Veg Models EmMeans
Jonathan Spiess
October 14, 2021
#Broad FG models
##Grass
TSF only: RB < NYB and 3yr
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Grass
## Chisq Df Pr(>Chisq)
## TSF 23.4592 3 3.239e-05 ***
## Management 0.2547 1 0.6138
## TSF:Management 1.9236 3 0.5884
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 34.4 1.90 15.5 30.3 38.4
## Intermediate 39.3 1.86 14.0 35.3 43.3
## 3 Years Since Fire 45.7 3.25 110.3 39.2 52.1
## Not Yet Burned 41.5 1.82 12.8 37.5 45.4
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -4.92 1.85 285 -2.657 0.0413
## Recently Burned - 3 Years Since Fire -11.31 3.24 293 -3.484 0.0032
## Recently Burned - Not Yet Burned -7.10 1.81 289 -3.912 0.0007
## Intermediate - 3 Years Since Fire -6.39 3.10 289 -2.062 0.1681
## Intermediate - Not Yet Burned -2.18 1.92 283 -1.135 0.6682
## 3 Years Since Fire - Not Yet Burned 4.21 3.39 288 1.242 0.6005
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 34.4 1.90 15.5 30.3 38.4
## Intermediate 39.3 1.86 14.0 35.3 43.3
## 3 Years Since Fire 45.7 3.25 110.3 39.2 52.1
## Not Yet Burned 41.5 1.82 12.8 37.5 45.4
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -4.92 1.85 285 -9.70 -0.135
## Recently Burned - 3 Years Since Fire -11.31 3.24 293 -19.69 -2.922
## Recently Burned - Not Yet Burned -7.10 1.81 289 -11.79 -2.409
## Intermediate - 3 Years Since Fire -6.39 3.10 289 -14.40 1.617
## Intermediate - Not Yet Burned -2.18 1.92 283 -7.15 2.785
## 3 Years Since Fire - Not Yet Burned 4.21 3.39 288 -4.55 12.963
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates##Forb
TSF, Grazer, and interaction significant
Overall TSF: Intermediate > NYB
Overall Grazer: Cattle > Sheep
Interaction: No tsf differences in sheep. RB & Intermediate > NYB in cattle
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Forb + 1)
## Chisq Df Pr(>Chisq)
## TSF 9.8304 3 0.02006 *
## Management 6.4838 1 0.01089 *
## TSF:Management 14.9841 3 0.00183 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.40 0.187 12.4 0.996 1.81
## Intermediate 1.52 0.186 11.9 1.113 1.92
## 3 Years Since Fire 1.47 0.232 36.7 1.002 1.94
## Not Yet Burned 1.22 0.185 11.5 0.814 1.62
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.1159 0.0974 286 -1.190 0.6336
## Recently Burned - 3 Years Since Fire -0.0710 0.1702 291 -0.417 0.9755
## Recently Burned - Not Yet Burned 0.1841 0.0953 289 1.931 0.2174
## Intermediate - 3 Years Since Fire 0.0448 0.1629 289 0.275 0.9927
## Intermediate - Not Yet Burned 0.3000 0.1002 265 2.995 0.0158
## 3 Years Since Fire - Not Yet Burned 0.2551 0.1768 273 1.443 0.4736
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.40 0.187 12.4 0.996 1.81
## Intermediate 1.52 0.186 11.9 1.113 1.92
## 3 Years Since Fire 1.47 0.232 36.7 1.002 1.94
## Not Yet Burned 1.22 0.185 11.5 0.814 1.62
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.1159 0.0974 286 -0.3675 0.136
## Recently Burned - 3 Years Since Fire -0.0710 0.1702 291 -0.5109 0.369
## Recently Burned - Not Yet Burned 0.1841 0.0953 289 -0.0623 0.430
## Intermediate - 3 Years Since Fire 0.0448 0.1629 289 -0.3761 0.466
## Intermediate - Not Yet Burned 0.3000 0.1002 265 0.0410 0.559
## 3 Years Since Fire - Not Yet Burned 0.2551 0.1768 273 -0.2019 0.712
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Management emmean SE df lower.CL upper.CL
## Cattle 1.823 0.254 9.81 1.257 2.39
## Sheep 0.983 0.254 9.82 0.416 1.55
##
## Results are averaged over the levels of: TSF
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Cattle - Sheep 0.84 0.359 9.82 2.343 0.0416
##
## Results are averaged over the levels of: TSF
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Management emmean SE df lower.CL upper.CL
## Cattle 1.823 0.254 9.81 1.257 2.39
## Sheep 0.983 0.254 9.82 0.416 1.55
##
## Results are averaged over the levels of: TSF
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Cattle - Sheep 0.84 0.359 9.82 0.039 1.64
##
## Results are averaged over the levels of: TSF
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95## $emmeans
## Management = Cattle:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.909 0.264 12.4 1.335 2.48
## Intermediate 1.973 0.262 11.9 1.401 2.55
## 3 Years Since Fire 2.021 0.329 36.7 1.355 2.69
## Not Yet Burned 1.389 0.261 11.5 0.818 1.96
##
## Management = Sheep:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 0.895 0.264 12.4 0.321 1.47
## Intermediate 1.063 0.263 12.0 0.490 1.64
## 3 Years Since Fire 0.925 0.329 36.7 0.259 1.59
## Not Yet Burned 1.047 0.261 11.6 0.475 1.62
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Management = Cattle:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.0638 0.137 286 -0.465 0.9666
## Recently Burned - 3 Years Since Fire -0.1121 0.241 291 -0.466 0.9664
## Recently Burned - Not Yet Burned 0.5200 0.135 290 3.861 0.0008
## Intermediate - 3 Years Since Fire -0.0484 0.230 289 -0.210 0.9967
## Intermediate - Not Yet Burned 0.5838 0.141 264 4.141 0.0003
## 3 Years Since Fire - Not Yet Burned 0.6321 0.250 273 2.530 0.0576
##
## Management = Sheep:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.1680 0.138 286 -1.215 0.6178
## Recently Burned - 3 Years Since Fire -0.0300 0.241 291 -0.124 0.9993
## Recently Burned - Not Yet Burned -0.1518 0.135 289 -1.125 0.6745
## Intermediate - 3 Years Since Fire 0.1380 0.230 289 0.599 0.9323
## Intermediate - Not Yet Burned 0.0162 0.142 266 0.114 0.9995
## 3 Years Since Fire - Not Yet Burned -0.1219 0.250 273 -0.487 0.9619
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Management = Cattle:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.909 0.264 12.4 1.335 2.48
## Intermediate 1.973 0.262 11.9 1.401 2.55
## 3 Years Since Fire 2.021 0.329 36.7 1.355 2.69
## Not Yet Burned 1.389 0.261 11.5 0.818 1.96
##
## Management = Sheep:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 0.895 0.264 12.4 0.321 1.47
## Intermediate 1.063 0.263 12.0 0.490 1.64
## 3 Years Since Fire 0.925 0.329 36.7 0.259 1.59
## Not Yet Burned 1.047 0.261 11.6 0.475 1.62
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Management = Cattle:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.0638 0.137 286 -0.4181 0.291
