CLOSER Statistics Report
Máté Váczy-Földi
2022-05-04
Diversity indices
Alpha diversity
The upper row contains bacteria, the lower contains eukaryotes.
Green = connected Red = fragmented
Beta diversity
The upper row contains bacteria, the lower contains eukaryotes
Green = connected Red = fragmented
Gamma diversity
The upper row contains bacteria, the lower contains eukaryotes
Green = connected Red = fragmented
Species accumulation curves
The upper row contains bacteria, the lower contains eukaryotes
Green = connected Red = fragmented
Non-metric multidimensional scaling
The upper row contains bacteria, the lower contains eukaryotes
NMDS on all samplings
These plots contain all the samplings in one NMDS
Adonis (PERMANOVA) and Bray-Curtis distance model results
Bacteria week 4
Adonis results
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = V_abund_mat_bact ~ V_attr_list_adonis_bact$Treatment + V_attr_list_adonis_bact$Treatment:V_attr_list_adonis_bact$Metacom_ID)
## Df
## V_attr_list_adonis_bact$Treatment 1
## V_attr_list_adonis_bact$Treatment:V_attr_list_adonis_bact$Metacom_ID 4
## Residual 24
## Total 29
## SumOfSqs
## V_attr_list_adonis_bact$Treatment 0.12521
## V_attr_list_adonis_bact$Treatment:V_attr_list_adonis_bact$Metacom_ID 0.36894
## Residual 1.80016
## Total 2.29432
## R2
## V_attr_list_adonis_bact$Treatment 0.05458
## V_attr_list_adonis_bact$Treatment:V_attr_list_adonis_bact$Metacom_ID 0.16081
## Residual 0.78462
## Total 1.00000
## F
## V_attr_list_adonis_bact$Treatment 1.6694
## V_attr_list_adonis_bact$Treatment:V_attr_list_adonis_bact$Metacom_ID 1.2297
## Residual
## Total
## Pr(>F)
## V_attr_list_adonis_bact$Treatment 0.076 .
## V_attr_list_adonis_bact$Treatment:V_attr_list_adonis_bact$Metacom_ID 0.165
## Residual
## Total
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Bray-Curtis distance model summaries
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = V_dis_bact, group =
## V_attr_list_adonis_bact$Treatment)
##
## No. of Positive Eigenvalues: 22
## No. of Negative Eigenvalues: 7
##
## Average distance to median:
## connected fragmented
## 0.2554 0.2578
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 29 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 0.53560 0.37851 0.29319 0.26741 0.18572 0.15709 0.12302 0.09185## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.000041 0.0000408 0.0053 0.9423
## Residuals 28 0.214550 0.0076625##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = V_dis_bact, group =
## V_attr_list_adonis_bact$Treatment:V_attr_list_adonis_bact$Metacom_ID)
##
## No. of Positive Eigenvalues: 22
## No. of Negative Eigenvalues: 7
##
## Average distance to median:
## connected:M1 connected:M2 connected:M3 fragmented:M4 fragmented:M5
## 0.2006 0.2220 0.2669 0.2247 0.2208
## fragmented:M6
## 0.2612
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 29 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 0.53560 0.37851 0.29319 0.26741 0.18572 0.15709 0.12302 0.09185## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 5 0.016662 0.0033324 0.4017 0.8428
## Residuals 24 0.199100 0.0082958Bacteria week 8
Adonis results
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = IX_abund_mat_bact ~ IX_attr_list_adonis_bact$Treatment + IX_attr_list_adonis_bact$Treatment:IX_attr_list_adonis_bact$Metacom_ID)
## Df
## IX_attr_list_adonis_bact$Treatment 1
## IX_attr_list_adonis_bact$Treatment:IX_attr_list_adonis_bact$Metacom_ID 4
## Residual 24
## Total 29
## SumOfSqs
## IX_attr_list_adonis_bact$Treatment 0.1637
## IX_attr_list_adonis_bact$Treatment:IX_attr_list_adonis_bact$Metacom_ID 0.7370
## Residual 3.0743
## Total 3.9749
## R2
## IX_attr_list_adonis_bact$Treatment 0.04118
## IX_attr_list_adonis_bact$Treatment:IX_attr_list_adonis_bact$Metacom_ID 0.18541
## Residual 0.77341
## Total 1.00000
## F
## IX_attr_list_adonis_bact$Treatment 1.2778
## IX_attr_list_adonis_bact$Treatment:IX_attr_list_adonis_bact$Metacom_ID 1.4384
## Residual
## Total
## Pr(>F)
## IX_attr_list_adonis_bact$Treatment 0.211
## IX_attr_list_adonis_bact$Treatment:IX_attr_list_adonis_bact$Metacom_ID 0.030 *
## Residual
## Total
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Bray-Curtis distance model summaries
