NEWS

JANE 2.1.0 (2025-11-03)

Add website with vignette to "URL" section of DESCRIPTION
Fix bug in JANE when class is added to NULL optimal_starting
Add more comprehensive tests
Replace some helper functions with more numerically stable variants
Use .registration = T for useDynLib
@useDynLib only included once in zzz.R. Removed all other instances in other R scripts
Create header file for helper functions
Create helper functions for inverse logit, density for ZTP and log-normal, and solve_only_sympd (checks for sympd before running arma::solve)
Update scripts to work with helper functions
Fix deprecated methods::as(A, "dgCMatrix") in JANE.R
Update specify_priors and check_priors to check user input, also remove redundant code
Add dimension checks for user supplied mus, omegas, and p in sim_A

Update prior specification functionality
Make new S3 class for priors and initial values
Improve documentation - add information about connection strength heterogeneity, fix priors in 'details' of specify_priors, and fix typos
Add vignette "JANE User Guide"

Add importFrom progress progress_bar to NAMESPACE to address note in checks
Add option to plotting function to remove noise edges if JANE was run with noise_weights = TRUE
Add citation information

JANE is now able to handle weighted networks, specifically for applications that involve the presence of noise edges in the network

Improve plotting function:
- Add options for user-specified titles (i.e., main, xlab, and ylab)
- Add option for user-specified colors for clusters

Fix plotting scripts to include immediate call to on.exit to reset user settings
Add testthat functionality for automatic testing of package functions