To Do List for MCSim:
====================

Fix bug: Mod: Problem with spaces before ";", does not exist in Sim.


Fix bug: Sim: Problem with assigning an output in the scale section.
Also, using an output or a state variable on the right hand side in
Scale results in an error at compilation.


Fix bug: Sim: An input cannot be used to define a parameter in the
global section, i suspect that an output or state cannot either. This
should be corrected or mentioned in the manual.


Fix bug: Sim: ExpisDept condition in mh.c may not be correctly set. 
F. Bois temptatively fixed it with an "if plevel->pext != NULL" in
ConvertMCLists, but this should be thoroughly checked.


Document: PerRate(), after debugging it.


Web pages: The MCSim pages are missing web references. Like what people 
contributed to it, which free programms can help or assists, where it 
is linked to. And so on... Possible users could see more examples and 
opinions about MCSim. Link to http://www.gnu.ai.mit.edu/home.html.
Talk about the texinfo file.


To do: Mod: warn about inputs used in scale (check what manual says
about that). Only the initial value of the input is used and the
assignment is not recomputed when the input changes with time.


To do: Sim: Prediction() should be usable with any model var at any
position. This will require modifications at least to simi.c and mh.c
(LnLikeData).


To do: Mod and Sim: hide compilation from the user. use different
names for the model.c file.


To do: Sim: Reinstall data files.


To do: Sim: Phase out SimType (make it obsolete).


To do: Mod: Check that outputs are actually computed.


To do: Sim: Report all errors through ReportErrors.


To do: Sim: A relatively minor matter: the code shows a rather casual
attitude toward freeing malloc'd variables. This will not cause
problems with unix, but may with PCs (and MACs?). I have formally
freed all of the malloc'd pointers in my new LEVEL structures, but
there are a number of fatal errors in the code which do not contain
pointers to the analysis structure, so that when these errors occur,
variables cannot be freed (these are ReportError(NULL, ...)
statements). We should, at some point, ensure that all malloc'd
variables are freed under all conditions.


To do: Sim: Multiple variables in a PrintStep should be allowed.


To do: Sim: Reintroduce scaling of inputs by dMag, allow it in mod.


To do: Sim: Check that negative times are ok for UpdateInputs, if yes
correct the mention of positive only times in UpdateInputs.


To do: Sim: Allow redefinition of the likelihood for a variable.


To do: Sim: There should not be a code distinction between likelihood
and prior.


To do: Sim: Define a Density synonym for Distrib, and implement
Density(x,ÊUserSpecified,ÊPrediction(something));


To do: Sim: it should be possible to set the value of a parameter
to another in the input file. This is not allowed now.


To do: Mod and Sim: Implement matrices and indices with wildcards.


To think about: Sim: How to treat parameters that are set by the model
and for which we still want a parent to depend upon ?


To think about: Sim: MCMC: what to do if several measurements are made
at the same time ? Do another experiment (that's expensive) ?


To think about: Sim: Stochastic sims: there should be a way to collect
their results and produce summary stats.


To think about: Sim: Do a separate optimization routine ? or fix
kernel adjustment in case of non-zero InitRuns


To think about: Sim: Put tempering in MCMC.


To think about: Sim: Do a Print (y for input_x, <values for input_x>);


To think about: Sim: Implement Wishart.


To think about: Sim: define several dependent variables, which could
be integration variables; that could lead to partial differential
equations solving.


