Forage Pub Update
Jonathan Spiess
May, 2022
#Nutritive Values
##Biomass
TSF and interaction significant
Overall TSF: RB < others, 3yr > intermediate and NYB
Interaction: Cattle: RB < others; Sheep: RB < others, Intermediate & 3yr > NYB
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(KgHa + 1)
## Chisq Df Pr(>Chisq)
## TSF 414.132 3 < 2.2e-16 ***
## Treatment 0.932 1 0.3344
## TSF:Treatment 52.976 3 1.855e-11 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see help('isSingular')## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 7.51 0.0736 11.9 7.35 7.67
## Intermediate 8.11 0.0730 11.4 7.95 8.27
## 3 Years Since Fire 8.27 0.0875 30.2 8.09 8.45
## Not Yet Burned 8.03 0.0734 11.8 7.87 8.19
##
## Results are averaged over the levels of: Treatment
## 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 -0.6004 0.0348 1944 -17.253 <.0001
## Recently Burned - 3 Years Since Fire -0.7608 0.0594 1975 -12.819 <.0001
## Recently Burned - Not Yet Burned -0.5271 0.0359 1974 -14.685 <.0001
## Intermediate - 3 Years Since Fire -0.1604 0.0565 1961 -2.840 0.0236
## Intermediate - Not Yet Burned 0.0733 0.0374 1928 1.961 0.2032
## 3 Years Since Fire - Not Yet Burned 0.2337 0.0633 1935 3.694 0.0013
##
## Results are averaged over the levels of: Treatment
## Note: contrasts are still on the log(mu + 1) scale
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see help('isSingular')
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 7.51 0.0736 11.9 7.35 7.67
## Intermediate 8.11 0.0730 11.4 7.95 8.27
## 3 Years Since Fire 8.27 0.0875 30.2 8.09 8.45
## Not Yet Burned 8.03 0.0734 11.8 7.87 8.19
##
## Results are averaged over the levels of: Treatment
## 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 -0.6004 0.0348 1944 -0.6899 -0.5110
## Recently Burned - 3 Years Since Fire -0.7608 0.0594 1975 -0.9134 -0.6082
## Recently Burned - Not Yet Burned -0.5271 0.0359 1974 -0.6194 -0.4348
## Intermediate - 3 Years Since Fire -0.1604 0.0565 1961 -0.3056 -0.0152
## Intermediate - Not Yet Burned 0.0733 0.0374 1928 -0.0228 0.1695
## 3 Years Since Fire - Not Yet Burned 0.2337 0.0633 1935 0.0710 0.3964
##
## Results are averaged over the levels of: Treatment
## Note: contrasts are still on the log(mu + 1) scale
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see help('isSingular')## $emmeans
## Treatment = Cattle:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 7.67 0.104 12.1 7.45 7.90
## Intermediate 8.05 0.104 11.5 7.82 8.28
## 3 Years Since Fire 8.14 0.126 32.6 7.88 8.40
## Not Yet Burned 8.15 0.104 11.8 7.92 8.38
##
## Treatment = Sheep:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 7.34 0.104 11.9 7.11 7.56
## Intermediate 8.16 0.103 11.3 7.94 8.39
## 3 Years Since Fire 8.40 0.121 27.8 8.15 8.64
## Not Yet Burned 7.91 0.104 11.8 7.69 8.14
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Treatment = Cattle:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.3749 0.0496 1947 -7.552 <.0001
## Recently Burned - 3 Years Since Fire -0.4644 0.0872 1973 -5.328 <.0001
## Recently Burned - Not Yet Burned -0.4776 0.0505 1969 -9.463 <.0001
## Intermediate - 3 Years Since Fire -0.0895 0.0829 1962 -1.079 0.7024
## Intermediate - Not Yet Burned -0.1027 0.0528 1931 -1.946 0.2093
## 3 Years Since Fire - Not Yet Burned -0.0133 0.0922 1934 -0.144 0.9989
##
## Treatment = Sheep:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.8260 0.0488 1941 -16.931 <.0001
## Recently Burned - 3 Years Since Fire -1.0573 0.0806 1975 -13.121 <.0001
## Recently Burned - Not Yet Burned -0.5766 0.0510 1977 -11.295 <.0001
## Intermediate - 3 Years Since Fire -0.2313 0.0767 1959 -3.017 0.0138
## Intermediate - Not Yet Burned 0.2494 0.0530 1924 4.709 <.0001
## 3 Years Since Fire - Not Yet Burned 0.4807 0.0867 1935 5.546 <.0001
##
## Note: contrasts are still on the log(mu + 1) scale
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see help('isSingular')## $emmeans
