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Permanova_results_all.txt
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> perm<-adonis2(dist.clr~Condition*Treatment*Collection.month,as(sample_data(ps5_BS2),"data.frame"))
> print(perm)
Permutation test for adonis under reduced model
Terms added sequentially (first to last)
Permutation: free
Number of permutations: 999
adonis2(formula = dist.clr ~ Condition * Treatment * Collection.month, data = as(sample_data(ps5_BS2), "data.frame"))
Df SumOfSqs R2 F Pr(>F)
Condition 2 15127 0.03271 3.5368 0.001 ***
Treatment 5 21612 0.04674 2.0212 0.001 ***
Collection.month 2 35736 0.07728 8.3553 0.001 ***
Condition:Treatment 4 7950 0.01719 0.9293 0.613
Condition:Collection.month 4 7389 0.01598 0.8638 0.735
Treatment:Collection.month 5 8850 0.01914 0.8277 0.845
Condition:Treatment:Collection.month 4 8627 0.01866 1.0085 0.429
Residual 167 357136 0.77231
Total 193 462427 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> perm2<-pairwise.adonis2(dist.clr~Condition*Treatment*Collection.month,as(sample_data(ps5_BS2),"data.frame"))
> print(perm2)
$parent_call
[1] "dist.clr ~ Condition * Treatment * Collection.month , strata = Null , permutations 999"
$HH_vs_DD
Df SumOfSqs R2 F Pr(>F)
Condition 1 6814 0.02321 2.5997 0.008 **
Treatment 5 20309 0.06917 1.5497 0.010 **
Collection.month 2 20122 0.06853 3.8386 0.001 ***
Condition:Collection.month 2 4277 0.01457 0.8159 0.714
Treatment:Collection.month 5 11440 0.03896 0.8729 0.716
Residual 88 230654 0.78556
Total 103 293616 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$HH_vs_HD
Df SumOfSqs R2 F Pr(>F)
Condition 1 1206 0.00602 0.7633 0.717
Treatment 5 13522 0.06747 1.7117 0.002 **
Collection.month 2 19658 0.09808 6.2207 0.001 ***
Condition:Collection.month 2 2437 0.01216 0.7713 0.764
Treatment:Collection.month 5 7185 0.03585 0.9094 0.642
Residual 99 156420 0.78043
Total 114 200428 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$DD_vs_HD
Df SumOfSqs R2 F Pr(>F)
Condition 1 12351 0.02934 5.5489 0.001 ***
Treatment 4 18943 0.04500 2.1277 0.001 ***
Collection.month 2 34026 0.08083 7.6433 0.001 ***
Condition:Treatment 4 7876 0.01871 0.8846 0.736
Condition:Collection.month 2 4203 0.00999 0.9442 0.505
Treatment:Collection.month 4 7702 0.01830 0.8651 0.764
Condition:Treatment:Collection.month 4 8627 0.02050 0.9690 0.512
Residual 147 327198 0.77733
Total 168 420927 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
attr(,"class")
[1] "pwadstrata" "list"
> perm3<-pairwise.adonis2(dist.clr~Treatment/Collection.month,as(sample_data(ps5_BS2),"data.frame"), strata='Collection.month')
> print(perm3)
$parent_call
[1] "dist.clr ~ Treatment/Collection.month , strata = Collection.month , permutations 999"
$`none_vs_probiotic paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 6153 0.02265 2.6988 0.394
Treatment:Collection.month 3 21538 0.07929 3.1492 0.232
Residual 107 243937 0.89805
Total 111 271628 1.00000
$`none_vs_probiotic bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 4968 0.01980 2.2571 0.684
Treatment:Collection.month 3 21402 0.08531 3.2410 0.443
Residual 102 224512 0.89489
Total 106 250882 1.00000
$`none_vs_control bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 6058 0.02185 2.6284 0.409
Treatment:Collection.month 3 22287 0.08039 3.2235 0.252
Residual 108 248906 0.89776
Total 112 277251 1.00000
$`none_vs_control paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 7491 0.02738 3.3532 0.176
Treatment:Collection.month 3 22643 0.08275 3.3785 0.716
Residual 109 243503 0.88988
Total 113 273637 1.00000
$none_vs_resistant
Df SumOfSqs R2 F Pr(>F)
Treatment 1 3250 0.01455 1.4721 0.503
Treatment:Collection.month 3 19166 0.08581 2.8932 0.330
Residual 91 200938 0.89964
Total 95 223354 1.00000
$`probiotic paste_vs_probiotic bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2042 0.02038 0.9696 0.507
Treatment:Collection.month 2 11794 0.11772 2.7999 0.326
Residual 41 86351 0.86190
Total 44 100187 1.00000
$`probiotic paste_vs_control bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2062 0.01643 0.8750 0.610
Treatment:Collection.month 2 12680 0.10104 2.6906 0.105
Residual 47 110745 0.88253
Total 50 125486 1.00000
$`probiotic paste_vs_control paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2462 0.02038 1.1220 0.256
Treatment:Collection.month 2 13035 0.10787 2.9697 0.236
Residual 48 105342 0.87175
Total 51 120839 1.00000
$`probiotic paste_vs_resistant`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 1846 0.02489 0.8824 0.571
Treatment:Collection.month 2 9558 0.12885 2.2838 0.402
Residual 30 62777 0.84626
Total 33 74181 1.00000
$`probiotic bag_vs_control bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2189 0.02064 1.0069 0.407
Treatment:Collection.month 2 12543 0.11827 2.8843 0.308
Residual 42 91320 0.86109
Total 45 106052 1.00000
$`probiotic bag_vs_control paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2190 0.02168 1.0959 0.451
Treatment:Collection.month 2 12898 0.12770 3.2277 0.375
Residual 43 85916 0.85062
Total 46 101004 1.00000
$`probiotic bag_vs_resistant`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 1520 0.02801 0.8768 0.574
Treatment:Collection.month 2 9421 0.17353 2.7165 0.579
Residual 25 43351 0.79847
Total 28 54293 1.00000
$`control bag_vs_control paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 1893 0.01503 0.8410 0.644
Treatment:Collection.month 2 13784 0.10941 3.0614 0.890
Residual 49 110311 0.87557
Total 52 125988 1.00000
$`control bag_vs_resistant`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 1412 0.01777 0.6463 0.884
Treatment:Collection.month 2 10307 0.12970 2.3582 0.819
Residual 31 67746 0.85252
Total 34 79465 1.00000
$`control paste_vs_resistant`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 1104 0.01490 0.5668 0.998
Treatment:Collection.month 2 10662 0.14387 2.7364 0.825
Residual 32 62343 0.84123
Total 35 74109 1.00000
attr(,"class")
[1] "pwadstrata" "list"
> perm4<-pairwise.adonis2(dist.clr~Condition/Collection.month,as(sample_data(ps5_BS2),"data.frame"), strata='Collection.month')
> print(perm4)
$parent_call
[1] "dist.clr ~ Condition/Collection.month , strata = Collection.month , permutations 999"
$HH_vs_DD
Df SumOfSqs R2 F Pr(>F)
Condition 1 6814 0.02321 2.6694 0.017 *
Condition:Collection.month 4 36642 0.12480 3.5887 0.027 *
Residual 98 250160 0.85200
Total 103 293616 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$HH_vs_HD
Df SumOfSqs R2 F Pr(>F)
Condition 1 1206 0.00602 0.7691 0.982
Condition:Collection.month 4 28292 0.14116 4.5103 0.073 .