## Recently Burned - 3 Years Since Fire -0.1121 0.241 291 -0.7339 0.510
## Recently Burned - Not Yet Burned 0.5200 0.135 290 0.1720 0.868
## Intermediate - 3 Years Since Fire -0.0484 0.230 289 -0.6435 0.547
## Intermediate - Not Yet Burned 0.5838 0.141 264 0.2193 0.948
## 3 Years Since Fire - Not Yet Burned 0.6321 0.250 273 -0.0138 1.278
##
## Management = Sheep:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.1680 0.138 286 -0.5253 0.189
## Recently Burned - 3 Years Since Fire -0.0300 0.241 291 -0.6522 0.592
## Recently Burned - Not Yet Burned -0.1518 0.135 289 -0.5006 0.197
## Intermediate - 3 Years Since Fire 0.1380 0.230 289 -0.4575 0.734
## Intermediate - Not Yet Burned 0.0162 0.142 266 -0.3518 0.384
## 3 Years Since Fire - Not Yet Burned -0.1219 0.250 273 -0.7685 0.525
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates##Legume
TSF, Grazer, and interaction significant
Overall TSF: Intermediate < NYB
Overall Grazer: Cattle almost > Sheep
Interaction: No tsf differences in sheep. RB, NYB, 3yr > Intermediate
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Legume + 1)
## Chisq Df Pr(>Chisq)
## TSF 15.0395 3 0.001783 **
## Management 9.6675 1 0.001876 **
## TSF:Management 13.4867 3 0.003694 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see ?isSingular## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 2.06 0.142 9.25 1.74 2.38
## Intermediate 1.81 0.141 8.81 1.49 2.13
## 3 Years Since Fire 1.71 0.219 50.18 1.27 2.14
## Not Yet Burned 2.25 0.139 8.37 1.93 2.57
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate 0.246 0.115 281 2.136 0.1444
## Recently Burned - 3 Years Since Fire 0.354 0.203 288 1.740 0.3048
## Recently Burned - Not Yet Burned -0.191 0.113 284 -1.685 0.3337
## Intermediate - 3 Years Since Fire 0.108 0.193 283 0.557 0.9447
## Intermediate - Not Yet Burned -0.437 0.122 294 -3.587 0.0022
## 3 Years Since Fire - Not Yet Burned -0.544 0.214 294 -2.541 0.0558
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 2.06 0.142 9.25 1.74 2.38
## Intermediate 1.81 0.141 8.81 1.49 2.13
## 3 Years Since Fire 1.71 0.219 50.18 1.27 2.14
## Not Yet Burned 2.25 0.139 8.37 1.93 2.57
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate 0.246 0.115 281 -0.0517 0.54383
## Recently Burned - 3 Years Since Fire 0.354 0.203 288 -0.1715 0.87876
## Recently Burned - Not Yet Burned -0.191 0.113 284 -0.4835 0.10192
## Intermediate - 3 Years Since Fire 0.108 0.193 283 -0.3918 0.60694
## Intermediate - Not Yet Burned -0.437 0.122 294 -0.7516 -0.12220
## 3 Years Since Fire - Not Yet Burned -0.544 0.214 294 -1.0980 0.00914
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Management emmean SE df lower.CL upper.CL
## Cattle 2.26 0.181 5.95 1.81 2.7
## Sheep 1.66 0.182 5.97 1.21 2.1
##
## Results are averaged over the levels of: TSF
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Cattle - Sheep 0.602 0.257 5.96 2.347 0.0576
##
## Results are averaged over the levels of: TSF
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Management emmean SE df lower.CL upper.CL
## Cattle 2.26 0.181 5.95 1.81 2.7
## Sheep 1.66 0.182 5.97 1.21 2.1
##
## Results are averaged over the levels of: TSF
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Cattle - Sheep 0.602 0.257 5.96 -0.0268 1.23
##
## Results are averaged over the levels of: TSF
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95## boundary (singular) fit: see ?isSingular## $emmeans
## Management = Cattle:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 2.51 0.201 9.25 2.05 2.96
## Intermediate 1.95 0.198 8.71 1.50 2.40
## 3 Years Since Fire 1.78 0.309 50.13 1.16 2.40
## Not Yet Burned 2.79 0.197 8.35 2.34 3.24
##
## Management = Sheep:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.61 0.201 9.25 1.16 2.07
## Intermediate 1.67 0.200 8.91 1.22 2.13
## 3 Years Since Fire 1.63 0.309 50.23 1.01 2.25
## Not Yet Burned 1.71 0.197 8.39 1.26 2.16
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Management = Cattle:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate 0.5530 0.162 281 3.408 0.0042
## Recently Burned - 3 Years Since Fire 0.7231 0.287 288 2.517 0.0594
## Recently Burned - Not Yet Burned -0.2869 0.160 284 -1.793 0.2789
## Intermediate - 3 Years Since Fire 0.1701 0.273 283 0.623 0.9248
## Intermediate - Not Yet Burned -0.8399 0.171 294 -4.899 <.0001
## 3 Years Since Fire - Not Yet Burned -1.0100 0.303 294 -3.336 0.0053
##
## Management = Sheep:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.0609 0.164 281 -0.372 0.9824
## Recently Burned - 3 Years Since Fire -0.0159 0.288 288 -0.055 0.9999
## Recently Burned - Not Yet Burned -0.0947 0.160 284 -0.591 0.9349
## Intermediate - 3 Years Since Fire 0.0450 0.273 283 0.165 0.9984
## Intermediate - Not Yet Burned -0.0338 0.173 294 -0.195 0.9974
## 3 Years Since Fire - Not Yet Burned -0.0788 0.303 294 -0.260 0.9938
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see ?isSingular## $emmeans
## Management = Cattle:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 2.51 0.201 9.25 2.05 2.96
## Intermediate 1.95 0.198 8.71 1.50 2.40
## 3 Years Since Fire 1.78 0.309 50.13 1.16 2.40
## Not Yet Burned 2.79 0.197 8.35 2.34 3.24
##
## Management = Sheep:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.61 0.201 9.25 1.16 2.07
## Intermediate 1.67 0.200 8.91 1.22 2.13
## 3 Years Since Fire 1.63 0.309 50.23 1.01 2.25
## Not Yet Burned 1.71 0.197 8.39 1.26 2.16
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Management = Cattle:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate 0.5530 0.162 281 0.1336 0.972
## Recently Burned - 3 Years Since Fire 0.7231 0.287 288 -0.0192 1.465
## Recently Burned - Not Yet Burned -0.2869 0.160 284 -0.7005 0.127
## Intermediate - 3 Years Since Fire 0.1701 0.273 283 -0.5359 0.876
## Intermediate - Not Yet Burned -0.8399 0.171 294 -1.2829 -0.397
## 3 Years Since Fire - Not Yet Burned -1.0100 0.303 294 -1.7924 -0.228
##
## Management = Sheep:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.0609 0.164 281 -0.4837 0.362
## Recently Burned - 3 Years Since Fire -0.0159 0.288 288 -0.7588 0.727
## Recently Burned - Not Yet Burned -0.0947 0.160 284 -0.5091 0.320
## Intermediate - 3 Years Since Fire 0.0450 0.273 283 -0.6614 0.751
## Intermediate - Not Yet Burned -0.0338 0.173 294 -0.4809 0.413
## 3 Years Since Fire - Not Yet Burned -0.0788 0.303 294 -0.8623 0.705
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates#Structure