## Treatment = Cattle:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 7.67 0.104 12.1 7.45 7.90
## Intermediate 8.05 0.104 11.5 7.82 8.28
## 3 Years Since Fire 8.14 0.126 32.6 7.88 8.40
## Not Yet Burned 8.15 0.104 11.8 7.92 8.38
##
## Treatment = Sheep:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 7.34 0.104 11.9 7.11 7.56
## Intermediate 8.16 0.103 11.3 7.94 8.39
## 3 Years Since Fire 8.40 0.121 27.8 8.15 8.64
## Not Yet Burned 7.91 0.104 11.8 7.69 8.14
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Treatment = Cattle:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.3749 0.0496 1947 -0.503 -0.2473
## Recently Burned - 3 Years Since Fire -0.4644 0.0872 1973 -0.689 -0.2403
## Recently Burned - Not Yet Burned -0.4776 0.0505 1969 -0.607 -0.3479
## Intermediate - 3 Years Since Fire -0.0895 0.0829 1962 -0.303 0.1237
## Intermediate - Not Yet Burned -0.1027 0.0528 1931 -0.238 0.0330
## 3 Years Since Fire - Not Yet Burned -0.0133 0.0922 1934 -0.250 0.2238
##
## Treatment = Sheep:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.8260 0.0488 1941 -0.951 -0.7005
## Recently Burned - 3 Years Since Fire -1.0573 0.0806 1975 -1.264 -0.8501
## Recently Burned - Not Yet Burned -0.5766 0.0510 1977 -0.708 -0.4453
## Intermediate - 3 Years Since Fire -0.2313 0.0767 1959 -0.428 -0.0341
## Intermediate - Not Yet Burned 0.2494 0.0530 1924 0.113 0.3855
## 3 Years Since Fire - Not Yet Burned 0.4807 0.0867 1935 0.258 0.7035
##
## Note: contrasts are still on the log(mu + 1) scale
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates##ADF
Only TSF
Overall TSF: 3yr & intermediate > NYB > RB
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: ADF
## Chisq Df Pr(>Chisq)
## TSF 388.6719 3 <2e-16 ***
## Treatment 1.6678 1 0.1965
## TSF:Treatment 4.2453 3 0.2362
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see help('isSingular')## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 33.2 0.304 5.92 32.5 34.0
## Intermediate 35.8 0.301 5.67 35.1 36.6
## 3 Years Since Fire 36.4 0.363 12.59 35.6 37.2
## Not Yet Burned 35.2 0.304 5.91 34.5 35.9
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -2.625 0.148 1946 -17.722 <.0001
## Recently Burned - 3 Years Since Fire -3.191 0.252 1974 -12.646 <.0001
## Recently Burned - Not Yet Burned -1.978 0.153 1973 -12.959 <.0001
## Intermediate - 3 Years Since Fire -0.567 0.240 1964 -2.359 0.0855
## Intermediate - Not Yet Burned 0.646 0.159 1896 4.071 0.0003
## 3 Years Since Fire - Not Yet Burned 1.213 0.269 1910 4.515 <.0001
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see help('isSingular')
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 33.2 0.304 5.92 32.5 34.0
## Intermediate 35.8 0.301 5.67 35.1 36.6
## 3 Years Since Fire 36.4 0.363 12.59 35.6 37.2
## Not Yet Burned 35.2 0.304 5.91 34.5 35.9
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -2.625 0.148 1946 -3.005 -2.244
## Recently Burned - 3 Years Since Fire -3.191 0.252 1974 -3.840 -2.542
## Recently Burned - Not Yet Burned -1.978 0.153 1973 -2.371 -1.586
## Intermediate - 3 Years Since Fire -0.567 0.240 1964 -1.184 0.051
## Intermediate - Not Yet Burned 0.646 0.159 1896 0.238 1.054
## 3 Years Since Fire - Not Yet Burned 1.213 0.269 1910 0.522 1.904
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates##NDF
TSF and Grazer significant, Interaction almost
Overall TSF: 3yr & intermediate > NYB > RB Overall Grazer: no difference (cattle almost lower)
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: NDF
## Chisq Df Pr(>Chisq)
## TSF 244.1510 3 < 2.2e-16 ***
## Treatment 7.6097 1 0.005806 **
## TSF:Treatment 7.1030 3 0.068686 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see help('isSingular')## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 62.0 0.422 6.24 60.9 63.0
## Intermediate 65.2 0.417 5.95 64.2 66.2
## 3 Years Since Fire 65.7 0.518 14.96 64.5 66.8
## Not Yet Burned 64.2 0.422 6.24 63.2 65.3
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -3.217 0.223 1942 -14.439 <.0001
