NEWS
biometryassist 1.4.0 (2026-02-03)
Major changes
- Deprecated
des_info(). This function has been superseded by design(), and will be removed in a future version.
- Implement
arcsin transformation handling in multiple_comparisons() (#60).
- Demonstrated how to add orientation information to design plots via a vignette (#126).
- Major refactoring of
design() in preparation for moving to a new backend later (#102). No user-facing changes.
- Added strip-plot designs (#134).
- Enabled output of p-value matrix from
multiple_comparisons(). This required changing the multiple_comparisons() output object to a list, but printing to console and autoplot(<multiple_comparisons>) still work as before (#22).
Minor changes
- Add interval type 'none' for
multiple_comparisons() (#125).
- Added a print method for
satab() to reliably get the same output (#133).
- Switched from cowplot to patchwork to speed up resplot (and variogram) (#29).
- Added and refactored numerous tests throughout to achieve 100% test coverage and speed up tests (#104, #143, #144, #135, #148)
- Added asreml downloads for more operating systems and versions (#158).
Bug Fixes
- Fixed a bug where hex colours don't work with
export_design_to_excel() (#124).
- Fixed a bug where buffers weren't added to the plot if they are added after initial design creation (#123).
- Fixed a bug in
install_asreml() where it threw an error with more than one new version (#122).
- Fixed a bug where calculate_differences clashed with package "MuMIn" (#131).
biometryassist 1.3.3 (2025-09-15)
Bug Fixes
- Fixing test issues identified by CRAN after ggplot2 4.0.0 release
biometryassist 1.3.2 (2025-09-11)
Bug Fixes
- Updates to tests and histograms for compatibility with upcoming ggplot2 release.
- Fixed a bug where standard errors that were too small would produce plots with missing upper or lower confidence limits due to rounding the SE to zero. (#119)
- Fixed a bug that made rotated axis labels overlap the plot area (#113)
biometryassist 1.3.1 (2025-07-04)
Bug Fixes
- Update to ensure compatibility with upcoming ggplot2 release (#111)
biometryassist 1.3.0 (2025-06-11)
Major changes
- Switched to using S3 methods for
resplot() to enable easier expansion to different models in future. (#100)
- Introduced a new function
export_design_to_excel(). An excel file can now be created from a design dataframe, instead of just a graphical plot. (#74)
- Introduced a new comparison interval type in
multiple_comparisons().
The new option int.type = 'tukey' will now create comparison intervals using Tukey's distribution rather than a t-distribution for a regular confidence interval.
This has been a point of confusion when intervals don't overlap but share letters. (#66)
Minor changes
- Model inputs are now checked for potential transformations that haven't been supplied in
multiple_comparisons(). (#83)
- Enabled a
verbose option for the quiet parameter in install_asreml() to give more detailed output when required. (#81)
- Added ability to group multiple resplots and variograms into a single grid via a
onepage argument. (#73)
- Buffer plots are now implemented within the design data frame, rather than just the plotting logic (#68)
Bug Fixes
- Fixed a bug introduced in v1.2.2 where arguments weren't passed through properly to asreml. (#98)
- Fixed a bug which broke the messages about deprecated parameters in resplot. (#97)
- Fixed a long-standing bug where logl_test would work if random terms were given in resid. (#7)
biometryassist 1.2.2 (2025-04-23)
Major changes
- Switched to using S3 methods to get predictions in
multiple_comparisons() to enable easier expansion to different models in future. (#92)
Minor changes
- Added ability to produce column plots from
multiple_comparisons() (#90)
- Add option in multiple_comparisons() to disable letter comparisons (#85)
- Enable custom colour palettes for design plots (#84)
Bug Fixes
- Fixed CRAN warnings due to changes in the sommer package (#89)
- Fixed errors in
shapiro.test() within resplot() with too many data points (#87)
- Fixed a bug where
heat_map() didn't work properly with factor columns (#86)
- Split-plot design dataframe doesn't have the required columns (#82)
biometryassist 1.2.1 (2024-06-05)
Bug Fixes
- The new
summary_graph() function was accidentally left out of the CRAN submission.
biometryassist 1.2.0 (2024-05-31)
Major changes
- Introduced the
summary_graph() (#75) and heat_map() (#19) functions
- Enabled arbitrary
row, column, block and treatment columns to be provided in the autoplot.design() function, to enable more general plotting of designs. (#28)
Minor changes
- Implemented the ability to plot designs with buffer plots. (#68)
- Changed
install_asreml() to check if there is a later version before downloading.
- Enabled non-standard evaluation input of column names in
autoplot.design().
biometryassist 1.1.3 (2023-07-19)
Bug fixes
- Better checking of column names in data provided to
multiple_comparisons() to prevent breaking. (#53)
- Updated install_asreml() to work with ARM chip macOS devices. (#54)
- Wrote a vignette with instructions for installing ASReml-R. (#55)
- Fixed variogram to enable it to work with dsum models (i.e. MET models). (#61)
biometryassist 1.1.2 (2022-11-25)
Bug fixes
- Fixed a bug introduced due to a change in names by
predictmeans(). (#50)
- Added a check for missing
ar1() component in variogram(). (#49)
- Added an error check for terms provided in the wrong order to
multiple_comparisons() via classify. (#48)
- Checked if model needs the
present argument passed to predict.asreml(). (#41)
biometryassist 1.1.1 (2022-10-27)
Minor changes
multiple_comparisons() now accepts power transformations and automatically back-transforms. It gains a new argument power to provide the transformation power applied in the model to undo. This enables more general Box-Cox transformations. (#36)
multiple_comparisons() no longer produces an error when the trans argument is supplied and offset is not. It now produces a warning and sets offset to 0 when not provided. (#37)
- Added an option to turn off the start up message and version check. Add
options(biometryassist.check = FALSE) to your .Rprofile file to disable. Partially fixes #6.
- Enabled new colour-blind friendly palettes (#39)
Bug fixes
- Updated the required version of rlang (>=1.0.0)
- Fixed a bug that didn't allow labels and the x axis to be rotated independently for
autoplot.mct() (#35)
- Fixed an issue where treatment columns were not determined correctly in
multiple_comparisons() (#33)
- Fixed a problem with variograms displaying grey values where
NAs have been produced. (#24 and #25)
- Fixed some warnings that would be introduced with the forthcoming version of ggplot2 (#42)
biometryassist 1.1.0 (2022-04-14)
Major changes
multiple_comparisons() no longer requires calls to predict.asreml() to be passed into the function, as the predicted values are now calculated internally. Additional arguments can be passed to predict.asreml() via the ... argument. (#27)
Minor changes
- The
order argument of multiple_comparisons() has been deprecated in favour of a new argument descending. This takes logical (TRUE or FALSE) values only, so default is no longer possible as it was producing incorrect results. (#8)
resplt() has been deprecated in favour of resplot() and will be removed in a future version (#20).
- Warnings about lack of convergence are no longer output in
logl_test(). (#17)
Bug fixes
- Aliased levels are printed properly in
multiple_comparisons() now. (#14)
- R.param and G.param are removed from the
asreml() call on resplot() if not explicitly provided. (#21)
- Fixed a bug where
install_asreml() would not work on macOS Monterey. (#16)
biometryassist 1.0.0 (2022-01-28)
Minor changes
mct.out() has been renamed to multiple_comparisons()
logl.test() has been renamed to logl_test()
des.info() has been renamed to des_info()
Previous versions
For changes prior to biometryassist 1.0.0 see the BiometryTraining package at https://biometryhub.github.io/BiometryTraining/news/index.html.