Finalise Documentation

[jakobjassmann]

@logan-berner I finished with a first full run through of the documentation. Here are the most critical points that need to be addressed.

• You can find the PDF user manual in "man/manuscript/lsatTS_0.8.0.pdf".

We need to:

• [x] Add an example to: lsat_calc_trend
• [x] Add an example to: lsat_evaluate_phenological_max
• [x] Add an example to: lsat_fit_phenological_curves
• [x] Add an example to: lsat_summarize_growing_seasons
• [x] Document all arguments for lsat_calc_trend (‘legend.position’ are ‘legend.dir’ are missing)
• [x] Add line breaks to lines exceeding 100 characters in documentation for: lsat_calibrate_rf
• [x] Add line breaks to lines exceeding 100 characters in documentation for: lsat_clean_data
• [x] Run over Logan's functions to look for typos, grammar etc.
• [x] Run over Jakob's functions to look for typos, grammer etc.
• [x] Check headers, tag line, title etc. for completeness and appropriateness (I had a first stab at it already)

If you have devtools and tinytext installed, then you can regenerate the PDF with devtools::build_manual(path = "man/manuscript/").

Personally, I found it easier to spot issues in the PDF than in the roxygen documentation.

Very happy to help with a final read through once you have polished the documentation for all your functions! Just let me know :)

[jakobjassmann]

Forgot to say @logan-berner you will also have to run devtools::document() before regenerating the PDF manual with devtools::build_manual(path = "man/manuscript/"). Sorry!

[logan-berner]

@jakobjassmann - I added examples to all functions and then cleaned up and rebuilt the documentation. The examples rely on an example dataset that I generated using your example for lsat_export_ts(). Those data are located in data/. I wasn't able to run devtools::build_manual(path = "man/manuscript/")... evidently because tinytext isn't installed, isn't available for R/4.0.2, and out of my bandwidth to track down today. Anyways, it would be great if you could do a final read through and package build!

[jakobjassmann]

Nice job Logan! I just ran the checks and rebuild the manual.

During the checks I receive the following errors:

• Unmatched braces/quotes in two functions:

Warning: [lsat_evaluate_phenological_max.R:29] @examples mismatched braces or quotes
Warning: [lsat_fit_phenological_curves.R:45] @examples mismatched braces or quotes

• The example for "lsat_calc_trend" fails testing due to a missing single quote:

   Error: unexpected symbol in:
   "lsat.pheno.dt <- lsat_fit_phenological_curves(lsat.dt, si = 'ndvi) 
   lsat.gs.dt <- lsat_summarize_growing_seasons(lsat.pheno.dt, si = 'ndvi"

• The checks complain that the "lsat.example.dt" dataset is not documented!

I suggest we add a documentation for the dataset. The r-pkgs books has a chapter on that: https://r-pkgs.org/data.html#documenting-data with some simple guidelines. In brief: You have to create an .R file with the name of the dataset in /R and write a roxygen header. There are some important details on how a dataset roxygen header differs to a fucntion - see link.

I rebuild the manual for you. 1fda742576920cf3b0d55ac7903afb0cea347ab3

[logan-berner]

Thanks @jakobjassmann! That was all a stupid missing quote that I accidently propagated while copy/pasting examples between functions. I fixed those errors, updated function documentation, and added documentation for lsat.example.dt dataset following the guidelines you sent.