## Recently Burned - 3 Years Since Fire -3.683 0.380 1972 -9.687 <.0001
## Recently Burned - Not Yet Burned -2.267 0.230 1970 -9.857 <.0001
## Intermediate - 3 Years Since Fire -0.466 0.362 1959 -1.289 0.5703
## Intermediate - Not Yet Burned 0.950 0.240 1935 3.962 0.0004
## 3 Years Since Fire - Not Yet Burned 1.416 0.406 1943 3.490 0.0028
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see help('isSingular')
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 62.0 0.422 6.24 60.9 63.0
## Intermediate 65.2 0.417 5.95 64.2 66.2
## 3 Years Since Fire 65.7 0.518 14.96 64.5 66.8
## Not Yet Burned 64.2 0.422 6.24 63.2 65.3
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -3.217 0.223 1942 -3.790 -2.644
## Recently Burned - 3 Years Since Fire -3.683 0.380 1972 -4.660 -2.705
## Recently Burned - Not Yet Burned -2.267 0.230 1970 -2.858 -1.675
## Intermediate - 3 Years Since Fire -0.466 0.362 1959 -1.396 0.464
## Intermediate - Not Yet Burned 0.950 0.240 1935 0.334 1.567
## 3 Years Since Fire - Not Yet Burned 1.416 0.406 1943 0.373 2.460
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see help('isSingular')
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Treatment emmean SE df lower.CL upper.CL
## Cattle 63.3 0.586 5.78 61.8 64.7
## Sheep 65.2 0.552 4.46 63.8 66.7
##
## Results are averaged over the levels of: TSF
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Cattle - Sheep -1.94 0.805 5.1 -2.412 0.0597
##
## Results are averaged over the levels of: TSF
## Degrees-of-freedom method: kenward-roger## boundary (singular) fit: see help('isSingular')
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Treatment emmean SE df lower.CL upper.CL
## Cattle 63.3 0.586 5.78 61.8 64.7
## Sheep 65.2 0.552 4.46 63.8 66.7
##
## Results are averaged over the levels of: TSF
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Cattle - Sheep -1.94 0.805 5.1 -4 0.115
##
## Results are averaged over the levels of: TSF
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95##ADL
TSF only
Overall TSF: RB < others
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: ADL
## Chisq Df Pr(>Chisq)
## TSF 288.5586 3 <2e-16 ***
## Treatment 0.5675 1 0.4513
## TSF:Treatment 4.5166 3 0.2108
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see help('isSingular')## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 4.15 0.155 5.00 3.75 4.54
## Intermediate 4.67 0.155 4.96 4.27 5.07
## 3 Years Since Fire 4.64 0.163 6.28 4.24 5.03
## Not Yet Burned 4.71 0.155 5.02 4.31 5.11
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.5237 0.0378 1915 -13.858 <.0001
## Recently Burned - 3 Years Since Fire -0.4909 0.0649 1929 -7.561 <.0001
## Recently Burned - Not Yet Burned -0.5627 0.0392 1927 -14.343 <.0001
## Intermediate - 3 Years Since Fire 0.0328 0.0615 1921 0.533 0.9510
## Intermediate - Not Yet Burned -0.0390 0.0415 1951 -0.940 0.7835
## 3 Years Since Fire - Not Yet Burned -0.0718 0.0701 1949 -1.024 0.7355
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see help('isSingular')
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 4.15 0.155 5.00 3.75 4.54
## Intermediate 4.67 0.155 4.96 4.27 5.07
## 3 Years Since Fire 4.64 0.163 6.28 4.24 5.03
## Not Yet Burned 4.71 0.155 5.02 4.31 5.11
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.5237 0.0378 1915 -0.621 -0.4265
## Recently Burned - 3 Years Since Fire -0.4909 0.0649 1929 -0.658 -0.3239
## Recently Burned - Not Yet Burned -0.5627 0.0392 1927 -0.664 -0.4618
## Intermediate - 3 Years Since Fire 0.0328 0.0615 1921 -0.125 0.1909
## Intermediate - Not Yet Burned -0.0390 0.0415 1951 -0.146 0.0677
## 3 Years Since Fire - Not Yet Burned -0.0718 0.0701 1949 -0.252 0.1085
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates##CP
TSF and interaction
Overall TSF: RB > NYB > Intermediate > 3Yr
Interaction Sheep: RB > NYB > Intermediate = 3Yr Cattle: RB = NYB > Intermediate > 3Yr
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(CP + 1)
