as.data.frame.kdetrees: Convert kdetrees object to data.frame
In kdetrees: Nonparametric method for identifying discordant phylogenetic trees
Description
Usage
Arguments
Value
Author(s)
Examples
Description
Converts a kdetrees object to a data.frame suitable for saving as
output. It contains the density estimates for each tree, a Boolean
value indicating if the tree was selected as an outlier, and
optionally the newick string corresponding to the tree.
Usage
1
2
## S3 method for class 'kdetrees'
as.data.frame(x, row.names, optional, trees = NULL, ...)
Arguments
x
kdetrees object to be converted
row.names
ignored
optional
ignored
trees
If given the original list of trees, will convert to
newick and add a column to the output
...
unused
Value
a data.frame
Author(s)
Grady Weyenberg
Examples
1
2
result <- kdetrees(apicomplexa)
as.data.frame(result)
Example output
density outlier
457.tre 100.6815592 FALSE
458.tre 61.4589835 FALSE
459.tre 100.5284096 FALSE
460.tre 95.4116339 FALSE
461.tre 92.5330682 FALSE
462.tre 106.1323081 FALSE
463.tre 44.3366766 FALSE
464.tre 110.4847943 FALSE
466.tre 87.1344328 FALSE
467.tre 99.7250559 FALSE
468.tre 65.0511726 FALSE
470.tre 95.7676477 FALSE
471.tre 35.6669431 FALSE
472.tre 34.1649735 FALSE
474.tre 73.3627993 FALSE
475.tre 89.8177786 FALSE
476.tre 101.5971551 FALSE
477.tre 87.6910994 FALSE
478.tre 52.4652583 FALSE
479.tre 86.7123820 FALSE
480.tre 94.7815063 FALSE
481.tre 94.1967610 FALSE
482.tre 34.9675917 FALSE
483.tre 85.9213913 FALSE
485.tre 53.8423933 FALSE
486.tre 100.3801383 FALSE
487.tre 68.5444764 FALSE
488.tre 13.6771954 TRUE
489.tre 24.6531206 FALSE
490.tre 85.8695049 FALSE
491.tre 99.9126119 FALSE
492.tre 78.6112114 FALSE
493.tre 89.0152096 FALSE
495.tre 81.3041651 FALSE
496.tre 86.1480207 FALSE
497.tre 0.9963762 TRUE
499.tre 88.5657491 FALSE
500.tre 54.7665659 FALSE
502.tre 66.5809850 FALSE
503.tre 98.8779857 FALSE
504.tre 78.9559326 FALSE
505.tre 58.9012020 FALSE
506.tre 81.7785399 FALSE
507.tre 70.3671678 FALSE
508.tre 84.4043904 FALSE
509.tre 89.7489805 FALSE
510.tre 71.5348209 FALSE
511.tre 77.8473961 FALSE
512.tre 98.0762836 FALSE
513.tre 100.2457023 FALSE
515.tre 0.9962957 TRUE
516.tre 65.9064966 FALSE
517.tre 84.3107652 FALSE
518.tre 93.7481223 FALSE
519.tre 94.8433065 FALSE
520.tre 92.6928206 FALSE
521.tre 91.2340212 FALSE
523.tre 99.4589229 FALSE
524.tre 78.0884662 FALSE
525.tre 95.3259579 FALSE
526.tre 86.4087178 FALSE
527.tre 65.4416155 FALSE
528.tre 76.7279591 FALSE
529.tre 70.5288986 FALSE
530.tre 96.2826312 FALSE
531.tre 94.8241391 FALSE
534.tre 93.5056666 FALSE
535.tre 80.1978217 FALSE
536.tre 93.8016197 FALSE
537.tre 96.3502529 FALSE
538.tre 106.5880329 FALSE
