by cleaning up the R code

Removes functions
* mkObj
* create_rcpp_interface_object
* use_module
* %>%
* FIMSFrameAge

Adds importFrom(TMB, MakeADFun) to package b/c TMB is no longer
explicitly used in the codebase. And, experimented with removing usethis
b/c it was also used in ./R/ but is still used in data-raw. It is now a
suggested package. Uses :: instead of importing functions, e.g.,
utils::head().

* Constricts line width to 80 characters
* Use full stops at the end of sentences
* Implement more spacing in between roxygen tags
* Move export tag to the end in most instances
* Use explicit brackets for if statements
* Remove duplicated code in gtest by calling run_gtest()
* Parameter and object names to snake_case
* Parameter, function, and object names, largely, w/o abbreviations

fix(run_gtest): Use paste() instead of paste0() to ensure proper spacing
which is not explicit in the instructions. With paste()
they can input as many additional arguments as they want and they are
all automatically separated, e.g.,
`run_gtest("--something", "--something-else")`

Close #588
Close #564
Close #590

- document units in code snippets of the fims-demo vignette
- add units to output figures in the fims-demo vignette and add a spawning biomass comparison figure
- add an R test to confirm that age composition intput can be in numbers or proportions
- add units for index_data and age_data in data_mile1.R

Co-authored-by: Kelli Johnson <kelli.johnson@noaa.gov>

This is necessary because changes were made to
codecov.io so that a token is required to upload.

- post documentation for users, developers, and project managers
- reorganize vignettes under appropriate sectionss
- remove the navbar for articles to ensure no articles are hidden

* Fixes the triage label to "status: triage_needed"
* Adds text on where to find documentation of reprex and that you should
  use one. Copied from the dplyr issue template.

Close NOAA-FIMS/collaborative_workflow#136

We no longer import the magrittr pipe

For catch and index data the measurement of uncertainty should be the
standard deviation (sd) of the logged observations. The operating model
outputs a CV. I added a temporary function in data_mile1.R to calculate
the sd from the CV. In the future we will need to, behind the scenes,
take the log of the sd so the parameters stay within the bounds, which
is what the vignette is doing now. This time series of uncertainty can
later be fed to the modules but I did not change the vignette.

Close #136

For users and developers, where the information for the latter was
moved to the collaborative workflow see
NOAA-FIMS/collaborative_workflow#146.

A badge for R-universe was placed in the list of all badges!

Work was done by @k-doering-NOAA with suggestions by @kellijohnson-NOAA

Part of NOAA-FIMS/collaborative_workflow#98

They have been moved and updated in NOAA-FIMS/.github/.github
with NOAA-FIMS/.github@33c261d. Now they are available to all repositories
not just NOAA-FIMS/FIMS. I did not migrate over the refactor_request
issue template because it was largely redundant with the developer_other_issue
template and I thought it was not needed.

Co-authored-by: Cole-Monnahan-NOAA <Cole-Monnahan-NOAA@users.noreply.github.com>

and check column names in FIMSFrame

The column names of the S4@data object were being checked with the
validation function but there was no check in FIMSFrame and to do the
calculations within FIMSFrame all of the columns need to be present.
Right now we are checking it twice, once in FIMSFrame and once in the
validator of the FIMSFrame class. We might need a different class like an
input data class and we could check the class upon input to FIMSFrame but
this works for right now. @k-doering-NOAA do you have any ideas here?

Had to change the test of a data frame without the proper columns to just
error out because no warnings are given just a stop() command.

When writing a data frame to a csv and reading it back in, the date
formatting can be lost, e.g., 0001-01-01 turns into 1-1-1. FIMS requires
a yyyy-mm-dd format. Now the use of the as.Date() function will create
a date object from a character object but only if it is in the correct
format. If it is in the wrong format, e.g., yyyy/mm/dd, then the function
will error out.

Right now the start_year and end_year are formatted as integers because for
plotting, I thought it would be better to have year 1 versus year 0001 but
we can change this. @ian-taylor-NOAA what do you think?

Close #639 
---------

Co-authored-by: Kelli.Johnson <1536491690113302@mil>