## Chisq Df Pr(>Chisq)
## TSF 436.1178 3 < 2.2e-16 ***
## Treatment 3.2467 1 0.07157 .
## TSF:Treatment 54.7090 3 7.921e-12 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see help('isSingular')## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 2.33 0.0315 5.43 2.25 2.41
## Intermediate 2.12 0.0313 5.30 2.04 2.19
## 3 Years Since Fire 2.00 0.0353 8.87 1.92 2.08
## Not Yet Burned 2.26 0.0315 5.45 2.18 2.33
##
## Results are averaged over the levels of: Treatment
## 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 0.2165 0.0119 1937 18.256 <.0001
## Recently Burned - 3 Years Since Fire 0.3288 0.0203 1967 16.222 <.0001
## Recently Burned - Not Yet Burned 0.0765 0.0123 1964 6.244 <.0001
## Intermediate - 3 Years Since Fire 0.1123 0.0193 1952 5.830 <.0001
## Intermediate - Not Yet Burned -0.1400 0.0128 1956 -10.915 <.0001
## 3 Years Since Fire - Not Yet Burned -0.2523 0.0217 1962 -11.630 <.0001
##
## Results are averaged over the levels of: Treatment
## Note: contrasts are still on the log(mu + 1) scale
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see help('isSingular')
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 2.33 0.0315 5.43 2.25 2.41
## Intermediate 2.12 0.0313 5.30 2.04 2.19
## 3 Years Since Fire 2.00 0.0353 8.87 1.92 2.08
## Not Yet Burned 2.26 0.0315 5.45 2.18 2.33
##
## Results are averaged over the levels of: Treatment
## 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 0.2165 0.0119 1937 0.1860 0.247
## Recently Burned - 3 Years Since Fire 0.3288 0.0203 1967 0.2767 0.381
## Recently Burned - Not Yet Burned 0.0765 0.0123 1964 0.0450 0.108
## Intermediate - 3 Years Since Fire 0.1123 0.0193 1952 0.0628 0.162
## Intermediate - Not Yet Burned -0.1400 0.0128 1956 -0.1730 -0.107
## 3 Years Since Fire - Not Yet Burned -0.2523 0.0217 1962 -0.3081 -0.197
##
## Results are averaged over the levels of: Treatment
## Note: contrasts are still on the log(mu + 1) scale
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see help('isSingular')## $emmeans
## Treatment = Cattle:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 2.37 0.0460 6.24 2.26 2.48
## Intermediate 2.15 0.0458 6.11 2.03 2.26
## 3 Years Since Fire 1.98 0.0519 10.44 1.86 2.09
## Not Yet Burned 2.36 0.0459 6.19 2.25 2.47
##
## Treatment = Sheep:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 2.29 0.0429 4.66 2.18 2.41
## Intermediate 2.08 0.0427 4.53 1.97 2.20
## 3 Years Since Fire 2.03 0.0478 7.40 1.92 2.14
## Not Yet Burned 2.15 0.0431 4.74 2.04 2.26
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Treatment = Cattle:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate 0.22267 0.0169 1940 13.159 <.0001
## Recently Burned - 3 Years Since Fire 0.39205 0.0298 1968 13.173 <.0001
## Recently Burned - Not Yet Burned 0.00679 0.0172 1960 0.394 0.9793
## Intermediate - 3 Years Since Fire 0.16937 0.0283 1955 5.989 <.0001
## Intermediate - Not Yet Burned -0.21589 0.0181 1954 -11.931 <.0001
## 3 Years Since Fire - Not Yet Burned -0.38526 0.0316 1956 -12.201 <.0001
##
## Treatment = Sheep:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate 0.21042 0.0166 1934 12.656 <.0001
## Recently Burned - 3 Years Since Fire 0.26565 0.0275 1965 9.648 <.0001
## Recently Burned - Not Yet Burned 0.14630 0.0174 1968 8.386 <.0001
## Intermediate - 3 Years Since Fire 0.05522 0.0262 1949 2.111 0.1499
## Intermediate - Not Yet Burned -0.06412 0.0182 1959 -3.526 0.0024
## 3 Years Since Fire - Not Yet Burned -0.11935 0.0298 1967 -4.011 0.0004
##
## Note: contrasts are still on the log(mu + 1) scale
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see help('isSingular')## $emmeans
## Treatment = Cattle:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 2.37 0.0460 6.24 2.26 2.48
## Intermediate 2.15 0.0458 6.11 2.03 2.26
## 3 Years Since Fire 1.98 0.0519 10.44 1.86 2.09
## Not Yet Burned 2.36 0.0459 6.19 2.25 2.47
##
## Treatment = Sheep:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 2.29 0.0429 4.66 2.18 2.41
## Intermediate 2.08 0.0427 4.53 1.97 2.20
## 3 Years Since Fire 2.03 0.0478 7.40 1.92 2.14
## Not Yet Burned 2.15 0.0431 4.74 2.04 2.26
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Treatment = Cattle:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate 0.22267 0.0169 1940 0.1792 0.2662