539.tre 53.3835800 FALSE
540.tre 106.3665938 FALSE
541.tre 94.0580906 FALSE
542.tre 94.4461847 FALSE
543.tre 97.3529546 FALSE
544.tre 82.5242257 FALSE
545.tre 90.8305415 FALSE
546.tre 1.0017186 TRUE
547.tre 0.9963805 TRUE
549.tre 97.3785361 FALSE
550.tre 98.6693569 FALSE
551.tre 91.2176257 FALSE
552.tre 107.9340480 FALSE
553.tre 63.4652168 FALSE
554.tre 90.7095582 FALSE
555.tre 97.1893301 FALSE
556.tre 93.9001906 FALSE
557.tre 88.8456664 FALSE
558.tre 27.1180371 FALSE
559.tre 97.7428758 FALSE
562.tre 96.0413900 FALSE
563.tre 50.1664166 FALSE
565.tre 100.9667419 FALSE
566.tre 102.0648816 FALSE
568.tre 62.3865805 FALSE
569.tre 64.2613231 FALSE
570.tre 80.0012859 FALSE
571.tre 72.8114438 FALSE
573.tre 53.2684582 FALSE
574.tre 65.7408463 FALSE
575.tre 93.1400594 FALSE
577.tre 109.7846239 FALSE
578.tre 26.4758642 FALSE
579.tre 48.4307392 FALSE
580.tre 100.4474024 FALSE
581.tre 56.3108062 FALSE
582.tre 80.7786217 FALSE
583.tre 80.2125031 FALSE
584.tre 89.6262907 FALSE
585.tre 56.0867532 FALSE
587.tre 79.2498699 FALSE
588.tre 65.2576381 FALSE
589.tre 90.5782183 FALSE
590.tre 79.9815780 FALSE
591.tre 74.9296210 FALSE
592.tre 74.0018752 FALSE
594.tre 105.5769891 FALSE
595.tre 80.4979103 FALSE
596.tre 93.5370726 FALSE
597.tre 82.0564078 FALSE
598.tre 84.5657803 FALSE
599.tre 99.1193575 FALSE
600.tre 102.5182229 FALSE
601.tre 84.6417960 FALSE
602.tre 33.1315894 FALSE
603.tre 98.6246903 FALSE
604.tre 97.9404625 FALSE
605.tre 93.3196378 FALSE
607.tre 78.5403891 FALSE
608.tre 58.9009217 FALSE
609.tre 89.0358059 FALSE
610.tre 60.3001177 FALSE
612.tre 70.2619543 FALSE
613.tre 78.1239264 FALSE
614.tre 108.6750817 FALSE
615.tre 62.0430593 FALSE
616.tre 74.0826654 FALSE
617.tre 80.9410265 FALSE
618.tre 85.2206483 FALSE
619.tre 97.0279862 FALSE
620.tre 79.2352205 FALSE
621.tre 92.9694887 FALSE
622.tre 98.5463288 FALSE
623.tre 88.8554030 FALSE
625.tre 75.2946965 FALSE
626.tre 72.9140212 FALSE
627.tre 96.5584500 FALSE
628.tre 86.3507066 FALSE
630.tre 62.0880670 FALSE
631.tre 78.1256244 FALSE
632.tre 41.3759152 FALSE
633.tre 43.3769362 FALSE
634.tre 97.8583941 FALSE
635.tre 94.0354616 FALSE
637.tre 71.9680175 FALSE
638.tre 81.2073474 FALSE
639.tre 99.8243293 FALSE
640.tre 81.8164549 FALSE
641.tre 7.3614018 TRUE
642.tre 70.4815808 FALSE
644.tre 84.2153377 FALSE
645.tre 65.4246024 FALSE
646.tre 98.3965522 FALSE
648.tre 48.5335762 FALSE
649.tre 89.8216582 FALSE
650.tre 86.5843783 FALSE
651.tre 76.9742439 FALSE
652.tre 89.8739493 FALSE
653.tre 44.0862684 FALSE
654.tre 77.4033451 FALSE
655.tre 101.4740445 FALSE
656.tre 84.5291497 FALSE
657.tre 57.7891209 FALSE
659.tre 101.9977450 FALSE
660.tre 4.4693869 TRUE
662.tre 1.0017483 TRUE