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = IX_dis_bact, group =
## IX_attr_list_adonis_bact$Treatment)
##
## No. of Positive Eigenvalues: 22
## No. of Negative Eigenvalues: 7
##
## Average distance to median:
## connected fragmented
## 0.3667 0.3282
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 29 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 0.7564 0.6702 0.4748 0.3954 0.2851 0.2579 0.2038 0.1888## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.011136 0.0111362 1.5609 0.2219
## Residuals 28 0.199763 0.0071344##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = IX_dis_bact, group =
## IX_attr_list_adonis_bact$Treatment:IX_attr_list_adonis_bact$Metacom_ID)
##
## No. of Positive Eigenvalues: 22
## No. of Negative Eigenvalues: 7
##
## Average distance to median:
## connected:M1 connected:M2 connected:M3 fragmented:M4 fragmented:M5
## 0.2718 0.2819 0.3853 0.2382 0.3046
## fragmented:M6
## 0.3663
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 29 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 0.7564 0.6702 0.4748 0.3954 0.2851 0.2579 0.2038 0.1888## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 5 0.081277 0.0162555 1.952 0.1227
## Residuals 24 0.199860 0.0083275Bacteria week 12
Adonis results
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = X_abund_mat_bact ~ X_attr_list_adonis_bact$Treatment + X_attr_list_adonis_bact$Treatment:X_attr_list_adonis_bact$Metacom_ID)
## Df
## X_attr_list_adonis_bact$Treatment 1
## X_attr_list_adonis_bact$Treatment:X_attr_list_adonis_bact$Metacom_ID 4
## Residual 23
## Total 28
## SumOfSqs
## X_attr_list_adonis_bact$Treatment 0.3132
## X_attr_list_adonis_bact$Treatment:X_attr_list_adonis_bact$Metacom_ID 1.1343
## Residual 3.9554
## Total 5.4029
## R2
## X_attr_list_adonis_bact$Treatment 0.05797
## X_attr_list_adonis_bact$Treatment:X_attr_list_adonis_bact$Metacom_ID 0.20994
## Residual 0.73209
## Total 1.00000
## F
## X_attr_list_adonis_bact$Treatment 1.8211
## X_attr_list_adonis_bact$Treatment:X_attr_list_adonis_bact$Metacom_ID 1.6489
## Residual
## Total
## Pr(>F)
## X_attr_list_adonis_bact$Treatment 0.024 *
## X_attr_list_adonis_bact$Treatment:X_attr_list_adonis_bact$Metacom_ID 0.005 **
## Residual
## Total
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Bray-Curtis distance model summaries
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = X_dis_bact, group =
## X_attr_list_adonis_bact$Treatment)
##
## No. of Positive Eigenvalues: 23
## No. of Negative Eigenvalues: 5
##
## Average distance to median:
## connected fragmented
## 0.3851 0.4286
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 28 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 1.0379 0.7295 0.6469 0.4631 0.3913 0.3838 0.3240 0.2515## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.013701 0.013702 1.2596 0.2716
## Residuals 27 0.293703 0.010878##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = X_dis_bact, group =
## X_attr_list_adonis_bact$Treatment:X_attr_list_adonis_bact$Metacom_ID)
##
## No. of Positive Eigenvalues: 23
## No. of Negative Eigenvalues: 5
##
## Average distance to median:
## connected:M1 connected:M2 connected:M3 fragmented:M4 fragmented:M5
## 0.3353 0.2897 0.4013 0.3542 0.4011
## fragmented:M6
## 0.3645
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 28 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 1.0379 0.7295 0.6469 0.4631 0.3913 0.3838 0.3240 0.2515## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 5 0.04286 0.0085715 0.6055 0.6964
