Error code with known fate analysis

[tarai]

Hi,

I'm trying to redo a known fate analysis on several birds that were radiotagged a few years ago. Unfortunately my house burnt down and I lost the original analysis. I also have used MARK in several years, so this has been a bit of a re-learning process!

I think I've properly coded the encounter histories for the birds (although the format doesn't look quite right here - there is staggered entry). I have 3 covariates: sex (0=female, 1=male), max dispersal distance and release group (1=early, 0=late).

/*LS01*/ 101010101010101010101010101010100000101010101010001011000000000000000000000000000000000000000000000000000000000000 0 0 1;
/*LS02*/ 1010101010101010101010101010100000101000000000000000000000000000000000000000000000000000000000000000000000000000 0 0 1;
/*LS03*/ 101010101010101010100000101010101010001000100010101010101010000000000000000000000000000000000000000000 1 0 1;
/*LS04*/ 101010101010101010100000101010101010001000100010101010001000000000000000000000000000000000000000000000 1 0 1;
/*LS05*/ 101010101010101010100000101010101010001000100010101010101010000000000011000000000000000000000000000000 0 0 1;
/*LS08*/ 1010100000101010101010001000100011000000000000000000000000000000000000000000000000000000 0 0 1;
/*LS09*/ 1010100000101010101010001000100010101010100000000000000000000000000000000000000000000000 0 2.92 1;
/*LS10*/ 1010100000101010101010001000100010100000000000000000000000000000000000000000000000000000 1 0 1;
/*LS11*/ 1010100000101010101010001000100010101010101000000000000000000000000000000000000000000000 1 0 1;
/*LS12*/ 1010101010101010000000000000001000000000000000000000000000 1 0 0;
/*LS13*/ 1010000000000000000000000000001000000000000000000000000000 1 6.18 0;
/*LS14*/ 1010101010101010000000000000001000000000000000000000000000 1 0 0;
/*LS15*/ 1010100000000000000000000000001000000000000000000000000000 0 2.33 0;
/*LS16*/ 1010000010101000001000000000000000000000000000000000000000 0 8.75 0;
/*LS17*/ 1010000010101000000010000000000000000000000000000000000000 0 14.9 0;
/*LS18*/ 1010101010101010000000000000000000000000000000100000000000 0 1.9 0;
/*LS19*/ 101010000000100000001100000000000000000000 0 0.89 0;
/*LS20*/ 101010000000000000000000000000000000000000 0 0 0;
/*LS21*/10101010101010101010101010101010101010101010101010101010101010100000000000000000000000000000000000000000000000000000000000 1 2.97 1;
/*LS22*/10101010101010101010101010101010101010101010101010101000000000000000000000000000000000000000000000000000000000000000000000 1 5.26 1;
/*LS23*/10101010101010101010101010101010101010101000000000000000000000000000000000000000000000000000000000000000000000000000000000 1 4.63 1;
/*LS24*/ 1010101010101010101010101010101010000000000000000000000000000000000000000000000000000000000000000000000000000000000000 1 0 1;
/*LS25*/ 1010101010101010101010101010101010101010001010101010101010101000000000000000000000000000000000000000000000000000000000 0 4.09 1;
/*LS27*/ 1010101010101010101010101010101010101010101010101010101010101010101010101000000000000000000000000000000000000000000000 1 0 1;
/*LS28*/ 1010101010101010101010101011000000000000000000000000000000000000000000000000000000000000000000000000 0 8.92 1;
/*LS29*/ 1010101010101010101010000000000000000000000000000000000000000000000000000000000000000000000000000000 0 5.61 1;
/*LS30*/ 1010101010101010101010101011101010101010100000000000000000000000000000000000000000000000000000000000 0 0 1;
/*LS31*/ 10101010100000000000000000000000000000000000000000000000000000000000 0 8.61 0;
/*LS32*/ 10101010101010101010101010100000000000000000000000000000000000000000 0 0 0;
/*LS33*/ 10101010101010101010101010101010101010101010101011000000000000000000 1 0 0;
/*LS34*/ 10101010101010101010101010101010101010101010101010101000000000000000 1 0 0;
/*LS35*/ 10101010101010101010101010101000000000000000 1 1.98 0;
/*LS36*/ 10101010101010101010101010101010101010101010 0 1.37 0;
/*LS37*/ 10101010101100000000000000000000000000000000 0 0 0;
/*LS38*/ 10101010101010101010101010101000000000000000 1 0 0;
/*LS39*/ 101010101010101010101100000000000000000000 0 5.09 0;
/*LS40*/ 101010101010101100000000000000000000000000 1 4.73 0;

I'm trying to look at survival rates up to migration (when the birds are right-censored), but I can't seem to run even the most basic analysis without getting the same error: "ERROR -- Encounter history must only consist of these characters '10' Exit code (weird symbols)"

I've tried searching the forum and reading the book, but I'm not really sure what I've done wrong. Help!

