NEWS.md

In graphsim: Simulate Expression Data from 'igraph' Networks

graphsim 1.0.4

Minor update to pass CRAN checks

• updates citation for retain on CRAN

• avoids deprecated use of S3 methods

graphsim 1.0.3

Minor update to pass CRAN checks

• removed imports for unused packages

• removed dependency on deprecated sparse matrices

• correct links in citations and vignettes

graphsim 1.0.2

Updates maintainer contact details.

• resolves vignette formatting #11

• passes updated CRAN checks (links updated)

graphsim 1.0.1

• Update citation to reflect acceptance at JOSS

• Update documentation (package help page, links and cross-references)

• Critical changes to vignettes to reduce build time (required for regular CRAN checks)

graphsim 1.0.0

• Major stable release: note changes to results are possible! (legacy code should run without breaking)

• Expanded documentation and examples (consolidate into fewer vignettes for clarity)

• Resolves errors handling inhibiting edges

• Efficiently compute a state matrix from a vector of edge properties from paths

• Enables passing "sd" (standard deviation) to alter covariance of Sigma matrix

• Adds methods for computing using Laplacian matrices

• Adds function to compute simulations directly from an adjacency matrix

• Migrates computing states to sigma (these matrices include inhibitions)

graphsim 0.1.1

• Initial CRAN release

• Unit testing for all functions

• Checking for compatible inputs

• Passing layout parameters to plotting function

graphsim 0.1.1

• Full vignette of biological pathway

• Merge plot_directed from function from plot.igraph to avoid github dependencies

• Added example data for reactome pathways

graphsim 0.1.0

• Initial version of the package for generating simulated data

graphsim documentation built on June 8, 2025, 11:53 a.m.