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# Untitled

a guest Jun 18th, 2019 56 Never
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1. lowest_AIC <- mixed_model(yield ~ stock,
2.                     random = ~  1 | groups,
3.                     data = trees,
4.                     family = hurdle.lognormal(), n_phis = 1,
5.                     zi_fixed = ~ stock
6. )
7.
8. > AIC(lowest_AIC)
9. [1] 2784.14
10. > mean(residuals(lowest_AIC)^2)
11. [1] 0.1474714
12. > summary(lowest_AIC)
13.
14. Call:
15. mixed_model(fixed = yield ~ stock, random = ~1 | groups, data = trees,
16.     family = hurdle.lognormal(), zi_fixed = ~stock, n_phis = 1)
17.
18. Data Descriptives:
19. Number of Observations: 20583
20. Number of Groups: 2
21.
22. Model:
23.  family: hurdle log-normal
25.
26. Fit statistics:
27.   log.Lik     AIC      BIC
28.  -1386.07 2784.14 2776.299
29.
30. Random effects covariance matrix:
31.               StdDev
32. (Intercept) 1.396311
33.
34. Fixed effects:
35.             Estimate Std.Err  z-value p-value
36. (Intercept)   0.0004  0.0061   0.0731 0.94177
37. stock        -0.0907  0.0062 -14.7410 < 1e-04
38.
39. Zero-part coefficients:
40.             Estimate Std.Err  z-value p-value
41. (Intercept)  -2.4295  0.0257 -94.3862 < 1e-04
42. stock         0.1934  0.0238   8.1089 < 1e-04
43.
44. log(residual std. dev.):
45.   Estimate Std.Err
46.    -0.1746  0.0051
47.
48. Integration:
51.
52. Optimization:
53. method: EM
54. converged: TRUE
55.
56. best <- mixed_model(yield ~ stock + slope + precipitation + n_trees + soil_depth + rocks  + position,
57.                     random = ~  1 | groups,
58.                     data = trees,
59.                     family = hurdle.lognormal(), n_phis = 1,
60.                     zi_fixed = ~ stock + slope + precipitation + rocks + position,
61.                     zi_random = ~  1 | groups
62.
63. )
64.
65. > AIC(best)
66. [1] 2839.902
67. > mean(residuals(best)^2)
68. [1] 0.1890385
69. > summary(best)
70.
71. Call:
72. mixed_model(fixed = yield ~ stock + slope + precipitation + n_trees +
73.     soil_depth + rocks + position, random = ~1 | groups, data = trees,
74.     family = hurdle.lognormal(), zi_fixed = ~stock + slope +
75.         precipitation + rocks + position, zi_random = ~1 | groups,
76.     n_phis = 1)
77.
78. Data Descriptives:
79. Number of Observations: 20528
80. Number of Groups: 2
81.
82. Model:
83.  family: hurdle log-normal
85.
86. Fit statistics:
87.    log.Lik      AIC      BIC
88.  -1387.951 2839.902 2798.083
89.
90. Random effects covariance matrix:
91.                 StdDev    Corr
92. (Intercept)     1.4117
93. zi_(Intercept)  0.1331  0.0477
94.
95. Fixed effects:
96.                            Estimate Std.Err  z-value p-value
97. (Intercept)                  0.4576  0.0176  25.9341 < 1e-04
98. stock                       -0.0644  0.0059 -10.8639 < 1e-04
99. slope                       -0.0593  0.0059 -10.1307 < 1e-04
100. precipitation               -0.0858  0.0061 -14.1035 < 1e-04
101. n_trees                     -0.0630  0.0060 -10.5368 < 1e-04
102. soil_depth                   0.0590  0.0061   9.7462 < 1e-04
103. rocks2                      -0.0847  0.0155  -5.4514 < 1e-04
104. rocks3                      -0.0942  0.0178  -5.2897 < 1e-04
105. rocks4                      -0.1437  0.0184  -7.8039 < 1e-04
106. rocks5                      -0.1933  0.0258  -7.5044 < 1e-04
107. rocks6                      -0.4962  0.0574  -8.6376 < 1e-04
108. position-0.561514296868636  -0.2333  0.0180 -12.9644 < 1e-04
109. position0.381120787744946   -0.4953  0.0193 -25.6413 < 1e-04
110. position1.32375587235853    -0.8913  0.0234 -38.0653 < 1e-04
111. position2.26639095697211    -1.0993  0.0276 -39.8970 < 1e-04
112.
113. Zero-part coefficients:
114.                            Estimate Std.Err  z-value  p-value
115. (Intercept)                 -3.5587  0.1180 -30.1541  < 1e-04
116. stock                        0.1724  0.0255   6.7729  < 1e-04
117. slope                        0.2517  0.0272   9.2508  < 1e-04
118. precipitation               -0.1457  0.0296  -4.9197  < 1e-04
119. rocks2                       0.3587  0.0719   4.9900  < 1e-04
120. rocks3                       0.3497  0.0823   4.2506  < 1e-04
121. rocks4                       0.3951  0.0845   4.6742  < 1e-04
122. rocks5                       0.5387  0.1110   4.8507  < 1e-04
123. rocks6                       0.5434  0.2539   2.1404 0.032319
124. position-0.561514296868636   0.3085  0.1215   2.5384 0.011136
125. position0.381120787744946    0.8707  0.1219   7.1406  < 1e-04
126. position1.32375587235853     1.5953  0.1251  12.7515  < 1e-04
127. position2.26639095697211     2.0707  0.1270  16.3061  < 1e-04
128.
129. log(residual std. dev.):
130.   Estimate Std.Err
131.    -0.2856  0.0052
132.
133. Integration: