Merge Staging to Master

[ahmedjoubest]

I reviewed the R Package GitHub Repository management and made the following updates:

Created a staging branch (https://github.com/CIAT/cleaned/tree/staging) from master, merged it with cleaned_v0.6.0, and resolved some conflicts (conflicts were limited to the visualization files, which I manage, so I was confident in resolving them)
Merged changes from cleaned_dev_prs into staging without conflicts
Staging now contains all recent changes and is functioning smoothly

However, I noticed two issues:

1. Compilation Issue: The package fails to compile due to the input_mappings.R file (commited previously in the cleaned_dev_prs). I removed it in staging. It doesn't seem core to CLEANED, but if it's important, you may want to investigate the issue (remotes::install_github("CIAT/cleaned@cleaned_dev_prs")). Error looks to something like this: Error : cannot create dir 'data\mappings', reason 'No such file or directory' -- lexical error: invalid char in json text. data/qt_example.json

2. Nitrogen Balance Error: After merging the fertilizer issue fix, the previous error no longer occurs, but there's a new error message in the nitrogen_balance function, when the fertilizer is missing.

[M-Emmanuel]

Please ignore the input_mappings.R file, it is something under development and isn't linked to the CLEANED package at the moment. Could you please provide more details on the new error message in the nitrogen_balance function? I think this is what Stephen addressed last time. Happy to jump on a call.

[M-Emmanuel]

I would approve this given there's an upcoming training that will rely on these changes. Otherwise it would make sense to address the nitrogen_balance in the next commit. Hopefully you have tested this locally and everything seems to work except the above?

[ymutua]

Please ignore the input_mappings.R file, it is something under development and isn't linked to the CLEANED package at the moment. Could you please provide more details on the new error message in the nitrogen_balance function? I think this is what Stephen addressed last time. Happy to jump on a call.

How high can you jump @M-Emmanuel? Great to see the work going on here anyways!

[ahmedjoubest]

Could you please provide more details on the new error message in the nitrogen_balance function? I think this is what Stephen addressed last time. Happy to jump on a call.

Please find the error message below for reference.

Browse[1]> nitrogen_balance <- n_balance(
+           para = para,
+           land_required = land_required,
+           soil_erosion = soil_erosion
+         )
Error in para[["fertilizer"]][which(para[["fertilizer"]]$fertilizer_desc ==  : 
  incorrect number of dimensions

[M-Emmanuel]

Great

Could you please provide more details on the new error message in the nitrogen_balance function? I think this is what Stephen addressed last time. Happy to jump on a call.

Please find the error message below for reference.

Browse[1]> nitrogen_balance <- n_balance(
+           para = para,
+           land_required = land_required,
+           soil_erosion = soil_erosion
+         )
Error in para[["fertilizer"]][which(para[["fertilizer"]]$fertilizer_desc ==  : 
  incorrect number of dimensions

Great, I'll probe this.