cbiomes / bayesian_cbiomes Goto Github PK

After installation I figured everyone should try running a model to make sure everything is installed correctly. Would you mind taking a quick peek before I send it around to the group?

Now, leading to the virtual meet, seems like a good time to transfer this repo to https://github.com/CBIOMES

@jpmattern do you want to do that?

It's pretty easy, takes a few clicks, although you just want to be careful -- it's all explained in https://help.github.com/en/github/administering-a-repository/transferring-a-repository in case you have never done this

After a truly horrendous, atrocious experience with trying to run Stan in Julia, I now tried Python instead. It went very smoothly! I have learned my lesson: go for the tried and tested!

R users may not be familiar with jupyter notebooks, but may be used to working with R studio.

I have converted the R versions in juypter notebooks to R markdown documents for use with Rstudio. These are in my fork: andrewirwin/bayesian_cbiomes. The script for doing the conversion is there too (remove_output.py and convert_ipynb_to_rmd.sh)

Andrew

Wu (lab mate) and I tried installing and running Stan in Julia yesterday and had a bitch of a time. It's still not working on my PC. Wu was able to get it to work on his Mac after having to fix several weird paths and settings. (I remember folks in the past having a harder time with Julia). Could you give it a go on your system and let me know if you run into issues? We'll have to sort out potential issues if we're going to support Julia in the workshop..
I'm going to give it another go on my PC and will post a question to the author of CmdStan.jl/Stan.jl
I'm also going to try it on my old Mac to see how it goes.