Changes in version 1.8.1                        

  - Requires dplyr >=1.1.0 due to change of sorting order in arrange()

                        Changes in version 1.8.0                        

  - Release version for Bioconductor 3.17.

                        Changes in version 1.6.1                        

  - Discontinue the use of .data due to its deprecation since
    tidyselect 1.2.0.
  - Update minimum required versions for some tidyverse related packages
    due to function deprecation.

                        Changes in version 1.6.0                        

  - Release version for Bioconductor 3.16. See changes for 1.5.x.

                         Changes in version 1.5                         

  - Added different modeling functions. Might not be completely
    backwards compatible!

                        Changes in version 1.4.0                        

  - Release version for Bioconductor 3.15. See changes for 1.3.x.

                         Changes in version 1.3                         

  - Switched from Louvain to Leiden algorithm for community detection
    (requires igraph >= 1.2.7).
  - The metamodel is now build by ridge regression. Intercept p-values
    are not calculated, the values are set to NA for backwards
    compatibility.
  - Unique value error for cv folds is downgraded to warning.
  - Prefix can be added to the column names generated by the fucntions
    add_juxtaview and add_paraview. This allows modeling the maker
    expression by its own juxtaview and paraview.
  - Bug fixes.

                        Changes in version 1.2.1                        

  - Fixed a separator issue in results aggregation and signature
    generation that might cause issues with variable names containing
    "_".

                        Changes in version 1.2.0                        

  - Release version for Bioconductor 3.14. See changes for 1.1.x.

                         Changes in version 1.1                         

  - Added functions for view manipulation, including view filtering and
    marker selection.
  - Added functions for performance, contribution and importance
    signature extraction from results.
  - Aggregation and signature generation is generalized for samples with
    non-identical targets by working on the intersection.
  - Modeling of intraview can be bypassed.
  - Added families of distances to calculate paraview.
  - Paraview can exlcude measurements within a used defined zone of
    indifference around each spatial unit.
  - Improved plotting control.
  - Complete test coverage.

IMPORTANT: R2 is now reported in percentages for intra, multi and gain.
Collecting results from running mistyR < 1.1.11 will lead to
miscalculation of gain.R2. Update the performance.txt files by
multiplying the values in columns intra.R2 and multi.R2 by 100.

                        Changes in version 1.0.3                        

  - Fixed display of messages and progress during view generation.
  - Improved plotting control and display.
  - Fixed handling of NaN in results.
  - Vignette output switched from BiocStyle to rmarkdown for pdfs due to
    BiocStyle issue.

                        Changes in version 1.0.2                        

  - Bugfix: models built with different parameters stored and retrieved
    from the same cache file.
  - Avoid calls to os-dependent file.info in tests.

                        Changes in version 1.0.1                        

  - Bugfix: passing arguments to ranger.
  - Warnings on clearing nonexistent cache folders and tests of
    performance.
  - Increased test coverage.

                        Changes in version 1.0.0                        

  - Release version for Bioconductor 3.13.

                       Changes in version 0.99.11                       

  - Fixed a bug in Nystrom approximation for creating paraview.
  - Added a suite of tests with high coverage.
  - Cleaner cache control.

                       Changes in version 0.99.9                        

Revisions requested by Bioconductor

  - Removed magrittr from dependencies. Reexported pipe operator.
    Removed from examples.
  - Caching turned off by default.
  - Added parameter for appending performance and coefficient files in
    run_misty.
  - Internal functions in views.R are now explicit.
  - Removed alternatives and additional examples for function use from
    documentation.
  - Removed redundant messages, escalated to warnings where required.
  - run_misty cleans up empty cache directories.
  - Vignette compatibility with the new release of SpatialExperiment.
  - Remove Seurat vignette from package due to missing hdf5r binary for
    R 4.1 on CRAN for MacOS.

Other changes

  - README.md figures moved to the cloud.
  - All passed paths and cache location are normalized.
  - Changes in the mistyR vignette to reflect changes to insilico
    evaluation from the paper.

                       Changes in version 0.99.0                        

  - Version with vignettes ready to submit to Bioconductor.

                        Changes in version 0.1.0                        

  - Initial beta release of mistyR (named as MISTy) with function
    documentation.