Species Matrix
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 0.38711297 550
## 2 0 2 0.24222866 550
## 3 0 3 0.16078237 550
## 4 0 4 0.11954148 550
## 5 0 5 0.09866497 550
## 6 0 6 0.08298410 550
## 7 0 7 0.07217471 550
## 8 0 8 0.06469312 550
## 9 1 1 0.38527192 358
## 10 1 2 0.24142802 358
## 11 1 3 0.16039409 358
## 12 1 4 0.11919480 358
## 13 1 5 0.09822518 358
## 14 1 6 0.08249494 358
## 15 1 7 0.07174614 358
## 16 1 8 0.06427661 358
## 17 3 1 0.38997384 208
## 18 3 2 0.24015118 208
## 19 3 3 0.16014430 208
## 20 3 4 0.11871759 208
## 21 3 5 0.09760716 208
## 22 3 6 0.08173640 208
## 23 3 7 0.07085879 208
## 24 3 8 0.06339706 208
## 25 5 1 0.38890659 154
## 26 5 2 0.23840062 154
## 27 5 3 0.15964342 154
## 28 5 4 0.11819719 154
## 29 5 5 0.09698724 154
## 30 5 6 0.08100519 154
## 31 5 7 0.07025112 154
## 32 5 8 0.06280129 154
## 33 10 1 0.38697659 82
## 34 10 2 0.23719685 82
## 35 10 3 0.15900872 82
## 36 10 4 0.11673975 82
## 37 10 5 0.09550392 82
## 38 10 6 0.07954828 82
## 39 10 7 0.06914625 82
## 40 10 8 0.06160040 82
Scree Plots
Final NMDS
## Run 0 stress 0.1195461
## Run 1 stress 0.119542
## ... New best solution
## ... Procrustes: rmse 0.0009741319 max resid 0.01133963
## Run 2 stress 0.1195421
## ... Procrustes: rmse 0.0004486076 max resid 0.00332522
## ... Similar to previous best
## Run 3 stress 0.1196013
## ... Procrustes: rmse 0.004785988 max resid 0.06006632
## Run 4 stress 0.1199822
## ... Procrustes: rmse 0.007121642 max resid 0.0718691
## Run 5 stress 0.1195415
## ... New best solution
## ... Procrustes: rmse 0.000398396 max resid 0.003925513
## ... Similar to previous best
## Run 6 stress 0.119569
## ... Procrustes: rmse 0.003643356 max resid 0.03210011
## Run 7 stress 0.1196603
## ... Procrustes: rmse 0.006126221 max resid 0.05820723
## Run 8 stress 0.1195426
## ... Procrustes: rmse 0.0004588069 max resid 0.00528717
## ... Similar to previous best
## Run 9 stress 0.1195527
## ... Procrustes: rmse 0.002434481 max resid 0.03104018
## Run 10 stress 0.1199665
## ... Procrustes: rmse 0.007307479 max resid 0.07201575
## Run 11 stress 0.1195981
## ... Procrustes: rmse 0.004799453 max resid 0.06139769
## Run 12 stress 0.1199011
## ... Procrustes: rmse 0.005806804 max resid 0.07233544
## Run 13 stress 0.1195425
## ... Procrustes: rmse 0.0002797275 max resid 0.002678431
## ... Similar to previous best
## Run 14 stress 0.1199015
## ... Procrustes: rmse 0.005687182 max resid 0.07228929
## Run 15 stress 0.1195985
## ... Procrustes: rmse 0.004845361 max resid 0.0620395
## Run 16 stress 0.1196225
## ... Procrustes: rmse 0.004774197 max resid 0.05462412
## Run 17 stress 0.119542
## ... Procrustes: rmse 0.0002344686 max resid 0.002062469
## ... Similar to previous best
## Run 18 stress 0.1195532
## ... Procrustes: rmse 0.002259107 max resid 0.03036973
## Run 19 stress 0.1195529
## ... Procrustes: rmse 0.002330175 max resid 0.03026088
## Run 20 stress 0.1196199
## ... Procrustes: rmse 0.004087998 max resid 0.03817144
## *** Best solution repeated 4 times
## [1] 0.1195415
Justification Plot
Main Ordination Plot (Community Composition)
Ordination with Environmental Overlay
## [1] "Latitude" "Longitude" "BurnYear"
## [4] "Avg_Cogongrass_Cover"
Patchwork
