Rebuild `taxmap` on top of `taxonomy` about taxa

[sckott]

Okay, let me know if I can help

[zachary-foster]

Ok, thanks!

[zachary-foster]

Hi @sckott. So this is finally done. Sorry it took so long. Everything is working as far as I can tell and all the new functions have examples that you can test out. There are no tests yet and I have not perfected the documentation since I wanted your input before investing more time in the details, but there is hopefully enough there for you to get what I am going for.

I know there is a lot of changes in this branch. Normally I would make change more incrementally, but most of the added functions are part of a theme or depend on each other. Most of this seems intuitive to me, but I have been thinking about it for a while so its hard for me to gauge how easily others will understand it. Feel free to suggest or make changes, even ones that fundamentally alter or remove things.

The taxmap.R is huge now and needs to be split up, but im not sure how best to do that.

This is the last part of metacoder I plan on migrating to taxa, so taxa can be developed in a more regular incremental way now since most of the building blocks are in place. I have lots of ideas for minor improvements that I would like your input on, but too many to discuss in one issue. If you like the overall structure of what I did so far, I will make new issues for each idea independently.

[sckott]

No worries about the time.

Great news. Will have a look through the pull request, and see if anything we should change.

The taxmap.R is huge now and needs to be split up, but im not sure how best to do that.

taking a look at it now, first thing to do is to split out helper functions in that file into other files as makes sense.

I suppose you're also or primarily referring to the Taxmap class - which yeah is pretty big. A few thoughts on that:

• could use inheritance in R6 https://cran.rstudio.com/web/packages/R6/vignettes/Introduction.html#inheritance - if that makes sense in this case, haven't thought about it enough to know
• i see a number of helper functions inside the Taxmap class that could be pulled out and put elsewhere since they aren't using self references

[zachary-foster]

could use inheritance in R6 ...

Perhaps. A few of the functions that only deal with taxon relationships could be reinstalled in the taxonomy class, but some would have to be partially overwritten by taxmap since they have options that affect the data variable in taxmap, even if that is not their main effect (e.g. filter_taxa). Im not sure if there is much room conceptually to put a class in between taxonomy and taxmap, but I am open to ideas.

i see a number of helper functions inside the Taxmap class that could be pulled out and put elsewhere ...

Yea, I think this should be done. There are also some similar chunks of code shared by multiple functions that could be made into helper functions I think.

[sckott]

for R6 inheritance, i've no idea if that even makes sense in this case, its just the only thing i can think of to allow breaking up Taxmap into smaller parts

Yea, I think this should be done.

cool, always a fan of DRYing out code

[sckott]

Seems like this issue is done, right? can I close?

If you like the overall structure of what I did so far, I will make new issues for each idea independently.

sounds good to open new issues

[zachary-foster]

Yea, it can be closed

[sckott]

thanks