Progress file functionality

[triphook]

Folding in the progress file functionality to make future merges less complicated

[cristinamullin]

I ran devtools::check() locally and found and addressed a few notes:

❯ checking top-level files ... NOTE
Non-standard file/directory found at top level:
'flagged.csv'

Removed flagged.csv

❯ checking R code for possible problems ... [41s] NOTE
mod_TADA_summary_server : : : no visible global
function definition for 'zip'
mod_data_flagging_server : : no visible global function
definition for 'updateRadioButtons'

added utils::zip
added shiny::updateRadioButtons

Undefined global functions or variables:
Field characteristicName characteristicType countycode endDate
example_data huc m2f nd_method nd_mult od_method org_table
organization original_source proj sampleMedia selected_filters
selected_flags siteType siteid startDate statecode

added these to utilities.R

**Three comments remain (below). We can ignore these for now but at some point we should look into addressing these as well.

── R CMD check results ────────────────────────────────── TADAShiny 0.0.0.9000 ────
Duration: 3m 12.9s

❯ checking package dependencies ... NOTE
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.

❯ checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.devcontainer
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.

❯ checking installed package size ... NOTE
installed size is 23.7Mb
sub-directories of 1Mb or more:
R 11.4Mb
app 1.0Mb
extdata 11.3Mb

0 errors ✔ | 0 warnings ✔ | 3 notes ✖

[cristinamullin]

Using the Utah Nutrients dataset, run though the flag page and then hit "compose synonym table" on the Harmonize and Calculate tab.

@triphook can you review the edits I made to make sure they look OK, and also look into this warning?

[1] "Warning: This dataframe is missing TADA QC flagging columns, indicating that you have not yet run the TADA_FlagResultUnit, TADA_FlagFraction, or TADA_FlagSpeciation functions. It is highly recommended you run these flagging functions and remove Invalid combinations before proceeding to this step."
Warning: Error in tidyr::pivot_longer: cols must select at least one column.
3: runApp
2: print.shiny.appobj
1: