leiden 0.4.3

Minor update to pass CRAN checks

• removed deprecated method to create sparse matrices

• correct links in citations and vignettes

leiden 0.4.2

• migrates bug fixes to conda environment and limit on total cells to refactored package

• allows calling igraph::community_leiden for supported parameters (requires igraph v1.2.7 or later)

• automatically calls native R version of leiden rather than Python to improve performance

leiden 0.4.1

• migrates changes to retain on CRAN to leiden 0.4.0 (alpha)

leiden 0.4.0

• migrate to calling community_leiden in igraph

leiden 0.3.10

• removes limitation on number of cells (disables scientific notation within function call): resolves #12

• resolves conflict between base and r-reticulate conda environments on loading: resolves #20

• updates conda environment in interactive sessions only for compliance to CRAN checks

• resolves formatting error in Rmarkdown vignettes (https://github.com/yihui/knitr/issues/2057)

• update testing for bipartite graphs for compatibility with newer version

leiden 0.3.9

Updates maintainer contact details. >>>>>>> master

leiden 0.3.8

• bug fixes for vignettes to retain on CRAN

leiden 0.3.7

• remove cairo graphics from vignette to retain on CRAN

leiden 0.3.6

• add methods for multiplex community detection from a list of graphs (requires leidenalg 0.7.1)

• add support for maximum community size (depends on leidenalg 0.8.2), if available

leiden 0.3.5

• background changes to build vignettes on CRAN

leiden 0.3.4

• add support for bipartite graphs (requires leidenalg 0.6.1 or later)

• changes to install python leidenalg from vtraag channel on Windows

• bug fixes to install documentation

• improve automated conda configuration in background on loading library

• optionally derive edge weights from the Laplacian matrix

leiden 0.3.3

• bug fixes for documentation in response to changes to R

see development version: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16223

leiden 0.3.2

• added support for passing weighted igraph objects

• improved handling of sparse matrices

• bug fixes to ensure same results from matrix and igraph methods

leiden 0.3.1

• method for sparse matrices that passes to igraph without casting to dense

• added seed and n_iterations to find_partitions

leiden 0.3.0

• Implements calling leiden directly on an igraph object

• Separate methods for igraph objects and adjacency matrices

• Support for sparse matrices

• Benchmarking added to vignettes

leiden 0.2.3

• Adds passing weighted adjacency matrices to derive weight parameters

leiden 0.2.2

• Changes to ensure compatibility with CRAN. Updates to vignettes and documentation.

leiden 0.2.1

• Enable passing arguments to Python functions: initial_membership, weights, and node_sizes.

leiden 0.2.0

• Adds passing arguments to the Python implementation: the partition_type and resolution_parameter. Runs the RBConfigurationVertexPartition by default (which is equivalent to ModularityVertexPartition with a resolution_parameter of 1).

leiden 0.1.1

• Removes dependancy on igraph R package and avoids writing to disk (compatible with CRAN). Passes adjacency matrix directly to python as a numpy array.

leiden 0.1.0

• Implements the Leiden algorithm in R by calling the leidenalg python library. Runs ModularityVertexPartition with defaults.