##VOR
TSFsignificant
Overall TSF: RB < others; Intermediate & 3yr > NYB
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(VOR_Mean + 1)
## Chisq Df Pr(>Chisq)
## TSF 77.8325 3 <2e-16 ***
## Management 0.9452 1 0.3310
## TSF:Management 0.9507 3 0.8132
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df asymp.LCL asymp.UCL
## Recently Burned 0.738 0.0399 Inf 0.659 0.816
## Intermediate 1.152 0.0371 Inf 1.080 1.225
## 3 Years Since Fire 1.236 0.0787 Inf 1.082 1.390
## Not Yet Burned 0.984 0.0349 Inf 0.915 1.052
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df z.ratio p.value
## Recently Burned - Intermediate -0.4147 0.0505 Inf -8.221 <.0001
## Recently Burned - 3 Years Since Fire -0.4984 0.0858 Inf -5.810 <.0001
## Recently Burned - Not Yet Burned -0.2460 0.0489 Inf -5.033 <.0001
## Intermediate - 3 Years Since Fire -0.0837 0.0833 Inf -1.005 0.7465
## Intermediate - Not Yet Burned 0.1688 0.0482 Inf 3.503 0.0026
## 3 Years Since Fire - Not Yet Burned 0.2525 0.0855 Inf 2.953 0.0166
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df asymp.LCL asymp.UCL
## Recently Burned 0.738 0.0399 Inf 0.659 0.816
## Intermediate 1.152 0.0371 Inf 1.080 1.225
## 3 Years Since Fire 1.236 0.0787 Inf 1.082 1.390
## Not Yet Burned 0.984 0.0349 Inf 0.915 1.052
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df asymp.LCL asymp.UCL
## Recently Burned - Intermediate -0.4147 0.0505 Inf -0.5443 -0.285
## Recently Burned - 3 Years Since Fire -0.4984 0.0858 Inf -0.7188 -0.278
## Recently Burned - Not Yet Burned -0.2460 0.0489 Inf -0.3715 -0.120
## Intermediate - 3 Years Since Fire -0.0837 0.0833 Inf -0.2977 0.130
## Intermediate - Not Yet Burned 0.1688 0.0482 Inf 0.0450 0.293
## 3 Years Since Fire - Not Yet Burned 0.2525 0.0855 Inf 0.0329 0.472
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates
##MaxLive
TSFsignificant
Overall TSF: RB < Intermediate; Intermediate > NYB
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: MaxLive
## Chisq Df Pr(>Chisq)
## TSF 32.8300 3 3.498e-07 ***
## Management 1.4061 1 0.2357
## TSF:Management 2.0785 3 0.5563
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df asymp.LCL asymp.UCL
## Recently Burned 5.12 0.222 Inf 4.69 5.56
## Intermediate 6.74 0.204 Inf 6.34 7.14
## 3 Years Since Fire 6.16 0.443 Inf 5.29 7.03
## Not Yet Burned 5.73 0.190 Inf 5.36 6.11
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df z.ratio p.value
## Recently Burned - Intermediate -1.621 0.288 Inf -5.620 <.0001
## Recently Burned - 3 Years Since Fire -1.035 0.487 Inf -2.124 0.1455
## Recently Burned - Not Yet Burned -0.609 0.279 Inf -2.184 0.1276
## Intermediate - 3 Years Since Fire 0.586 0.475 Inf 1.234 0.6053
## Intermediate - Not Yet Burned 1.012 0.270 Inf 3.745 0.0010
## 3 Years Since Fire - Not Yet Burned 0.426 0.480 Inf 0.887 0.8119
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## P value adjustment: tukey method for comparing a family of 4 estimates## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df asymp.LCL asymp.UCL
## Recently Burned 5.12 0.222 Inf 4.69 5.56
## Intermediate 6.74 0.204 Inf 6.34 7.14
## 3 Years Since Fire 6.16 0.443 Inf 5.29 7.03
## Not Yet Burned 5.73 0.190 Inf 5.36 6.11
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df asymp.LCL asymp.UCL
## Recently Burned - Intermediate -1.621 0.288 Inf -2.361 -0.880
## Recently Burned - 3 Years Since Fire -1.035 0.487 Inf -2.287 0.217
## Recently Burned - Not Yet Burned -0.609 0.279 Inf -1.325 0.107
## Intermediate - 3 Years Since Fire 0.586 0.475 Inf -0.634 1.805
## Intermediate - Not Yet Burned 1.012 0.270 Inf 0.318 1.705
## 3 Years Since Fire - Not Yet Burned 0.426 0.480 Inf -0.808 1.660
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates##MaxDead
TSFsignificant
Overall TSF: RB < all patches, 3yr > NYB & Intermediate, Intermediate > NYB
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: MaxDead
## Chisq Df Pr(>Chisq)
## TSF 266.5123 3 <2e-16 ***
## Management 1.9035 1 0.1677
## TSF:Management 3.8931 3 0.2732
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df asymp.LCL asymp.UCL
## Recently Burned 1.01 0.134 Inf 0.745 1.27
## Intermediate 3.02 0.124 Inf 2.781 3.27
## 3 Years Since Fire 5.23 0.265 Inf 4.711 5.75
## Not Yet Burned 2.13 0.117 Inf 1.899 2.36
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df z.ratio p.value
## Recently Burned - Intermediate -2.017 0.171 Inf -11.817 <.0001
## Recently Burned - 3 Years Since Fire -4.223 0.290 Inf -14.575 <.0001
## Recently Burned - Not Yet Burned -1.120 0.165 Inf -6.781 <.0001
## Intermediate - 3 Years Since Fire -2.206 0.282 Inf -7.832 <.0001
## Intermediate - Not Yet Burned 0.897 0.162 Inf 5.530 <.0001
## 3 Years Since Fire - Not Yet Burned 3.102 0.288 Inf 10.776 <.0001
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## P value adjustment: tukey method for comparing a family of 4 estimates## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df asymp.LCL asymp.UCL
## Recently Burned 1.01 0.134 Inf 0.745 1.27
## Intermediate 3.02 0.124 Inf 2.781 3.27
## 3 Years Since Fire 5.23 0.265 Inf 4.711 5.75
## Not Yet Burned 2.13 0.117 Inf 1.899 2.36
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df asymp.LCL asymp.UCL
## Recently Burned - Intermediate -2.017 0.171 Inf -2.46 -1.579
## Recently Burned - 3 Years Since Fire -4.223 0.290 Inf -4.97 -3.478
## Recently Burned - Not Yet Burned -1.120 0.165 Inf -1.54 -0.696
## Intermediate - 3 Years Since Fire -2.206 0.282 Inf -2.93 -1.482
## Intermediate - Not Yet Burned 0.897 0.162 Inf 0.48 1.313
## 3 Years Since Fire - Not Yet Burned 3.102 0.288 Inf 2.36 3.842
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates##LitMean
TSFsignificant
Overall TSF: RB < others, 3yr > Intermediate & NYB
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(LitMean + 1)
## Chisq Df Pr(>Chisq)
## TSF 113.6207 3 <2e-16 ***
## Management 0.9511 1 0.3294
## TSF:Management 1.1601 3 0.7626
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df asymp.LCL asymp.UCL
## Recently Burned 0.548 0.0389 Inf 0.472 0.625
## Intermediate 0.859 0.0347 Inf 0.791 0.927
## 3 Years Since Fire 1.370 0.0778 Inf 1.218 1.523
## Not Yet Burned 0.943 0.0317 Inf 0.881 1.005
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df z.ratio p.value
