000 1;
/* 5 */ 00000000010000001000001000000000000000 1;
/* 6 */ 00000000000000100000000000000001000000 1;
/* 7 */ 00000000000000001000000000000000000000 1;
/* 8 */ 00000000000000000000000000000000100000 1;
/* 9 */ 00000000000000000000000000000001000000 1;
/* a */ 00000000000000000000000000000001000000 1;
/* b */ 00000000000000000000000000000000000010 1;
/* c */ 00000000000000000000000000000000100000 1;


Thanks for any suggestions,

K88

Several comments:

1\ You get the 'warning' any time the number of occasions is > number of lines in the data file. You can prove this to yourself simply by making a copy of your .in file, but quadrupling the number of lines (easy enough -- just copy and paste your histories 3 times below your current histories. If you do, the warning message disappears.)

2\ in general, do not put blank lines anywhere in the .inp file. So, better to delete the blank line between the title comment and the first encounter history. In other words, it should look like the following.

/* P.n W MARK data 2010-2011 */
/* 1 */ 00000000000000100000000000000000000000 1;
/* 2 */ 00000000000100000000000010000000000000 1;
<snip>

3\ Brett is correct -- your data are so sparse (if this is in fact your data set), that you're not going to get much out of them. Based on the 3 standard models (M0, Mt, Mb -- see chapter 14), the most parsimonious is Mb. Estimate of N from this model is 16132.879 (which is clearly nonsense), and the CI is basically ~100 -> >1,000,000 (which is also nonsense). If you drop that model (based on the 'stupid nonsense criteria'), then estimates (based on M0 and Mt) are more 'reasonable' (N ~17), but with an encounter probability (per occasion) < 0.03 (more or less), you going to have a really hard time getting an estimate you're likely to be very comfortable with.

[Kamerus88]

Thank you both so much for the replies and help instructions.

Cooch,

I removed the blank space, and also copied and pasted the data 4 times without and spaces between the copies, I went to run the closed analysis again and the semicolon error message disappeared however it took me straight to an abort error message. I've reinstalled/installed MARK 3 times since starting this thread and I'm still not having any luck with getting any sort of Parameters index to display for my own data, the sample Kahna Tiger however goes through just fine. A Data file from another student's project is also being run through MARK and I've also attempted to run this one, it does the same thing as my own. I've tried this analysis on 3 different computers as well, I just don't understand why it won't advance to the PIM displays.


Thanks you for the data interpretation and explanation as well, from what everyone has suggested it's probably not going to be an extremely accurate or viable estimate value. I Just wish I could dissect and diagnose it myself!

K88

[cooch]

Thank you both so much for the replies and help instructions.

Cooch,

I removed the blank space, and also copied and pasted the data 4 times without and spaces between the copies, I went to run the closed analysis again and the semicolon error message disappeared however it took me straight to an abort error message. I've reinstalled/installed MARK 3 times since starting this thread and I'm still not having any luck with getting any sort of Parameters index to display for my own data, the sample Kahna Tiger however goes through just fine. A Data file from another student's project is also being run through MARK and I've also attempted to run this one, it does the same thing as my own. I've tried this analysis on 3 different computers as well, I just don't understand why it won't advance to the PIM displays.


Thanks you for the data interpretation and explanation as well, from what everyone has suggested it's probably not going to be an extremely accurate or viable estimate value. I Just wish I could dissect and diagnose it myself!

K88

1\ look for any/all files ending in .tmp in the directory where you were working with your data

2\ delete any such .tmp file

3\ reboot

4\ try again

[jhines]

K88,

Assuming that you're still interested in getting a sample data-file to run in Mark, are you able to run any of the Mark examples? What version of Windows are you using (XP, Vista, 7)? Is it an English-language version? If you'd like to send me your input file, I'd be happy to take a look at it for problems. (It would be best to create a zip archive containing the file and send me (jhines@usgs.gov) the zipfile.)

Jim