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add support for time_windows in getTimeIntervalSubstitutionRatios R-CMD-check.yaml #31: Commit ecce203 pushed by SamT123
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Add date_column argument to toChronumentalTree R-CMD-check.yaml #30: Commit 096806e pushed by SamT123
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compute exposure from parental node R-CMD-check.yaml #29: Commit 8ab9bfe pushed by SamT123
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four_fold_syn_nuc_positions from ATCG only R-CMD-check.yaml #28: Commit 16fda65 pushed by SamT123
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use reference sequence for fa2vcf R-CMD-check.yaml #27: Commit 32ad69e pushed by SamT123
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use reference sequence for fa2vcf R-CMD-check.yaml #26: Commit dad4f25 pushed by SamT123
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tidy up selection of positions for which to calculate p-values R-CMD-check.yaml #25: Commit d8edf45 pushed by SamT123
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bugfix R-CMD-check.yaml #24: Commit 9f1238b pushed by SamT123
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bug fix R-CMD-check.yaml #23: Commit 351aaf8 pushed by SamT123
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add calculate_p_values option to getTimeIntervalSubstitutionRatios R-CMD-check.yaml #22: Commit ce43fe3 pushed by SamT123
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Change | -> & for choosing mutations to calculate p-values for R-CMD-check.yaml #21: Commit 4591b06 pushed by SamT123
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build docs R-CMD-check.yaml #20: Commit 0e50fef pushed by SamT123
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update docs R-CMD-check.yaml #19: Commit 061c8ca pushed by SamT123
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Allow specifying hypothesis test alternative R-CMD-check.yaml #18: Commit 4c928ec pushed by SamT123
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More options for which p-values to calculate R-CMD-check.yaml #17: Commit ff6826f pushed by SamT123
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Update docs R-CMD-check.yaml #16: Commit cb78b98 pushed by SamT123
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Add option to skip p-values, and report on progress in getSubstitutio… R-CMD-check.yaml #15: Commit 7d2e1b8 pushed by SamT123
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small fix R-CMD-check.yaml #14: Commit 8802532 pushed by SamT123
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Don't group ratio tables R-CMD-check.yaml #13: Commit 4c1de4f pushed by SamT123
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fix docs R-CMD-check.yaml #12: Commit 8ee345c pushed by SamT123
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more renaming R-CMD-check.yaml #11: Commit c96d828 pushed by SamT123
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rename syn_nucs to nucs R-CMD-check.yaml #10: Commit 7d863a9 pushed by SamT123
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Add reoptimiseTreeAndSequences R-CMD-check.yaml #9: Commit c2987fa pushed by SamT123
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Update node sequence reconstruction R-CMD-check.yaml #8: Commit c0881cc pushed by SamT123
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Report progress during node reconstruction R-CMD-check.yaml #7: Commit 0c8da0f pushed by SamT123
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