663.tre 75.9670289 FALSE
664.tre 80.3441302 FALSE
667.tre 55.1864362 FALSE
668.tre 48.1960461 FALSE
671.tre 82.8290244 FALSE
672.tre 94.1621150 FALSE
674.tre 63.9776388 FALSE
675.tre 95.8801197 FALSE
677.tre 73.6903343 FALSE
678.tre 103.3664019 FALSE
680.tre 60.3853297 FALSE
682.tre 93.3171811 FALSE
683.tre 76.9592712 FALSE
684.tre 62.4199586 FALSE
685.tre 49.9025168 FALSE
686.tre 72.9818236 FALSE
687.tre 102.6789892 FALSE
689.tre 99.6223200 FALSE
690.tre 40.4675155 FALSE
691.tre 105.8747955 FALSE
693.tre 94.0316581 FALSE
694.tre 72.1610415 FALSE
695.tre 94.0358985 FALSE
696.tre 99.2329732 FALSE
699.tre 86.9108587 FALSE
700.tre 61.3291444 FALSE
701.tre 63.4926128 FALSE
702.tre 96.4202860 FALSE
703.tre 78.0784036 FALSE
704.tre 95.4957866 FALSE
705.tre 96.5862220 FALSE
706.tre 85.3225659 FALSE
708.tre 83.5969107 FALSE
709.tre 99.0745255 FALSE
712.tre 97.3916977 FALSE
713.tre 94.1414403 FALSE
714.tre 69.6456036 FALSE
716.tre 54.8717534 FALSE
718.tre 42.7655069 FALSE
720.tre 60.4456974 FALSE
722.tre 72.3580435 FALSE
723.tre 84.3458695 FALSE
725.tre 67.3677181 FALSE
726.tre 97.3928192 FALSE
727.tre 102.2379489 FALSE
728.tre 1.0017574 TRUE
730.tre 68.6410426 FALSE
731.tre 89.2071592 FALSE
732.tre 79.9019242 FALSE
733.tre 96.2014973 FALSE
734.tre 93.1308572 FALSE
735.tre 98.8445744 FALSE
738.tre 114.5457898 FALSE
739.tre 66.0109124 FALSE
740.tre 84.7464990 FALSE
741.tre 77.5421615 FALSE
742.tre 76.6563663 FALSE
743.tre 58.4212036 FALSE
744.tre 101.6924449 FALSE
745.tre 59.3812182 FALSE
746.tre 82.7571152 FALSE
747.tre 1.0016920 TRUE
748.tre 90.8141387 FALSE
749.tre 86.4547070 FALSE
750.tre 60.4247890 FALSE
755.tre 89.3958795 FALSE
756.tre 56.8065199 FALSE
757.tre 74.7978171 FALSE
758.tre 90.5862014 FALSE
759.tre 52.4949066 FALSE
760.tre 74.7578842 FALSE
761.tre 105.4226543 FALSE
762.tre 71.3106746 FALSE
763.tre 56.9534066 FALSE
764.tre 93.3402361 FALSE
765.tre 74.7102624 FALSE
766.tre 53.9822681 FALSE
767.tre 77.4971791 FALSE
768.tre 79.4696790 FALSE
769.tre 93.6356323 FALSE
770.tre 66.8506088 FALSE
773.tre 1.0016828 TRUE
774.tre 78.0690226 FALSE
775.tre 106.1678559 FALSE
776.tre 82.1553072 FALSE
777.tre 85.4292220 FALSE
778.tre 75.6841545 FALSE
779.tre 86.6809660 FALSE
780.tre 0.9964220 TRUE
783.tre 94.6350376 FALSE
784.tre 67.3916358 FALSE
kdetrees documentation built on May 1, 2019, 9:35 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Author(s) Examples
Description
Converts a kdetrees object to a data.frame suitable for saving as output. It contains the density estimates for each tree, a Boolean value indicating if the tree was selected as an outlier, and optionally the newick string corresponding to the tree.