Residual 109 170930 0.85283
Total 114 200428 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$DD_vs_HD
Df SumOfSqs R2 F Pr(>F)
Condition 1 12351 0.02934 5.6338 0.001 ***
Condition:Collection.month 4 51229 0.12171 5.8419 0.012 *
Residual 163 357347 0.84895
Total 168 420927 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
attr(,"class")
[1] "pwadstrata" "list"
perm5<-pairwise.adonis2(dist.clr~Treatment*Condition/Collection.month,as(sample_data(ps5_BS2),"data.frame"), strata='Collection.month')
print(perm5)
$parent_call
[1] "dist.clr ~ Treatment * Condition/Collection.month , strata = Collection.month , permutations 999"
$`none_vs_probiotic paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 6153 0.02265 2.8289 0.195
Condition 2 16097 0.05926 3.7005 0.001 ***
Treatment:Condition 1 2227 0.00820 1.0241 0.228
Treatment:Condition:Collection.month 8 31827 0.11717 1.8292 0.103
Residual 99 215324 0.79272
Total 111 271628 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`none_vs_probiotic bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 4968 0.01980 2.3183 0.547
Condition 2 12550 0.05003 2.9282 0.002 **
Treatment:Condition 1 3351 0.01336 1.5638 0.055 .
Treatment:Condition:Collection.month 8 28569 0.11387 1.6664 0.395
Residual 94 201443 0.80294
Total 106 250882 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`none_vs_control bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 6058 0.02185 2.7150 0.328
Condition 2 14717 0.05308 3.2982 0.003 **
Treatment:Condition 1 2333 0.00841 1.0455 0.266
Treatment:Condition:Collection.month 8 31028 0.11191 1.7384 0.305
Residual 100 223115 0.80474
Total 112 277251 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`none_vs_control paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 7491 0.02738 3.4579 0.125
Condition 2 13678 0.04999 3.1570 0.002 **
Treatment:Condition 1 2550 0.00932 1.1769 0.124
Treatment:Condition:Collection.month 8 31124 0.11374 1.7959 0.421
Residual 101 218794 0.79958
Total 113 273637 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$none_vs_resistant
Df SumOfSqs R2 F Pr(>F)
Treatment 1 3250 0.01455 1.5318 0.355
Condition 2 13766 0.06163 3.2438 0.001 ***
Treatment:Condition:Collection.month 7 25973 0.11628 1.7486 0.109
Residual 85 180365 0.80753
Total 95 223354 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`probiotic paste_vs_probiotic bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2042 0.02038 0.9966 0.474
Condition 1 3786 0.03779 1.8479 0.051 .
Treatment:Condition 1 2907 0.02902 1.4189 0.163
Treatment:Condition:Collection.month 4 15636 0.15607 1.9078 0.454
Residual 37 75814 0.75673
Total 44 100187 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`probiotic paste_vs_control bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2062 0.01643 0.9094 0.555
Condition 1 5641 0.04495 2.4882 0.007 **
Treatment:Condition 1 2201 0.01754 0.9709 0.476
Treatment:Condition:Collection.month 4 18096 0.14421 1.9955 0.079 .
Residual 43 97487 0.77687
Total 50 125486 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`probiotic paste_vs_control paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2462 0.02038 1.1630 0.248
Condition 1 4980 0.04122 2.3521 0.005 **
Treatment:Condition 1 2039 0.01688 0.9631 0.452
Treatment:Condition:Collection.month 4 18191 0.15054 2.1478 0.097 .
Residual 44 93166 0.77099
Total 51 120839 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`probiotic paste_vs_resistant`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 1846 0.02489 0.9445 0.442
Condition 1 4558 0.06145 2.3318 0.005 **
Treatment:Condition:Collection.month 3 13040 0.17579 2.2235 0.046 *
Residual 28 54736 0.73787
Total 33 74181 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`probiotic bag_vs_control bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2189 0.02064 0.9951 0.413
Condition 1 3443 0.03247 1.5650 0.223
Treatment:Condition 1 1976 0.01863 0.8982 0.511
Treatment:Condition:Collection.month 4 14838 0.13991 1.6860 0.727
Residual 38 83606 0.78835
Total 45 106052 1.00000
$`probiotic bag_vs_control paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2190 0.02168 1.0771 0.433
Condition 1 2725 0.02698 1.3407 0.317
Treatment:Condition 1 1871 0.01853 0.9205 0.575
Treatment:Condition:Collection.month 4 14933 0.14785 1.8364 0.741
Residual 39 79285 0.78496
Total 46 101004 1.00000
$`probiotic bag_vs_resistant`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 1520 0.02801 0.8560 0.598
Condition 1 2135 0.03933 1.2022 0.474
Treatment:Condition:Collection.month 3 9782 0.18017 1.8356 0.729
Residual 23 40855 0.75250
Total 28 54293 1.00000
$`control bag_vs_control paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 1893 0.01503 0.8439 0.643
Condition 1 4018 0.03189 1.7909 0.060 .
