Code quality issues

[fabian-s]

Running goodpractice::gp on ALUES yields the suggestions I pasted below.
Fixing/improving (some of) them is not required for JOSS publications, but recommended.

It is good practice to

✖ write unit tests for all functions, and all package code in
general. 78% of code lines are covered by test cases.

R/overall_suit.R:101:NA
R/overall_suit.R:104:NA
R/overall_suit.R:105:NA
R/overall_suit.R:110:NA
R/overall_suit.R:113:NA
... and 219 more lines

✖ write short and simple functions. These functions have high
cyclomatic complexity:suitability (171).
✖ not use "Depends" in DESCRIPTION, as it can cause name
clashes, and poor interaction with other packages. Use "Imports"
instead.
✖ omit "Date" in DESCRIPTION. It is not required and it gets
invalid quite often. A build date will be added to the package when
you perform R CMD build on it.
✖ use '<-' for assignment instead of '='. '<-' is the
standard, and R users and developers are used it and it is easier
to read your code for them if you use '<-'.

R/overall_suit.R:137:8
R/overall_suit.R:137:16
R/overall_suit.R:137:27
R/overall_suit.R:137:37
R/overall_suit.R:137:48
... and 153 more lines

✖ avoid long code lines, it is bad for readability. Also,
many people prefer editor windows that are about 80 characters
wide. Try make your lines shorter than 80 characters

R/ALFALFASoil.R:3:1
R/ALFALFASoil.R:24:1
R/ALFALFATemp.R:3:1
R/ALFALFATemp.R:13:1
R/ALFALFATerrain.R:3:1
... and 1395 more lines

✖ omit trailing semicolons from code lines. They are not
needed and most R coding standards forbid them

R/overall_suit.R:137:52
tests/testthat/test_suitability_min.R:63:31
tests/testthat/test_suitability_min.R:117:35
tests/testthat/test_suitability_sowmonth.R:60:137
tests/testthat/test_suitability_sowmonth.R:91:137
... and 30 more lines

✖ avoid sapply(), it is not type safe. It might return a
vector, or a list, depending on the input data. Consider using
vapply() instead.

R/overall_suit.R:163:16

✖ avoid 1:length(...), 1:nrow(...), 1:ncol(...), 1:NROW(...)
and 1:NCOL(...) expressions. They are error prone and result 1:0 if
the expression on the right hand side is zero. Use seq_len() or
seq_along() instead.

R/suitability.R:69:15
R/suitability.R:70:17
R/suitability.R:188:12
tests/testthat/test_suitability.R:75:13

✖ not import packages as a whole, as this can cause name
clashes between the imported packages. Instead, import only the
specific functions you need.
✖ fix this R CMD check NOTE: installed size is 6.6Mb
sub-directories of 1Mb or more: doc 2.4Mb help 2.0Mb libs 1.9Mb

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part of this JOSS review

[alstat]

Noted on these @fabian-s, thank you. These are indeed useful suggestions and will consider these on next release.