## Recently Burned - Intermediate -0.311 0.0521 Inf -5.969 <.0001
## Recently Burned - 3 Years Since Fire -0.822 0.0869 Inf -9.456 <.0001
## Recently Burned - Not Yet Burned -0.395 0.0502 Inf -7.867 <.0001
## Intermediate - 3 Years Since Fire -0.511 0.0851 Inf -6.004 <.0001
## Intermediate - Not Yet Burned -0.084 0.0470 Inf -1.786 0.2799
## 3 Years Since Fire - Not Yet Burned 0.427 0.0840 Inf 5.087 <.0001
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 6328' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 6328)' or larger];
## but be warned that this may result in large computation time and memory use.## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df asymp.LCL asymp.UCL
## Recently Burned 0.548 0.0389 Inf 0.472 0.625
## Intermediate 0.859 0.0347 Inf 0.791 0.927
## 3 Years Since Fire 1.370 0.0778 Inf 1.218 1.523
## Not Yet Burned 0.943 0.0317 Inf 0.881 1.005
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df asymp.LCL asymp.UCL
## Recently Burned - Intermediate -0.311 0.0521 Inf -0.445 -0.1771
## Recently Burned - 3 Years Since Fire -0.822 0.0869 Inf -1.045 -0.5987
## Recently Burned - Not Yet Burned -0.395 0.0502 Inf -0.524 -0.2659
## Intermediate - 3 Years Since Fire -0.511 0.0851 Inf -0.730 -0.2925
## Intermediate - Not Yet Burned -0.084 0.0470 Inf -0.205 0.0368
## 3 Years Since Fire - Not Yet Burned 0.427 0.0840 Inf 0.211 0.6431
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: asymptotic
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates##BGCover
TSF only: RB < others, intermediate < 3yr & NYB
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(BGCover + 1)
## Chisq Df Pr(>Chisq)
## TSF 117.1671 3 <2e-16 ***
## Management 0.1240 1 0.7247
## TSF:Management 1.9868 3 0.5752
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 2.450 0.117 14.9 2.201 2.70
## Intermediate 1.805 0.114 13.5 1.559 2.05
## 3 Years Since Fire 0.945 0.200 106.6 0.548 1.34
## Not Yet Burned 1.451 0.112 12.3 1.207 1.69
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate 0.645 0.114 285 5.665 <.0001
## Recently Burned - 3 Years Since Fire 1.505 0.200 293 7.537 <.0001
## Recently Burned - Not Yet Burned 0.999 0.112 289 8.946 <.0001
## Intermediate - 3 Years Since Fire 0.860 0.191 289 4.511 0.0001
## Intermediate - Not Yet Burned 0.354 0.118 284 2.992 0.0159
## 3 Years Since Fire - Not Yet Burned -0.506 0.209 288 -2.427 0.0743
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 2.450 0.117 14.9 2.201 2.70
## Intermediate 1.805 0.114 13.5 1.559 2.05
## 3 Years Since Fire 0.945 0.200 106.6 0.548 1.34
## Not Yet Burned 1.451 0.112 12.3 1.207 1.69
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate 0.645 0.114 285 0.3507 0.9392
## Recently Burned - 3 Years Since Fire 1.505 0.200 293 0.9891 2.0210
## Recently Burned - Not Yet Burned 0.999 0.112 289 0.7104 1.2874
## Intermediate - 3 Years Since Fire 0.860 0.191 289 0.3674 1.3528
## Intermediate - Not Yet Burned 0.354 0.118 284 0.0482 0.6597
## 3 Years Since Fire - Not Yet Burned -0.506 0.209 288 -1.0451 0.0327
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates##GCover
TSF only: RB < others
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: GCover
## Chisq Df Pr(>Chisq)
## TSF 55.3614 3 5.749e-12 ***
## Management 3.7464 1 0.05292 .
## TSF:Management 4.3244 3 0.22850
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 23.32 1.19 59.4 20.94 25.7
## Intermediate 15.29 1.11 42.7 13.05 17.5
## 3 Years Since Fire 9.65 2.36 233.3 5.01 14.3
## Not Yet Burned 14.49 1.05 32.8 12.35 16.6
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate 8.033 1.50 292 5.365 <.0001
## Recently Burned - 3 Years Since Fire 13.673 2.56 279 5.338 <.0001
## Recently Burned - Not Yet Burned 8.836 1.45 293 6.080 <.0001
## Intermediate - 3 Years Since Fire 5.641 2.49 291 2.269 0.1078
## Intermediate - Not Yet Burned 0.803 1.44 173 0.558 0.9442
## 3 Years Since Fire - Not Yet Burned -4.838 2.56 195 -1.889 0.2363
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 23.32 1.19 59.4 20.94 25.7
## Intermediate 15.29 1.11 42.7 13.05 17.5
## 3 Years Since Fire 9.65 2.36 233.3 5.01 14.3
## Not Yet Burned 14.49 1.05 32.8 12.35 16.6
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate 8.033 1.50 292 4.164 11.90
## Recently Burned - 3 Years Since Fire 13.673 2.56 279 7.053 20.29
## Recently Burned - Not Yet Burned 8.836 1.45 293 5.081 12.59
## Intermediate - 3 Years Since Fire 5.641 2.49 291 -0.784 12.07
## Intermediate - Not Yet Burned 0.803 1.44 173 -2.929 4.53
## 3 Years Since Fire - Not Yet Burned -4.838 2.56 195 -11.475 1.80
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates##LitCover
TSF only: RB < others, 3yr > interediate and NYB
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: LitCover
## Chisq Df Pr(>Chisq)
## TSF 160.0804 3 <2e-16 ***
## Management 0.5545 1 0.4565
## TSF:Management 4.3092 3 0.2300
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see ?isSingular## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.38 1.23 15.6 3.76 8.99
## Intermediate 16.65 1.20 13.9 14.07 19.23
## 3 Years Since Fire 28.57 2.19 118.0 24.23 32.91
## Not Yet Burned 17.92 1.18 12.5 15.37 20.47
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -10.27 1.28 286 -8.052 <.0001
## Recently Burned - 3 Years Since Fire -22.19 2.23 294 -9.938 <.0001
## Recently Burned - Not Yet Burned -11.55 1.25 291 -9.238 <.0001
## Intermediate - 3 Years Since Fire -11.92 2.14 290 -5.583 <.0001
## Intermediate - Not Yet Burned -1.27 1.32 278 -0.967 0.7682
## 3 Years Since Fire - Not Yet Burned 10.65 2.32 284 4.580 <.0001
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.38 1.23 15.6 3.76 8.99
## Intermediate 16.65 1.20 13.9 14.07 19.23
## 3 Years Since Fire 28.57 2.19 118.0 24.23 32.91
## Not Yet Burned 17.92 1.18 12.5 15.37 20.47
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -10.27 1.28 286 -13.57 -6.98
## Recently Burned - 3 Years Since Fire -22.19 2.23 294 -27.97 -16.42
## Recently Burned - Not Yet Burned -11.55 1.25 291 -14.78 -8.32
## Intermediate - 3 Years Since Fire -11.92 2.14 290 -17.44 -6.40
## Intermediate - Not Yet Burned -1.27 1.32 278 -4.68 2.13
## 3 Years Since Fire - Not Yet Burned 10.65 2.32 284 4.64 16.65
##
## Results are averaged over the levels of: Management
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates#Ordinations ## Species Ordination1
