Check - make CRAN ready

[leppott]

Run Check and make the package CRAN ready.

[leppott]

Will have to cut down on file size. Extdata is 23.5 MB.

Several other things to fix but shouldn't affect functionality of the package at this time.

[leppott]

R CMD check results
1 error | 4 warnings | 5 notes

v1.0.2.9005 (2017-07-31)

checking for portable file names ... WARNING
Found the following files with non-portable file names:
data-raw/December 2016 - Salt Results - Final.xlsx
inst/extdata/BIBI 1998 (Stribling et al.) (ea-99-6).pdf
inst/extdata/MBSS Install Guide.pdf
inst/extdata/PHI Worksheet_from MP (Erik20170329).xls
inst/extdata/Paul et al. 2003_MBSS (ea-03-4_phi).pdf
inst/extdata/Southerland et al_2005 (MBSS_new_ibi) (ea-05-13).pdf

checking for missing documentation entries ... WARNING
Undocumented code objects:
'metric.values.algae' 'metric.values.bugs' 'metric.values.fish'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.

checking for unstated dependencies in examples ... WARNING
Warning: parse error in file 'MBSStools-Ex.R':
16: unexpected ','
29: #write.table(flow.sample,paste0("SumFlow",myYear,"_",datetime,".tab"),
30: row.names=FALSE,
^

checking data for non-ASCII characters ... WARNING
Warning: found non-ASCII strings
'ATKI-102-X-2016 ' in object 'taxa_bugs_family'
'ATKI-102-X-2016 ' in object 'taxa_bugs_genus'

[leppott]

Addressing CMD check issues with help of CodeFactor, codecov, lintr, and goodpractices.