[Developers] ADMB Getting Started Guide

[Arni Magnusson]

Hi Jim,

I believe you volunteered to coordinate comments from the La Jolla 
participants, before they are sent on to Kiersten. Please find my comments 
below.

First of all, the guide is an excellent addition to the existing 
documentation. Definitely the place to start for beginners, before opening 
the main ADMB manual. The amount of overlap is not excessive and one could 
almost call them part I and II, although perhaps they will be merged 
eventually.

The guide uses many external web links (in magenta) to 
https://code.nceas.ucsb.edu, e.g. in Sections 1.2, 7.1, 7.2, 7.3, and 7.4. 
These are currently useless for readers who don't have username and 
password.

The first paragraph in Section 2.1 should say "ADMB runs on Windows, 
Linux, Mac OS, and OpenSolaris."

The 'Make' application is not required to use ADMB, and will not be 
included in upcoming releases of ADMB. To reflect this change, references 
to 'Make' should be removed from Sections 2.1, 2.2.1, 2.2.1.8, and 2.2.6.

Sections 2.1 and 2.2 should mention ADMB-IDE as an alternative setup, 
providing a full-featured IDE.

Section 5.1 - and other instances of 'makeadm' - should use the 'admb' 
compilation script.

Section 6.5 should mention the 'R2admb' package, and not the 'scape' 
package.

Chapter 8 should be extended, based on keywords.txt 
(http://admb-project.org/documentation/api/keywords.txt/view), to include 
functions like 'colfill', 'sfabs', and the 'rand*' functions.

In Table 8.1, 'extract_row' can be replaced with 'row'. The definition of 
'mfexp' should mention that it is safer than 'exp' (see ADMB manual). The 
definition of 'regression' should start with "Calculates the concentrated 
log-likelihood of ...". The functions 'initialize', 'column', 
'extract_row' (or 'row'), and 'regression' should probably be moved to 
Sections 8.2 and 8.3.

The mathematical notation in Tables 8.2 and 8.3 should have subscripts in 
rendered in subscript.

---

Thanks to Kiersten for putting this manual together, and to you for 
coordinating the comments!

Arni