TODO.md
In R2admb: ADMB to R interface functions

newer

change checkdata and checkparams: try to detect existing info, write only if necessary
incorporate Jeff Laake's intro document as an alternate vignette (get comments on vignette) -- subdivide into quickstart (or quickstart for R users/quickstart for ADMB users/details)?

older

make sure strategy for copying modifying TPL files is robust: should work reliably even for mixed-case input file names, and should always survive a crash well. e.g. rather than moving the original tpl file out of the way, use the _gen file, then move _gen results when finished.
clean up argument list
make sure strategy for guessing/specifying mode of data (esp. numeric/integer) is robust
modularize run: should be able to do any one of
write data and input files
write modified TPL file based on data/input
compile
run
read results back into R
implement: phases, 'fixed' argument (set phase < 0); check bounds relative to starting values
accessors: confint, coeftab, coefplot
attach data as well when checking bounds in DATA section
weaken/eliminate ggplot2 dependency
comparisons with PBSadmb?
support for transformations (on the fly)?
better setup detection, error trapping: comments on adcomp/adlink/admb scripts
test/document examples of random effects in vignette:
?? formula interface???
read bar (binary) rather than par file?
read hessian file?
evaluate objective function by fixing vals
finish bounds support: check bounds on initial parameters?
better strategy for saving originals when changing case/auto-generating inputs -- temporary filenames, or temp directory??
TEST check for variables with "." in the name: stop? change to "_" and warn?
check for random effects vectors (don't redefine if already there)
more checks/flags of compiling step -- stop if error
more info on thinning etc. of MCMC saved/printed in final object