boot.vc: Bootstrap confidence intervals for variance components

Description Usage Arguments Value References See Also Examples

Description

Provides a bootstrap confidence interval (over loci) for sums of the different variance components (equivalent to gene diversity estimates at the different levels), and the derived F-statistics, as suggested by Weir and Cockerham (1984). Will not run with less than 5 loci. Raymond and Rousset (199X) points out shortcomings of this method.

Usage

1
boot.vc(levels=levels,loci=loci,diploid=TRUE,nboot=1000,quant=c(0.025,0.5,0.975))

Arguments

levels

a data frame containing the different levels (factors) from the outermost (e.g. region) to the innermost before the individual

loci

a data frame containing the different loci

diploid

Specify whether the data are coming from diploid or haploid organisms (diploid is the default)

nboot

Specify the number of bootstrap to carry out. Default is 1000

quant

Specify which quantile to produce. Default is c(0.025,0.5,0.975) giving the percentile 95% CI and the median

Value

boot

a data frame with the bootstrapped variance components. Could be used for obtaining bootstrap ci of statistics not listed here.

res

a data frame with the bootstrap derived statistics. H stands for gene diversity, F for F-statistics

ci

Confidence interval for each statistic.

References

Raymond M and Rousset F, 1995. An exact test for population differentiation. Evolution. 49:1280-1283

Weir, B.S. (1996) Genetic Data Analysis II. Sinauer Associates.

Weir BS and Cockerham CC, 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370.

See Also

varcomp.glob.

Examples

1
2
3
#load data set
data(gtrunchier)
boot.vc(gtrunchier[,c(1:2)],gtrunchier[,-c(1:2)],nboot=100)

Example output

$boot
    Locality  Patch    Ind  Error
1     2.3274 0.5823 1.2018 0.3886
2     2.4596 0.4532 1.0673 0.3979
3     2.3985 0.6631 1.5619 0.3896
4     2.3533 0.5629 1.1633 0.4106
5     2.5524 0.4313 1.1588 0.3779
6     2.0887 0.7496 1.3843 0.4149
7     1.9655 0.7577 1.1619 0.4103
8     2.4339 0.3509 0.9968 0.3582
9     2.1161 0.5596 0.9725 0.3775
10    2.4686 0.5553 1.4301 0.3916
11    2.3240 0.6160 1.4155 0.3675
12    2.5220 0.3459 0.9798 0.3761
13    2.4201 0.5246 1.2692 0.3801
14    2.3819 0.4755 1.1586 0.3432
15    2.1827 0.6072 1.1632 0.3759
16    2.4780 0.3484 0.9883 0.3672
17    2.3196 0.5828 1.2461 0.3650
18    2.0719 0.6479 1.0659 0.3975
19    2.2572 0.6901 1.3336 0.3867
20    2.5006 0.4343 1.2116 0.3453
21    1.8469 0.8348 1.1329 0.3969
22    2.3500 0.6324 1.4011 0.3781
23    2.3455 0.5634 1.2077 0.3870
24    2.4596 0.4532 1.0673 0.3979
25    2.1023 0.6975 1.2208 0.4107
26    2.2270 0.5188 1.0698 0.3559
27    2.5750 0.4814 1.3580 0.3674
28    2.3533 0.5629 1.1633 0.4106
29    2.6148 0.3240 1.0712 0.3562
30    2.1646 0.5903 1.1333 0.3890
31    2.2313 0.6737 1.3481 0.3761
32    2.3897 0.4392 1.0903 0.3783
33    2.6814 0.4075 1.2860 0.3433
34    2.1463 0.7309 1.2363 0.4083
35    2.2270 0.4830 1.0458 0.3672
36    2.3454 0.5276 1.1837 0.3983
37    2.3014 0.5659 1.2162 0.3780
38    2.2710 0.5163 1.0613 0.3648
39    2.0505 0.7363 1.2977 0.3667
40    2.4246 0.5578 1.4386 0.3826
41    2.3457 0.4417 1.0988 0.3693
42    2.4111 0.4225 0.9065 0.3864
43    2.3240 0.6160 1.4155 0.3675
44    2.2391 0.6374 1.2797 0.4111
45    2.4563 0.5227 1.3050 0.3654
46    2.0764 0.7169 1.2592 0.3887
47    2.2436 0.7064 1.4731 0.4023
48    2.4460 0.5053 1.2308 0.4021
49    2.2833 0.5490 1.1863 0.3910
50    2.3316 0.7014 1.4560 0.4202
51    2.3075 0.4284 1.0122 0.3211
52    2.3334 0.4090 0.9738 0.3431
53    2.5129 0.4670 1.3366 0.3715
54    2.5343 0.4144 1.1288 0.3910
55    2.0583 0.7000 1.2293 0.4017
56    2.4521 0.3678 1.0268 0.3452
57    2.3379 0.4780 1.1672 0.3343
58    2.3761 0.4913 1.2537 0.3824
59    2.7151 0.3518 1.1792 0.4003
60    2.4702 0.3847 1.0567 0.3321
61    2.4244 0.6437 1.5235 0.4116
62    2.5524 0.3955 1.1347 0.3893
63    2.1827 0.6072 1.1632 0.3759
64    2.3940 0.6300 1.3926 0.3871
65    2.4460 0.5053 1.2308 0.4021
66    2.3578 0.5961 1.3327 0.4132
67    2.4123 0.5251 1.3136 0.3564
68    2.3014 0.5659 1.2162 0.3780
69    2.3681 0.6493 1.4310 0.3651
70    2.2529 0.4994 1.0314 0.3779
71    2.2788 0.5158 1.0169 0.3885
72    2.2132 0.6568 1.3182 0.3891
73    2.4216 0.3182 0.8718 0.3320
74    2.2936 0.5664 1.2606 0.3543
75    2.3273 0.5465 1.1778 0.4000
76    2.2617 0.7233 1.5030 0.3892
77    2.3455 0.5634 1.2077 0.3870
78    2.2346 0.6400 1.1344 0.3972
79    2.6847 0.3022 1.0243 0.3872
80    2.3455 0.5634 1.2077 0.3870
81    2.3593 0.4255 0.9593 0.3537
82    2.1647 0.6261 1.1573 0.3776
83    2.3286 0.6850 1.6089 0.3587
84    2.3014 0.5659 1.2162 0.3780
85    2.2346 0.6400 1.1344 0.3972
86    2.5524 0.4313 1.1588 0.3779
87    2.5126 0.5529 1.4215 0.4005
88    2.1785 0.4523 0.8849 0.3557
89    2.3897 0.4392 1.0903 0.3783
90    1.9974 0.6008 0.9195 0.3754
91    2.4597 0.4890 1.0913 0.3865
92    2.6985 0.1642 0.7759 0.3539
93    2.3057 0.7208 1.4945 0.3982
94    2.3059 0.5991 1.3856 0.3805
95    2.3942 0.5082 1.2836 0.3694
96    2.5220 0.3817 1.0038 0.3648
97    2.0902 0.5431 0.9869 0.3668
98    2.2529 0.4994 1.0314 0.3779
99    2.1251 0.6617 1.3352 0.3711
100   1.9974 0.6008 0.9195 0.3754

