Code

King test#30

Code

Merged

dramanica merged 77 commits intomainEvolEcolGroup/tidypopgen:mainfrom king_testEvolEcolGroup/tidypopgen:king_testCopy head branch name to clipboardMay 3, 2024

+6,196-16,880

Commits

Commits on Apr 17, 2024

• Fix king to use equation 11

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• clean up

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Commits on Apr 18, 2024

• stray n_cores

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• test snp_king and sp_ibs against plink output

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Commits on Apr 19, 2024

• filter_high_relatedness function

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Commits on Apr 20, 2024

• Add filter_high_relatedness to namespace, edit files for ibs and king tests

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Commits on Apr 23, 2024

• Alter snp_ibs output and adjust test

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• Start to remove gt_write_bed_from_dfs

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• add dimnames for FBM

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• Merge branch 'king_test' of github.com:EvolEcolGroup/tidypopgen into king_test

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• make tests quiet

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• Merge branch 'main' into king_test

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• a few fixes and some problems

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• plink mibs and test fixes

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• Remove gt_write_bed_from_dfs from all tests

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• Test for filter_high_relatedness

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• filter_high_relatedness document

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• types for ibs

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• Merge branch 'king_test' of github.com:EvolEcolGroup/tidypopgen into king_test

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• implement all types for ibs

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• more ibd exploration

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• Merge branch 'king_test' of github.com:EvolEcolGroup/tidypopgen into king_test

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Commits on Apr 24, 2024

• minor missing allele bug

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• hail examples

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• remove dimnames for fbm

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• clean up some internal functions

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• More function names clean up

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• udpate file names

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• More name fixing

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• more name cleanups

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• implement allele sharing

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Commits on Apr 25, 2024

• implement pop_fst and pop_fis

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• More on fst

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Commits on Apr 26, 2024

• small clean up of pairwise fst

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• tidy allele sharing

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• fix row and cols being swapped when reading vcf

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Commits on Apr 28, 2024

• more work on fst

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• more wc

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Commits on Apr 29, 2024

• Some work on exporting data

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• implement gt_as_genlight

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• minor cleanup

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• Add tider to pairwise_king

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• Add tidier to pairwise_ibs

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• implement nei73 with new framework

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• Merge branch 'king_test' of github.com:EvolEcolGroup/tidypopgen into king_test

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• Adapt set_impute in PCA and LD functions

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• Merge branch 'king_test' of github.com:EvolEcolGroup/tidypopgen into king_test

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• improve check

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• Update indiv_qc_report to include relatedness

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• Merge branch 'king_test' of github.com:EvolEcolGroup/tidypopgen into king_test

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• fix

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• compare to hierfstat

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Commits on Apr 30, 2024

• Temporary test files for QC vignette

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• Merge branch 'king_test' of github.com:EvolEcolGroup/tidypopgen into king_test

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• test files too large

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• more hierfstat

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• Merge branch 'king_test' of github.com:EvolEcolGroup/tidypopgen into king_test

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Commits on May 1, 2024

• QC and plink cheatsheet vignettes

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• add more missingness families data

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• pairwise fst

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• treat NA as FALSE in select_loci()

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• loci_names() and loci_chromosomes()

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• Minor doc fixes

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• small fixes

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Commits on May 2, 2024

• qc_report function name changes

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• change parameter names in qc_report_loci, qc_report_indiv, and filter_high_relatedness

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• Add note on allele swapping

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• Autoplot documentation

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Commits on May 3, 2024

• loci_clump_ld() now returns boolean by default

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• gt_write_plink() is now gt_as_plink()

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• clean up

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• More cleaning up

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• Relatedness plot

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• Merge branch 'king_test' of github.com:EvolEcolGroup/tidypopgen into king_test

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• read ped files

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• Merge branch 'king_test' of github.com:EvolEcolGroup/tidypopgen into king_test

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• Fix warnings.

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