Usage
1 2 | ## S3 method for class 'kdetrees'
as.data.frame(x, row.names, optional, trees = NULL, ...)
|
Arguments
x |
kdetrees object to be converted |
row.names |
ignored |
optional |
ignored |
trees |
If given the original list of trees, will convert to newick and add a column to the output |
... |
unused |
Value
a data.frame
Author(s)
Grady Weyenberg
Examples
1 2 | result <- kdetrees(apicomplexa)
as.data.frame(result)
|
Example output
density outlier
457.tre 100.6815592 FALSE
458.tre 61.4589835 FALSE
459.tre 100.5284096 FALSE
460.tre 95.4116339 FALSE
461.tre 92.5330682 FALSE
462.tre 106.1323081 FALSE
463.tre 44.3366766 FALSE
464.tre 110.4847943 FALSE
466.tre 87.1344328 FALSE
467.tre 99.7250559 FALSE
468.tre 65.0511726 FALSE
470.tre 95.7676477 FALSE
471.tre 35.6669431 FALSE
472.tre 34.1649735 FALSE
474.tre 73.3627993 FALSE
475.tre 89.8177786 FALSE
476.tre 101.5971551 FALSE
477.tre 87.6910994 FALSE
478.tre 52.4652583 FALSE
479.tre 86.7123820 FALSE
480.tre 94.7815063 FALSE
481.tre 94.1967610 FALSE
482.tre 34.9675917 FALSE
483.tre 85.9213913 FALSE
485.tre 53.8423933 FALSE
486.tre 100.3801383 FALSE
487.tre 68.5444764 FALSE
488.tre 13.6771954 TRUE
489.tre 24.6531206 FALSE
490.tre 85.8695049 FALSE
491.tre 99.9126119 FALSE
492.tre 78.6112114 FALSE
493.tre 89.0152096 FALSE
495.tre 81.3041651 FALSE
496.tre 86.1480207 FALSE
497.tre 0.9963762 TRUE
499.tre 88.5657491 FALSE
500.tre 54.7665659 FALSE
502.tre 66.5809850 FALSE
503.tre 98.8779857 FALSE
504.tre 78.9559326 FALSE
505.tre 58.9012020 FALSE
506.tre 81.7785399 FALSE
507.tre 70.3671678 FALSE
508.tre 84.4043904 FALSE
509.tre 89.7489805 FALSE
510.tre 71.5348209 FALSE
511.tre 77.8473961 FALSE
512.tre 98.0762836 FALSE
513.tre 100.2457023 FALSE
515.tre 0.9962957 TRUE
516.tre 65.9064966 FALSE
517.tre 84.3107652 FALSE
518.tre 93.7481223 FALSE
519.tre 94.8433065 FALSE
520.tre 92.6928206 FALSE
521.tre 91.2340212 FALSE
523.tre 99.4589229 FALSE
524.tre 78.0884662 FALSE
525.tre 95.3259579 FALSE
526.tre 86.4087178 FALSE
527.tre 65.4416155 FALSE
528.tre 76.7279591 FALSE
529.tre 70.5288986 FALSE
530.tre 96.2826312 FALSE
531.tre 94.8241391 FALSE
534.tre 93.5056666 FALSE
535.tre 80.1978217 FALSE
536.tre 93.8016197 FALSE
537.tre 96.3502529 FALSE
538.tre 106.5880329 FALSE
539.tre 53.3835800 FALSE
540.tre 106.3665938 FALSE
541.tre 94.0580906 FALSE
542.tre 94.4461847 FALSE
543.tre 97.3529546 FALSE
544.tre 82.5242257 FALSE
545.tre 90.8305415 FALSE
