2nd draft

README.md

@@ -1,3 +1,109 @@
-# Course announcement
+# Workshop announcement
 
-first draft to come shortly...
+## Preamble
+
+The general structure of the workshop is that mornings will be lectures and demonstrations (how to build TMB models), while afternoons 
+will be explorations of different software components (how to contribute to TMB development). Throughout the workshop, we will get an overview of the existing TMB documentation and identify where enhancements are needed.
+
+People who are unable to attend the whole workshop are encouraged to drop in whenever they can.
+
+The afternoons will not follow a rigid structure, so participants can focus on a particular software component in their area of expertise and interest. In particular, from Wednesday afternoon it is planned that users will be able to implement their model of interest for their own research.
+
+## Schedule
+| Day | AM/PM | Activity |
+|-----|-------|----------|
+|Mon|am| Intro to TMB, building simple models |
+|Mon|pm| Closer look at installation, GitHub, RStudio/Emacs/other |
+|Tue |am| Working with parameters, nonlinear models |
+|Tue |pm| Anatomy of the TMB package, objects, and overall design |
+|Tue (Fat) |ppm| Some sort of Mardi gras celebration... |
+|Wed|am| Stock assessment models, uncertainty, debugging |
+|Wed|pm| Implementing uncertainty analysis in TMB |
+|Thu|am| Random effects, geostatistical methods |
+|Thu|pm| Related C++ libraries and R packages, CppAD, glmmTMB |
+|Fri|am| Geostatistical and spatio-temporal models continued |
+|Fri|pm| TBD (one degree of freedom) |
+
+## Topics to consider for breakout groups
+Below are some case studies that might be of interest for different groups
+
+  * Random effects for estimating future fishery weights at age (Jim I.)
+  * Time series modeling (building from examples)
+
+## Remote access
+1.  Please join my meeting. https://global.gotomeeting.com/join/534027645
+
+2.  Use your microphone and speakers (VoIP) - a headset is recommended.  Or, call in using your telephone.
+
+  * Dial +1 (224) 501-3312
+  * Access Code: 534-027-645
+  * Audio PIN: Shown after joining the meeting
+
+  * Meeting ID: 534-027-645
+
+
+Arni, did you have an updated sense of how to structure the workshop given then exchanges we had yesterday?  I think we had settled on a morning-lecture, afternoon-workshop format with 2 days devoted to the geostatistical index standardization tool and spatio-temporal models. do you have ideas for teh remaining 3 days?
+
+## TMB Improvement efforts
+Below is a list provided from the core developer (Kasper Kristiansen) on ways the workshop may contribute to the TMB work.
+
+1. Documentation. Some example tasks:
+   * Create text versions of Latex displaymath formulas (so that formulas show up nicely not only in the pdf docs).
+   * Doxygen documentation clean up.
+   * Roxygen documentation clean up.
+
+2. More streamlined testing workflow. Could be something like travis
+   (Ben Bolker set it up for glmmTMB). But travis might not be sufficient. 
+   The ideal setup should run *all* tests on *all* combinations of
+   * Operating system
+   * With/without precompile
+   * CRAN version / not CRAN version
+   It should further be able to detect performance regressions - both
+   in terms of runtime, compilation time and memory usage.
+   (BTW we should keep an eye on https://github.com/r-hub/proposal )
+
+3. Make debugging work on windows.
+
+4. Make good consistent test scripts of e.g. the TMB array class,
+   matrices etc. Purpose is to demonstrate syntax and test for
+   correctness. There are some tests in "adcomp/tmb_syntax" but it
+   needs improvement.
+
+5. The C++ code could also need some re-structuring and cleanup but
+   that is not something I recommend for this workshop.
+
+# Participants
+
+
+| name | email | notes | N |
+| --- | --- | --- | --- |
+|Arni Magnusson |arnima@hafro.is |Hafro, Instructor! |1|
+|Jim Thorson |James.Thorson@noaa.gov |NOAA, Instructor! |2|
+|Jim Ianelli |jim.ianelli@noaa.gov |NOAA, limited to Excel©| 3|
+|Kirstin Holsman |Kirstin.Holsman@noaa.gov|NOAA, sublime experience |4|
+|Martin Dorn |martin.dorn@noaa.gov  |NOAA, limited experience |5|
+|Steve Martell |Martell.Steve@gmail.com |SS, Mac fanboy |6|
+|Lee Qi |leeqi@uw.edu |UW |7|
+|Teresa A’mar |teresa.amar@noaa.gov |HQ, Guru extraordinare |8|
+|Gwladys Lambert |gwladys.lambert@noaa.gov |NOAA Post doc |9|
+|Johnoel Ancheta |johnoel@hawaii.edu |Univ of Hawaii, ADMB dude |10|
+|Felipe Carvalho |felipe.carvalho@noaa.gov |JIMAR/NOAA |11|
+|Yi-Jay Chang |yi-jay.chang@noaa.gov |JIMAR |12|
+|Marc Nadon |marc.nadon@noaa.gov |JIMAR |13|
+|Jessica Hale |jrh33@uw.edu |UW |14|
+|Paul Spencer |Paul.Spencer@noaa.gov |NOAA |15|
+|Anne Hollowed |Anne.Hollowed@noaa.gov |NOAA First day or 2 |16|
+|Marie Ferguson |marie.ferguson@noaa.gov |NOAA |17|
+|Andre Punt |Aepunt@uw.edu |UW |18|
+|Brandon Chasco |brandon.chasco@gmail.com |UW/OSU |19|
+|Cole Monnahan| | | |
+|Bill Clark| | | |
+|Kotaro| | ||
+|Kelli | | | | 
+|Allan Hicks | |  | | 
+
+## Remote access interest
+SEFSC Beaufort lab
+NWFSC  / Newport lab
+SWFSC (Huihua, 5-10 people)
+Remote A