Staging tables

[sam1mitchell1-hub]

Bulk of checkpointing and staging tables code.

Things to note:

• Tables in checkpointing section has NAs and not zeros. Everything I tried to make the default entry a zero and not a NA caused the code to stop working. Tried 4 or 5 different ways of doing it. Shy of re-running the loop to the have is.na condition I don't know how to change that.
• Adding checkpointing actually slows the R code down.
• Some R code produces unnecessary outputs i.e. just outputs a 0. It is possible to suppress them by using invisible() but thats not best practice. They could be removed from the markdown file by hand but also didn't know if to do that or not.
• no R code for the insertInto section as I couldn't make that work in R either.

For review:

• Build book to ensure all files are in the right place and the markdown file is formatted correctly.
• decision about zeros of the first tables
• decision about needless R outputs
• decision about whether or not to put in a section of text regarding the checkpointing slowing the R code.

[NathanKelly-ONS]

Just working my way through the R code - one thing I noticed is that the file path set in the config for the animal_rescue csv is set to the animal_rescue.csv in Johanna's user area so I had to change it to read it in - might not be a problem once it's merged as the config might be accurate on the main branch but just wanted to flag just in case.

[robertswh]

Just working my way through the R code - one thing I noticed is that the file path set in the config for the animal_rescue csv is set to the animal_rescue.csv in Johanna's user area so I had to change it to read it in - might not be a problem once it's merged as the config might be accurate on the main branch but just wanted to flag just in case.

Well spotted @NathanKelly-ONS. This is fixed in another pull request.