datafarming 1.4.0 → 2.2.0

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Files changed (21) hide show
  1. checksums.yaml +4 -4
  2. data/LICENSE.md +1 -1
  3. data/README.md +10 -6
  4. data/datafarming.gemspec +11 -6
  5. data/exe/datafarming.rb +33 -27
  6. data/exe/generate_design.rb +306 -0
  7. data/lib/datafarming/freq_sets.rb +52 -243
  8. data/lib/datafarming/nolh_designs.rb +19105 -4483
  9. data/lib/datafarming/res_v_seqs.rb +57 -0
  10. data/lib/datafarming/scale_design.rb +29 -0
  11. data/lib/datafarming/screen_freq_sets.rb +143 -0
  12. data/lib/datafarming/version.rb +5 -0
  13. data/lib/datafarming.rb +8 -0
  14. metadata +42 -18
  15. data/DESCRIPTIONS.html +0 -1107
  16. data/DESCRIPTIONS.md +0 -45
  17. data/exe/augment_design.rb +0 -66
  18. data/exe/scaled_fde.rb +0 -169
  19. data/exe/scaled_rf_cubed.rb +0 -173
  20. data/exe/stack_nolhs.rb +0 -174
  21. data/lib/datafarming/factorial_generator.rb +0 -49
data/DESCRIPTIONS.html DELETED
@@ -1,1107 +0,0 @@
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- <!DOCTYPE html>
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- <html>
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- <head>
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- <title>DESCRIPTIONS</title>
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273
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303
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324
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327
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331
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332
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333
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334
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338
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345
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346
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347
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348
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349
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350
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351
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352
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353
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354
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355
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356
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357
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358
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359
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360
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361
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362
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363
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364
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365
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366
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367
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368
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369
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370
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371
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372
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373
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374
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375
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376
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377
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378
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379
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380
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381
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382
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383
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384
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385
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386
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387
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388
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389
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390
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391
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392
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393
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394
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395
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396
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397
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398
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399
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400
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401
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402
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403
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404
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405
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406
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407
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408
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409
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410
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411
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412
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413
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414
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418
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419
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435
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471
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484
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498
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526
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527
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528
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529
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531