## Residuals 23 0.32560 0.0141566Bacteria week 16
Adonis results
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = XI_abund_mat_bact ~ XI_attr_list_adonis_bact$Treatment + XI_attr_list_adonis_bact$Treatment:XI_attr_list_adonis_bact$Metacom_ID)
## Df
## XI_attr_list_adonis_bact$Treatment 1
## XI_attr_list_adonis_bact$Treatment:XI_attr_list_adonis_bact$Metacom_ID 4
## Residual 24
## Total 29
## SumOfSqs
## XI_attr_list_adonis_bact$Treatment 0.4541
## XI_attr_list_adonis_bact$Treatment:XI_attr_list_adonis_bact$Metacom_ID 1.4587
## Residual 4.8333
## Total 6.7461
## R2
## XI_attr_list_adonis_bact$Treatment 0.06731
## XI_attr_list_adonis_bact$Treatment:XI_attr_list_adonis_bact$Metacom_ID 0.21623
## Residual 0.71646
## Total 1.00000
## F
## XI_attr_list_adonis_bact$Treatment 2.2547
## XI_attr_list_adonis_bact$Treatment:XI_attr_list_adonis_bact$Metacom_ID 1.8108
## Residual
## Total
## Pr(>F)
## XI_attr_list_adonis_bact$Treatment 0.008
## XI_attr_list_adonis_bact$Treatment:XI_attr_list_adonis_bact$Metacom_ID 0.001
## Residual
## Total
##
## XI_attr_list_adonis_bact$Treatment **
## XI_attr_list_adonis_bact$Treatment:XI_attr_list_adonis_bact$Metacom_ID ***
## Residual
## Total
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Bray-Curtis distance model summaries
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = XI_dis_bact, group =
## XI_attr_list_adonis_bact$Treatment)
##
## No. of Positive Eigenvalues: 25
## No. of Negative Eigenvalues: 4
##
## Average distance to median:
## connected fragmented
## 0.4237 0.4751
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 29 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 1.3697 0.8231 0.7198 0.6063 0.5092 0.4090 0.3771 0.3065## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.019789 0.019790 2.0442 0.1639
## Residuals 28 0.271068 0.009681##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = XI_dis_bact, group =
## XI_attr_list_adonis_bact$Treatment:XI_attr_list_adonis_bact$Metacom_ID)
##
## No. of Positive Eigenvalues: 25
## No. of Negative Eigenvalues: 4
##
## Average distance to median:
## connected:M1 connected:M2 connected:M3 fragmented:M4 fragmented:M5
## 0.2869 0.3166 0.4190 0.4574 0.4223
## fragmented:M6
## 0.4346
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 29 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 1.3697 0.8231 0.7198 0.6063 0.5092 0.4090 0.3771 0.3065## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 5 0.12221 0.024442 2.6349 0.04907 *
## Residuals 24 0.22262 0.009276
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Eukaryotes week 4
Adonis results
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = V_abund_mat_euk ~ V_attr_list_adonis_euk$Treatment + V_attr_list_adonis_euk$Treatment:V_attr_list_adonis_euk$Metacom_ID)
## Df SumOfSqs
## V_attr_list_adonis_euk$Treatment 1 0.3038
## V_attr_list_adonis_euk$Treatment:V_attr_list_adonis_euk$Metacom_ID 4 1.0456
## Residual 23 5.6656
## Total 28 7.0151
## R2
## V_attr_list_adonis_euk$Treatment 0.04331
## V_attr_list_adonis_euk$Treatment:V_attr_list_adonis_euk$Metacom_ID 0.14906
## Residual 0.80763
## Total 1.00000
## F
## V_attr_list_adonis_euk$Treatment 1.2335
## V_attr_list_adonis_euk$Treatment:V_attr_list_adonis_euk$Metacom_ID 1.0612
## Residual
## Total
## Pr(>F)
## V_attr_list_adonis_euk$Treatment 0.252
## V_attr_list_adonis_euk$Treatment:V_attr_list_adonis_euk$Metacom_ID 0.369
## Residual
## TotalBray-Curtis distance model summaries
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = V_dis_euk, group =
## V_attr_list_adonis_euk$Treatment)
##
## No. of Positive Eigenvalues: 22
## No. of Negative Eigenvalues: 6
##
## Average distance to median:
## connected fragmented
## 0.4841 0.4586
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 28 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 2.1296 1.3515 0.8027 0.5912 0.4740 0.3737 0.2615 0.2186## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.00472 0.0047249 0.3925 0.5363