## Recently Burned - 3 Years Since Fire 0.39205 0.0298 1968 0.3155 0.4686
## Recently Burned - Not Yet Burned 0.00679 0.0172 1960 -0.0375 0.0511
## Intermediate - 3 Years Since Fire 0.16937 0.0283 1955 0.0967 0.2421
## Intermediate - Not Yet Burned -0.21589 0.0181 1954 -0.2624 -0.1694
## 3 Years Since Fire - Not Yet Burned -0.38526 0.0316 1956 -0.4664 -0.3041
##
## Treatment = Sheep:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate 0.21042 0.0166 1934 0.1677 0.2532
## Recently Burned - 3 Years Since Fire 0.26565 0.0275 1965 0.1949 0.3364
## Recently Burned - Not Yet Burned 0.14630 0.0174 1968 0.1014 0.1912
## Intermediate - 3 Years Since Fire 0.05522 0.0262 1949 -0.0120 0.1225
## Intermediate - Not Yet Burned -0.06412 0.0182 1959 -0.1109 -0.0174
## 3 Years Since Fire - Not Yet Burned -0.11935 0.0298 1967 -0.1959 -0.0428
##
## Note: contrasts are still on the log(mu + 1) scale
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates##Moisture
TSF only
Overall TSF: RB > Intermediate = NYB > 3yr
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Moisture
## Chisq Df Pr(>Chisq)
## TSF 410.1747 3 <2e-16 ***
## Treatment 1.3448 1 0.2462
## TSF:Treatment 0.2121 3 0.9756
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see help('isSingular')## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 50.9 1.79 5.00 46.3 55.5
## Intermediate 43.6 1.78 4.95 39.0 48.2
## 3 Years Since Fire 40.9 1.89 6.30 36.3 45.4
## Not Yet Burned 44.1 1.79 5.01 39.5 48.7
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate 7.308 0.441 1914 16.583 <.0001
## Recently Burned - 3 Years Since Fire 10.031 0.757 1928 13.248 <.0001
## Recently Burned - Not Yet Burned 6.822 0.458 1926 14.911 <.0001
## Intermediate - 3 Years Since Fire 2.723 0.717 1920 3.796 0.0009
## Intermediate - Not Yet Burned -0.486 0.484 1949 -1.004 0.7469
## 3 Years Since Fire - Not Yet Burned -3.209 0.818 1948 -3.924 0.0005
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see help('isSingular')
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 50.9 1.79 5.00 46.3 55.5
## Intermediate 43.6 1.78 4.95 39.0 48.2
## 3 Years Since Fire 40.9 1.89 6.30 36.3 45.4
## Not Yet Burned 44.1 1.79 5.01 39.5 48.7
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate 7.308 0.441 1914 6.175 8.442
## Recently Burned - 3 Years Since Fire 10.031 0.757 1928 8.084 11.978
## Recently Burned - Not Yet Burned 6.822 0.458 1926 5.646 7.999
## Intermediate - 3 Years Since Fire 2.723 0.717 1920 0.879 4.567
## Intermediate - Not Yet Burned -0.486 0.484 1949 -1.730 0.758
## 3 Years Since Fire - Not Yet Burned -3.209 0.818 1948 -5.312 -1.106
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates##SI
something still isn’t right with the glmer. the post hoc test results are flipped (directionally)
TSF only
Overall TSF: RB > Intermediate = NYB > 3yr
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: (Powell + 0.001)
## Chisq Df Pr(>Chisq)
## TSF 130.9634 3 <2e-16 ***
## Treatment 0.0043 1 0.9475
## TSF:Treatment 4.5163 3 0.2108
## ---
## 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 asymp.LCL asymp.UCL
## Recently Burned 0.508 0.0438 Inf 0.422 0.594
## Intermediate 1.700 0.1283 Inf 1.449 1.952
## 3 Years Since Fire 3.848 0.6302 Inf 2.613 5.084
## Not Yet Burned 1.201 0.0883 Inf 1.028 1.374
##
## Results are averaged over the levels of: Treatment
## Results are given on the inverse(mu + 0.001) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df z.ratio p.value
## Recently Burned - Intermediate -1.192 0.1356 Inf -8.789 <.0001
## Recently Burned - 3 Years Since Fire -3.340 0.6317 Inf -5.288 <.0001
## Recently Burned - Not Yet Burned -0.693 0.0986 Inf -7.024 <.0001
## Intermediate - 3 Years Since Fire -2.148 0.6431 Inf -3.341 0.0046
## Intermediate - Not Yet Burned 0.499 0.1558 Inf 3.205 0.0074
## 3 Years Since Fire - Not Yet Burned 2.648 0.6363 Inf 4.161 0.0002
##
## Results are averaged over the levels of: Treatment
## Note: contrasts are still on the inverse(mu + 0.001) scale
## Results are given on the ( (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 asymp.LCL asymp.UCL
## Recently Burned 0.508 0.0438 Inf 0.422 0.594
## Intermediate 