Tara

[sbonner]

Hey Tara,

All of the encounter histories need to have the same length. To indicate the staggered entries you need to pad the beginning of each capture history with '00' entries until the first time it was observed. E.g. 0010... would be used to indicate that the individual was first captured on the second occasion.

Cheers...

[egc]

Hey Tara,

All of the encounter histories need to have the same length. To indicate the staggered entries you need to pad the beginning of each capture history with '00' entries until the first time it was observed. E.g. 0010... would be used to indicate that the individual was first captured on the second occasion.

Cheers...

Which is, in fact, noted in Chapter 2, and in the known-fate chapter.

[tarai]

Thanks for the quick responses. I've modified my inp files, but now I get the an error code saying that several of my animals were never released, even though every line has at least one 10 in it. Could this be due to the long lead of 00 in front of many of my encounter histories?

[sbonner]

Hey Tara,

There is another problem with your inp file. Every line needs to end with the number of individuals sharing that capture history. In your case, you need to add another 1 to the end of each line (before the semicolon). This gives me a different error message, but it's at least part of the problem. Before anyone else pipes in -- looks like you need to review the material on data formatting.

Let me know if that works.

Cheers...

[cooch]

...looks like you need to review the material on data formatting...

Agreed - again (as noted earlier), Chapter 2, and various parts of the helpfile.

[tarai]

Thanks again. I'll go back though chapter 2 again.

[tarai]

Well I've been through chapter 2 again and the help files but I still can't figure out the problem with my inp file. I'm getting a message about one of the animals not being released, but all of them have at least one 10 in the encounter history and all the 10 are lined up properly. When I click on the "list data" checkbox before running the analysis, the problem seems to be with LS20. But I've tried rerunning the analysis with LS20 removed from the file and then another animal seems to be problem. I've tried removing several different individuals, but it still doesn't seem to work. I don't know where to go from here...


