Minor edits.
Step 1 in implementing new model for containers. Also changed the return type of RevLanguage::Function functions from RevObject to RevPtr<Variable>. The wrapping into variables happened previously in SyntaxFunctionCall but some functions need to return variables rather than Rev objects. The code compiles but some bug remains to be sorted out.
Completely reworked the container classes.
Loop variables are now real control variables and the replaceVariableWithConstant hack in parser classes is now removed. Fixed a few container bugs; RevLanguageBasicsTutorial.Rev now runs to completion, apparently without problems.
Some bug fixes to new container implementation.
New model for managing parent nodes of dynamic DAG nodes (delegate to derived classes).
Delegated management of DAG node parents of dynamic nodes to the derived dynamic node classes. Stochastic nodes delegate their parent management to their distributions, so that triple book-keeping of parents in stochastic nodes now is replaced by single local management of parents / parameters.
Fixed the cloning of DAGs for container nodes, and a few other minor problems related to DAG node management.
Fixing bug with lazy evaluation in vector function.
Playing around with substCTMC
Merge branch 'master' of ssh://git.code.sf.net/p/revbayes/code-git
added functions to multivariatePhyloProcess class
Merge branch 'master' of ssh://git.code.sf.net/p/revbayes/code-git
Final fix to the new lazy evaluation to get it working again for the GTR+Gamma model.
debugging Brownian models
Merge branch 'master' of ssh://git.code.sf.net/p/revbayes/code-git
Small changes to biogeo CH model during VectorFunction debug
Merge branch 'master' of ssh://git.code.sf.net/p/revbayes/code-git
multivariate brownian clocks now seem to work
minor changes to some test files