Treatment:Condition 1 1727 0.01371 0.7699 0.668
Treatment:Condition:Collection.month 4 17393 0.13805 1.9381 0.824
Residual 45 100957 0.80132
Total 52 125988 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`control bag_vs_resistant`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 1412 0.01777 0.6551 0.876
Condition 1 3284 0.04132 1.5230 0.132
Treatment:Condition:Collection.month 3 12241 0.15405 1.8925 0.648
Residual 29 62528 0.78686
Total 34 79465 1.00000
$`control paste_vs_resistant`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 1104 0.01490 0.5691 0.995
Condition 1 2461 0.03321 1.2686 0.225
Treatment:Condition:Collection.month 3 12337 0.16647 2.1195 0.773
Residual 30 58207 0.78542
Total 35 74109 1.00000
attr(,"class")
[1] "pwadstrata" "list"
##### Diseased samples only
perm6<-pairwise.adonis2(dist.clr2~Treatment/Collection.month,as(sample_data(ps5_BS2_DD),"data.frame"), strata='Collection.month')
print(perm6)
phyloseq-class experiment-level object
otu_table() OTU Table: [ 756 taxa and 79 samples ]
sample_data() Sample Data: [ 79 samples by 13 sample variables ]
tax_table() Taxonomy Table: [ 756 taxa by 6 taxonomic ranks ]
No. adjusted imputations: 25046
$parent_call
[1] "dist.clr2 ~ Treatment/Collection.month , strata = Collection.month , permutations 999"
$`none_vs_probiotic paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 6107 0.04156 2.0340 0.615
Treatment:Collection.month 3 17734 0.12069 1.9689 0.950
Residual 41 123093 0.83775
Total 45 146933 1.00000
$`none_vs_probiotic bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 5649 0.04468 1.8970 0.558
Treatment:Collection.month 3 13573 0.10735 1.5191 0.471
Residual 36 107214 0.84797
Total 40 126436 1.00000
$`none_vs_control bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 5377 0.03517 1.6458 0.736
Treatment:Collection.month 3 16832 0.11009 1.7174 0.528
Residual 40 130677 0.85474
Total 44 152886 1.00000
$`none_vs_control paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 6827 0.04642 2.2425 0.491
Treatment:Collection.month 3 15410 0.10479 1.6872 0.840
Residual 41 124820 0.84879
Total 45 147057 1.00000
$`probiotic paste_vs_probiotic bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2741 0.04979 1.0817 0.553
Treatment:Collection.month 2 9235 0.16773 1.8220 0.624
Residual 17 43086 0.78249
Total 20 55063 1.00000
$`probiotic paste_vs_control bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2168 0.02669 0.6841 0.935
Treatment:Collection.month 2 12495 0.15385 1.9714 0.063 .
Residual 21 66549 0.81945
Total 24 81212 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`probiotic paste_vs_control paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2362 0.03186 0.8562 0.698
Treatment:Collection.month 2 11073 0.14937 2.0068 0.083 .
Residual 22 60693 0.81876
Total 25 74127 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`probiotic bag_vs_control bag`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2581 0.04191 0.8150 0.579
Treatment:Collection.month 2 8333 0.13531 1.3157 0.875
Residual 16 50670 0.82277
Total 19 61585 1.00000
$`probiotic bag_vs_control paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2286 0.04233 0.8672 0.733
Treatment:Collection.month 2 6911 0.12796 1.3109 0.854
Residual 17 44813 0.82971
Total 20 54011 1.00000
$`control bag_vs_control paste`
Df SumOfSqs R2 F Pr(>F)
Treatment 1 2649 0.03266 0.8147 0.637
Treatment:Collection.month 2 10171 0.12541 1.5641 0.863
Residual 21 68277 0.84192
Total 24 81096 1.00000
attr(,"class")
[1] "pwadstrata" "list"