8 1992 full system analyses

8.1 Total leaf area in 1992.

This analysis uses all systems that have a non-NA value for total leaf area of the front and back in 1991, excluding those systems for which 1990 leaf area was NA.

8.1.1 Data & visualization

Read in data

Select the total leaf area variable, and the independent variables. Also filtering out rows that don’t have a leaf area record in 1990. We need to do this in order to be able to compare models from model set A (which don’t include leaf area, and so wouldn’t naturally be affected by the missing data) with models from model set B (which do include leaf area and would be affected by the missing data). In other words, removing these rows means that model set A and model set B will run using the exact same dataset, which is necessary in order for us to compare the models.

8.1.2 Model selection with leaf area in 1990 and 1991

(Intercept) Lf_90 Lftot_91 Sever Sex_90 Time Sever:Sex_90 Sever:Time Sex_90:Time Sever:Sex_90:Time df logLik AICc delta weight
6 -18.98414 0.2778212 0.7753865
NA
NA NA NA NA 10 -1455.489 2932.022 0.0000000 0.18486575
2 -11.40856 0.3133500 0.7830574
NA NA NA NA NA NA 8 -1457.689 2932.055 0.0332159 0.18182086
1 -14.75243 0.3049134 0.7980890 NA NA NA NA NA NA NA 5 -1461.208 2932.694 0.6728440 0.13205360
5 -24.40721 0.2699304 0.7914756 NA NA
NA NA NA NA 7 -1459.182 2932.888 0.8663366 0.11987644
4 -44.03431 0.3534655 0.7845174
NA NA NA NA NA 9 -1457.382 2933.613 1.5908845 0.08344499
40 -44.46533 0.2972305 0.7771511
NA NA
NA 13 -1453.031 2933.813 1.7913502 0.07548657
8 -29.18421 0.2918686 0.7761747
NA NA NA NA 11 -1455.459 2934.176 2.1543934 0.06295582
39 -45.87488 0.2827734 0.7913642 NA
NA NA
NA 10 -1456.590 2934.223 2.2009571 0.06150702
3 -40.25139 0.3382077 0.7985259 NA
NA NA NA NA NA 6 -1460.998 2934.387 2.3654655 0.05665029
7 -30.35397 0.2786637 0.7917473 NA
NA NA NA NA 8 -1459.171 2935.017 2.9956628 0.04133867

From this round of model selection, when Lf_90 and LfFtot_91 are required to be in the models that are considered, there are six models within two AICc units: (1) Lf_90, Lft_91, Sever, and Time (AICc 2932.0) (2) Lf_90, Lft_91, and Sever (AICc 2932.1) (3) Lf_90 and Lft_91 (AICc 2932.7) (4) Lf_90, Lft_91, and Time (AICc 2932.9) (5) Lf_90, Lft_91, Sever, and Sex_90 (AICc 2933.6) (6) Lf_90, Lft_91, Sever, Time, Sex_90, and the Sex_90 x Time interaction (AICc 2933.8)

8.1.3 Model selection with leaf area in 1991

(Intercept) Lf_90 Lftot_91 Sever Sex_90 Time Sever:Sex_90 Sever:Time Sex_90:Time Sever:Sex_90:Time df logLik AICc delta weight
12 -18.98414 0.2778212 0.7753865
NA
NA NA NA NA 10 -1455.489 2932.022 0.0000000 0.18486575
4 -11.40856 0.3133500 0.7830574
NA NA NA NA NA NA 8 -1457.689 2932.055 0.0332159 0.18182086
2 -14.75243 0.3049134 0.7980890 NA NA NA NA NA NA NA 5 -1461.208 2932.694 0.6728440 0.13205360
10 -24.40721 0.2699304 0.7914756 NA NA
NA NA NA NA 7 -1459.182 2932.888 0.8663366 0.11987644
8 -44.03431 0.3534655 0.7845174
NA NA NA NA NA 9 -1457.382 2933.613 1.5908845 0.08344499
80 -44.46533 0.2972305 0.7771511
NA NA
NA 13 -1453.031 2933.813 1.7913502 0.07548657
16 -29.18421 0.2918686 0.7761747
NA NA NA NA 11 -1455.459 2934.176 2.1543934 0.06295582
78 -45.87488 0.2827734 0.7913642 NA
NA NA
NA 10 -1456.590 2934.223 2.2009571 0.06150702
6 -40.25139 0.3382077 0.7985259 NA
NA NA NA NA NA 6 -1460.998 2934.387 2.3654655 0.05665029
14 -30.35397 0.2786637 0.7917473 NA
NA NA NA NA 8 -1459.171 2935.017 2.9956628 0.04133867

From this round of model selection, when LfFtot_91 only is required to be in the models that are considered, the same six best models are returned as above.

