Appendix C. Results tables for GLMM and GEE models of seedling survival.
| TABLE C1. Effect of seedling and adult neighborhoods (of varying sizes) on individual seedling survival over the first year (GEE). Seedling neighbors are found within the same 1-m2 seedling plot as each focal seedling, and tree neighborhoods contain adults > 10 cm DBH in circles with the indicated radii surrounding each plot. See Methods for a description of the regression model. Coefficient estimates are expressed as odds ratios for the fixed-factor predictors in a generalized estimating equation model. Significant predictor variables are highlighted in bold. Odds ratios >1 have a positive relationship with increased survival, and ratios <1 have a negative relationship with survival. An asterisk (*) indicates the predictor had a P value <0.1, and is included for heuristic purposes to show changes in the strength of the signal with changes in the size of the adult neighborhood included in the model. Model ROC values > 0.7 indicate acceptable discrimination ability. |
5-m radius |
10-m radius |
15-m radius |
20-m radius |
|
Conspecific adult basal area |
0.001 |
0.030 |
* 0.096 |
* 0.252 |
Heterospecific adult basal area |
0.715 |
0.844 |
1.142 |
0.950 |
Phylogenetic distance (adults) 1 |
0.909 |
0.945 |
0.950 |
0.958 |
Conspecific seedling density |
0.979 |
0.978 |
0.973 |
0.975 |
Heterospecific seedling density |
1.001 |
1.000 |
1.000 |
1.000 |
Phylogenetic distance (seedlings) 1 |
0.982 |
0.972 |
0.968 |
0.965 |
Seedling species diversity |
1.005 |
1.011 |
0.973 |
0.999 |
Initial seedling height |
1.032 |
1.032 |
1.048 |
1.007 |
Height × Conspecific adult basal area |
1.300 |
* 1.122 |
1.015 |
1.020 |
Height × Heterospecific adult basal area |
1.037 |
1.010 |
0.995 |
1.010 |
Height × Conspecific seedling density |
1.002 |
1.002 |
1.002 |
1.002 |
Height × Heterospecific seedling density |
1.000 |
1.000 |
1.000 |
1.000 |
Height × Seedling diversity |
1.015 |
1.014 |
1.017 |
1.016 |
Recruit Year = 2004 |
0.385 |
0.379 |
0.382 |
0.379 |
Recruit Year = 2005 |
0.284 |
0.284 |
0.285 |
0.288 |
Recruit Year = 2006 |
0.251 |
0.248 |
0.243 |
0.244 |
Recruit Year = 2007 |
0.242 |
0.240 |
0.238 |
0.236 |
ROC |
0.684 |
0.679 |
0.685 |
0.679 |
1 Phylogenetic distance measured as an effect size with values >0 indicating phylogenetic clustering (neighborhood is more closely related than expected by null model) and values <0 indicating phylogenetic dispersion (neighborhood is more distantly related than expected from null model). Positive effects (odds ratios >1) indicate better survival with increased phylogenetic clustering; negative effects (odds ratios <1) indicate survival is decreased when neighbors are more closely related.
TABLE C2. Neighborhood effects on survival beyond the first year (GEE, 5-m adult radius). Regression coefficients expressed as odds ratios for, from left to right, survival of new recruits over the first two years, survival of new recruits over the first three years, and survival of one-year old seedlings through the second year. See Methods for a description of the generalized estimating equation model; the 5-m radius is used for the adult neighborhood in this model. Significant predictor variables are highlighted in bold. Odds ratios >1 have a positive relationship with increased survival, and ratios <1 have a negative relationship with survival. Model ROC values > 0.7 indicate acceptable discrimination ability.
Survival 0 to 2 1 |
Survival 0 to 3 2 |
Survival 1 to 2 3 |
|
Conspecific adult basal area |
0.002 |
0.000 |
0.027 |
Heterospecific adult basal area |
0.755 |
1.449 |
0.989 |
Phylogenetic distance (adults) 4 |
1.013 |
1.031 |
1.201 |
Conspecific seedling density |
0.989 |
0.982 |
1.017 |
Heterospecific seedling density |
0.997 |
1.001 |
0.991 |
Phylogenetic distance (seedlings) 4 |
0.921 |
0.870 |
0.889 |
Seedling species diversity |
1.315 |
1.135 |
1.568 |
Initial seedling height |
1.041 |
1.028 |
1.035 |
Height × Conspecific adult basal area |
1.120 |
1.287 |
0.992 |
Height × Heterospecific adult basal area |
1.012 |
0.978 |
0.956 |
Height × Conspecific seedling density |
1.002 |
1.003 |
1.000 |
Height × Heterospecific seedling density |
1.001 |
1.001 |
1.001 |
Height × Seedling diversity |
1.004 |
1.017 |
0.999 |
Recruit Year = 2004 5 |
0.500 |
0.455 |
0.902 |
Recruit Year = 2005 5 |
0.343 |
0.326 |
0.646 |
Recruit Year = 2006 5 |
0.319 |
-- |
0.688 |
ROC |
0.677 |
0.678 |
0.622 |
1 Analysis included 3690 seedlings from 160 species and four recruit cohorts.
2 Analysis included 2844 seedlings from 153 species and three recruit cohorts.
3 Analysis included 1950 seedlings from 151 species and four recruit cohorts.
4 Phylogenetic distance measured as an effect size with values >0 indicating phylogenetic clustering (neighborhood is more closely related than expected by null model) and values <0 indicating phylogenetic dispersion (neighborhood is more distantly related than expected from null model). Positive effects (odds ratios >1) indicate better survival with increased phylogenetic clustering; negative effects (odds ratios <1) indicate survival is decreased when neighbors are more closely related.
