Changes in version 1.9 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.