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534
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536
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537
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538
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539
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541
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544
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545
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546
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551
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552
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553
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554
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555
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556
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557
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558
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559
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560
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561
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562
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563
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564
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565
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566
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567
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568
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569
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570
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571
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572
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573
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574
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575
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576
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577
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578
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579
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580
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581
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583
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586
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589
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591
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592
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595
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596
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599
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600
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601
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603
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606
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608
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611
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612
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614
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615
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618
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619
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621
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622
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623
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625
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626
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627
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628
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629
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630
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631
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632
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633
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634
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635
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636
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637
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639
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640
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641
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642
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643
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644
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645
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646
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647
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648
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649
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650
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652
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653
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654
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655
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656
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657
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658
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659
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661
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662
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664
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666
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667
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668
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669
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670
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671
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672
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673
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674
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676
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677
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679
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680
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681
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682
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683
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684
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685
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686
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687
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688
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689
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690
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691
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692
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693
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694
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695
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696
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697
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698
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700
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701
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702
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703
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704
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707
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710
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712
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721
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724
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725
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728
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729
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731
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732
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733
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734
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735
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736
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737
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738
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740
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741
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742
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743
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744
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745
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746
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747
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748
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749
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750
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751
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752
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753
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754
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755
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756
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757
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758
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759
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760
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761
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762
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763
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764
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765
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768
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769
- }
770
- .syntax--entity.syntax--other.syntax--attribute-name.syntax--pseudo-element {
771
- color: #C792EA;
772
- }
773
- .syntax--entity.syntax--other.syntax--attribute-name.syntax--attribute {
774
- color: #C792EA;
775
- }
776
- .syntax--entity.syntax--name.syntax--class,
777
- .syntax--entity.syntax--name.syntax--type.syntax--class {
778
- color: #FFCB6B;
779
- }
780
- .syntax--entity.syntax--name.syntax--section {
781
- color: #82AAFF;
782
- }
783
- .syntax--entity.syntax--name.syntax--tag {
784
- color: #F07178;
785
- }
786
- .syntax--entity.syntax--other.syntax--attribute-name {
787
- color: #FFCB6B;
788
- }
789
- .syntax--meta.syntax--class {
790
- color: #FFE082;
791
- }
792
- .syntax--meta.syntax--delimiter.syntax--period {
793
- color: #89DDF3;
794
- }
795
- .syntax--meta.syntax--link {
796
- color: #FFCB6B;
797
- }
798
- .syntax--meta.syntax--require {
799
- color: #82AAFF;
800
- }
801
- .syntax--meta.syntax--selector {
802
- color: #C792EA;
803
- }
804
- .syntax--meta.syntax--separator {
805
- background-color: #373b41;
806
- color: #EEFFFF;
807
- }
808
- .syntax--meta.syntax--brace.syntax--round,
809
- .syntax--meta.syntax--brace.syntax--square {
810
- color: #89DDF3;
811
- }
812
- .syntax--none {
813
- color: #EEFFFF;
814
- }
815
- .syntax--markup.syntax--bold {
816
- color: #FFCB6B;
817
- font-weight: bold;
818
- }
819
- .syntax--markup.syntax--changed {
820
- color: #C792EA;
821
- }
822
- .syntax--markup.syntax--deleted {
823
- color: #F07178;
824
- }
825
- .syntax--markup.syntax--italic {
826
- color: #C792EA;
827
- font-style: italic;
828
- }
829
- .syntax--markup.syntax--heading .syntax--punctuation.syntax--definition.syntax--heading {
830
- color: #82AAFF;
831
- }
832
- .syntax--markup.syntax--inserted {
833
- color: #C3E88D;
834
- }
835
- .syntax--markup.syntax--list {
836
- color: #F07178;
837
- }
838
- .syntax--markup.syntax--quote {
839
- color: #FFCB6B;
840
- }
841
- .syntax--markup.syntax--raw.syntax--inline {
842
- color: #C3E88D;
843
- }
844
- .syntax--source.syntax--gfm .syntax--markup {
845
- -webkit-font-smoothing: auto;
846
- }
847
- .syntax--source.syntax--gfm .syntax--markup.syntax--heading {
848
- color: #C3E88D;
849
- }
850
- pre.editor-colors[mini] .scroll-view {
851
- padding-left: 1px;
852
- }
853
- pre.editor-colors .highlight .region.bracket-matcher {
854
- z-index: inherit;
855
- }
856
- .bracket-matcher .region {
857
- border-bottom: 1px solid #009688;
858
- box-sizing: border-box;
859
- background-color: rgba(238, 255, 255, 0.1);
860
- box-shadow: inset 0 -1px 0 #009688;
861
- }
862
- pre.editor-colors .spell-check-misspelling .region {
863
- z-index: auto;
864
- }
865
- .syntax--jsx.syntax--component {