Setup1
##
## Call:
## metaMDS(comm = SpHRECProp10, distance = "euclidean", k = 3, trymax = 50)
##
## global Multidimensional Scaling using monoMDS
##
## Data: wisconsin(SpHRECProp10)
## Distance: euclidean
##
## Dimensions: 3
## Stress: 0.09811844
## Stress type 1, weak ties
## Two convergent solutions found after 20 tries
## Scaling: centring, PC rotation
## Species: expanded scores based on 'wisconsin(SpHRECProp10)'## importance.MDS1 importance.MDS2 importance.MDS3
## Eigenvalue 3.24 3.08 1.17
## Proportion Explained 0.32 0.30 0.11
## Cumulative Proportion 0.32 0.62 0.73
## importance.MDS4 importance.MDS5 importance.MDS6
## Eigenvalue 0.83 0.76 0.51
## Proportion Explained 0.08 0.07 0.05
## Cumulative Proportion 0.81 0.89 0.94
## importance.MDS7 importance.MDS8
## Eigenvalue 0.40 0.26
## Proportion Explained 0.04 0.03
## Cumulative Proportion 0.97 1.00
Env Fit
##
## ***VECTORS
##
## NMDS1 NMDS2 NMDS3 r2 Pr(>r)
## BGCover 0.54513 -0.30006 0.78281 0.0533 0.188
## GCover -0.41302 -0.73730 0.53460 0.0215 0.512
## LitCover -0.46591 0.76106 0.45136 0.0048 0.812
## LitMean -0.11823 -0.67049 0.73244 0.0018 0.924
## MaxDead 0.63739 -0.41995 0.64605 0.0530 0.538
## MaxLive -0.18196 -0.32032 0.92967 0.0527 0.370
## VOR_Mean -0.62569 -0.49066 0.60644 0.0611 0.100
## Blocks: strata
## Permutation: free
## Number of permutations: 499
##
## ***FACTORS:
##
## Centroids:
## NMDS1 NMDS2 NMDS3
## TSFRB -0.0122 0.0066 0.0166
## TSF1yr2yr 0.0747 -0.0211 -0.0102
## TSF2yr3yr 0.1042 -0.0653 -0.0327
## TSF3yr4yr 0.0768 -0.0672 -0.0430
## TSFUnburned -0.0767 0.0391 0.0121
## ManagementCattle -0.0082 0.0758 -0.0385
## ManagementSheep 0.0082 -0.0758 0.0385
##
## Goodness of fit:
## r2 Pr(>r)
## TSF 0.0814 0.096 .
## Management 0.0861 1.000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499##
## ***FACTORS:
##
## Centroids:
## NMDS1 NMDS2 NMDS3
## TSFRB -0.0122 0.0066 0.0166
## TSF1yr2yr 0.0747 -0.0211 -0.0102
## TSF2yr3yr 0.1042 -0.0653 -0.0327
## TSF3yr4yr 0.0768 -0.0672 -0.0430
## TSFUnburned -0.0767 0.0391 0.0121
##
## Goodness of fit:
## r2 Pr(>r)
## TSF 0.0814 0.108
## Blocks: strata
## Permutation: free
## Number of permutations: 499
Species Ordination2
Setup2
##
## Call:
## metaMDS(comm = SpHRECProp10Int, distance = "euclidean", k = 3, trymax = 50)
##
## global Multidimensional Scaling using monoMDS
##
## Data: wisconsin(SpHRECProp10Int)
## Distance: euclidean
##
## Dimensions: 3
## Stress: 0.09811844
## Stress type 1, weak ties
## Two convergent solutions found after 28 tries
## Scaling: centring, PC rotation
## Species: expanded scores based on 'wisconsin(SpHRECProp10Int)'## importance.MDS1 importance.MDS2 importance.MDS3
## Eigenvalue 3.24 3.08 1.17
## Proportion Explained 0.32 0.30 0.11
## Cumulative Proportion 0.32 0.62 0.73
## importance.MDS4 importance.MDS5 importance.MDS6
## Eigenvalue 0.83 0.76 0.51
## Proportion Explained 0.08 0.07 0.05
## Cumulative Proportion 0.81 0.89 0.94
## importance.MDS7 importance.MDS8
## Eigenvalue 0.40 0.26
## Proportion Explained 0.04 0.03
## Cumulative Proportion 0.97 1.00
Env Fit2
##
## ***VECTORS
##
## NMDS1 NMDS2 NMDS3 r2 Pr(>r)
## BGCover 0.54478 -0.30021 0.78300 0.0534 0.184
## GCover -0.41347 -0.73712 0.53451 0.0215 0.538
## LitCover -0.46560 0.76105 0.45168 0.0048 0.868
## LitMean -0.11877 -0.66960 0.73317 0.0018 0.932
## MaxDead 0.63701 -0.42027 0.64622 0.0530 0.538
## MaxLive -0.18223 -0.32040 0.92959 0.0526 0.352
## VOR_Mean -0.62621 -0.49055 0.60599 0.0611 0.106
## Blocks: strata
## Permutation: free
## Number of permutations: 499
##
## ***FACTORS:
##
## Centroids:
## NMDS1 NMDS2 NMDS3
## TSFRecently Burned -0.0122 0.0066 0.0166
## TSFIntermediate 0.0865 -0.0388 -0.0192
## TSF3 Years Since Fire 0.0767 -0.0672 -0.0430
## TSFNot Yet Burned -0.0767 0.0392 0.0122
## ManagementCattle -0.0082 0.0758 -0.0385
## ManagementSheep 0.0082 -0.0758 0.0385
##
## Goodness of fit:
## r2 Pr(>r)
## TSF 0.0784 0.102
## Management 0.0861 1.000
## Blocks: strata
## Permutation: free
## Number of permutations: 499##
## ***FACTORS:
##
## Centroids:
## NMDS1 NMDS2 NMDS3
## TSFRecently Burned -0.0122 0.0066 0.0166
## TSFIntermediate 0.0865 -0.0388 -0.0192
## TSF3 Years Since Fire 0.0767 -0.0672 -0.0430
## TSFNot Yet Burned -0.0767 0.0392 0.0122
##
## Goodness of fit:
## r2 Pr(>r)
## TSF 0.0784 0.092 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499
Functional Group Ordination1
Setup
##
## Call:
## metaMDS(comm = FGFineHREC, distance = "euclidean", k = 3, trymax = 50)
##
## global Multidimensional Scaling using monoMDS
##
## Data: wisconsin(sqrt(FGFineHREC))
## Distance: euclidean
##
## Dimensions: 3
## Stress: 0.06718037
## Stress type 1, weak ties
## Two convergent solutions found after 20 tries
## Scaling: centring, PC rotation
## Species: expanded scores based on 'wisconsin(sqrt(FGFineHREC))'## importance.MDS1 importance.MDS2 importance.MDS3
## Eigenvalue 3.07 1.18 0.87
## Proportion Explained 0.51 0.20 0.15
## Cumulative Proportion 0.51 0.70 0.85
## importance.MDS4 importance.MDS5 importance.MDS6
## Eigenvalue 0.47 0.24 0.19
## Proportion Explained 0.08 0.04 0.03
## Cumulative Proportion 0.93 0.97 1.00
Env Fit
##
## ***VECTORS
##
## NMDS1 NMDS2 NMDS3 r2 Pr(>r)
## BGCover 0.61000 -0.72931 -0.30984 0.0276 0.530
## GCover -0.96481 -0.02108 -0.26212 0.0385 0.690
## LitCover 0.00500 0.71266 -0.70149 0.0874 0.098 .
## LitMean -0.18004 0.59741 -0.78147 0.0980 0.126
## MaxDead 0.10795 0.23781 -0.96529 0.0950 0.076 .
## MaxLive 0.20291 -0.92067 0.33347 0.1217 0.984
## VOR_Mean -0.05783 -0.94684 0.31646 0.0657 0.972
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499
##
## ***FACTORS:
##
## Centroids:
## NMDS1 NMDS2 NMDS3
## TSFRB 0.0178 -0.0059 0.0133
## TSF1yr2yr 0.0234 -0.0397 0.0007
## TSF2yr3yr 0.0650 -0.0342 -0.0210
## TSF3yr4yr -0.1017 -0.0501 -0.0550
## TSFUnburned -0.0283 0.0435 0.0070
## ManagementCattle 0.0408 -0.0008 0.0461
## ManagementSheep -0.0408 0.0008 -0.0461
##
## Goodness of fit:
## r2 Pr(>r)
## TSF 0.0643 0.2
## Management 0.0745 1.0
## Blocks: strata
## Permutation: free
## Number of permutations: 499
Functional Group Ordination2
Setup2
