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Jun 17th, 2019
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  1. > dat
  2. num_bloc F E y
  3. 1 bloc1 T B 0.0695
  4. 2 bloc2 T B 0.1540
  5. 3 bloc3 T B 0.0634
  6. 4 bloc1 C B 0.0770
  7. 5 bloc2 C B 0.0746
  8. 6 bloc3 C B 0.1020
  9. 7 bloc1 P B 0.0825
  10. 8 bloc2 P B 0.0559
  11. 9 bloc3 P B 0.0832
  12. 10 bloc1 T B.Br 0.0891
  13. 11 bloc2 T B.Br 0.1050
  14. 12 bloc3 T B.Br 0.1150
  15. 13 bloc1 C B.Br 0.1580
  16. 14 bloc2 C B.Br 0.0989
  17. 15 bloc3 C B.Br 0.1510
  18. 16 bloc1 P B.Br 0.1020
  19. 17 bloc2 P B.Br 0.0751
  20. 18 bloc3 P B.Br 0.0655
  21. 19 bloc1 T B.S 0.1020
  22. 20 bloc2 T B.S 0.0755
  23. 21 bloc3 T B.S 0.0631
  24. 22 bloc1 C B.S 0.0705
  25. 23 bloc2 C B.S 0.0782
  26. 24 bloc3 C B.S 0.0751
  27. 25 bloc1 P B.S 0.0826
  28. 26 bloc2 P B.S 0.0800
  29. 27 bloc3 P B.S 0.0996
  30. 28 bloc1 T B.S.Br 0.0850
  31. 29 bloc2 T B.S.Br 0.0688
  32. 30 bloc3 T B.S.Br 0.0727
  33. 31 bloc1 C B.S.Br 0.0762
  34. 32 bloc2 C B.S.Br 0.0880
  35. 33 bloc3 C B.S.Br 0.0751
  36. 34 bloc1 P B.S.Br 0.0694
  37. 35 bloc2 P B.S.Br 0.0619
  38. 36 bloc3 P B.S.Br 0.0627
  39. >
  40.  
  41. full0 <- lme(y~F*E,control=lmeControl(opt = "optim"),
  42. random=~1|num_bloc/E,data=dat,method='ML',
  43. contrasts = list(F='contr.treatment'),na.action="na.exclude")
  44.  
  45. full <- update(full0,weight=varIdent(form = ~ 1 | E*F))
  46.  
  47. main0 <- lme(y~F+E,control=lmeControl(opt = "optim"),
  48. random=~1|num_bloc/E,data=dat,method='ML',
  49. contrasts = list(F='contr.treatment'),na.action="na.exclude")
  50. main <- update(main0,weight=varIdent(form = ~ 1 | E*F))
  51.  
  52. anova(full,main)
  53. Model df AIC BIC logLik Test L.Ratio p-value
  54. full 1 26 -174.1895 -133.0180 113.0948
  55. main 2 20 -175.5688 -143.8985 107.7844 1 vs 2 10.62064 0.1008
  56.  
  57. > contrast(emmeans(full0,~F),method="trt.vs.ctrl")
  58. NOTE: Results may be misleading due to involvement in interactions
  59. contrast estimate SE df t.ratio p.value
  60. C - T 0.00513 0.00856 16 0.599 0.7690
  61. P - T -0.01189 0.00856 16 -1.390 0.3123
  62.  
  63. Results are averaged over the levels of: E
  64. P value adjustment: dunnettx method for 2 tests
  65.  
  66. > contrast(emmeans(full,~F),method="trt.vs.ctrl")
  67. NOTE: Results may be misleading due to involvement in interactions
  68. contrast estimate SE df t.ratio p.value
  69. C - T 0.00513 0.00973 16 0.527 0.8110
  70. P - T -0.01189 0.00905 16 -1.314 0.3482
  71.  
  72. Results are averaged over the levels of: E
  73. P value adjustment: dunnettx method for 2 tests
  74.  
  75. > contrast(emmeans(main0,~F),method="trt.vs.ctrl")
  76. contrast estimate SE df t.ratio p.value
  77. C - T 0.00513 0.00902 22 0.568 0.7857
  78. P - T -0.01189 0.00902 22 -1.318 0.3392
  79.  
  80. Results are averaged over the levels of: E
  81. P value adjustment: dunnettx method for 2 tests
  82.  
  83. > contrast(emmeans(main,~F),method="trt.vs.ctrl")
  84. contrast estimate SE df t.ratio p.value
  85. C - T 0.000686 0.00469 22 0.146 0.9773
  86. P - T -0.011254 0.00222 22 -5.072 0.0001
  87.  
  88. Results are averaged over the levels of: E
  89. P value adjustment: dunnettx method for 2 tests
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