### Minor changes

• Sample names in calculate_diversities() are not required to be numeric values. Previously, this column was converted to numeric so if character values were present, these values became NA. This allows for greater flexibility when analysing the data as sample names are often more descriptive than just a numerical value.

• Spelling corrections in code comments

• Clean up CITATION file

• README is now more complete with information and links to the MPMI paper

### Minor changes

• Improved documentation formatting

• Update roxygen details

• Fixes incomplete end of line in test-create_binary_matrix.R

• Add wordlist of allowed words for spellchecking

• More consistent code styling in vignettes

• Prefer “_” to “*” for italics

• More verbose handling of importing data.table as a whole package using “R/utils-data.table.R” in place of “R/zzz.R”

### Minor Changes

• Use ape, vegan, dplyr and vidiffr packages conditionally

• Remove covr from Suggests

• Better documentation formatting

### Major Changes

• Add new function, create_binary_matrix() to format data for exporting beta diversity matrices representing the pathotype of each isolate. Users can export a binary pathotype data matrix which could then be used to visualize beta-diversity of pathotypes using vegan or ape in R

• Add new vignette, “Beta-diversity Analyses”, to illustrate the use of the new functionality

### Minor Changes

• Use ROxygen 7.1.1

• Spell check and correct spelling errors

### Minor Changes

• Update citation with full MPMI citation

• Fix issue in CITATION file where nasapower was referred to in text

• Use ROxygen 7.0.0

• Remove an extra “/” in the CITATION’s DOI

### 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

### Minor Changes

• 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 field

• Initial CRAN release

• Completely new R-package format rather than just Rmd and script files

• Initial release of Rmd and script files by A. McCoy and Z. Noel