$res
    H-Total F-Locality/Total F-Patch/Total F-Ind/Total H-Locality
1    0.7500           0.5172        0.6466      0.9136     0.3621
2    0.7297           0.5618        0.6653      0.9091     0.3197
3    0.8355           0.4784        0.6107      0.9223     0.4358
4    0.7484           0.5241        0.6495      0.9085     0.3562
5    0.7534           0.5646        0.6601      0.9164     0.3280
6    0.7729           0.4504        0.6120      0.9105     0.4248
7    0.7159           0.4576        0.6340      0.9045     0.3883
8    0.6900           0.5879        0.6727      0.9135     0.2843
9    0.6709           0.5257        0.6647      0.9062     0.3182
10   0.8076           0.5095        0.6241      0.9192     0.3962
11   0.7872           0.4921        0.6225      0.9222     0.3998
12   0.7040           0.5971        0.6790      0.9109     0.2836
13   0.7657           0.5268        0.6410      0.9173     0.3623
14   0.7266           0.5464        0.6555      0.9213     0.3296
15   0.7215           0.5042        0.6445      0.9132     0.3577
16   0.6970           0.5926        0.6759      0.9122     0.2840
17   0.7523           0.5139        0.6430      0.9191     0.3657
18   0.6972           0.4953        0.6502      0.9050     0.3519
19   0.7780           0.4836        0.6314      0.9171     0.4017
20   0.7486           0.5567        0.6534      0.9231     0.3319
21   0.7019           0.4385        0.6368      0.9058     0.3941
22   0.7936           0.4935        0.6263      0.9206     0.4019
23   0.7506           0.5208        0.6459      0.9141     0.3597
24   0.7297           0.5618        0.6653      0.9091     0.3197
25   0.7386           0.4744        0.6318      0.9073     0.3882
26   0.6952           0.5339        0.6582      0.9147     0.3241
27   0.7970           0.5385        0.6392      0.9232     0.3678
28   0.7484           0.5241        0.6495      0.9085     0.3562
29   0.7277           0.5989        0.6731      0.9184     0.2919
30   0.7129           0.5061        0.6441      0.9091     0.3521
31   0.7715           0.4820        0.6275      0.9188     0.3996
32   0.7162           0.5561        0.6583      0.9120     0.3180
33   0.7864           0.5683        0.6547      0.9272     0.3395
34   0.7536           0.4747        0.6363      0.9097     0.3959
35   0.6872           0.5401        0.6573      0.9109     0.3160
36   0.7425           0.5265        0.6449      0.9106     0.3516
37   0.7436           0.5158        0.6427      0.9153     0.3600
38   0.7022           0.5390        0.6615      0.9134     0.3237
39   0.7419           0.4607        0.6261      0.9176     0.4001
40   0.8006           0.5048        0.6209      0.9204     0.3965
41   0.7092           0.5512        0.6550      0.9132     0.3183
42   0.6877           0.5843        0.6867      0.9064     0.2859
43   0.7872           0.4921        0.6225      0.9222     0.3998
44   0.7612           0.4902        0.6298      0.9100     0.3880
45   0.7749           0.5283        0.6407      0.9214     0.3655
46   0.7402           0.4675        0.6289      0.9125     0.3941
47   0.8042           0.4650        0.6113      0.9166     0.4303
48   0.7640           0.5336        0.6438      0.9123     0.3563
49   0.7349           0.5178        0.6423      0.9113     0.3544
50   0.8182           0.4749        0.6178      0.9144     0.4296
51   0.6782           0.5671        0.6723      0.9211     0.2936
52   0.6765           0.5748        0.6756      0.9155     0.2877
53   0.7813           0.5360        0.6356      0.9208     0.3625
54   0.7447           0.5672        0.6599      0.9125     0.3224
55   0.7316           0.4689        0.6284      0.9085     0.3885
56   0.6986           0.5850        0.6727      0.9177     0.2900
57   0.7196           0.5415        0.6522      0.9226     0.3299
58   0.7506           0.5276        0.6367      0.9151     0.3546
59   0.7744           0.5843        0.6601      0.9138     0.3219
60   0.7073           0.5821        0.6727      0.9217     0.2956
61   0.8339           0.4846        0.6132      0.9177     0.4298
62   0.7453           0.5708        0.6592      0.9129     0.3199
63   0.7215           0.5042        0.6445      0.9132     0.3577
64   0.8006           0.4984        0.6295      0.9194     0.4016
65   0.7640           0.5336        0.6438      0.9123     0.3563
66   0.7833           0.5017        0.6285      0.9121     0.3903
67   0.7679           0.5236        0.6375      0.9226     0.3659
68   0.7436           0.5158        0.6427      0.9153     0.3600
