Error creating/reading .inp files for mark-resight analysis

[mpitman]

I am trying to run a mark-resight Immigration-emigration log-normal estimator (IELNE) model on a data set containing 91 observations (not split up into primary/secondary events) where each observation represents one day of 91 continuous camera trapping days. We have capture histories for 4 marked individuals, and have created an encounter history file that is formatted exactly as is the example in Chapter 18 of "Guide...". Trying to initially run model I get

"ERROR - Encounter history must consist of only these characters: 'ABO.' Exit code (something in strange characters)"
- What does this error mean? Is there a problem with our .inp file?

Also tried creating own version of example dataset from "Guide..." called "IELNE_IndividualMarks_OneGroup.inp", but got same ERROR as above.
- Again seems to be problem with .inp file.

Tried finding example dataset referenced on p 18-17 in markdata unzipped file (IELNE_IndividualMarks_OneGroup.inp), but it is not there to test out?
- I have followed along with other examples and successfully imported .inp files in markdata folder before so if I had the file available I could run it making sure there is no problem with MARK running mark-resight analysis on my computer.

To my knowledge I have tried all methods of correctly creating an .inp file from using jedit to saving the file as text MS DOS format in Wordpad, on MAC parallels running XP and Desktop PC running Windows XP.

Are there any other things I should try or anything else that could be wrong? Anyone who knows about running Mark-Resight analysis who could help with step by step instructions for running this model that might get around this problem?

Working on my masters thesis and NEED HELP!
Thanks!

Megan

[mpitman]

Update - have found IELNE_IndividualMarks_OneGroup.inp example data file, and tried to run initial analysis with IELNE mark-resight model, but got the same error, with the .inp datafile provided for example!!!!!

This seems to suggest that the problem may not be with our .inp file but with not setting up the model to run correctly for the first time. Chapter 18 in "A Gentle guide..." is my only source for running this analysis. Unfortunately those examples aren't step by step enough for me to even reproduce given the sample data, much less start my own data analysis.

Any insight into running Mark-Resight models (specifically IELNE) would be helpful! Especially some instruction on how to set up analysis so that model will run without errors for example data.

Megan

[bmcclintock]

Hi Megan,

Without further details, I am unable to recreate your error message. For the time being, let's ignore the fact that you only have 4 marked individuals and see if we can get the example analysis up and running. I've installed the most recent version of MARK and can successfully setup and run an analysis using the "IELNE_IndividualMarks.inp" input file, so this doesn't appear to be a problem with MARK 6.0 or the input file. Have you installed the latest version of MARK? If not, that's the first step.

In your previous message you said you were using the "IELNE_IndividualMarks_OneGroup.inp" example input file, but that's a typo in The Book because there is no such file in the "MARK Examples" folder (I'll ask Evan to correct this for me). I therefore assume you're using "IELNE_IndividualMarks.inp" (and you aren't trying to use the "Logit_IndividualMarks_OneGroup.inp" example input file for an IELNE analysis!).

To setup an analysis using "IELNE_IndividualMarks.inp":

1. open MARK, click File>New
2. select "Mark-Resight" bullet
3. highlight "Immigration-Emigration Logit-Normal" and click OK
4. enter a title for this set of data
5. select "Click to Select File" and open "IELNE_IndividualMarks.inp"
6. change the "Results File Name" to avoid overwriting the original results file (e.g., "C:\Program Files\MARK\Examples\IELNE_IndividualMarks_Megan.DBF")
7. for "Encounter Occasions", enter "12"
8. click on "Easy Robust Design Times", enter "3" for the number of Primary Occasions and click OK, leave the number of secondary occasions at the default "4" for each primary occasion, and click OK.
9. you're done, click OK.

To run the most general {p(session*t) sigma(session) Nbar(session) alpha(session*t) Nstar(session)} model,

1. select Run>Current Model
2. enter the model name
3. select "OK to run"
4. when asked about the identity design matrix, click "Yes"
5. after the model runs, append the results by clicking "Yes"

Barring other problems like a corrupted input file or MARK installation, that should do it.

Cheers,
Brett

[cooch]

Tried finding example dataset referenced on p 18-17 in markdata unzipped file (IELNE_IndividualMarks_OneGroup.inp), but it is not there to test out?
- I have followed along with other examples and successfully imported .inp files in markdata folder before so if I had the file available I could run it making sure there is no problem with MARK running mark-resight analysis on my computer.

A bit confusing - this particular example input file is in fact in the /Examples subdirectory that gets created when you install MARK (i.e., look in /MARK/Examples for the file). I suppose I should also add it to markdata.zip

[mpitman]

Thank you for the quick response!

It turns out (according to an email replay from Dr. Gary White) that until he corrected it last night, there was a bug in the software probably introduced in December that was probably causing the problem. I downloaded the new version of MARK this morning and was able to run the example analysis without a problem, thanks so much for the detailed instruction!

Unfortunately running my own analysis is coming up with errors, the most memorable being the error: "could not import the variance covariance matrix".

I'm taking the same steps as in the example, so I am wondering if my low number of marked individuals is the issue. We have 91 days of continuous observations with camera traps (1day=1observation) and 5 marked pumas (although one who has been available to be detected has not been captured yet). This is not very many marked individuals, but in terms of proportion of the larger population, since it is with large solitary wide-ranging carnivores who live at relatively low population densities, the number of marked individuals almost definitely represents a majority of the total population for the study area.

We've been trying splitting the data into multiple primary occassion to see if it would help, but so far it hasn't. Any suggestions?