Old tidyverse SE functions are deprecated

[Jason Vander Heiden]

Test messages

testDiversity.R:8: warning: calcCoverage
group_by_() is deprecated.
Please use group_by() instead

testDiversity.R:8: warning: calcCoverage
mutate_() is deprecated.
Please use mutate() instead

testDiversity.R:8: warning: calcCoverage
arrange_() is deprecated.
Please use arrange() instead

testDiversity.R:8: warning: calcCoverage
rename_() is deprecated.
Please use rename() instead

testDiversity.R:24: warning: countClones
summarise_() is deprecated.
Please use summarise() instead

testTopology.R:40: warning: Test getMRCA and testMRCA
filter_() is deprecated.
Please use filter() instead

Fix

Remove all usage of _ tidyverse functions in favor of new quosure proceedure:

https://dplyr.tidyverse.org/articles/programming.html

And set appropriate tidyverse package version requirements.

[Jason Vander Heiden]

Link to an easier to understand explanation of the fix:

https://edwinth.github.io/blog/dplyr-recipes/

[Jason Vander Heiden]

We should probably also remove all use of `.dots` in favor of `!!!syms()`.

[ssnn]

.dots removed in fed7d3b

[ssnn]

several commits after dc5137a