1.700 0.1283 Inf 1.449 1.952
## 3 Years Since Fire 3.848 0.6302 Inf 2.613 5.084
## Not Yet Burned 1.201 0.0883 Inf 1.028 1.374
##
## Results are averaged over the levels of: Treatment
## Results are given on the inverse(mu + 0.001) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df asymp.LCL asymp.UCL
## Recently Burned - Intermediate -1.192 0.1356 Inf -1.540 -0.843
## Recently Burned - 3 Years Since Fire -3.340 0.6317 Inf -4.963 -1.717
## Recently Burned - Not Yet Burned -0.693 0.0986 Inf -0.946 -0.439
## Intermediate - 3 Years Since Fire -2.148 0.6431 Inf -3.801 -0.496
## Intermediate - Not Yet Burned 0.499 0.1558 Inf 0.099 0.900
## 3 Years Since Fire - Not Yet Burned 2.648 0.6363 Inf 1.013 4.282
##
## Results are averaged over the levels of: Treatment
## Note: contrasts are still on the inverse(mu + 0.001) scale
## Results are given on the ( (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesOrdination Setup2
## importance.MDS1 importance.MDS2 importance.MDS3
## Eigenvalue 1.16 0.46 0.01
## Proportion Explained 0.71 0.28 0.01
## Cumulative Proportion 0.71 0.99 1.00##
## ***VECTORS
##
## MDS1 MDS2 r2 Pr(>r)
## Moisture 0.96876 -0.24800 0.6353 0.002 **
## Powell 0.88571 0.46423 0.1112 0.002 **
## KgHa -0.90003 -0.43584 0.1967 0.002 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499
##
## ***FACTORS:
##
## Centroids:
## MDS1 MDS2
## TSFRecently Burned 0.1048 0.0303
## TSFIntermediate -0.0299 -0.0791
## TSF3 Years Since Fire -0.1366 -0.0435
## TSFNot Yet Burned -0.0223 0.0607
## ESDClayey 0.0092 0.0237
## ESDLoamy 0.0132 -0.0215
## ESDSaline Lowland -0.0221 -0.0122
## ESDSandy 0.0084 0.0058
## ESDThin Claypan -0.0130 -0.0813
## MonthJune 0.2576 -0.0473
## MonthJuly 0.0126 -0.0337
## MonthAugust -0.0876 0.0020
## MonthSeptember -0.1181 0.0672
## TreatmentCattle 0.0232 0.0548
## TreatmentSheep -0.0288 -0.0680
##
## Goodness of fit:
## r2 Pr(>r)
## TSF 0.0923 0.002 **
## ESD 0.0062 0.602
## Month 0.2390 0.002 **
## Treatment 0.0500 1.000
## ---
## 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: NIR.cap3a by NIREnv_2a$TSF
## 999 permutations
##
## Recently Burned Intermediate 3 Years Since Fire
## Intermediate 0.001 - -
## 3 Years Since Fire 0.001 0.001 -
## Not Yet Burned 0.001 0.001 0.001
##
## P value adjustment method: fdr##
## Pairwise comparisons using factor fitting to an ordination
##
## data: NIR.cap3a by NIREnv_2a$Month
## 999 permutations
##
## June July August
## July 0.001 - -
## August 0.001 0.001 -
## September 0.001 0.001 0.001
##
## P value adjustment method: fdr
#Weight gains
versus 0
##
## Simultaneous Tests for General Linear Hypotheses
##
## Fit: lmer(formula = ADG ~ Year + 0 + (1 | Pasture1/Year), data = HrecEwe,
## REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Year2016 == 0 0.257578 0.008247 31.23 <2e-16 ***
## Year2017 == 0 0.289330 0.008433 34.31 <2e-16 ***
## Year2018 == 0 0.347227 0.008408 41.30 <2e-16 ***
## Year2019 == 0 0.289061 0.008572 33.72 <2e-16 ***
## Year2020 == 0 0.227955 0.008526 26.74 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)##
## Simultaneous Confidence Intervals
##
## Fit: lmer(formula = ADG ~ Year + 0 + (1 | Pasture1/Year), data = HrecEwe,
## REML = FALSE)
##
## Quantile = 2.565
## 95% family-wise confidence level
##
##
## Linear Hypotheses:
## Estimate lwr upr
## Year2016 == 0 0.2576 0.2364 0.2787
## Year2017 == 0 0.2893 0.2677 0.3110
## Year2018 == 0 0.3472 0.3257 0.3688
## Year2019 == 0 0.2891 0.2671 0.3110
## Year2020 == 0 0.2280 0.2061 0.2498##
## Simultaneous Tests for General Linear Hypotheses
##
## Fit: lmer(formula = ADG ~ Year + 0 + (1 | Pasture1/Year), data = HrecCow,
## REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Year2016 == 0 0.64684 0.08892 7.275 1.74e-12 ***
## Year2017 == 0 0.45185 0.08955 5.046 2.26e-06 ***
## Year2018 == 0 1.28594 0.08812 14.593 < 2e-16 ***
## Year2019 == 0 0.62724 0.09316 6.733 8.30e-11 ***
## Year2020 == 0 0.61921 0.09363 6.614 1.87e-10 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)##
## Simultaneous Confidence Intervals
##
## Fit: lmer(formula = ADG ~ Year + 0 + (1 | Pasture1/Year), data = HrecCow,
## REML = FALSE)
##
## Quantile = 2.569
## 95% family-wise confidence level
##
##
## Linear Hypotheses:
## Estimate lwr upr
## Year2016 == 0 0.6468 0.4184 0.8753
## Year2017 == 0 0.4519 0.2218 0.6819
## Year2018 == 0 1.2859 1.0596 1.5123
## Year2019 == 0 0.6272 0.3879 0.8666
## Year2020 == 0 0.6192 0.3787 0.8597##
## Simultaneous Tests for General Linear Hypotheses
##
## Fit: lmer(formula = ADG ~ Year + 0 + (1 | Pasture1/Year), data = HrecCalf,
## REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Year2016 == 0 2.98717 0.04546 65.72 <2e-16 ***
## Year2017 == 0 3.09392 0.04520 68.44 <2e-16 ***
## Year2018 == 0 2.64443 0.04505 58.70 <2e-16 ***
## Year2019 == 0 2.96073 0.04691 63.11 <2e-16 ***
## Year2020 == 0 2.97068 0.04751 62.52 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)##
## Simultaneous Confidence Intervals
##
## Fit: lmer(formula = ADG ~ Year + 0 + (1 | Pasture1/Year), data = HrecCalf,
## REML = FALSE)
##
## Quantile = 2.569
## 95% family-wise confidence level
##
##
## Linear Hypotheses:
## Estimate lwr upr
## Year2016 == 0 2.9872 2.8704 3.1039
## Year2017 == 0 3.0939 2.9778 3.2100
## Year2018 == 0 2.6444 2.5287 2.7602
## Year2019 == 0 2.9607 2.8402 3.0813
## Year2020 == 0 2.9707 2.8486 3.0927##
## Simultaneous Tests for General Linear Hypotheses
##
## Fit: lmer(formula = ADG ~ Type + 0 + (1 | Pasture1/Year), data = HrecAdgRaw,
## REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## TypeEwe == 0 0.28220 0.01995 14.14 <2e-16 ***
## TypeCalf == 0 2.92754 0.02410 121.49 <2e-16 ***
## TypeCow == 0 0.73571 0.02388 30.81 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)##
## Simultaneous Confidence Intervals
##
## Fit: lmer(formula = ADG ~ Type + 0 + (1 | Pasture1/Year), data = HrecAdgRaw,
## REML = FALSE)
##
## Quantile = 2.3625
## 95% family-wise confidence level
##
##
## Linear Hypotheses:
## Estimate lwr upr
## TypeEwe == 0 0.2822 0.2351 0.3293
## TypeCalf == 0 2.9275 2.8706 2.9845
## TypeCow == 0 0.7357 0.6793 0.7921Year Test
Ewe
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: ADG
## Chisq Df Pr(>Chisq)
## Year 129.4 4 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2016 0.258 0.0102 19.9 0.236 0.279
## 2017 0.289 0.0103 20.6 0.268 0.311
## 2018 0.347 0.0103 20.5 0.326 0.369
## 2019 0.289 0.0104 21.1 0.267 0.311
## 2020 0.228 0.0104 20.9 0.206 0.250
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2016 - Year2017 -0.031753 0.0134 17.8 -2.370 0.1696
## Year2016 - Year2018 -0.089650 0.0134 17.7 -6.698 <.0001
## Year2016 - Year2019 -0.031484 0.0135 18.0 -2.334 0.1795
## Year2016 - Year2020 0.029623 0.0135 17.9 2.201 0.2239
## Year2017 - Year2018 -0.057897 0.0135 18.0 -4.289 0.0035
## Year2017 - Year2019 0.000269 0.0136 18.3 0.020 1.0000
## Year2017 - Year2020 0.061375 0.0136 18.2 4.522 0.0021
## Year2018 - Year2019 0.058166 0.0136 18.3 4.281 0.0035
## Year2018 - Year2020 0.119272 0.0136 18.2 8.797 <.0001
## Year2019 - Year2020 0.061107 0.0137 18.5 4.473 0.0023
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 5 estimates## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2016 0.258 0.0102 19.9 0.236 0.279
## 2017 0.289 0.0103 20.6 0.268 0.311
## 2018 0.347 0.0103 20.5 0.326 0.369
## 2019 0.289 0.0104 21.1 0.267 0.311
## 2020 0.228 0.0104 20.9 0.206 0.250
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2016 - Year2017 -0.031753 0.0134 17.8 -0.0723 0.00882
## Year2016 - Year2018 -0.089650 0.0134 17.7 -0.1302 -0.04911
## Year2016 - Year2019 -0.031484 0.0135 18.0 -0.0723 0.00930
## Year2016 - Year2020 0.029623 0.0135 17.9 -0.0111 0.07034
## Year2017 - Year2018 -0.057897 0.0135 18.0 -0.0987 -0.01708
## Year2017 - Year2019 0.000269 0.0136 18.3 -0.0408 0.04133
## Year2017 - Year2020 0.061375 0.0136 18.2 0.0204 0.10237
## Year2018 - Year2019 0.058166 0.0136 18.3 0.0171 0.09919
## Year2018 - Year2020 0.119272 0.0136 18.2 0.0783 0.16023
## Year2019 - Year2020 0.061107 0.0137 18.5 0.0199 0.10231
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 5 estimatesCalf
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: ADG
## Chisq Df Pr(>Chisq)
## Year 56.267 4 1.763e-11 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see help('isSingular')## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2016 2.99 0.0561 22.3 2.87 3.10
## 2017 3.09 0.0558 22.1 2.98 3.21
## 2018 2.64 0.0557 22.1 2.53 2.76
## 2019 2.96 0.0572 23.2 2.84 3.08
## 2020 2.97 0.0577 23.7 2.85 3.09
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2016 - Year2017 -0.10675 0.0791 17.9 -1.349 0.6657
