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.
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.
@autoglobal tag, which has been added.Add Cain et al. paper to README.
Minor grammar edits.
Use {roxyglobals}.
Format package names as {package name} not package name or package name in documentation.
.create_summary_isolate(), an internal function, was exported. It should not be user-facing and is now no longer exported or documented.Improved documentation formatting.
Improved handling of internal global variables.
Further updates to test infrastructure.
Update CITATION to follow CRAN’s desired format.
Update outdated URLs.
Update test infrastructure.
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
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”
Use {ape}, {vegan}, {dplyr} and {vidiffr} packages conditionally
Remove {covr} from Suggests
Better documentation formatting
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
Use ROxygen 7.1.1
Spell check and correct spelling errors
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
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 plotRename 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
Initial CRAN release
Completely new R-package format rather than just Rmd and script files