Features

Now exporting the previously internal but potentially useful function denest_sleuth_boots() for extracting and consolidating bootstrapped abundances from a Sleuth object.
Also exporting the previously internal group_samples() which restructures the information from the sample_to_covariates table of a Sleuth object.
Also exporting the previously internal version of g.test() that performs our G-test.
plot_gene() now allows customisation of the information layers and colours used. You can choose what (if any) information is encoded as colour, fill and shape, as well as what colours are used. Please consult the Plots vignette for details on how to use them.

Other changes

Revised default values. Following false positive benchmarking, abund_thresh was lowered from 10 to 5 and dprop_thresh was increased from 0.1 to 0.2.
dtu_summary() and get_dtu_ids() have been clarified and extended. Additional categories are now reported and the names used for the categories are now shared between the two functions. Please consult the Raw Output vignette for details.
plot_gene() styles have been revised. Some were no longer necessary, after the customisation options added. The two remaining styles have been renamed to be clearer and a new third style was added. The old style names "lines" and "merged" are still recognised.
The Output and Plots vignette has been split into two separate vignettes, one for the raw output and one for the plots.
Four types of plot_overview() have been removed. The types had been left undocumented and should not affect your user experience. "volcano" and "maxdprop" are still valid types.
Development will now take place on a separate branch. Even/Odd version number convention for tagging release and developmental version will remain. The current developmental stage can be obtained via devtools::install_github("bartongroup/rats", ref="development")

Switched vignette engine to knitr::knitr. This should prevent some rendering issues.
Corrected the missing title from the LICENSE document.
Input checks for validity of structure of bootstrapped data are now performed correctly and more thoroughly. Previously they applied only to Sleuth objects, not to generically formatted data.