## Residuals 27 0.32506 0.0120391##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = V_dis_euk, group =
## V_attr_list_adonis_euk$Treatment:V_attr_list_adonis_euk$Metacom_ID)
##
## No. of Positive Eigenvalues: 22
## No. of Negative Eigenvalues: 6
##
## Average distance to median:
## connected:M1 connected:M2 connected:M3 fragmented:M4 fragmented:M5
## 0.3515 0.4673 0.4631 0.4353 0.4432
## fragmented:M6
## 0.3758
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 28 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 2.1296 1.3515 0.8027 0.5912 0.4740 0.3737 0.2615 0.2186## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 5 0.05212 0.010424 0.4523 0.8073
## Residuals 23 0.53012 0.023049Eukaryotes week 8
Adonis results
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = IX_abund_mat_euk ~ IX_attr_list_adonis_euk$Treatment + IX_attr_list_adonis_euk$Treatment:IX_attr_list_adonis_euk$Metacom_ID)
## Df
## IX_attr_list_adonis_euk$Treatment 1
## IX_attr_list_adonis_euk$Treatment:IX_attr_list_adonis_euk$Metacom_ID 4
## Residual 24
## Total 29
## SumOfSqs
## IX_attr_list_adonis_euk$Treatment 0.1809
## IX_attr_list_adonis_euk$Treatment:IX_attr_list_adonis_euk$Metacom_ID 0.8361
## Residual 4.4308
## Total 5.4478
## R2
## IX_attr_list_adonis_euk$Treatment 0.03321
## IX_attr_list_adonis_euk$Treatment:IX_attr_list_adonis_euk$Metacom_ID 0.15348
## Residual 0.81332
## Total 1.00000
## F
## IX_attr_list_adonis_euk$Treatment 0.9799
## IX_attr_list_adonis_euk$Treatment:IX_attr_list_adonis_euk$Metacom_ID 1.1322
## Residual
## Total
## Pr(>F)
## IX_attr_list_adonis_euk$Treatment 0.426
## IX_attr_list_adonis_euk$Treatment:IX_attr_list_adonis_euk$Metacom_ID 0.294
## Residual
## TotalBray-Curtis distance model summaries
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = IX_dis_euk, group =
## IX_attr_list_adonis_euk$Treatment)
##
## No. of Positive Eigenvalues: 20
## No. of Negative Eigenvalues: 9
##
## Average distance to median:
## connected fragmented
## 0.4205 0.3803
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 29 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 1.8622 0.9760 0.7010 0.4761 0.4094 0.3184 0.2271 0.1941## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.01216 0.012155 0.6603 0.4233
## Residuals 28 0.51544 0.018409##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = IX_dis_euk, group =
## IX_attr_list_adonis_euk$Treatment:IX_attr_list_adonis_euk$Metacom_ID)
##
## No. of Positive Eigenvalues: 20
## No. of Negative Eigenvalues: 9
##
## Average distance to median:
## connected:M1 connected:M2 connected:M3 fragmented:M4 fragmented:M5
## 0.4040 0.3464 0.4110 0.3482 0.3255
## fragmented:M6
## 0.3228
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 29 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 1.8622 0.9760 0.7010 0.4761 0.4094 0.3184 0.2271 0.1941## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 5 0.03713 0.0074252 0.2395 0.941
## Residuals 24 0.74421 0.0310089Eukaryotes week 12
Adonis results
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = X_abund_mat_euk ~ X_attr_list_adonis_euk$Treatment + X_attr_list_adonis_euk$Treatment:X_attr_list_adonis_euk$Metacom_ID)
## Df SumOfSqs
## X_attr_list_adonis_euk$Treatment 1 0.1557
## X_attr_list_adonis_euk$Treatment:X_attr_list_adonis_euk$Metacom_ID 4 1.8725
## Residual 23 3.8267
## Total 28 5.8548
## R2
## X_attr_list_adonis_euk$Treatment 0.02659
## X_attr_list_adonis_euk$Treatment:X_attr_list_adonis_euk$Metacom_ID 0.31982
## Residual 0.65360
## Total 1.00000
## F
## X_attr_list_adonis_euk$Treatment 0.9356
## X_attr_list_adonis_euk$Treatment:X_attr_list_adonis_euk$Metacom_ID 2.8136
## Residual
## Total
## Pr(>F)
## X_attr_list_adonis_euk$Treatment 0.406
## X_attr_list_adonis_euk$Treatment:X_attr_list_adonis_euk$Metacom_ID 0.002 **
## Residual
## Total
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Bray-Curtis distance model summaries