866
- color: #F07178;
867
- }
868
- pre.editor-colors .syntax--source.syntax--js.syntax--jsx .syntax--jsx .syntax--entity.syntax--other.syntax--attribute-name {
869
- font-style: normal;
870
- }
871
- .syntax--css .syntax--support.syntax--constant {
872
- color: #89DDF3;
873
- }
874
- .syntax--css .syntax--support.syntax--property-name {
875
- color: #73d1c8;
876
- }
877
- .syntax--css .syntax--keyword.syntax--unit {
878
- color: #F78C6A;
879
- }
880
- .syntax--css .syntax--constant.syntax--numeric {
881
- color: #FFE082;
882
- }
883
- .syntax--css .syntax--constant.syntax--color {
884
- color: #FFE082;
885
- }
886
- .syntax--css .syntax--constant.syntax--color .syntax--punctuation {
887
- color: currentColor;
888
- }
889
- .syntax--css .syntax--entity.syntax--tag {
890
- color: #B2CCD6;
891
- }
892
- .syntax--css .syntax--entity.syntax--id {
893
- color: #C792EA;
894
- }
895
- .syntax--css .syntax--punctuation.syntax--delimiter {
896
- color: #89DDF3;
897
- }
898
- .syntax--css .syntax--punctuation.syntax--delimiter + .syntax--constant.syntax--numeric:not(.syntax--color) {
899
- color: #F78C6A;
900
- }
901
- [data-grammar*="gfm"] .syntax--markup.syntax--underline.syntax--link {
902
- color: #ff869a;
903
- }
904
- [data-grammar*="gfm"] .syntax--markup.syntax--underline.syntax--link span.syntax--punctuation {
905
- color: #FF5370;
906
- }
907
- [data-grammar*="gfm"] .syntax--markup.syntax--strike {
908
- position: relative;
909
- color: rgba(238, 255, 255, 0.5);
910
- }
911
- [data-grammar*="gfm"] .syntax--markup.syntax--strike::after {
912
- content: "";
913
- position: absolute;
914
- top: calc(54%);
915
- left: 0;
916
- right: 0;
917
- height: 1px;
918
- background-color: rgba(238, 255, 255, 0.5);
919
- }
920
- [data-grammar*="gfm"] .syntax--table .syntax--border {
921
- color: rgba(238, 255, 255, 0.5);
922
- }
923
- [data-grammar*="gfm"] .syntax--markup.syntax--heading {
924
- color: #82AAFF;
925
- }
926
- [data-grammar*="gfm"] .syntax--punctuation.syntax--definition.syntax--begin,
927
- [data-grammar*="gfm"] .syntax--punctuation.syntax--definition.syntax--end {
928
- color: #82AAFF;
929
- }
930
- [data-grammar*="gfm"] .syntax--punctuation.syntax--definition.syntax--begin + span:not(.syntax--function.syntax--parameter) {
931
- color: #9cbbff;
932
- }
933
- .syntax--html .syntax--meta.syntax--tag.syntax--doctype,
934
- .syntax--jsx .syntax--meta.syntax--tag.syntax--doctype {
935
- color: #C792EA;
936
- }
937
- .syntax--html .syntax--punctuation.syntax--tag,
938
- .syntax--jsx .syntax--punctuation.syntax--tag {
939
- color: #89DDF3;
940
- }
941
- .syntax--js.syntax--constant {
942
- color: #EEFFFF;
943
- }
944
- .syntax--js.syntax--support.syntax--variable.syntax--property {
945
- color: #EEFFFF;
946
- }
947
- .syntax--js.syntax--support.syntax--variable.syntax--property.syntax--dom {
948
- color: #82AAFF;
949
- }
950
- .syntax--js.syntax--entity.syntax--name.syntax--type {
951
- color: #FFCB6B;
952
- }
953
- .syntax--js.syntax--variable.syntax--property {
954
- color: #82AAFF;
955
- }
956
- .syntax--js.syntax--variable.syntax--other.syntax--object {
957
- color: #EEFFFF;
958
- }
959
- .syntax--js.syntax--variable.syntax--other.syntax--object.syntax--property {
960
- color: #82AAFF;
961
- }
962
- .syntax--js.syntax--string.syntax--quoted.syntax--template .syntax--other.syntax--object.syntax--property {
963
- color: #C3E88D;
964
- }
965
- .syntax--js.syntax--constant.syntax--numeric {
966
- color: #F78C6A;
967
- }
968
- .syntax--js.syntax--constant.syntax--boolean {
969
- color: #F07178;
970
- }
971
- .syntax--js.syntax--punctuation.syntax--begin,
972
- .syntax--js.syntax--punctuation.syntax--end,
973
- .syntax--js.syntax--delimiter.syntax--object.syntax--comma,
974
- .syntax--js.syntax--brace.syntax--curly {
975
- color: #89DDF3;
976
- }
977
- .syntax--comment .syntax--js.syntax--punctuation.syntax--begin,
978
- .syntax--comment .syntax--js.syntax--punctuation.syntax--end,
979
- .syntax--comment .syntax--js.syntax--delimiter.syntax--object.syntax--comma,
980
- .syntax--comment .syntax--js.syntax--brace.syntax--curly {
981
- color: #4f6875;
982
- }
983
- .syntax--js.syntax--export .syntax--variable.syntax--default {
984
- color: #C792EA;
985
- }
986
- .syntax--json .syntax--meta.syntax--array.syntax--structure .syntax--string.syntax--quoted.syntax--double {
987
- color: #C3E88D;
988
- }
989
- .syntax--json .syntax--meta.syntax--array.syntax--structure .syntax--string.syntax--quoted.syntax--double > * {
990
- color: currentColor;
991
- }
992
- .syntax--json .syntax--meta.syntax--array.syntax--structure .syntax--string.syntax--quoted.syntax--double > *.syntax--punctuation.syntax--begin,
993
- .syntax--json .syntax--meta.syntax--array.syntax--structure .syntax--string.syntax--quoted.syntax--double > *.syntax--punctuation.syntax--end {
994
- color: #89DDF3;
995
- }
996
- .syntax--json .syntax--meta .syntax--punctuation.syntax--separator.syntax--key-value + .syntax--string.syntax--quoted {
997
- color: #C3E88D;
998
- }
999
- .syntax--json .syntax--meta .syntax--punctuation.syntax--separator.syntax--key-value + .syntax--string.syntax--quoted * {
1000
- color: currentColor;
1001
- }
1002
- .syntax--json .syntax--meta .syntax--punctuation.syntax--separator.syntax--key-value + .syntax--string.syntax--quoted *.syntax--punctuation.syntax--begin,
1003
- .syntax--json .syntax--meta .syntax--punctuation.syntax--separator.syntax--key-value + .syntax--string.syntax--quoted *.syntax--punctuation.syntax--end {
1004
- color: #89DDF3;
1005
- }
1006
- .syntax--json .syntax--meta.syntax--structure.syntax--dictionary .syntax--string.syntax--quoted {
1007
- color: #C792EA;
1008
- }
1009
- .syntax--json .syntax--meta.syntax--structure.syntax--dictionary .syntax--string.syntax--quoted .syntax--punctuation.syntax--string {
1010
- color: currentColor;
1011
- }
1012
- .syntax--php.syntax--keyword.syntax--operator.syntax--assignment {
1013
- color: #C792EA;
1014
- }
1015
- .syntax--php.syntax--meta.syntax--object {
1016
- color: #82AAFF;
1017
- }
1018
- .syntax--php.syntax--meta.syntax--arguments {
1019
- color: #C792EA;
1020
- }
1021
- .syntax--python .syntax--meta.syntax--function-call {
1022
- color: #82AAFF;
1023
- }
1024
- .syntax--python .syntax--meta.syntax--function-call .syntax--punctuation {
1025
- color: #89DDF3;
1026
- }
1027
- .syntax--python .syntax--meta.syntax--function-call .syntax--arguments {
1028
