new GNU/Linux verson

announcements (new versions, changes, bugs, installation problems...) related to program MARK

new GNU/Linux verson

Postby cooch » Mon Jan 02, 2017 8:02 pm

As of 10 minutes ago -- latest and greatest code-base compiled (separately as either a dynamic, or a statically-linked executable -- one or the other is likely to work on your distro, provided you're running a 64-bit distribution), and uploaded. You can grab from links on the following page:

Extract the file (mark.64.dynamic or mark.64.static) from, rename it to mark (or whatever you want -- if interfcing with RMark, following the3 naming conventions Jeff has discussed elsewhere), copy it to a directory in the path (typically, /usr/local/bin ), and make it executable using chmod. Make sure it runs by typing mark from the command line (or ./mark if trying to run it from the directory in which you placed the executable)

The new version reflects the following changes/updates/additions:

July, 2016

267. The capability to specify the number of nodes to use in Gaussian-Hermite quadrature (used in random effects individual heterogenity models) was added to the File | Preferences dialog window. The default value is 101 nodes, with minimum of 15 and maximum of 505.

November, 2016

268. Processing of individual covariates in the mark-resight data types (114, 115, 120, 158, 159, and 160) was updated based on changes provided by Brett McClintock. These data types now give identical answers when an individual covariate of all 1's is used in a model compared to the same model with no individual covariate.

December, 2016

269. The Poisson mark-resight models were updated to add a data type with a zero-inflated Poisson distribution, useful for modeling animals that are marked but that may not be available in the next resighting occasion. The additional parameter (w) is the probability that a newly marked animal remains alive and on the study area during its first resighting occasion. In addition, all 3 of the Poisson models were extended to assume the same individual random effect across primary periods, rather than the current implementation of individual random effects changing between primary periods. There are now 6 Poisson mark-resight data types (see main MARK page for details).

This version of MARK was compiled using gfortran 5.3.1. (Simply type gfortran -v in a terminal window to see what your system is running). There is some chance that the libraries on your distribution may be in different locations than the MARK executable is expecting. You can either (i) LDD the MARK executable to find out what it 'requires', then tweak the LD_LIBRARY_PATH as needed (if the preceding sentence doesn't make sense to you, you should probably quit now, and ask a local 'guru' for help... ;-), or (ii) try the statically compiled version.
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