## Year2016 - Year2018 0.34274 0.0790 17.9 4.337 0.0033
## Year2016 - Year2019 0.02644 0.0802 18.4 0.330 0.9972
## Year2016 - Year2020 0.01649 0.0805 18.5 0.205 0.9996
## Year2017 - Year2018 0.44949 0.0788 17.8 5.701 0.0002
## Year2017 - Year2019 0.13319 0.0799 18.3 1.666 0.4774
## Year2017 - Year2020 0.12324 0.0803 18.5 1.535 0.5539
## Year2018 - Year2019 -0.31630 0.0799 18.3 -3.960 0.0070
## Year2018 - Year2020 -0.32625 0.0802 18.4 -4.069 0.0055
## Year2019 - Year2020 -0.00995 0.0813 18.9 -0.122 0.9999
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 5 estimates## boundary (singular) fit: see help('isSingular')## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2016 2.99 0.0561 22.3 2.87 3.10
## 2017 3.09 0.0558 22.1 2.98 3.21
## 2018 2.64 0.0557 22.1 2.53 2.76
## 2019 2.96 0.0572 23.2 2.84 3.08
## 2020 2.97 0.0577 23.7 2.85 3.09
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2016 - Year2017 -0.10675 0.0791 17.9 -0.346 0.1326
## Year2016 - Year2018 0.34274 0.0790 17.9 0.104 0.5819
## Year2016 - Year2019 0.02644 0.0802 18.4 -0.215 0.2683
## Year2016 - Year2020 0.01649 0.0805 18.5 -0.226 0.2591
## Year2017 - Year2018 0.44949 0.0788 17.8 0.211 0.6882
## Year2017 - Year2019 0.13319 0.0799 18.3 -0.108 0.3745
## Year2017 - Year2020 0.12324 0.0803 18.5 -0.119 0.3653
## Year2018 - Year2019 -0.31630 0.0799 18.3 -0.557 -0.0751
## Year2018 - Year2020 -0.32625 0.0802 18.4 -0.568 -0.0844
## Year2019 - Year2020 -0.00995 0.0813 18.9 -0.255 0.2346
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 5 estimatesCow
## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: ADG
## Chisq Df Pr(>Chisq)
## Year 52.936 4 8.79e-11 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see help('isSingular')## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2016 0.647 0.110 22.3 0.419 0.875
## 2017 0.452 0.111 22.5 0.223 0.681
## 2018 1.286 0.109 22.1 1.059 1.513
## 2019 0.627 0.113 23.7 0.393 0.862
## 2020 0.619 0.114 23.9 0.384 0.854
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2016 - Year2017 0.19498 0.156 17.9 1.249 0.7238
## Year2016 - Year2018 -0.63910 0.155 17.7 -4.117 0.0053
## Year2016 - Year2019 0.01959 0.158 18.4 0.124 0.9999
## Year2016 - Year2020 0.02762 0.158 18.5 0.174 0.9998
## Year2017 - Year2018 -0.83409 0.156 17.8 -5.362 0.0004
## Year2017 - Year2019 -0.17539 0.158 18.5 -1.107 0.8008
## Year2017 - Year2020 -0.16736 0.159 18.6 -1.054 0.8269
## Year2018 - Year2019 0.65870 0.158 18.3 4.179 0.0044
## Year2018 - Year2020 0.66673 0.158 18.4 4.222 0.0039
## Year2019 - Year2020 0.00803 0.161 19.0 0.050 1.0000
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 5 estimates## boundary (singular) fit: see help('isSingular')## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2016 0.647 0.110 22.3 0.419 0.875
## 2017 0.452 0.111 22.5 0.223 0.681
## 2018 1.286 0.109 22.1 1.059 1.513
## 2019 0.627 0.113 23.7 0.393 0.862
## 2020 0.619 0.114 23.9 0.384 0.854
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2016 - Year2017 0.19498 0.156 17.9 -0.277 0.667
## Year2016 - Year2018 -0.63910 0.155 17.7 -1.109 -0.169
## Year2016 - Year2019 0.01959 0.158 18.4 -0.458 0.497
## Year2016 - Year2020 0.02762 0.158 18.5 -0.450 0.505
## Year2017 - Year2018 -0.83409 0.156 17.8 -1.305 -0.363
## Year2017 - Year2019 -0.17539 0.158 18.5 -0.653 0.302
## Year2017 - Year2020 -0.16736 0.159 18.6 -0.646 0.311
## Year2018 - Year2019 0.65870 0.158 18.3 0.183 1.134
## Year2018 - Year2020 0.66673 0.158 18.4 0.190 1.143
## Year2019 - Year2020 0.00803 0.161 19.0 -0.475 0.491
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 5 estimatesADG Graph Stack
cowplot::plot_grid( CowPlot,CalfPlot, EwePlot, nrow = 3 )
#Graphs
##Biomass
##Moisture
##Protein
##NDF
##ADF
##ADL
##SI
Stacks
Bio CP Moisture
cowplot::plot_grid( BioPlot,MoiPlot, CPRPlot, nrow = 3)
Fiber stack
cowplot::plot_grid( NDFPlot,ADFPlot, ADLPlot, nrow = 3)
Ordi stack1
cowplot::plot_grid( Plot1, NULL, Plot2, Plot3, nrow = 2, labels=c('A','','B','C') )
Ordi stack2
cowplot::plot_grid( Plot1b, Plot2b, Plot3b, nrow = 3, labels=c('A','B','C') )