NEWS

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tidypopgen 0.4.4 (2026-05-19)

• fix seed argument of gt_admixture()
• implement our own upset plot function to avoid dependency on UpSetR package, which is no longer maintained
• fix reading of VCFs when genotype separator symbol is present in the sample information
• fix loci_ functions output when calculating across groups for a single loci
• fix gt_update_backingfile() to preserve imputation metadata when backing files are updated
• add validation in gt_impute_simple() to detect and report SNP dimension mismatches caused by excluded SNPs
• add outdir argument in gt_admixture() to store partial outputs for large jobs
• fix gt_admixture() output file names when n_runs > 1

tidypopgen 0.4.3 (2026-01-23)

• fix occasional test failure when temporary file names contained certain patterns

tidypopgen 0.4.2 (2026-01-22)

• allow least squares projection of multiple components at once in gt_project_pca()

tidypopgen 0.4.1 (2025-12-20)

• duplicate-distance checks removed in is_loci_table_ordered()
• make qc_report_* functions work with pseudohaploids

tidypopgen 0.4.0 (2025-10-24)

• store chromosomes as factors, and remove redundant column storing chromosome as integer

tidypopgen 0.3.3

• only use the FBM backend (rather than a complete bigsnpr object)
• fix a few minor bugs

tidypopgen 0.3.2 (2025-08-27)

• tidy up for CRAN submission

tidypopgen 0.3.0

• add gt_pseudohaploid() and adapt appropriate functions to work with pseudohaploids

tidypopgen 0.2.0

• Lots of optimisations to speed up processing of large datasets.
• Added an sf backend to tidypopgen for spatial data.
• Windowed statistics.

tidypopgen 0.1.0

• Initial public version of tidypopgen released on r-universe.