##
## Call:
## metaMDS(comm = FGFineHRECInt, distance = "euclidean", k = 3, trymax = 50)
##
## global Multidimensional Scaling using monoMDS
##
## Data: wisconsin(sqrt(FGFineHRECInt))
## Distance: euclidean
##
## Dimensions: 3
## Stress: 0.06718037
## Stress type 1, weak ties
## Two convergent solutions found after 20 tries
## Scaling: centring, PC rotation
## Species: expanded scores based on 'wisconsin(sqrt(FGFineHRECInt))'## importance.MDS1 importance.MDS2 importance.MDS3
## Eigenvalue 3.07 1.18 0.87
## Proportion Explained 0.51 0.20 0.15
## Cumulative Proportion 0.51 0.70 0.85
## importance.MDS4 importance.MDS5 importance.MDS6
## Eigenvalue 0.47 0.24 0.19
## Proportion Explained 0.08 0.04 0.03
## Cumulative Proportion 0.93 0.97 1.00
Env Fit2
##
## ***VECTORS
##
## NMDS1 NMDS2 NMDS3 r2 Pr(>r)
## BGCover 0.50199 -0.86190 -0.07164 0.0266 0.542
## GCover -0.72232 0.54896 -0.42059 0.0350 0.750
## LitCover 0.00162 0.71865 -0.69537 0.0877 0.094 .
## LitMean -0.16832 0.64783 -0.74296 0.0991 0.132
## MaxDead 0.11750 0.21458 -0.96961 0.0900 0.070 .
## MaxLive 0.19963 -0.93053 0.30701 0.1234 0.988
## VOR_Mean -0.00510 -0.96600 0.25848 0.0576 0.988
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499
##
## ***FACTORS:
##
## Centroids:
## NMDS1 NMDS2 NMDS3
## TSFRecently Burned 0.0178 -0.0059 0.0133
## TSFIntermediate 0.0400 -0.0375 -0.0080
## TSF3 Years Since Fire -0.1017 -0.0501 -0.0550
## TSFNot Yet Burned -0.0283 0.0435 0.0070
## ManagementCattle 0.0408 -0.0008 0.0461
## ManagementSheep -0.0408 0.0008 -0.0461
##
## Goodness of fit:
## r2 Pr(>r)
## TSF 0.0610 0.09 .
## Management 0.0745 1.00
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499
Structure Ordination 1
Setup
##
## Call:
## metaMDS(comm = StrSpeHREC, distance = "euclidean", k = 3, trymax = 50)
##
## global Multidimensional Scaling using monoMDS
##
## Data: wisconsin(StrSpeHREC)
## Distance: euclidean
##
## Dimensions: 3
## Stress: 0.04695268
## Stress type 1, weak ties
## Two convergent solutions found after 20 tries
## Scaling: centring, PC rotation
## Species: expanded scores based on 'wisconsin(StrSpeHREC)'## importance.MDS1 importance.MDS2 importance.MDS3
## Eigenvalue 2.07 0.72 0.50
## Proportion Explained 0.58 0.20 0.14
## Cumulative Proportion 0.58 0.78 0.92
## importance.MDS4 importance.MDS5 importance.MDS6
## Eigenvalue 0.17 0.07 0.04
## Proportion Explained 0.05 0.02 0.01
## Cumulative Proportion 0.97 0.99 1.00
Env Fit
##
## ***FACTORS:
##
## Centroids:
## NMDS1 NMDS2 NMDS3
## TSFRB -0.1822 -0.0164 -0.0123
## TSF1yr2yr 0.0173 -0.0309 0.0142
## TSF2yr3yr 0.0803 -0.0040 0.0075
## TSF3yr4yr 0.1736 0.0727 0.0531
## TSFUnburned 0.0571 0.0157 -0.0102
## ManagementCattle 0.0040 -0.0147 0.0042
## ManagementSheep -0.0040 0.0147 -0.0042
##
## Goodness of fit:
## r2 Pr(>r)
## TSF 0.3879 0.002 **
## Management 0.0073 1.000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499##
## ***FACTORS:
##
## Centroids:
## NMDS1 NMDS2 NMDS3
## ManagementCattle 0.0040 -0.0147 0.0042
## ManagementSheep -0.0040 0.0147 -0.0042
##
## Goodness of fit:
## r2 Pr(>r)
## Management 0.0073 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499##
## ***FACTORS:
##
## Centroids:
## NMDS1 NMDS2 NMDS3
## TSFRB -0.1822 -0.0164 -0.0123
## TSF1yr2yr 0.0173 -0.0309 0.0142
## TSF2yr3yr 0.0803 -0.0040 0.0075
## TSF3yr4yr 0.1736 0.0727 0.0531
## TSFUnburned 0.0571 0.0157 -0.0102
##
## Goodness of fit:
## r2 Pr(>r)
## TSF 0.3879 0.002 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499##
## Pairwise comparisons using factor fitting to an ordination
##
## data: StSp.MDSe by EnvPatchHREC2$TSF
## 999 permutations
##
## RB 1yr2yr 2yr3yr 3yr4yr
## 1yr2yr 0.002 - - -
## 2yr3yr 0.002 0.213 - -
## 3yr4yr 0.002 0.002 0.104 -
## Unburned 0.002 0.054 0.549 0.010
##
## P value adjustment method: fdr##
## Pairwise comparisons using factor fitting to an ordination
##
## data: StSp.MDSe by EnvPatchHREC2$Management
## 999 permutations
##
## Cattle
## Sheep 0.43
##
## P value adjustment method: fdr
Structure Ordination 2
Setup2
##
## Call:
## metaMDS(comm = StrSpeHRECInt, distance = "euclidean", k = 3, trymax = 50)
##
## global Multidimensional Scaling using monoMDS
##
## Data: wisconsin(StrSpeHRECInt)
## Distance: euclidean
##
## Dimensions: 3
## Stress: 0.04695262
## Stress type 1, weak ties
## Two convergent solutions found after 20 tries
## Scaling: centring, PC rotation
## Species: expanded scores based on 'wisconsin(StrSpeHRECInt)'## importance.MDS1 importance.MDS2 importance.MDS3
## Eigenvalue 2.07 0.72 0.50
## Proportion Explained 0.58 0.20 0.14
## Cumulative Proportion 0.58 0.78 0.92
## importance.MDS4 importance.MDS5 importance.MDS6
## Eigenvalue 0.17 0.07 0.04
## Proportion Explained 0.05 0.02 0.01
## Cumulative Proportion 0.97 0.99 1.00
Env Fit2
##
## ***FACTORS:
##
## Centroids:
## NMDS1 NMDS2 NMDS3
## TSFRecently Burned -0.1822 -0.0164 -0.0123
## TSFIntermediate 0.0425 -0.0202 0.0115
## TSF3 Years Since Fire 0.1736 0.0727 0.0531
## TSFNot Yet Burned 0.0571 0.0157 -0.0102
## ManagementCattle 0.0040 -0.0147 0.0042
## ManagementSheep -0.0040 0.0147 -0.0042
##
## Goodness of fit:
## r2 Pr(>r)
## TSF 0.3775 0.002 **
## Management 0.0073 1.000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499##
## ***FACTORS:
##
## Centroids:
## NMDS1 NMDS2 NMDS3
## ManagementCattle 0.0040 -0.0147 0.0042
## ManagementSheep -0.0040 0.0147 -0.0042
##
## Goodness of fit:
## r2 Pr(>r)
## Management 0.0073 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499##
## ***FACTORS:
##
## Centroids:
## NMDS1 NMDS2 NMDS3
## TSFRecently Burned -0.1822 -0.0164 -0.0123
## TSFIntermediate 0.0425 -0.0202 0.0115
## TSF3 Years Since Fire 0.1736 0.0727 0.0531
## TSFNot Yet Burned 0.0571 0.0157 -0.0102
##
## Goodness of fit:
## r2 Pr(>r)
## TSF 0.3775 0.002 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499##
## Pairwise comparisons using factor fitting to an ordination
##
## data: StSp.MDSeInt by EnvPatchHRECOrdi2$TSF
## 999 permutations
##
## Recently Burned Intermediate 3 Years Since Fire
## Intermediate 0.002 - -
## 3 Years Since Fire 0.002 0.006 -
## Not Yet Burned 0.002 0.220 0.003
##
## P value adjustment method: fdr##
## Pairwise comparisons using factor fitting to an ordination
##
## data: StSp.MDSeInt by EnvPatchHRECOrdi2$Management
## 999 permutations
##
## Cattle
## Sheep 0.44
##
## P value adjustment method: fdr
#Graphs
##Community Composition
##FG Stack Graph
cowplot::plot_grid( GrassPlot,ForbPlot,LegumePlot, nrow = 3)
##Structure Stack1
cowplot::plot_grid( VorPlot,MaxLivePlot,MaxDeadPlot,LitMeanPlot, nrow = 4)
##Structure Stack2
cowplot::plot_grid( BarePlot, GroundPlot,LitterPlot, nrow = 3)
#Heterogeneity Over Time
Setup
## `summarise()` has grouped output by 'Year', 'Variable'. You can override using the `.groups` argument.Tests
VOR
## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 0.03568 0.03568 10.56 0.0314 *
## Residuals 4 0.01351 0.00338
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.158 0.0336 4 0.0651 0.251
## 2020 0.313 0.0336 4 0.2193 0.406
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -0.154 0.0475 4 -3.250 0.0314## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.158 0.0336 4 0.0651 0.251
## 2020 0.313 0.0336 4 0.2193 0.406
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -0.154 0.0475 4 -0.286 -0.0225
##
## Confidence level used: 0.95## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 7.017e-11 7.017e-11 1.326 0.314
## Residuals 4 2.117e-10 5.293e-11## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 7.34e-07 4.2e-06 4 -1.09e-05 1.24e-05
## 2020 7.57e-06 4.2e-06 4 -4.09e-06 1.92e-05
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -6.84e-06 5.94e-06 4 -1.151 0.3137## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 7.34e-07 4.2e-06 4 -1.09e-05 1.24e-05
## 2020 7.57e-06 4.2e-06 4 -4.09e-06 1.92e-05
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -6.84e-06 5.94e-06 4 -2.33e-05 9.65e-06
##
## Confidence level used: 0.95Max Live
## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 1.4380 1.4380 19.63 0.0114 *
## Residuals 4 0.2931 0.0733
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.256 0.156 4 -0.178 0.69
## 2020 1.235 0.156 4 0.801 1.67
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -0.979 0.221 4 -4.430 0.0114## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.256 0.156 4 -0.178 0.69
## 2020 1.235 0.156 4 0.801 1.67
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -0.979 0.221 4 -1.59 -0.365
##
## Confidence level used: 0.95## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 0.02013 0.02013 1 0.374
## Residuals 4 0.08051 0.02013## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.116 0.0819 4 -0.112 0.343
## 2020 0.000 0.0819 4 -0.227 0.227
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 0.116 0.116 4 1.000 0.3739## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.116 0.0819 4 -0.112 0.343
## 2020 0.000 0.0819 4 -0.227 0.227
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 0.116 0.116 4 -0.206 0.437
##
## Confidence level used: 0.95Max Dead
## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 0.07551 0.07551 174.5 0.00019 ***
## Residuals 4 0.00173 0.00043
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.271 0.012 4 0.237 0.304
## 2020 0.495 0.012 4 0.462 0.528
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -0.224 0.017 4 -13.210 0.0002## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.271 0.012 4 0.237 0.304
## 2020 0.495 0.012 4 0.462 0.528
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -0.224 0.017 4 -0.272 -0.177
##
## Confidence level used: 0.95## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 1.098e-11 1.098e-11 3.488 0.135
## Residuals 4 1.259e-11 3.148e-12## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 2.71e-06 1.02e-06 4 -1.39e-07 5.55e-06
## 2020 0.00e+00 1.02e-06 4 -2.84e-06 2.84e-06
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 2.71e-06 1.45e-06 4 1.868 0.1352## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 2.71e-06 1.02e-06 4 -1.39e-07 5.55e-06
## 2020 0.00e+00 1.02e-06 4 -2.84e-06 2.84e-06
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 2.71e-06 1.45e-06 4 -1.32e-06 6.73e-06
##
## Confidence level used: 0.95Litter Depth
## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 0.19293 0.19293 58.8 0.00155 **
## Residuals 4 0.01312 0.00328
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.101 0.0331 4 0.00914 0.193
## 2020 0.460 0.0331 4 0.36778 0.551
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -0.359 0.0468 4 -7.668 0.0016## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.101 0.0331 4 0.00914 0.193
## 2020 0.460 0.0331 4 0.36778 0.551
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -0.359 0.0468 4 -0.488 -0.229
##
## Confidence level used: 0.95## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 0.000539 0.0005392 0.197 0.68
## Residuals 4 0.010922 0.0027306## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.0222 0.0302 4 -0.0615 0.106
## 2020 0.0412 0.0302 4 -0.0426 0.125
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -0.019 0.0427 4 -0.444 0.6798## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.0222 0.0302 4 -0.0615 0.106
## 2020 0.0412 0.0302 4 -0.0426 0.125
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -0.019 0.0427 4 -0.137 0.0995
##
## Confidence level used: 0.95Bare Ground Cover
## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 0.3431 0.3431 16.89 0.0147 *
## Residuals 4 0.0812 0.0203
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.366 0.0823 4 0.137 0.594
## 2020 0.844 0.0823 4 0.615 1.072
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -0.478 0.116 4 -4.110 0.0147## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.366 0.0823 4 0.137 0.594
## 2020 0.844 0.0823 4 0.615 1.072
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -0.478 0.116 4 -0.801 -0.155
##
## Confidence level used: 0.95## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 1.373e-09 1.373e-09 2.692 0.176
## Residuals 4 2.040e-09 5.101e-10## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 4.20e-11 1.3e-05 4 -3.62e-05 3.62e-05
## 2020 3.03e-05 1.3e-05 4 -5.95e-06 6.65e-05
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -3.03e-05 1.84e-05 4 -1.641 0.1762## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 4.20e-11 1.3e-05 4 -3.62e-05 3.62e-05
## 2020 3.03e-05 1.3e-05 4 -5.95e-06 6.65e-05
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -3.03e-05 1.84e-05 4 -8.15e-05 2.09e-05
##
## Confidence level used: 0.95Ground Litter
## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 25.899 25.899 19.17 0.0119 *
## Residuals 4 5.405 1.351
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 4.76 0.671 4 2.89 6.62
## 2020 8.91 0.671 4 7.05 10.78
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -4.16 0.949 4 -4.378 0.0119## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 4.76 0.671 4 2.89 6.62
## 2020 8.91 0.671 4 7.05 10.78
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -4.16 0.949 4 -6.79 -1.52
