NEWS

Sadiq, H. et al (2025), "scoup: Simulate Codon Sequences with
Darwinian Selection Incorporated as an Ornstein-Uhlenbeck
Process", Journal Name Vol(No.): ppA–ppZ.

This file documents package changes since first submission on Bioconductor.

1.5.1 - 1.5.5 (2026-03-17): JOSS Publication Update
+ Extended the vignettes/exData folder to incorporate reviewers suggestions.
+ Updated the paper, inst and vignettes folders in response to editor's queries.
+ Fine-tuned paper and necessary files as part of final JOSS requirements.
+ Updated citation.

1.1.1 - 1.1.4 (2025-01-07): Functional Update
+ Improved flexibility by allowing specification of mutation rate parameters.
+ Adjusted the `fixed` input in `codonCoeffs` function.
+ Reversed the mutation matrix flexibility due to expensive computational cost.
+ Updated help files to aptly emphasise episodic in-place of "deterministic".
+ Revised the `codonFreq` function so that it uses `softmax` identity.

0.99.16 - 0.99.17 (2024-10-23): Developmental Release Changes
+ Edited citation and vignette appropriately

0.99.15 (2024-10-09): Review Changes
+ Incorporated recommendations from @jianhong
+ Updated 'biTree' to include test and warning

0.99.2 - 0.99.12 (2024-08-14): Additional Pre-Review Changes
+ Updated temporary inst/CITATION file.
+ Updated seqDetails.R to accommodate NOTE from Bioc report about use of "is".
+ Updated NAMESPACE as recommended by Bioc report: imported "methods" & "is".
+ Incorporated Biostrings: used to generate colorful sequences.
+ Initiated unit tests.

0.99.1 (2024-08-13): Pre-Review Changes
+ Updated temporary inst/CITATION file.
+ Deleted redundant LICENSE file.
+ Removed patchlevel dependency attached to R in DESCRIPTION file.
+ Shortened code lengths and corrected T/F.
+ Adjusted spaces to size 4.
+ Bumped package version number to *.**.1.

0.99.0 (2024-08-01): First Submitted Version
+ Submitted on Bioconductor for review.
+ Edited the DESCRIPTION, README and vignettes with
  Bioconductor-esque installation instructions.