uqrmaie1/admixtools

Issues

• possible to get worst residuals from `find_graphs` models?

  #76 opened 7 months ago by laufran
  2

• eigenstrat_to_plink decouples sample ID and genotypes in plink outputs

  #80 opened 3 months ago by Kelzor
  1

• computing 𝑓3 - and 𝑓4 -statistics directly from genotype files

  #79 opened 3 months ago by Kelzor
  1

• Interpretation of qpadm results

  #78 opened 5 months ago by dosshra
  0

• Installation / Update error

  #77 opened 6 months ago by AimSmall37
  4

• Suggestion: Change to p_emp calculation in compare_fits()

  #75 opened 6 months ago by YourePrettyGood
  1

• Problem making f2 file from plink .bed .fam and .bim files

  #74 opened 7 months ago by sbird1000
  6

• Issue with extract_f2

  #73 opened 8 months ago by jaurbanChicago
  2

• running many replicates of find_graphs?

  #72 opened 8 months ago by laufran
  1

• Comparing graphs with compare_fits

  #67 opened 9 months ago by ndussex
  2

• auto_only: change default value to FALSE

  #68 opened 9 months ago by bergstand
  1

• Issue with f3 and f4

  #71 opened 8 months ago by freshspaceoctopus
  2

• qpWave returning one fewer ranks than expected

  #69 opened 9 months ago by breslie
  1

• qpAdm computation stucks when the num. of letf pops below 3

  #70 opened 8 months ago by nihilistshaman
  0

• keyword argument typo lack of error

  #66 opened 10 months ago by laufran
  3

• Inconsistent bootstrap significance testing

  #65 opened 10 months ago by theo-atkinson
  5

• please add tags/releases

  #64 opened 10 months ago by jowodo
  2

• Protocol Advice: Establishing a t hresholds for the number of allowed admixture events

  #56 opened a year ago by santiago1234
  3

• D statistic estimation

  #38 opened a year ago by juanenciso14
  4

• Zero drift edges

  #61 opened a year ago by santiago1234
  2

• Error in if (gimp > 0 && gimp%%plusminus_generations == 0) { : missing value where TRUE/FALSE needed

  #63 opened a year ago by diegovelizo
  2

• est_to_boo does not preserve the SNP block names (number of SNPs), but est_to_loo() does. Is that intended?

  #59 opened a year ago by diegovelizo
  2

• Behavior affected by other R packages?

  #62 opened a year ago by diegovelizo
  2

• Zero drift edges

  #35 opened 2 years ago by Agenetics
  2

• Error in parse_qpadm_output

  #53 opened a year ago by jaurbanChicago
  1

• large difference of f3 result between admixtools and admixtools2

  #60 opened a year ago by hungweichen0327
  1

• Do qpWave, qpAdm, and f5 have requirements on the minimum number of individuals for each population?

  #58 opened a year ago by maruiqi0710
  1

• qp3pop unique_only does not work as expected

  #57 opened a year ago by RvV1979
  2

• Explanation of the functions qpdstat and qpf4ratio

  #55 opened a year ago by maruiqi0710
  1

• The order of pops in outgroup f3 test

  #54 opened a year ago by hungweichen0327
  2

• evaluation nested too deeply: infinite recursion / options(expressions=)? in find_graphs() when using initgraph

  #51 opened a year ago by jaurbanChicago
  13

• Optimization unsuccessful (constraints inconsistent). Try increasing 'diag', when running qpgraph with a graph and upper and lower bounds

  #52 opened a year ago by jaurbanChicago
  2

• error when running extract_f2 and qpfstats set as TRUE

  #50 opened a year ago by jaurbanChicago
  1

• Feasibility inconsistency between qpadm_rotate with full_results and without full_results

  #49 opened a year ago by idaios
  7

• block_size_issues

  #47 opened a year ago by borletti
  6

• $f4 missing from qpAdm

  #48 opened a year ago
  1

• Error in satisfies_constraints(...) when using admix and event constraints with find_graphs

  #46 opened a year ago by Tharsikav
  2

• How to constrain find_graphs search?

  #33 opened 2 years ago by dosshra
  3

• Update tutorial page 'parallelization'

  #41 opened 2 years ago by Banthandor
  1

• slice_sample error in find_graphs

  #45 opened a year ago by rossibarra
  1

• running find_graphs with the initgraph parameter

  #43 opened a year ago by fangdm
  3

• Distances between populations.

  #36 opened 2 years ago by smd555
  1

• Outgroup f3 statistics not working with pseudohaploidized data.

  #44 opened a year ago by Hjorvik
  2

• How to determine whether the score is reasonable in qpgraph

  #40 opened 2 years ago by jackzhong1995
  1

• Do I need to run LD Prune before running ADMIXTOOLS 2?

  #42 opened 2 years ago by maruiqi0710
  1

• What should I do with "The 'plotly_click' event tied a source ID of 'src' is not registered"?

  #37 opened 2 years ago by sttongjai
  1

• extarct_f2_subset does not copy block_lengths file

  #32 opened 2 years ago by dosshra
  2

• Errors when reject_f4z applied in find_graphs

  #31 opened 2 years ago by ZheCai
  1

• Suggestion: Running extract_f2 for a very large dataset (600 ind. x 18,000,000 snp)

  #30 opened 2 years ago by wjaratlerdsiri
  2

• Question: The difference of qpAdm/qpWave model fitting between Admixtools 1 and 2.

  #29 opened 2 years ago by dongkeeeee
  3