##
## Confidence level used: 0.95## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 4.980e-08 4.976e-08 0.497 0.52
## Residuals 4 4.004e-07 1.001e-07## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 7.32e-05 0.000183 4 -0.000434 0.000580
## 2020 2.55e-04 0.000183 4 -0.000252 0.000762
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -0.000182 0.000258 4 -0.705 0.5197## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 7.32e-05 0.000183 4 -0.000434 0.000580
## 2020 2.55e-04 0.000183 4 -0.000252 0.000762
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -0.000182 0.000258 4 -0.000899 0.000535
##
## Confidence level used: 0.95Standing Litter
## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 30.343 30.343 38.81 0.00338 **
## Residuals 4 3.128 0.782
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 5.88 0.511 4 4.46 7.29
## 2020 10.37 0.511 4 8.96 11.79
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -4.5 0.722 4 -6.229 0.0034## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 5.88 0.511 4 4.46 7.29
## 2020 10.37 0.511 4 8.96 11.79
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -4.5 0.722 4 -6.5 -2.49
##
## Confidence level used: 0.95## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 1.399e-14 1.399e-14 1 0.374
## Residuals 4 5.596e-14 1.399e-14## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.00e+00 6.83e-08 4 -1.9e-07 1.90e-07
## 2020 9.66e-08 6.83e-08 4 -9.3e-08 2.86e-07
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -9.66e-08 9.66e-08 4 -1.000 0.3739## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.00e+00 6.83e-08 4 -1.9e-07 1.90e-07
## 2020 9.66e-08 6.83e-08 4 -9.3e-08 2.86e-07
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -9.66e-08 9.66e-08 4 -3.65e-07 1.72e-07
##
## Confidence level used: 0.95Forb
## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 0.08002 0.08002 1.168 0.341
## Residuals 4 0.27409 0.06852## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.485 0.151 4 0.0657 0.905
## 2020 0.254 0.151 4 -0.1652 0.674
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 0.231 0.214 4 1.081 0.3406## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.485 0.151 4 0.0657 0.905
## 2020 0.254 0.151 4 -0.1652 0.674
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 0.231 0.214 4 -0.362 0.824
##
## Confidence level used: 0.95## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 0.04715 0.04715 1.413 0.3
## Residuals 4 0.13348 0.03337## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.223 0.105 4 -0.0702 0.516
## 2020 0.400 0.105 4 0.1071 0.693
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -0.177 0.149 4 -1.189 0.3003## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.223 0.105 4 -0.0702 0.516
## 2020 0.400 0.105 4 0.1071 0.693
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -0.177 0.149 4 -0.591 0.237
##
## Confidence level used: 0.95Legume
## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 0.0188 0.01885 0.097 0.771
## Residuals 4 0.7755 0.19388## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.349 0.254 4 -0.357 1.05
## 2020 0.461 0.254 4 -0.245 1.17
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -0.112 0.36 4 -0.312 0.7708## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.349 0.254 4 -0.357 1.05
## 2020 0.461 0.254 4 -0.245 1.17
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -0.112 0.36 4 -1.11 0.886
##
## Confidence level used: 0.95## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 0.3206 0.3206 11.22 0.0286 *
## Residuals 4 0.1143 0.0286
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.106 0.0976 4 -0.165 0.377
## 2020 0.568 0.0976 4 0.297 0.839
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 -0.462 0.138 4 -3.350 0.0286## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.106 0.0976 4 -0.165 0.377
## 2020 0.568 0.0976 4 0.297 0.839
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 -0.462 0.138 4 -0.846 -0.0792
##
## Confidence level used: 0.95Grass
## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 0.18 0.18 0.005 0.946
## Residuals 4 143.61 35.90## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 7.50 3.46 4 -2.10 17.1
## 2020 7.15 3.46 4 -2.45 16.8
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 0.351 4.89 4 0.072 0.9463## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 7.50 3.46 4 -2.10 17.1
## 2020 7.15 3.46 4 -2.45 16.8
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 0.351 4.89 4 -13.2 13.9
##
## Confidence level used: 0.95## Df Sum Sq Mean Sq F value Pr(>F)
## Year 1 1.654e-05 1.654e-05 1 0.374
## Residuals 4 6.617e-05 1.654e-05## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.00332 0.00235 4 -0.00320 0.00984
## 2020 0.00000 0.00235 4 -0.00652 0.00652
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## 2017 - 2020 0.00332 0.00332 4 1.000 0.3739## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2017 0.00332 0.00235 4 -0.00320 0.00984
## 2020 0.00000 0.00235 4 -0.00652 0.00652
##
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## 2017 - 2020 0.00332 0.00332 4 -0.0059 0.0125
##
## Confidence level used: 0.95Stacked graphs
cowplot::plot_grid( VORvp,MLvp,MDvp, LDvp, nrow = 4)
cowplot::plot_grid( BGvp,GCvp,LCvp, nrow = 3)
cowplot::plot_grid( GRvp,FBvp,LGvp, nrow = 3)
Use Comparison
## `summarise()` has grouped output by 'Year', 'Variable', 'Use'. You can override using the `.groups` argument.## `summarise()` has grouped output by 'Variable', 'Use'. You can override using the `.groups` argument.## Warning in write.csv(VPUSESummaryGraph, file = "D:/R/data/
## VPUSESummaryGraph.csv", : attempt to set 'col.names' ignored## Warning in write.csv(VPUSESummaryGraph2, file = "D:/R/data/
## VPUSESummaryGraph2.csv", : attempt to set 'col.names' ignored
cowplot::plot_grid( UP1,UP2, nrow = 2)
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: sdcor
## Chisq Df Pr(>Chisq)
## Use 19.211 1 1.17e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Use emmean SE df lower.CL upper.CL
## Heterogeneous 0.1945 0.0262 17.82 0.13951 0.250
## Homogeneous 0.0564 0.0221 7.85 0.00518 0.108
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Heterogeneous - Homogeneous 0.138 0.0325 46.3 4.251 0.0001
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## Use emmean SE df lower.CL upper.CL
## Heterogeneous 0.1945 0.0262 17.82 0.13951 0.250
## Homogeneous 0.0564 0.0221 7.85 0.00518 0.108
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Heterogeneous - Homogeneous 0.138 0.0325 46.3 0.0728 0.204
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95