Nemo Files

N E M O v2.1.0 [01 Feb 2009]

This new release adds temporal parameters argument specifiers to the init
file. This new feature allows to dynamically modify the components state
during a simulation. It applies only to the life cycle events and the 
population parameters for now, and thus allows to change the number and/or
size of the patches at different time points during a simulation (among 
other possibilities...).

Genetic data can now be loaded in text mode to use as a starting source
for the population. This allows to load neutral markers data using FSTAT
files for instance and thus use field or experimental data in a simulation.

A couple new LCEs are also proposed, the 'resize', and 'crossing' LCEs. 
Some modifications to the aging and regulation LCEs have be made as well.
The User's and developer's documentation have been revized and augmented.

Changelog:

Users:
FIX: in aging, regulation was performed non-randomly
FIX: lattice models available with backward migration
CHG: regulation is back and acts on all age class in the same way
CHG: polygyny, the alpha male is set randomly
NEW: temporal parameter specifier (@g#), see the manual
NEW: added paramters:
     - simulation::run_mode
     - population::source_file_type, source_fill_age_class,
       source_start_at_replicate
CHG: parameters:
     - boolean parameters accept 1(=true/set) and 0(=false/unset)
     - dispersal_lattice_model -> dispersal_border_model, applies to 
       1D and 2D stepping stone models equally.
     - replicates and generations are now part of the simulation comp.
NEW: output file option for ntrl trait: allele frequencies and variance 
     components (for Weir & Cockerham Fst)
NEW: LCE: resize and crossing
NEW: compressed binary source files are uncompressed/compressed on the
     fly
CHG: stats:
     - weighted.fst -> weighted.fst.matrix for the complete Fst matrix
     - weighted.fst only output the average Fst (Weir&Hill 2002)
NEW: stats:
     - [adlt./off.]fstWC: Weir&Cockerham (1984) Fst estimate (theta)
CHG: output format for deleterious mutation genotypes changed
NEW: added genotype file reader for ntrl and delet traits

Framework:
CHG: SimComponent, LifeCycleEvent, Param, and ParamSet interfaces have
     changed, check the doc!
NEW: added the ParamUpdater, UpdaterService, etc.
CHG: SimManager change to SIMenv
CHG: the replicate and cycle loops have moved to the SimRunner
CHG: too many to list them all, check the source, and please report bugs!