# hagis 3.1.12

## Minor changes

* Standardise and tidy up text for functions' returned values in documentation.

## Bug fixes

* Fixes examples in "Beta-diversity Analysis with hagis" vignette to work with new versions of {vegan}.

* Corrects {vegan} example where $R^2$ was incorrectly reported.

# hagis 3.1.11

## Minor changes

* Put more guardrails in place for CRAN.
Ensure that all tests are skipped on CRAN using a universal statement rather than `skip_on_cran()`.

* Use `data.table::setDTthreads(1L)` at the top of both vignettes.

* Use `@examplesIf interactive()` for all examples so that they don't run on CRAN.

## Bug fixes

* Removes a redundant zzz.R file that had globals in it.
This revealed that one of the autoplot functions was missing the `@autoglobal` tag, which has been added.

# hagis 3.1.10

## Minor changes

* Skip _ALL_ tests on CRAN.
Because, y'know, CRAN...

# hagis 3.1.9

## "Bug" fixes

* Only run plotting examples if session is interactive to "fix" a "bug" with CRAN determining that the examples suddenly take too long to run.

# hagis 3.1.8

## Bug fixes

* Fix "long running" tests.

## Minor changes

* Add Cain _et al._ paper to README.

* Minor grammar edits.

# hagis 3.1.7

## Minor changes

* Use {roxyglobals}.

* Format package names as {package name} not `package name` or _package name_ in documentation.

## Bug fixes

* Use proper title case in function titles.

# hagis 3.1.6

## Bug fixes

* Fixes bug where `.create_summary_isolate()`, an internal function, was exported.
It should not be user-facing and is now no longer exported or documented.

# hagis 3.1.5

## Minor changes

* Improved documentation formatting.

* Improved handling of internal global variables.

* Further updates to test infrastructure.

* Update CITATION to follow CRAN's desired format.

# hagis 3.1.4

## Minor changes

* Update outdated URLs.

* Update test infrastructure.

# hagis 3.1.3

## 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

# hagis 3.1.2

## 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"

# hagis 3.1.1

## Minor Changes

* Use {ape}, {vegan}, {dplyr} and {vidiffr} packages conditionally

* Remove {covr} from Suggests

* Better documentation formatting

# hagis 3.1.0

## 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

# hagis 3.0.1

## 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

# 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

## 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 Authors@R field

# hagis 2.0.0

* Initial CRAN release

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

# hagis 1.0.0

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