Doc update v2.3.3

[brownag]

This is an update to function definitions and corresponding documentation, brought to my attention by jblindsay/whitebox-tools#382

settings.json takes priority over default arguments in function definitions.

The default values for compress_rasters and verbose_mode have been set to NULL to better reflect this behavior. If the user specifies a value for these arguments in the function call then the flag will be passed in command line call. Otherwise the null value is ignored. Links to the corresponding option-setting functions have been added to the documentation to aid in setting up options

I have another development branch https://github.com/opengeos/whiteboxR/tree/wd4 that would implement some more general tools for reading/writing the settings.json file. Having control over this on the R side would potentially make it easier to keep R package options and Whitebox settings in sync

[codecov-commenter]

Codecov Report

Merging #117 (b6d6170) into master (1165485) will not change coverage.
The diff coverage is 100.00%.

❗ Current head b6d6170 differs from pull request most recent head 5711dae. Consider uploading reports for the commit 5711dae to get more accurate results

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@@          Coverage Diff           @@
##           master    #117   +/-   ##
======================================
  Coverage    8.87%   8.87%           
======================================
  Files          21      21           
  Lines        8374    8374           
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  Hits          743     743           
  Misses       7631    7631           

Files	Coverage Δ
R/data_tools.R	0.00% <ø> (ø)
R/gis_analysis.R	0.00% <ø> (ø)
R/gis_analysis_distance.R	0.00% <ø> (ø)
R/gis_analysis_overlay.R	0.00% <ø> (ø)
R/gis_analysis_patch_shape.R	0.00% <ø> (ø)
R/hydro_analysis.R	0.00% <ø> (ø)
R/image_analysis.R	0.00% <ø> (ø)
R/image_analysis_classification.R	0.00% <ø> (ø)
R/image_analysis_enhancement.R	0.00% <ø> (ø)
R/image_analysis_filters.R	0.00% <ø> (ø)
... and 8 more

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