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Program MARK - FAQ

PostPosted: Mon May 26, 2003 1:09 pm
by egc
Many of the questions concerning MARK, especially those coming from 'new users', have been asked before. While you can always use the search facility to find answers (with a little work), to make it more efficient to find answers to common questions, we've posted this FAQ (which we will regularly edit, update and tweak).

1. Where can I get MARK? - there are 2 primary sources for the MARK installation file - the main page Gary White maintains (which can be found at here), or on this server, where a locally mirrored copy can be found here.

1(a) where can I get one of those cool MARK t-shirts? - Simply point your browser here

2. What kind of computer do I need to run MARK? - Ideally, a hot-rod PC - there is no such thing as 'too much computer' when using MARK. Minimally, a 3.0 GHz (or faster) PC running Windows 10 or better, with at least 8 Gb of RAM or more (more RAM is always better), and at least a 19 inch monitor. Although written for Windows, you can also run MARK on a Mac, or under Linux, with a bit of work - some details can be found here.

3. how can I learn to use MARK? - Well, if you can 'afford a semester' (in terms of both time and tuition), the best way is to take the class at Colorado State. If that is not an option, then the best way is to (i) start with the 'book' on teaching yourself MARK (you can find it here), (ii) once you've gone through the book, read the various lecture notes that several MARK users have online, and (iii) convince whoever is paying you to give you enough $$$$ to allow you to attend one of the various MARK workshops that are offered fairly regularly.

4. MARK is a big program, but my analysis needs are small - should I spend the time to learn to use it when I don't need it for my project? - short answer: yes. While MARK may be overkill for your present needs, your needs may grow and change. Further, time spent learning MARK will serve many purposes. You're ready for more complicated analyses, you'll have a better understanding of statistics in general (especially linear models and design matrices), what you learn for MARK can be ported to other high-level software (like POPAN, or M/E-SURGE) if the need arises, and besides....pulling up a big, ugly design matrix on the screen is bound to impress your friends. :lol:

5. I have a question, but suspect it might have been asked before. Rather than ask again, anywhere I can look to see if its already been addressed? - Congratulations and thank you for your consideration - asking a question that has already been answered is a sure way to get 'flamed'. You should approach the decision as to whether or not to post a question in 2 steps:

    (1) make sure you have thoroughly read and understood the documentation for MARK that is available first - this is the 'RTFM' request (RTFM = Read The F****** Manual). If you're sure can't find your answer there (note -- see point 7(d), below)., then

    (2) search the forum

6. OK, I've RTFM, and searched the forum, and still need help. What next? - Easy - post your question on the MARK forum. But, several things to keep in mind. First, resist the initial temptation to email Gary White (or anyone else) directly. Even if your thesis/project is due by the end of the week, resist. Post your question on the forum as the first step. And, it is recommended that you post your question (or, questions) in small, discrete pieces - again, resist strongly the temptation to post a several hundred line question containing multiple sub-questions. Once again, even if your thesis/project is due by the end of the week, resist. Many of the people who might want to help will look at a multi-line, multi-element question and figure they have better things to do with their time (and not answer you at all).

7. The MARK 'book' is pretty helpful - how should I cite it? - Well, first off - thanks. We're glad you find it helpful - its an organic document that is essentially the product of the various questions that have been asked over the years. But, how to cite it? Easy - in general, don't (but see below for the one exception). The book is not a technical reference, but a 'software manual' (more or less). The 'technical' bits in the book (e.g., suggestions on how to approach some sorts of analysis, guides to interpreting results...) are drawn from the primary literature, which should be cited in all cases.

The exception - some chapters in 'the MARK book' have been written by colleagues (Kendall for the RD chapter, Lukacs for the closed abundance chapter, Schwarz & Arnason for the POPAN chapter, Rotella for the nest survival chapter, McClintock for mark-resight, and so on). In that case, we think it is entirely appropriate to cite their individual chapter contributions, but in the end, leave that to those authors to decide one way or the other. In other words, it's entirely their prerogative. So, if you want to cite an 'authored' chapter, contact the author(s), and ask their recommendation.

For an interesting discussion about our request not to cite the book, have a look at the following. Its rather entertaining...

7(a). The MARK 'book' is sufficiently helpful I'd like to use some/all of it in a class (or for some other educational purpose). How do I get permission? Easy - check the general 'rights and permissions' notice at the bottom of the last page of the Forward. As long as your intended 'use' fits into the specified categories, consider permission granted.

7(b). The MARK 'book' makes reference to various example input files - many of which aren't distributed with MARK - where can I get them? - On the webpage for the MARK book, the last item of the drop-down menu where you select chapters (left-hand side of the page) is a link to the example files. If you can't find the files there, check the /mark/examples subdirectory that is created when you install MARK.

7(c). Which is more 'up-to-date' -- the individual chapters, or the fully collated book? - The individual book chapters and appendices are always the most recent -- the revision date for any individual chapter can be found in the lower right-hand corner of the first page. The fully collated book is more convenient (in the sense that it is single file, which can be searched in its entirety for references to a particular phrase), but the collation and indexing take a bit of time, and is generally only done every other month or so.

8. the literature related to this stuff (i.e., analysis of data from marked individuals) is pretty daunting - where should I start? - What? You mean you don't want to try to read the 150-200 papers per year that are published in this area? Don't feel too bad. No one reads all of the papers - with the exception of Jim Nichols, who is a special case. :wink:

But, fortunately, there is an option: run (don't walk) to your nearest bookstore (or, in the modern age, fire up the website for your favorite online bookstore) and order yourself two books:

    Williams, B.K., Nichols, J.D., and Conroy, M.D. (2002) Analysis and Management of Animal Populations. Academic Press. 1040 pp.

    Burnham, K.P. and Anderson, D.R. (2002). Model Selection and Multi-model Inference. 2nd Edition. Springer-Verlag. 496 pp.

These books are essential reading: the first covers pretty well everything you want to know about estimation, synthesizing a huge literature. The second is the de facto standard reference for model selection, using information theoretic approaches.

9. MARK isn't working - I keep getting a <insert weird gibberish code> error message - what should I do? Well, first, don't panic. The next thing you should do is re-install MARK, making sure you're using the most recent version of the software (see above on where to get MARK). When re-installing MARK, make sure that (i) you first completely uninstall the old version (using the Windows Uninstall Programs method), and then deleting the MARK subdirectory that was created when you originally installed MARK, and then (ii) installing MARK from the most recent build. If after re-installing MARK you still get the same error messages, try a different analysis, if the error message shows up during an analysis. If the error is 'analysis-specific', then it may (or may not) be related to your input file. Have a look to see if there are any problems with it. If the error is in simply getting MARK to run at all, then report the problem with full information (operating system, amount of RAM, what AV software are you running, are you running anything else that might be causing MARK to crash, and so forth...the more information you can report, the better.]).

9(a) 'garbage in, garbage out' - the input file - many of the problems people have getting started with MARK can ultimately be traced back to problems with the input (.inp) file. You are strongly encouraged to spend a lot of quality time reading the documentation about data formatting before you do anything else. Also, as a general suggestion, avoid - as in 'like the plague' - using Windows Notepad (or, even worse, Word) to do much of anything related to building/editing .inp files. Do yourself a favor and get yourself a real ASCII editor - there are a number of very good 'free' applications you can (and should) use instead of Notepad (e.g., Notepad++, EditPad Lite, jEdit, and so on...)

Then, if none of the above works, post your question in the 'software problems' sub-forum.