openplantpathology/hagis v3.0.0

hagis 3.0.0 Defunct functions

• plot() is now defunct. Use autoplot() to plot hagis objects in place of plot(). This is to avoid the side-effect of generating and displaying a plot every time plot() is called, which can be troublesome when using ggplot2 themes since it created two plots, the original with the base theme and the new themed plot

• Rename output column N_susc to N_virulent_isolates

• Don't round results from summarize_gene() or calculate_complexities() before returning values to user

• Implement fix suggested by @zkamvar to ensure that the user-input data is not changed from a data.frame or tibble object to a data.table object in the R session

• Add ability to sort graph x-axis in ascending or descending order based on the y-axis values rather than only by gene or complexity.

• Move example data set into internal data and provide documentation for them

• Provide documentation for how diversity indices are calculated along with mathematical notation where possible to display

• Calculate Shannon and Simpson indices internally rather than rely on vegan to reduce number of Dependencies

• Replace the term field with column in documentation

• Test coverage now 100 %

• Add funding agencies to DESCRIPTION Authors@R field