Scree Plots
Alan Ivory
2026-02-27
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 0.38521754 549
## 2 0 2 0.24221452 549
## 3 0 3 0.16077353 549
## 4 0 4 0.11951511 549
## 5 0 5 0.09864276 549
## 6 0 6 0.08296758 549
## 7 0 7 0.07216772 549
## 8 0 8 0.06468389 549
## 9 1 1 0.38527623 357
## 10 1 2 0.24140857 357
## 11 1 3 0.16040530 357
## 12 1 4 0.11919975 357
## 13 1 5 0.09823543 357
## 14 1 6 0.08249768 357
## 15 1 7 0.07177339 357
## 16 1 8 0.06428049 357
## 17 3 1 0.38999008 207
## 18 3 2 0.24014430 207
## 19 3 3 0.16014299 207
## 20 3 4 0.11871448 207
## 21 3 5 0.09759811 207
## 22 3 6 0.08173606 207
## 23 3 7 0.07086806 207
## 24 3 8 0.06339915 207
## 25 5 1 0.38933393 153
## 26 5 2 0.23835081 153
## 27 5 3 0.15964358 153
## 28 5 4 0.11819455 153
## 29 5 5 0.09698774 153
## 30 5 6 0.08100270 153
## 31 5 7 0.07025120 153
## 32 5 8 0.06279758 153
## 33 10 1 0.38698724 81
## 34 10 2 0.23719349 81
## 35 10 3 0.15901046 81
## 36 10 4 0.11674423 81
## 37 10 5 0.09550378 81
## 38 10 6 0.07955027 81
## 39 10 7 0.06915074 81
## 40 10 8 0.06160300 81Scree Plots
Final NMDS
## Run 0 stress 0.1195177
## Run 1 stress 0.1195151
## ... New best solution
## ... Procrustes: rmse 0.0009024113 max resid 0.01087575
## Run 2 stress 0.1195154
## ... Procrustes: rmse 0.00045647 max resid 0.003404618
## ... Similar to previous best
## Run 3 stress 0.1195766
## ... Procrustes: rmse 0.004947761 max resid 0.0617355
## Run 4 stress 0.1199226
## ... Procrustes: rmse 0.006798825 max resid 0.06868266
## Run 5 stress 0.1195153
## ... Procrustes: rmse 0.0004869649 max resid 0.004109183
## ... Similar to previous best
## Run 6 stress 0.119544
## ... Procrustes: rmse 0.00348909 max resid 0.03200252
## Run 7 stress 0.1195847
## ... Procrustes: rmse 0.004717148 max resid 0.04314792
## Run 8 stress 0.1195156
## ... Procrustes: rmse 0.0005672559 max resid 0.004734595
## ... Similar to previous best
## Run 9 stress 0.1195285
## ... Procrustes: rmse 0.002417111 max resid 0.03094708
## Run 10 stress 0.119931
## ... Procrustes: rmse 0.007112581 max resid 0.0686961
## Run 11 stress 0.1195728
## ... Procrustes: rmse 0.004911301 max resid 0.0625611
## Run 12 stress 0.1198741
## ... Procrustes: rmse 0.005550125 max resid 0.06910745
## Run 13 stress 0.1198612
## ... Procrustes: rmse 0.004992138 max resid 0.06877693
## Run 14 stress 0.1198752
## ... Procrustes: rmse 0.005474878 max resid 0.06906896
## Run 15 stress 0.1195722
## ... Procrustes: rmse 0.004891018 max resid 0.06239054
## Run 16 stress 0.1195997
## ... Procrustes: rmse 0.004950931 max resid 0.0579671
## Run 17 stress 0.1195157
## ... Procrustes: rmse 0.0004898192 max resid 0.004670872
## ... Similar to previous best
## Run 18 stress 0.1195295
## ... Procrustes: rmse 0.00221816 max resid 0.03009831
## Run 19 stress 0.1195991
## ... Procrustes: rmse 0.005152094 max resid 0.06091113
## Run 20 stress 0.1195999
## ... Procrustes: rmse 0.005128798 max resid 0.05798112
## *** Best solution repeated 4 times## [1] 0.1195151Justification 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 0.15693 37.973 0.001 ***
## Residual 204 31.957 0.84307
## Total 205 37.906 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: 0.1075255
## 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 3.2657 0.22463 22.308 0.001 ***
## Residual 77 11.2725 0.77537
## Total 78 14.5382 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