GAMA version 0.2.2

Author: JLewis-dev

CITATION.cff

@@ -1,8 +1,8 @@
 cff-version: 1.2.0
 message: 'If you use GAMA in your research, please cite it as below.'
 title: 'GAMA: Genomic Availability & Metadata Analysis Tool'
-version: 0.2.1
-date-released: 2026-02-27
+version: 0.2.2
+date-released: 2026-03-06
 authors:
   - family-names: Lewis
     given-names: James

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GAMA
 Title: Genomic Availability & Metadata Analysis Tool
-Version: 0.2.1
+Version: 0.2.2
 Authors@R:
     person('James', 'Lewis',
            email = 'James.Lewis-2022@outlook.com',
@@ -11,8 +11,9 @@ Description:
     data for user-defined sets of species. It unifies NCBI Assembly, SRA,
     and BioSample query searches to generate availability summaries with a
     composite data richness score, alongside ontology-based breakdowns of
-    SRA modalities and GEO experiment linkage. GAMA is intended to support
-    feasibility assessments for in silico research on underutilised plants.
+    SRA modalities, GEO experiment linkage, and BioSample/BioProject-level
+    replication skew. GAMA is intended to support feasibility assessments
+    for in silico research on underutilised plants.
 URL: https://github.com/JLewis-dev/GAMA
 BugReports: https://github.com/JLewis-dev/GAMA/issues
 License: MIT + file LICENSE
@@ -22,7 +23,6 @@ Imports:
     ggplot2,
     purrr,
     rentrez,
-    rlang,
     tibble,
     tidyr,
     xml2

NAMESPACE

@@ -5,7 +5,7 @@ export(extract_assembly_metadata)
 export(extract_sra_metadata)
 export(plot_availability)
 export(plot_sra_availability)
-export(plot_sra_geo_availability)
+export(plot_sra_geo)
 export(plot_sra_skew)
 export(query_species)
 export(summarise_availability)

NEWS.md

@@ -1,3 +1,19 @@
+# GAMA 0.2.2
+
+## Refactoring
+- Renamed `plot_sra_geo_availability()` to `plot_sra_geo()`
+- GEO linkage fields are now always cached in `summarise_sra_availability()` output via the attached `sra_profile`, regardless of `include_geo`
+- `include_geo = TRUE` now acts only as an output visibility option, appending species-level GEO summary columns without changing what is cached
+
+## Documentation
+- Updated roxygen documentation and examples to reflect the revised GEO caching and `plot_sra_geo()` workflow
+- Added `docs/GAMA_user_guide.pdf` as a comprehensive reference for GAMA functions and methods
+
+## Testing
+- Tested end-to-end SRA availability and GEO overlay workflow
+
+---
+
 # GAMA 0.2.1
 
 ## Refactoring