69   0.8023           0.4920        0.6269      0.9241     0.4076
70   0.6936           0.5414        0.6614      0.9092     0.3181
71   0.7000           0.5426        0.6654      0.9075     0.3202
72   0.7629           0.4835        0.6270      0.9150     0.3940
73   0.6573           0.6141        0.6947      0.9158     0.2537
74   0.7458           0.5125        0.6391      0.9208     0.3636
75   0.7419           0.5228        0.6456      0.9101     0.3540
76   0.8129           0.4637        0.6120      0.9202     0.4359
77   0.7506           0.5208        0.6459      0.9141     0.3597
78   0.7344           0.5072        0.6524      0.9099     0.3619
79   0.7331           0.6104        0.6791      0.9120     0.2856
80   0.7506           0.5208        0.6459      0.9141     0.3597
81   0.6830           0.5757        0.6796      0.9137     0.2898
82   0.7209           0.5004        0.6452      0.9127     0.3602
83   0.8302           0.4675        0.6050      0.9280     0.4421
84   0.7436           0.5158        0.6427      0.9153     0.3600
85   0.7344           0.5072        0.6524      0.9099     0.3619
86   0.7534           0.5646        0.6601      0.9164     0.3280
87   0.8146           0.5141        0.6272      0.9180     0.3958
88   0.6452           0.5627        0.6795      0.9081     0.2822
89   0.7162           0.5561        0.6583      0.9120     0.3180
90   0.6489           0.5131        0.6674      0.9036     0.3159
91   0.7378           0.5557        0.6661      0.9127     0.3278
92   0.6654           0.6759        0.7170      0.9114     0.2157
93   0.8199           0.4687        0.6152      0.9190     0.4356
94   0.7785           0.4937        0.6219      0.9185     0.3942
95   0.7592           0.5256        0.6371      0.9189     0.3602
96   0.7121           0.5903        0.6797      0.9146     0.2917
97   0.6645           0.5242        0.6605      0.9080     0.3161
98   0.6936           0.5414        0.6614      0.9092     0.3181
99   0.7489           0.4730        0.6202      0.9174     0.3947
100  0.6489           0.5131        0.6674      0.9036     0.3159
    F-Patch/Locality F-Ind/Locality H-Patch F-Ind/Patch   Hobs
1             0.2680         0.8211  0.2651      0.7556 0.0648
2             0.2362         0.7926  0.2442      0.7284 0.0663
3             0.2536         0.8510  0.3253      0.8003 0.0649
4             0.2634         0.8078  0.2623      0.7391 0.0684
5             0.2192         0.8080  0.2561      0.7541 0.0630
6             0.2941         0.8372  0.2999      0.7694 0.0691
7             0.3252         0.8239  0.2620      0.7390 0.0684
8             0.2057         0.7900  0.2258      0.7357 0.0597
9             0.2930         0.8023  0.2250      0.7204 0.0629
10            0.2336         0.8353  0.3036      0.7850 0.0653
11            0.2568         0.8468  0.2972      0.7939 0.0613
12            0.2033         0.7790  0.2260      0.7226 0.0627
13            0.2413         0.8252  0.2749      0.7696 0.0633
14            0.2405         0.8264  0.2503      0.7715 0.0572
15            0.2829         0.8248  0.2565      0.7557 0.0627
16            0.2045         0.7845  0.2259      0.7291 0.0612
17            0.2657         0.8336  0.2685      0.7735 0.0608
18            0.3069         0.8117  0.2439      0.7283 0.0663
19            0.2863         0.8396  0.2867      0.7752 0.0645
20            0.2181         0.8266  0.2595      0.7782 0.0576
21            0.3530         0.8322  0.2550      0.7406 0.0661
22            0.2622         0.8432  0.2965      0.7875 0.0630
23            0.2611         0.8207  0.2658      0.7573 0.0645
24            0.2362         0.7926  0.2442      0.7284 0.0663
25            0.2995         0.8237  0.2719      0.7483 0.0684
26            0.2668         0.8170  0.2376      0.7504 0.0593
27            0.2181         0.8335  0.2876      0.7871 0.0612
28            0.2634         0.8078  0.2623      0.7391 0.0684
29            0.1850         0.7966  0.2379      0.7505 0.0594
30            0.2794         0.8159  0.2537      0.7445 0.0648
31            0.2810         0.8432  0.2874      0.7819 0.0627
32            0.2302         0.8017  0.2448      0.7424 0.0630
33            0.2001         0.8314  0.2716      0.7893 0.0572
34            0.3077         0.8281  0.2741      0.7517 0.0681
35            0.2547         0.8063  0.2355      0.7401 0.0612
36            0.2501         0.8112  0.2637      0.7482 0.0664
37            0.2620         0.8250  0.2657      0.7629 0.0630
