more functions/drake about tes_spatial_access_2021 HOT 7 CLOSED

These are the plots it should create:

from tes_spatial_access_2021.

Wow, you've really got a namespace problem. Something is using the plyr package, but you're also using dplyr throughout, and I'm getting namespace collisions (e.g. summarize() calls are using plyr in some circumstances, which is not what you want and generates errors). That's one problem, and it's causing a lot of others.

To your question: the gg_totalcounts target calls do_gg_totalcounts, and here's the beginning of that routine:

do_gg_totalcounts <- function(peakcounts_core) {
  browser()
  totalcounts_label <- 
    peakcounts_core %>% 
    do_labels_totalcounts_intact(.$counts, .$Moisture, .$Amendments)

This is already looking weird and bad, but look at do_label_totalcounts_intact:

do_labels_totalcounts_intact = function(depvar, Moisture, Amendments, Wetting){
  # 1. p-values for moisture ----
  moisture_label = 
    peakcounts_core %>% 

The parameters don't match up, and the function is calling peakcounts_core which doesn't exist in this function. So yeah at this point the code throws up its hand and says wtf.

from tes_spatial_access_2021.

I'm opening a PR with fixes for some of the above. In particular look at my changes to 2f-fticr-pipeline_plotting.R. The pipeline now makes it through the R Markdown targets.

from tes_spatial_access_2021.

That makes sense, I think. I assumed I didn't have to add the file name in the function structure, because that isn't changing. I guess not.
Thanks!

from tes_spatial_access_2021.

Question for you: how to you get those very nice looking file references in your comments?

I mean these:

from tes_spatial_access_2021.

I get the permalink from the code file, and then add a line range
example:
https://github.com/kaizadp/tes_spatial_access/blob/5f34b22e8bf9d72448d70f224ba426224896f850/code/2f-fticr-pipeline_plotting.R #L414-L416
I added the space before the # so you can see the link

https://github.com/kaizadp/tes_spatial_access/blob/5f34b22e8bf9d72448d70f224ba426224896f850/code/2f-fticr-pipeline_plotting.R#L414-L416

from tes_spatial_access_2021.

Oh cool, thanks.

from tes_spatial_access_2021.