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = X_dis_euk, group =
## X_attr_list_adonis_euk$Treatment)
##
## No. of Positive Eigenvalues: 20
## No. of Negative Eigenvalues: 8
##
## Average distance to median:
## connected fragmented
## 0.4487 0.4138
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 28 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 2.6026 0.9759 0.4999 0.4778 0.3503 0.2304 0.2074 0.1586## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.00881 0.0088102 0.6691 0.4205
## Residuals 27 0.35550 0.0131668##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = X_dis_euk, group =
## X_attr_list_adonis_euk$Treatment:X_attr_list_adonis_euk$Metacom_ID)
##
## No. of Positive Eigenvalues: 20
## No. of Negative Eigenvalues: 8
##
## Average distance to median:
## connected:M1 connected:M2 connected:M3 fragmented:M4 fragmented:M5
## 0.2505 0.3741 0.3345 0.3474 0.2814
## fragmented:M6
## 0.3885
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 28 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 2.6026 0.9759 0.4999 0.4778 0.3503 0.2304 0.2074 0.1586## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 5 0.07181 0.014363 0.3818 0.856
## Residuals 23 0.86516 0.037616Eukaryotes week 16
Adonis results
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = XI_abund_mat_euk ~ XI_attr_list_adonis_euk$Treatment + XI_attr_list_adonis_euk$Treatment:XI_attr_list_adonis_euk$Metacom_ID)
## Df
## XI_attr_list_adonis_euk$Treatment 1
## XI_attr_list_adonis_euk$Treatment:XI_attr_list_adonis_euk$Metacom_ID 4
## Residual 24
## Total 29
## SumOfSqs
## XI_attr_list_adonis_euk$Treatment 0.6171
## XI_attr_list_adonis_euk$Treatment:XI_attr_list_adonis_euk$Metacom_ID 1.2410
## Residual 4.2162
## Total 6.0743
## R2
## XI_attr_list_adonis_euk$Treatment 0.10159
## XI_attr_list_adonis_euk$Treatment:XI_attr_list_adonis_euk$Metacom_ID 0.20431
## Residual 0.69410
## Total 1.00000
## F
## XI_attr_list_adonis_euk$Treatment 3.5126
## XI_attr_list_adonis_euk$Treatment:XI_attr_list_adonis_euk$Metacom_ID 1.7661
## Residual
## Total
## Pr(>F)
## XI_attr_list_adonis_euk$Treatment 0.001 ***
## XI_attr_list_adonis_euk$Treatment:XI_attr_list_adonis_euk$Metacom_ID 0.018 *
## Residual
## Total
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Bray-Curtis distance model summaries
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = XI_dis_euk, group =
## XI_attr_list_adonis_euk$Treatment)
##
## No. of Positive Eigenvalues: 24
## No. of Negative Eigenvalues: 5
##
## Average distance to median:
## connected fragmented
## 0.4413 0.3526
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 29 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 2.0064 0.9016 0.6599 0.5119 0.4158 0.3258 0.2838 0.2017## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.05898 0.058977 1.9932 0.169
## Residuals 28 0.82850 0.029589##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = XI_dis_euk, group =
## XI_attr_list_adonis_euk$Treatment:XI_attr_list_adonis_euk$Metacom_ID)
##
## No. of Positive Eigenvalues: 24
## No. of Negative Eigenvalues: 5
##
## Average distance to median:
## connected:M1 connected:M2 connected:M3 fragmented:M4 fragmented:M5
## 0.2491 0.4023 0.4747 0.3802 0.2670
## fragmented:M6
## 0.3551
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 29 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 2.0064 0.9016 0.6599 0.5119 0.4158 0.3258 0.2838 0.2017## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 5 0.1807 0.036140 2.5047 0.05831 .
## Residuals 24 0.3463 0.014429
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1