- color: #7986CB;
1029
- }
1030
- .syntax--python .syntax--meta.syntax--function-call .syntax--arguments.syntax--punctuation {
1031
- color: #89DDF3;
1032
- }
1033
- .syntax--python .syntax--variable.syntax--self {
1034
- color: #FF5370;
1035
- }
1036
- .syntax--python .syntax--meta .syntax--punctuation.syntax--inheritance,
1037
- .syntax--python .syntax--meta .syntax--punctuation.syntax--section {
1038
- color: #89DDF3;
1039
- }
1040
- .syntax--python .syntax--variable.syntax--parameter {
1041
- color: #89DDF3;
1042
- }
1043
- .syntax--python .syntax--keyword.syntax--operator {
1044
- color: #C792EA;
1045
- }
1046
- .syntax--ruby .syntax--punctuation.syntax--separator {
1047
- color: #89DDF3;
1048
- }
1049
- .syntax--ruby .syntax--variable.syntax--block {
1050
- color: #F07178;
1051
- }
1052
- .syntax--ruby .syntax--variable.syntax--instance {
1053
- color: #F07178;
1054
- }
1055
- .syntax--ruby .syntax--variable.syntax--instance .syntax--punctuation {
1056
- color: currentColor;
1057
- }
1058
- </style>
1059
- </head>
1060
- <body class='markdown-preview' data-use-github-style><h4 id="command-line-tools">COMMAND-LINE TOOLS</h4>
1061
- <p>Ruby is a powerful and concise object-oriented scripting language. Scripts are normally run from a command-line or terminal environment by typing the <code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">ruby</code> command followed by a script name, often followed by one or more command-line arguments. However, scripts installed as gems do not need the <code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">ruby</code> command to be typed explicitly. For example, typing <code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">stripheaderdups.rb my_file.txt</code> will invoke the <code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">stripheaderdups.rb</code> script and apply it to file <code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">my_file.txt</code> in your current working directory. Note that on Windows the <code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">.rb</code> suffix is not needed to run your scripts, e.g., <code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">stripheaderdups my_file.txt</code> will suffice.</p>
1062
- <p>All scripts in this distribution are self documenting if run with a <code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">--help</code>, <code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">-h</code>, or <code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">-?</code> option. Quick descriptions follow.</p>
1063
- <h4 id="data-manipulation">DATA MANIPULATION</h4>
1064
- <ul>
1065
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">blank2csv.rb</code> —
1066
- convert whitespace-delimited files to Comma Separated Values (CSV) files</li>
1067
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">cat.rb</code> —
1068
- Unix <code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">cat</code> program work-alike for Windows—for viewing or creating text files or concatenating multiple files, based on stdio</li>
1069
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">convert_line_endings.rb</code> —
1070
- convert text files (including CSV files) to your current operating system environment (e.g., DOS to Unix or Unix to DOS)</li>
1071
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">csv2blank.rb</code> —
1072
- convert CSV files to whitespace-delimited files</li>
1073
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">pool_files.rb</code> —
1074
- pool columns from separate files into a new file, useful for combining design file &amp; output files or multiple output files</li>
1075
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">stripheaders.rb</code>, <code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">stripheaderdups.rb</code> —
1076
- remove column headers from a file, or duplicate headers within a file, respectively</li>
1077
- </ul>
1078
- <h4 id="design-generators">DESIGN GENERATORS</h4>
1079
- <ul>
1080
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">augment_design.rb</code> —
1081
- generate star points to augment an already existing factorial design</li>
1082
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">cross.rb</code> —
1083
- create a combinatorial design by crossing all combinations of any # of individual smaller designs</li>
1084
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">scaled_fde.rb</code> —
1085
- generate fully orthogonal quadratic designs based on discrete Fourier frequencies, with factor scaling</li>
1086
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">scaled_rf_cubed.rb</code> —
1087
- generate 2-level Resolution V fractional factorial designs and Central Composite Designs (CCDs), with factor scaling</li>
1088
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">stack_nolhs.rb</code> —
1089
- generate designs by reassigning columns from pre-tabled NOLHs, with factor scaling, for up to 100 factors</li>
1090
- </ul>
1091
- <h4 id="run-control">RUN CONTROL</h4>
1092
- <ul>
1093
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">batchrunner.rb</code> —
1094
- run a model interactively with replication</li>
1095
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">rundesign_general.rb</code> —
1096
- run control to replicate a designed experiment applied to a model</li>
1097
- </ul>
1098
- <h4 id="confidence-intervals-for-time-series">CONFIDENCE INTERVALS FOR TIME SERIES</h4>
1099
- <ul>
1100
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">mser.rb</code> —
1101
- use MSER truncation to remove initial transient effects for time-series output, reporting truncated average and number of observations for each run to facilitate construction of a properly weighted confidence interval.</li>
1102
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">mser_nolbm.rb</code> —
1103
- use MSER truncation to remove initial transient effects for time-series output, then calculate a 95% confidence interval on the remaining data using non-overlapping batch means.</li>
1104
- <li><code style="font-family: Menlo, Consolas, &quot;DejaVu Sans Mono&quot;, monospace;">mser_olbm.rb</code> —
1105
- use MSER truncation to remove initial transient effects for time-series output, then calculate a 95% confidence interval on the remaining data using overlapping batch means.</li>
1106
- </ul></body>
1107
- </html>