38            0.2658         0.8122  0.2377      0.7442 0.0608
39            0.3067         0.8473  0.2774      0.7797 0.0611
40            0.2345         0.8392  0.3035      0.7899 0.0638
41            0.2313         0.8066  0.2447      0.7485 0.0615
42            0.2463         0.7748  0.2155      0.7011 0.0644
43            0.2568         0.8468  0.2972      0.7939 0.0613
44            0.2738         0.8234  0.2818      0.7569 0.0685
45            0.2383         0.8334  0.2784      0.7813 0.0609
46            0.3032         0.8356  0.2747      0.7641 0.0648
47            0.2736         0.8442  0.3126      0.7855 0.0670
48            0.2363         0.8120  0.2721      0.7538 0.0670
49            0.2582         0.8161  0.2629      0.7521 0.0652
50            0.2721         0.8370  0.3127      0.7760 0.0700
51            0.2432         0.8177  0.2222      0.7592 0.0535
52            0.2370         0.8012  0.2195      0.7395 0.0572
53            0.2147         0.8292  0.2847      0.7825 0.0619
54            0.2143         0.7979  0.2533      0.7428 0.0652
55            0.3003         0.8277  0.2718      0.7537 0.0670
56            0.2114         0.8016  0.2287      0.7484 0.0575
57            0.2415         0.8311  0.2502      0.7774 0.0557
58            0.2309         0.8202  0.2727      0.7663 0.0637
59            0.1821         0.7927  0.2633      0.7465 0.0667
60            0.2169         0.8127  0.2315      0.7608 0.0554
61            0.2496         0.8404  0.3225      0.7873 0.0686
62            0.2060         0.7972  0.2540      0.7446 0.0649
63            0.2829         0.8248  0.2565      0.7557 0.0627
64            0.2614         0.8393  0.2966      0.7825 0.0645
65            0.2363         0.8120  0.2721      0.7538 0.0670
66            0.2545         0.8236  0.2910      0.7633 0.0689
67            0.2392         0.8376  0.2783      0.7866 0.0594
68            0.2620         0.8250  0.2657      0.7629 0.0630
69            0.2655         0.8507  0.2994      0.7967 0.0609
70            0.2617         0.8020  0.2349      0.7319 0.0630
71            0.2685         0.7978  0.2342      0.7236 0.0647
72            0.2778         0.8354  0.2845      0.7721 0.0649
73            0.2091         0.7819  0.2006      0.7242 0.0553
74            0.2597         0.8376  0.2692      0.7806 0.0591
75            0.2573         0.8117  0.2630      0.7465 0.0667
76            0.2765         0.8512  0.3154      0.7943 0.0649
77            0.2611         0.8207  0.2658      0.7573 0.0645
78            0.2947         0.8171  0.2553      0.7406 0.0662
79            0.1763         0.7741  0.2352      0.7257 0.0645
80            0.2611         0.8207  0.2658      0.7573 0.0645
81            0.2447         0.7965  0.2188      0.7306 0.0590
82            0.2897         0.8253  0.2558      0.7540 0.0629
83            0.2582         0.8648  0.3279      0.8177 0.0598
84            0.2620         0.8250  0.2657      0.7629 0.0630
85            0.2947         0.8171  0.2553      0.7406 0.0662
86            0.2192         0.8080  0.2561      0.7541 0.0630
87            0.2328         0.8313  0.3037      0.7802 0.0668
88            0.2672         0.7899  0.2068      0.7133 0.0593
89            0.2302         0.8017  0.2448      0.7424 0.0630
90            0.3169         0.8020  0.2158      0.7101 0.0626
91            0.2486         0.8035  0.2463      0.7385 0.0644
92            0.1269         0.7265  0.1883      0.6867 0.0590
93            0.2758         0.8476  0.3155      0.7896 0.0664
94            0.2533         0.8391  0.2944      0.7845 0.0634
95            0.2351         0.8291  0.2755      0.7765 0.0616
96            0.2181         0.7916  0.2281      0.7335 0.0608
97            0.2863         0.8066  0.2256      0.7290 0.0611
98            0.2617         0.8020  0.2349      0.7319 0.0630
99            0.2794         0.8433  0.2844      0.7825 0.0619
100           0.3169         0.8020  0.2158      0.7101 0.0626

$ci
      H-Total F-Locality/Total F-Patch/Total F-Ind/Total H-Locality
2.5%   0.6529           0.4590        0.6117      0.9047     0.2829
50%    0.7436           0.5232        0.6454      0.9140     0.3570
97.5%  0.8253           0.6049        0.6834      0.9237     0.4357
      F-Patch/Locality F-Ind/Locality H-Patch F-Ind/Patch   Hobs
2.5%            0.1835         0.7768  0.2109      0.7101 0.0555
50%             0.2577         0.8207  0.2629      0.7541 0.0630
97.5%           0.3169         0.8508  0.3192      0.7956 0.0687

hierfstat documentation built on Nov. 17, 2021, 5:08 p.m.