8.1.4 Model selection with leaf area in 1990

(Intercept) Lf_90 Lftot_91 Sever Sex_90 Time Sever:Sex_90 Sever:Time Sex_90:Time Sever:Sex_90:Time df logLik AICc delta weight
12 -18.98414 0.2778212 0.7753865
NA
NA NA NA NA 10 -1455.489 2932.022 0.0000000 0.18486575
4 -11.40856 0.3133500 0.7830574
NA NA NA NA NA NA 8 -1457.689 2932.055 0.0332159 0.18182086
2 -14.75243 0.3049134 0.7980890 NA NA NA NA NA NA NA 5 -1461.208 2932.694 0.6728440 0.13205360
10 -24.40721 0.2699304 0.7914756 NA NA
NA NA NA NA 7 -1459.182 2932.888 0.8663366 0.11987644
8 -44.03431 0.3534655 0.7845174
NA NA NA NA NA 9 -1457.382 2933.613 1.5908845 0.08344499
80 -44.46533 0.2972305 0.7771511
NA NA
NA 13 -1453.031 2933.813 1.7913502 0.07548657
16 -29.18421 0.2918686 0.7761747
NA NA NA NA 11 -1455.459 2934.176 2.1543934 0.06295582
78 -45.87488 0.2827734 0.7913642 NA
NA NA
NA 10 -1456.590 2934.223 2.2009571 0.06150702
6 -40.25139 0.3382077 0.7985259 NA
NA NA NA NA NA 6 -1460.998 2934.387 2.3654655 0.05665029
14 -30.35397 0.2786637 0.7917473 NA
NA NA NA NA 8 -1459.171 2935.017 2.9956628 0.04133867

From this round of model selection, when Lf_90 is required to be in the models that are considered, the same six best models are returned as above.

8.1.5 Model selection without leaf area

## Fixed term is "(Intercept)"
(Intercept) Lf_90 Lftot_91 Sever Sex_90 Time Sever:Sex_90 Sever:Time Sex_90:Time Sever:Sex_90:Time df logLik AICc delta weight
24 -18.98414 0.2778212 0.7753865
NA
NA NA NA NA 10 -1455.489 2932.022 0.0000000 0.18486575
8 -11.40856 0.3133500 0.7830574
NA NA NA NA NA NA 8 -1457.689 2932.055 0.0332159 0.18182086
4 -14.75243 0.3049134 0.7980890 NA NA NA NA NA NA NA 5 -1461.208 2932.694 0.6728440 0.13205360
20 -24.40721 0.2699304 0.7914756 NA NA
NA NA NA NA 7 -1459.182 2932.888 0.8663366 0.11987644
16 -44.03431 0.3534655 0.7845174
NA NA NA NA NA 9 -1457.382 2933.613 1.5908845 0.08344499
160 -44.46533 0.2972305 0.7771511
NA NA
NA 13 -1453.031 2933.813 1.7913502 0.07548657
32 -29.18421 0.2918686 0.7761747
NA NA NA NA 11 -1455.459 2934.176 2.1543934 0.06295582
156 -45.87488 0.2827734 0.7913642 NA
NA NA
NA 10 -1456.590 2934.223 2.2009571 0.06150702
12 -40.25139 0.3382077 0.7985259 NA
NA NA NA NA NA 6 -1460.998 2934.387 2.3654655 0.05665029
28 -30.35397 0.2786637 0.7917473 NA
NA NA NA NA 8 -1459.171 2935.017 2.9956628 0.04133867

From this round of model selection, when the leaf area effects are not required to be in the models that are considered, the same six best models are returned as above.

8.1.6 Conclusion

The simplest and best model here includes fixed effects of total leaf area in 1991 and leaf area in 1990.