Scree Plots
Alan Ivory
2026-03-04
Species Matrix Function
Stress Runs
## Running for rarity threshold: 0 %
## Running for rarity threshold: 1 %
## Running for rarity threshold: 3 %
## Running for rarity threshold: 5 %
## Running for rarity threshold: 10 %## rarity k stress num_species
## 1 0 1 0.38520883 548
## 2 0 2 0.24220372 548
## 3 0 3 0.16074765 548
## 4 0 4 0.11950969 548
## 5 0 5 0.09863375 548
## 6 0 6 0.08297024 548
## 7 0 7 0.07216692 548
## 8 0 8 0.06467785 548
## 9 1 1 0.38718256 356
## 10 1 2 0.24139698 356
## 11 1 3 0.16038761 356
## 12 1 4 0.11919702 356
## 13 1 5 0.09823081 356
## 14 1 6 0.08250165 356
## 15 1 7 0.07174312 356
## 16 1 8 0.06427810 356
## 17 3 1 0.38997907 206
## 18 3 2 0.24013265 206
## 19 3 3 0.16012555 206
## 20 3 4 0.11871262 206
## 21 3 5 0.09759422 206
## 22 3 6 0.08173536 206
## 23 3 7 0.07084584 206
## 24 3 8 0.06339472 206
## 25 5 1 0.38929924 152
## 26 5 2 0.23834690 152
## 27 5 3 0.15961936 152
## 28 5 4 0.11818930 152
## 29 5 5 0.09697712 152
## 30 5 6 0.08100495 152
## 31 5 7 0.07024635 152
## 32 5 8 0.06279613 152
## 33 10 1 0.38896436 80
## 34 10 2 0.23718302 80
## 35 10 3 0.15898442 80
## 36 10 4 0.11673687 80
## 37 10 5 0.09549772 80
## 38 10 6 0.07955317 80
## 39 10 7 0.06914362 80
## 40 10 8 0.06160368 80Scree Plots
Final NMDS
## Run 0 stress 0.1195121
## Run 1 stress 0.1195097
## ... New best solution
## ... Procrustes: rmse 0.0009303014 max resid 0.01120289
## Run 2 stress 0.1195105
## ... Procrustes: rmse 0.0005461896 max resid 0.00412627
## ... Similar to previous best
## Run 3 stress 0.1195677
## ... Procrustes: rmse 0.004893949 max resid 0.06161007
## Run 4 stress 0.1199193
## ... Procrustes: rmse 0.006825636 max resid 0.0687013
## Run 5 stress 0.1195099
## ... Procrustes: rmse 0.0005013257 max resid 0.004357373
## ... Similar to previous best
## Run 6 stress 0.1195661
## ... Procrustes: rmse 0.003106919 max resid 0.03160956
## Run 7 stress 0.1195537
## ... Procrustes: rmse 0.004039909 max resid 0.03446183
## Run 8 stress 0.1195222
## ... Procrustes: rmse 0.002448576 max resid 0.03094683
## Run 9 stress 0.1195227
## ... Procrustes: rmse 0.002430515 max resid 0.03090869
## Run 10 stress 0.1199253
## ... Procrustes: rmse 0.007076496 max resid 0.06870056
## Run 11 stress 0.1195662
## ... Procrustes: rmse 0.004914426 max resid 0.06253942
## Run 12 stress 0.1198714
## ... Procrustes: rmse 0.005572213 max resid 0.06915403
## Run 13 stress 0.1199073
## ... Procrustes: rmse 0.005354754 max resid 0.06864509
## Run 14 stress 0.119872
## ... Procrustes: rmse 0.005466139 max resid 0.06911808
## Run 15 stress 0.119566
## ... Procrustes: rmse 0.004911941 max resid 0.06261103
## Run 16 stress 0.1195923
## ... Procrustes: rmse 0.004973774 max resid 0.05838658
## Run 17 stress 0.1195106
## ... Procrustes: rmse 0.0005206667 max resid 0.005465723
## ... Similar to previous best
## Run 18 stress 0.1195228
## ... Procrustes: rmse 0.002219364 max resid 0.03010937
## Run 19 stress 0.1195914
## ... Procrustes: rmse 0.004929944 max resid 0.05758632
## Run 20 stress 0.1195921
## ... Procrustes: rmse 0.005136055 max resid 0.05801794
## *** Best solution repeated 3 times## [1] 0.1195097Justification Plot
Ordination with Environmental Overlay
## [1] "Latitude" "Longitude" "BurnYear"
## [4] "Avg_Cogongrass_Cover"Patchwork
Plot of subplots B and C
PERMANOVA
## [1] TRUE## Permutation test for adonis under reduced model
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist_matrix ~ Avg_Cogongrass_Cover, data = plot_metadata, permutations = 999, strata = plot_metadata$Site)
## Df SumOfSqs R2 F Pr(>F)
## Model 1 5.949 0.15694 37.977 0.001 ***
## Residual 204 31.956 0.84306
## Total 205 37.905 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Regional NMDS and PERMANOVA
Regional Groups
Run Each Region
##
## =============================
## Region: Central FL
## Sites: ONF, WSF
## =============================
## Stress: 0.08978136
## Permutation test for adonis under reduced model
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist_matrix ~ Imperata_cylindrica, data = region_species_matrix, permutations = 999)
## Df SumOfSqs R2 F Pr(>F)
## Model 1 1.2467 0.15382 9.0893 0.001 ***
## Residual 50 6.8580 0.84618
## Total 51 8.1047 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## =============================
## Region: North FL
## Sites: BRSF, Escambia, Jay, Howell, Hooper
## =============================
## Stress: 0.100787
## Permutation test for adonis under reduced model
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist_matrix ~ Imperata_cylindrica, data = region_species_matrix, permutations = 999)
## Df SumOfSqs R2 F Pr(>F)
## Model 1 1.7588 0.16019 13.924 0.001 ***
## Residual 73 9.2211 0.83981
## Total 74 10.9800 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## =============================
## Region: South MS
## Sites: CNF, DSNF, BCNWR
## =============================
## Stress: 0.1075478
## Permutation test for adonis under reduced model
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist_matrix ~ Imperata_cylindrica, data = region_species_matrix, permutations = 999)
## Df SumOfSqs R2 F Pr(>F)
## Model 1 3.2659 0.22467 22.312 0.001 ***
## Residual 77 11.2708 0.77533
## Total 78 14.5367 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Central Florida Ordination Plot
North Florida Ordination Plot
South Mississippi Ordination Plot
Patchwork
combine the three regional NMDS plots into a single figure