Init development

[kellijohnson-NOAA]

@chantelwetzel-noaa I think it is time to merge this into main. It clearly is not "done" but nothing ever will be 😆. It is done enough to provide and index. One thing that I probably should do before merging this though would be to get copy the code from run_sdmtmb2() over to run_sdmtmb() so there is just one run function and call that function from run(). I asked for your review just to get your take on what you think about merging, you do NOT need to review the actual code unless you want to 😉.

[kellijohnson-NOAA]

Once merged, this will close #7

[chantelwetzel-noaa]

I agree that it is in a place where this branch can be moved into main. Nice work on this!

[chantelwetzel-noaa]

@kellijohnson-NOAA did you want to make any revisions based on @seananderson feedback prior to merging this pull request? I am fine either way but wanted to double check.

[kellijohnson-NOAA]

Thanks for asking @chantelwetzel-noaa and yes, there are a few things that I am still working out. The biggest one is being able to pass "formula" to accommodate removing of effects if they are not significant. I am almost done. Then, I will merge it into main and move the repository.

[seananderson]

If you're going to move/rename the repository, that might be a good time to clean out some giant files in the history with the BFG Repo-Cleaner. The one caveat being that anyone who is going to push would need to take a fresh clone or they'd re-introduce the history (so may not be worth the trouble). Anything > 245 KB should do, but it's mostly that 42 MB one:

4dd4ffc3c38c  246KiB sandbox/data/yelloweye_rockfish_catch_data.rdata
aabf57d17807  251KiB sandbox/data/widow_rockfish_catch_data.rdata
0d09fa358aac  255KiB sandbox/data/blackgill_rockfish_catch_data.rdata
ecbbdde3a019  259KiB sandbox/data/pacific_ocean_perch_catch_data.rdata
0ed522380acb  261KiB sandbox/data/bocaccio_catch_data.rdata
c38915ea8d30  274KiB sandbox/data/aurora_rockfish_catch_data.rdata
c4f04b9cdd8f  275KiB sandbox/data/big_skate_catch_data.rdata
5020a07d53b9  277KiB sandbox/data/chilipepper_rockfish_catch_data.rdata
3d5fdd090b60  282KiB sandbox/data/darkblotched_rockfish_catch_data.rdata
efbdfd0da64e  300KiB sandbox/data/pacific_spiny_dogfish_catch_data.rdata
2f0059fe0165  317KiB sandbox/data/arrowtooth_flounder_catch_data.rdata
30e28e53db26  331KiB sandbox/data/petrale_sole_catch_data.rdata
e2292744b57c  346KiB sandbox/data/shortspine_thornyhead_catch_data.rdata
b75ca34e5ee3  362KiB sandbox/data/rex_sole_catch_data.rdata
d569a0506177  365KiB sandbox/data/sablefish_catch_data.rdata
17a180f12ee6  396KiB sandbox/data/dover_sole_catch_data.rdata
8c2777086326  478KiB sandbox/data/rougheye_rockfish_catch_data.rdata
739d33baf4f9  488KiB sandbox/data/canary_rockfish_catch_data.rdata
3eec0f2f9509  4.0MiB data/california_current_grid.rda
f592aef3988d   42MiB sandbox/dover_example/sdmTMB_save.RData

[kellijohnson-NOAA]

Thanks @seananderson ... I thought I had removed the large files after discussion in #5 but I probably did something wrong. I will make sure that I run BFG prior to moving it.

[kellijohnson-NOAA]

Thanks to @chantelwetzel-noaa, @seananderson, and @ericward-noaa for making this happen. {sdmTMB} is great to work with and Chantel is the 💣 !