546.tre 1.0017186 TRUE
547.tre 0.9963805 TRUE
549.tre 97.3785361 FALSE
550.tre 98.6693569 FALSE
551.tre 91.2176257 FALSE
552.tre 107.9340480 FALSE
553.tre 63.4652168 FALSE
554.tre 90.7095582 FALSE
555.tre 97.1893301 FALSE
556.tre 93.9001906 FALSE
557.tre 88.8456664 FALSE
558.tre 27.1180371 FALSE
559.tre 97.7428758 FALSE
562.tre 96.0413900 FALSE
563.tre 50.1664166 FALSE
565.tre 100.9667419 FALSE
566.tre 102.0648816 FALSE
568.tre 62.3865805 FALSE
569.tre 64.2613231 FALSE
570.tre 80.0012859 FALSE
571.tre 72.8114438 FALSE
573.tre 53.2684582 FALSE
574.tre 65.7408463 FALSE
575.tre 93.1400594 FALSE
577.tre 109.7846239 FALSE
578.tre 26.4758642 FALSE
579.tre 48.4307392 FALSE
580.tre 100.4474024 FALSE
581.tre 56.3108062 FALSE
582.tre 80.7786217 FALSE
583.tre 80.2125031 FALSE
584.tre 89.6262907 FALSE
585.tre 56.0867532 FALSE
587.tre 79.2498699 FALSE
588.tre 65.2576381 FALSE
589.tre 90.5782183 FALSE
590.tre 79.9815780 FALSE
591.tre 74.9296210 FALSE
592.tre 74.0018752 FALSE
594.tre 105.5769891 FALSE
595.tre 80.4979103 FALSE
596.tre 93.5370726 FALSE
597.tre 82.0564078 FALSE
598.tre 84.5657803 FALSE
599.tre 99.1193575 FALSE
600.tre 102.5182229 FALSE
601.tre 84.6417960 FALSE
602.tre 33.1315894 FALSE
603.tre 98.6246903 FALSE
604.tre 97.9404625 FALSE
605.tre 93.3196378 FALSE
607.tre 78.5403891 FALSE
608.tre 58.9009217 FALSE
609.tre 89.0358059 FALSE
610.tre 60.3001177 FALSE
612.tre 70.2619543 FALSE
613.tre 78.1239264 FALSE
614.tre 108.6750817 FALSE
615.tre 62.0430593 FALSE
616.tre 74.0826654 FALSE
617.tre 80.9410265 FALSE
618.tre 85.2206483 FALSE
619.tre 97.0279862 FALSE
620.tre 79.2352205 FALSE
621.tre 92.9694887 FALSE
622.tre 98.5463288 FALSE
623.tre 88.8554030 FALSE
625.tre 75.2946965 FALSE
626.tre 72.9140212 FALSE
627.tre 96.5584500 FALSE
628.tre 86.3507066 FALSE
630.tre 62.0880670 FALSE
631.tre 78.1256244 FALSE
632.tre 41.3759152 FALSE
633.tre 43.3769362 FALSE
634.tre 97.8583941 FALSE
635.tre 94.0354616 FALSE
637.tre 71.9680175 FALSE
638.tre 81.2073474 FALSE
639.tre 99.8243293 FALSE
640.tre 81.8164549 FALSE
641.tre 7.3614018 TRUE
642.tre 70.4815808 FALSE
644.tre 84.2153377 FALSE
645.tre 65.4246024 FALSE
646.tre 98.3965522 FALSE
648.tre 48.5335762 FALSE
649.tre 89.8216582 FALSE
650.tre 86.5843783 FALSE
651.tre 76.9742439 FALSE
652.tre 89.8739493 FALSE
653.tre 44.0862684 FALSE
654.tre 77.4033451 FALSE
655.tre 101.4740445 FALSE
656.tre 84.5291497 FALSE
657.tre 57.7891209 FALSE
