Changelog

Source: NEWS.md

hagis (development version)

hagis 3.1.112023-09-06

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 3.1.62023-04-25

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 3.1.42022-08-15

Minor changes

  • Update outdated URLs.

  • Update test infrastructure.

hagis 3.1.32021-10-14

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 3.1.22021-09-30

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 3.1.12020-12-09

Minor Changes

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

  • Remove {covr} from Suggests

  • Better documentation formatting

hagis 3.1.02020-10-07

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 3.0.12019-11-18

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 3.0.02019-08-26

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

hagis 2.0.02019-06-24

  • 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