/*LS01*/00000000101010101010101010101010101010100000101010101010001011000000000000000000000000000000000000000000000000000000000000 1 0 0 1;
/*LS02*/00000000001010101010101010101010101010100000101000000000000000000000000000000000000000000000000000000000000000000000000000 1 0 0 1;
/*LS03*/00000000000000000000101010101010101010100000101010101010001000100010101010101010000000000000000000000000000000000000000000 1 1 0 1;
/*LS04*/00000000000000000000101010101010101010100000101010101010001000100010101010001000000000000000000000000000000000000000000000 1 1 0 1;
/*LS05*/00000000000000000000101010101010101010100000101010101010001000100010101010101010000000000011000000000000000000000000000000 1 0 0 1;
/*LS08*/00000000000000000000000000000000001010100000101010101010001000100011000000000000000000000000000000000000000000000000000000 1 0 0 1;
/*LS09*/00000000000000000000000000000000001010100000101010101010001000100010101010100000000000000000000000000000000000000000000000 1 0 2.92 1;
/*LS10*/00000000000000000000000000000000001010100000101010101010001000100010100000000000000000000000000000000000000000000000000000 1 1 0 1;
/*LS11*/00000000000000000000000000000000001010100000101010101010001000100010101010101000000000000000000000000000000000000000000000 1 1 0 1;
/*LS12*/00000000000000000000000000000000000000000000000000000000000000001010101010101010000000000000001000000000000000000000000000 1 1 0 0;
/*LS13*/00000000000000000000000000000000000000000000000000000000000000001010000000000000000000000000001000000000000000000000000000 1 1 6.18 0;
/*LS14*/00000000000000000000000000000000000000000000000000000000000000001010101010101010000000000000001000000000000000000000000000 1 1 0 0;
/*LS15*/00000000000000000000000000000000000000000000000000000000000000001010100000000000000000000000001000000000000000000000000000 1 0 2.33 0;
/*LS16*/00000000000000000000000000000000000000000000000000000000000000001010000010101000001000000000000000000000000000000000000000 1 0 8.75 0;
/*LS17*/00000000000000000000000000000000000000000000000000000000000000001010000010101000000010000000000000000000000000000000000000 1 0 14.9 0;
/*LS18*/00000000000000000000000000000000000000000000000000000000000000001010101010101010000000000000000000000000000000100000000000 1 0 1.9 0;
/*LS19*/00000000000000000000000000000000000000000000000000000000000000000000000000000000101010000000100000001100000000000000000000 1 0 0.89 0;
/*LS20*/00000000000000000000000000000000000000000000000000000000000000000000000000000000101010000000000000000000000000000000000000 1 0 0 0;
/*LS21*/10101010101010101010101010101010101010101010101010101010101010100000000000000000000000000000000000000000000000000000000000 1 1 2.97 1;
/*LS22*/10101010101010101010101010101010101010101010101010101000000000000000000000000000000000000000000000000000000000000000000000 1 1 5.26 1;
/*LS23*/10101010101010101010101010101010101010101000000000000000000000000000000000000000000000000000000000000000000000000000000000 1 1 4.63 1;
/*LS24*/00001010101010101010101010101010101010000000000000000000000000000000000000000000000000000000000000000000000000000000000000 1 1 0 1;
/*LS25*/00001010101010101010101010101010101010101010001010101010101010101000000000000000000000000000000000000000000000000000000000 1 0 4.09 1;
/*LS27*/00001010101010101010101010101010101010101010101010101010101010101010101010101000000000000000000000000000000000000000000000 1 1 0 1;
/*LS28*/00000000000000000000001010101010101010101010101011000000000000000000000000000000000000000000000000000000000000000000000000 1 0 8.92 1;
/*LS29*/00000000000000000000001010101010101010101010000000000000000000000000000000000000000000000000000000000000000000000000000000 1 0 5.61 1;
/*LS30*/00000000000000000000001010101010101010101010101011101010101010100000000000000000000000000000000000000000000000000000000000 1 0 0 1;
/*LS31*/00000000000000000000000000000000000000000000000000000010101010100000000000000000000000000000000000000000000000000000000000 1 0 8.61 0;
/*LS32*/00000000000000000000000000000000000000000000000000000010101010101010101010101010100000000000000000000000000000000000000000 1 0 0 0;
/*LS33*/00000000000000000000000000000000000000000000000000000010101010101010101010101010101010101010101010101011000000000000000000 1 1 0 0;
/*LS34*/00000000000000000000000000000000000000000000000000000010101010101010101010101010101010101010101010101010101000000000000000 1 1 0 0;
/*LS35*/00000000000000000000000000000000000000000000000000000000000000000000000000000010101010101010101010101010101000000000000000 1 1 1.98 0;
/*LS36*/00000000000000000000000000000000000000000000000000000000000000000000000000000010101010101010101010101010101010101010101010 1 0 1.37 0;
/*LS37*/00000000000000000000000000000000000000000000000000000000000000000000000000000010101010101100000000000000000000000000000000 1 0 0 0;
/*LS38*/00000000000000000000000000000000000000000000000000000000000000000000000000000010101010101010101010101010101000000000000000 1 1 0 0;
/*LS39*/00000000000000000000000000000000000000000000000000000000000000000000000000000000101010101010101010101100000000000000000000 1 0 5.09 0;
/*LS40*/00000000000000000000000000000000000000000000000000000000000000000000000000000000101010101010101100000000000000000000000000 1 1 4.73 0;

[sbonner]

Hmmm... works for me!

I copied your data directly from your post and copied it to an inp file, and everything seems to work fine. Known fate mode... 61 capture occasions... 3 individual covariates. Completely time dependent model gives estimates of survival of exactly 1 for most occasions, but that make sense with your data -- most individuals are recaptured consistently. Constant survival model fits much better and gives survival estimate of about .98 per occasion.

I've posted the files including the inp, DBF and FPT, and the output from the two models online at www.simon.bonners.ca/MARK/tarai.

[cooch]

Hmmm... works for me!

I copied your data directly from your post and copied it to an inp file, and everything seems to work fine. Known fate mode... 61 capture occasions... 3 individual covariates. Completely time dependent model gives estimates of survival of exactly 1 for most occasions, but that make sense with your data -- most individuals are recaptured consistently. Constant survival model fits much better and gives survival estimate of about .98 per occasion.

I've posted the files including the inp, DBF and FPT, and the output from the two models online at http://www.simon.bonners.ca/MARK/tarai.

I had similar success to what Simon reports. Worked just fine.