659.tre 101.9977450 FALSE
660.tre 4.4693869 TRUE
662.tre 1.0017483 TRUE
663.tre 75.9670289 FALSE
664.tre 80.3441302 FALSE
667.tre 55.1864362 FALSE
668.tre 48.1960461 FALSE
671.tre 82.8290244 FALSE
672.tre 94.1621150 FALSE
674.tre 63.9776388 FALSE
675.tre 95.8801197 FALSE
677.tre 73.6903343 FALSE
678.tre 103.3664019 FALSE
680.tre 60.3853297 FALSE
682.tre 93.3171811 FALSE
683.tre 76.9592712 FALSE
684.tre 62.4199586 FALSE
685.tre 49.9025168 FALSE
686.tre 72.9818236 FALSE
687.tre 102.6789892 FALSE
689.tre 99.6223200 FALSE
690.tre 40.4675155 FALSE
691.tre 105.8747955 FALSE
693.tre 94.0316581 FALSE
694.tre 72.1610415 FALSE
695.tre 94.0358985 FALSE
696.tre 99.2329732 FALSE
699.tre 86.9108587 FALSE
700.tre 61.3291444 FALSE
701.tre 63.4926128 FALSE
702.tre 96.4202860 FALSE
703.tre 78.0784036 FALSE
704.tre 95.4957866 FALSE
705.tre 96.5862220 FALSE
706.tre 85.3225659 FALSE
708.tre 83.5969107 FALSE
709.tre 99.0745255 FALSE
712.tre 97.3916977 FALSE
713.tre 94.1414403 FALSE
714.tre 69.6456036 FALSE
716.tre 54.8717534 FALSE
718.tre 42.7655069 FALSE
720.tre 60.4456974 FALSE
722.tre 72.3580435 FALSE
723.tre 84.3458695 FALSE
725.tre 67.3677181 FALSE
726.tre 97.3928192 FALSE
727.tre 102.2379489 FALSE
728.tre 1.0017574 TRUE
730.tre 68.6410426 FALSE
731.tre 89.2071592 FALSE
732.tre 79.9019242 FALSE
733.tre 96.2014973 FALSE
734.tre 93.1308572 FALSE
735.tre 98.8445744 FALSE
738.tre 114.5457898 FALSE
739.tre 66.0109124 FALSE
740.tre 84.7464990 FALSE
741.tre 77.5421615 FALSE
742.tre 76.6563663 FALSE
743.tre 58.4212036 FALSE
744.tre 101.6924449 FALSE
745.tre 59.3812182 FALSE
746.tre 82.7571152 FALSE
747.tre 1.0016920 TRUE
748.tre 90.8141387 FALSE
749.tre 86.4547070 FALSE
750.tre 60.4247890 FALSE
755.tre 89.3958795 FALSE
756.tre 56.8065199 FALSE
757.tre 74.7978171 FALSE
758.tre 90.5862014 FALSE
759.tre 52.4949066 FALSE
760.tre 74.7578842 FALSE
761.tre 105.4226543 FALSE
762.tre 71.3106746 FALSE
763.tre 56.9534066 FALSE
764.tre 93.3402361 FALSE
765.tre 74.7102624 FALSE
766.tre 53.9822681 FALSE
767.tre 77.4971791 FALSE
768.tre 79.4696790 FALSE
769.tre 93.6356323 FALSE
770.tre 66.8506088 FALSE
773.tre 1.0016828 TRUE
774.tre 78.0690226 FALSE
775.tre 106.1678559 FALSE
776.tre 82.1553072 FALSE
777.tre 85.4292220 FALSE
778.tre 75.6841545 FALSE
779.tre 86.6809660 FALSE
780.tre 0.9964220 TRUE
783.tre 94.6350376 FALSE
784.tre 67.3916358 FALSE
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