Input Files

[JFS321]

I ask forgiveness in advance if this post has already been covered or is not appropriate for the forum.

I am new to MARK and using it to analyze mark-recapture data from ambystomatid salamanders. Specifically, my question is: How are the input files created? I cannot seem to find any information on how to create these files (if any additional software is needed...etc.).

I greatly appreciate the help.

JFS

[cooch]

I ask forgiveness in advance if this post has already been covered or is not appropriate for the forum.

I am new to MARK and using it to analyze mark-recapture data from ambystomatid salamanders. Specifically, my question is: How are the input files created? I cannot seem to find any information on how to create these files (if any additional software is needed...etc.).

I greatly appreciate the help.

JFS

Given your 'newness', and the level of your question, you are *strongly* urged to stop worry about your data until you've read chapters 1 -> 7 of the following:

http://www.phidot.org/software/mark/docs/book/

This is the de facto starting point in learning to use MARK. Issues like data formatting (your specifi question) are covered there (chapter 2). But, resist the temptation to immediately dive into your data. Learn how to use MARK first, then worry about data you care about.

[dhewitt]

Chapter 2 of GIM is nice and clear about what the encounter history file should look like, so after reading that you should have a target for your .INP creation process. However, I think there is still a need for (somewhere) a more detailed description of how to get to that point with common software. Alas, I can't do that here and now, but I'll point you to some _free_ software I find handy for this purpose...

1.) A good database program, like OpenOffice.org BASE (MS Access is good too, but it ain't free).

OR, if your data set is relatively small,

2.) A good spreadsheet program, like OpenOffice.org CALC (which in my view has a number of features that make it superior to MS Excel).

Both of the above programs are free from, you guessed it -- www.openoffice.org

3.) A good plain text editor for checking the final file, like Notepad++ (available from http://notepad-plus.sourceforge.net/ -- beware of on-the-fly encoding changes that MS Notepad makes).

One of the common PITAs to be aware of is that spreadsheet software may strip the leading zeros from your encounter histories unless the column/field is designated as text when the file is opened.

Hope this helps.

[JFS321]

Thank you all.

I have all of my data in MS Excel, and I have used Notepad to list encounter histories, so I have damp feet with the data formatting. I'll continue the search for .inp creation.

[darryl]

Joe,
Presuming you have your data in Excel formatted such that there's 1 row per individual you can use the formula 'concatenate' or '&' to create a text string from values in a series of cells or text. So if you have your capture data in columns B-E, a single group and no covariates, for the first individual (row 1) you could enter the formula (inside single quotes)

'=B1&C1&D1&E1&" 1;"'

The " 1;" is to indicate the history applies to a single individual and you only have a single group, and the semi-colon indicating the end of the line.

You then copy this formula down for all individuals, then paste all the results into a text editor.

Cheers
Darryl

[darryl]

A couple of off-list queries about what you do if you have more than 1 group or covariates.

Really you only need the concatenation to get all the capture occasion outcomes into a single text string (column). After that you can have 1 column for each group and covariate. You'd then paste the series of columns (the capture history, groups, covariates, and don't forget the semi-colon) into your favourite text editor, which will probably automatically insert a tab between the columns, creating the 'white space' MARK expects in the input file between the various bits of information.

[darryl]

For info on formatting of encounter histories, read chapter 2 of The Book.

http://www.phidot.org/software/mark/doc ... /chap2.pdf

[cooch]

For info on formatting of encounter histories, read chapter 2 of The Book.

http://www.phidot.org/software/mark/doc ... /chap2.pdf

Said chapter covers the basics, but I haven't updated it to handle what I'll call the 'dot' notation (use of '.' to indicate a sampling occasion where a patch/site wasn't visited). No particular reason, except i need to take the time to integrate that particular notation into sections of other chapters which deal with other related sampling issues (like, uneven intervals between occasions).

[pcutter]

Hi Markers,

I'm trying to get the input file right for some of the Closed Robust Multi-state models. I have successfully set up and used an input file for a related analysis with just detection/non-detection data and a period-specific covariate (distance surveyed) resulting in 4 individual covariates.

Now I'm adding states (2 states (resulting really in 3 values: Present, Breeding, and 0), and two additional covariates to the four period-specific distance covariates. I have a feeling the problem es are presented to MARK. I am indicating 4 survey periods, a distance surveyed for each period (4 covariates), and 2 more individual covariates (for a total of 6 covariates). Not sure why it isn’t going in ok.

inp file is below. Any ideas?:

/* Robust Multi-state Design, 4 survey periods, 4 period-specific covariates + 2 additional covariates*/
/*Column Reference: siteID, capture history, dist97, dist98, dist99, dist00, size of site, preysum*/
/*ESU_126*/ PP.. 1 3.146 27.147 15.885 25.804 149.836 3.669;
/*ESU_055*/ PP.. 1 24.027 14.467 15.885 25.804 155.946 4.081;
/*ESU_004*/ P0P. 1 6.676 2.976 1.383 25.804 101.238 3.513;
/*ESU_121*/ P00B 1 4.085 17.207 6.493 3.934 112.517 2.534;
/*ESU_074*/ P00B 1 19.849 6.326 7.916 32.688 189.569 2.72;
/*ESU_076*/ P.PP 1 19.715 13.981 20.902 21.126 189.846 2.431;
/*ESU_054*/ P.PP 1 12.775 13.981 14.187 11.168 155.442 4.743;
/*ESU_148*/ P.P0 1 16.632 13.981 23.426 8.794 141.962 2.389;
/*ESU_147*/ P.P. 1 10.978 13.981 3.920 25.804 168.925 3.117;
/*ESU_085*/ P.BB 1 20.488 13.981 31.542 65.718 199.24 2.735;
/*ESU_091*/ B0P. 1 33.268 42.871 13.927 25.804 250.945 6.564;
/*ESU_122*/ B.P. 1 14.547 13.981 15.863 25.804 137.849 2.978;
/*ESU_038*/ 0P0P 1 0.412 33.256 2.688 14.273 137.713 2.833;
/*ESU_071*/ 0P0P 1 1.575 2.239 7.949 3.689 185.389 4.229;
/*ESU_128*/ 0P.. 1 12.947 8.176 15.885 25.804 175.487 4.202;
/*ESU_030*/ 0B.. 1 1.248 72.553 15.885 25.804 127.022 2.996;
/*ESU_025*/ 0.0. 1 0.360 13.981 0.102 25.804 121.385 1.943;
/*ESU_043*/ 0..0 1 5.898 13.981 15.885 8.002 141.852 1.402;
/*ESU_125*/ 0... 1 0.054 13.981 15.885 25.804 110.972 3.063;
/*ESU_060*/ .PP. 1 11.081 13.785 16.569 25.804 166.111 2.394;
/*ESU_127*/ .PB. 1 11.081 2.168 20.243 25.804 201.049 4.791;
/*ESU_006*/ .P0. 1 11.081 2.627 9.956 25.804 103.939 3.63;
/*ESU_068*/ .0P. 1 11.081 1.735 14.720 25.804 177.032 2.838;
/*ESU_087*/ .0B. 1 11.081 2.756 30.898 25.804 204.798 1.678;
/*ESU_059*/ .0.P 1 11.081 8.541 15.885 27.755 165.724 2.34;
/*ESU_028*/ .0.0 1 11.081 2.747 15.885 0.691 126.05 0.896;
/*ESU_048*/ .0.. 1 11.081 3.720 15.885 25.804 149.893 1.124;
/*ESU_049*/ .0.. 1 11.081 0.340 15.885 25.804 151.793 1.403;
/*ESU_063*/ ..P0 1 11.081 13.981 10.935 13.565 167.801 2.429;
/*ESU_130*/ ..P. 1 11.081 13.981 28.762 25.804 184.634 2.861;
/*ESU_051*/ ..P. 1 11.081 13.981 7.202 25.804 153.515 4.14;
/*ESU_065*/ ..B. 1 11.081 13.981 13.929 25.804 170.799 4.406;
/*ESU_146*/ ..0B 1 11.081 13.981 10.312 17.843 196.929 2.827;
/*ESU_117*/ ..00 1 11.081 13.981 17.790 33.255 151.852 1.637;
/*ESU_058*/ ..00 1 11.081 13.981 0.028 0.114 165.315 2.173;
/*ESU_083*/ ..00 1 11.081 13.981 0.847 104.391 196.253 2.367;
/*ESU_044*/ ..0. 1 11.081 13.981 10.071 25.804 142.206 1.366;
/*ESU_111*/ ..0. 1 11.081 13.981 15.937 25.804 107.004 1.487;
/*ESU_129*/ ..0. 1 11.081 13.981 8.860 25.804 103.032 1.734;
/*ESU_139*/ ..0. 1 11.081 13.981 18.965 25.804 133.026 1.777;
/*ESU_112*/ ..0. 1 11.081 13.981 15.344 25.804 160.38 1.804;
/*ESU_062*/ ..0. 1 11.081 13.981 17.263 25.804 167.281 2.062;
/*ESU_029*/ ..0. 1 11.081 13.981 0.264 25.804 126.35 2.149;
/*ESU_133*/ ..0. 1 11.081 13.981 0.057 25.804 139.802 2.228;
/*ESU_084*/ ..0. 1 11.081 13.981 51.134 25.804 196.631 2.367;
/*ESU_010*/ ..0. 1 11.081 13.981 11.689 25.804 106.706 2.435;
/*ESU_081*/ ...P 1 11.081 13.981 15.885 28.484 194.867 2.225;
/*ESU_123*/ ...B 1 11.081 13.981 15.885 21.352 166.963 2.825;
/*ESU_033*/ ...0 1 11.081 13.981 15.885 13.571 129.195 1.332;
/*ESU_018*/ ...0 1 11.081 13.981 15.885 23.423 115.087 1.567;
/*ESU_035*/ ...0 1 11.081 13.981 15.885 31.930 135.387 1.787;
/*ESU_009*/ ...0 1 11.081 13.981 15.885 44.582 106.058 1.822;
/*ESU_015*/ ...0 1 11.081 13.981 15.885 13.750 111.183 1.857;
/*ESU_008*/ ...0 1 11.081 13.981 15.885 7.281 105.786 2.038;
/*ESU_001*/ ...0 1 11.081 13.981 15.885 2.638 88.01 2.294;
/*ESU_096*/ ...0 1 11.081 13.981 15.885 0.410 197.687 2.774;
/*ESU_067*/ ...0 1 11.081 13.981 1.152 0.176 176.264 2.815;
/*ESU_116*/ 0.00 1 20.190 13.981 132.472 171.942 233.605 2.436;
/*ESU_145*/ 0.00 1 3.832 13.981 3.832 21.779 216.112 2.927;