5 Change in intercept relative to baseline cohort (recruit year = 2003).
TABLE C3. Neighborhood effects on survival beyond the first year (10-m adult radius). Regression coefficients expressed as odds ratios for, from left to right, survival of new recruits over the first two years, survival of new recruits over the first three years, and survival of one-year old seedlings through the second year. See Methods for a description of the GLMM and GEE models. Significant predictor variables are highlighted in bold. Odds ratios >1 have a positive relationship with increased survival, and ratios <1 have a negative relationship with survival. Model ROC values > 0.7 indicate acceptable discrimination ability.
Survival 0 to 2 1 |
Survival 0 to 3 2 |
Survival 1 to 2 3 |
||||
Analysis |
GLMM |
GEE |
GLMM |
GEE |
GLMM |
GEE |
Conspecific adult basal area |
0.069 |
0.130 |
0.091 |
0.211 |
0.962 |
0.768 |
Heterospecific adult basal area |
0.828 |
0.668 |
0.994 |
0.792 |
0.782 |
0.733 |
Phylogenetic distance (adults) 4 |
1.084 |
1.081 |
1.146 |
1.128 |
1.221 |
1.204 |
Conspecific seedling density |
0.978 |
0.990 |
0.967 |
0.980 |
1.011 |
1.017 |
Heterospecific seedling density |
0.995 |
0.997 |
1.000 |
1.001 |
0.992 |
0.993 |
Phylogenetic distance (seedlings) 4 |
0.872 |
0.885 |
0.789 |
0.825 |
0.860 |
0.872 |
Seedling species diversity |
1.180 |
1.351 |
1.081 |
1.158 |
1.597 |
1.674 |
Initial seedling height |
1.039 |
1.041 |
1.040 |
1.035 |
1.042 |
1.040 |
Height × Conspecific adult basal area |
0.967 |
0.968 |
0.951 |
0.931 |
0.871 |
0.892 |
Height × Heterospecific adult basal area |
1.001 |
1.009 |
0.984 |
0.995 |
0.990 |
0.996 |
Height × Conspecific seedling density |
1.002 |
1.002 |
1.004 |
1.003 |
1.000 |
1.000 |
Height × Heterospecific seedling density |
1.001 |
1.001 |
1.001 |
1.001 |
1.001 |
1.001 |
Height × Seedling diversity |
1.012 |
1.003 |
1.023 |
1.016 |
0.997 |
0.994 |
Recruit Year = 2004 5 |
0.444 |
0.502 |
0.403 |
0.461 |
0.915 |
0.929 |
Recruit Year = 2005 5 |
0.285 |
0.342 |
0.261 |
0.325 |
0.616 |
0.642 |
Recruit Year = 2006 5 |
0.261 |
0.307 |
- - |
- - |
0.679 |
0.679 |
ROC |
0.808 |
0.672 |
0.833 |
0.674 |
0.750 |
0.619 |
1 Analysis included 3690 seedlings from 160 species and four recruit cohorts.
2 Analysis included 2844 seedlings from 153 species and three recruit cohorts.
3 Analysis included 1950 seedlings from 151 species and four recruit cohorts.
4 Phylogenetic distance measured as an effect size with values >0 indicating phylogenetic clustering (neighborhood is more closely related than expected by null model) and values <0 indicating phylogenetic dispersion (neighborhood is more distantly related than expected from null model). Positive effects (odds ratios >1) indicate better survival with increased phylogenetic clustering; negative effects (odds ratios <1) indicate survival is decreased when neighbors are more closely related.
5 Change in intercept relative to baseline cohort (recruit year = 2003).
TABLE C4. Effect of seedling and adult neighborhoods (5–10 m radius) on individual seedling survival, excluding the most common species. Analysis includes 154 morphospecies and 2997 individuals; the nine most common seedling species (each with > 100 recruits) were excluded. Seedling neighbors are found within the same 1-m2 seedling plot as each focal seedling, and tree neighborhoods contain adults > 10 cm DBH in circles with the indicated radii surrounding each plot. See Methods for a description of the regression model. Coefficient estimates are expressed as odds ratios for the fixed-factor predictors in a GEE or GLMM model. Significant predictor variables are highlighted in bold. Odds ratios >1 have a positive relationship with increased survival, and ratios <1 have a negative relationship with survival.
|
GLMM |
GEE |
||
Adults: 5-m |
Adults:10-m |
Adults: 5-m |
Adults:10-m |
|
Conspecific adult basal area |
0.001 |
0.022 |
0.003 |
0.041 |
Heterospecific adult basal area |
0.612 |
0.949 |
0.613 |
0.903 |
Phylogenetic distance (adults) 1 |
0.810 |
0.861 |
0.815 |
0.871 |
Conspecific seedling density |
0.958 |
0.952 |
0.962 |
0.960 |
Heterospecific seedling density |
0.992 |
0.991 |
0.992 |
0.991 |
Phylogenetic distance (seedlings) 1 |
0.942 |
0.936 |
0.953 |
0.942 |
Seedling species diversity |
0.689 |
0.676 |
0.702 |
0.695 |
Initial seedling height |
1.002 |
1.003 |
1.000 |
0.999 |
Height × Conspecific adult basal area |
1.386 |
1.176 |
1.298 |
1.145 |
Height × Heterospecific adult basal area |
1.043 |
1.006 |
1.043 |
1.009 |
Height × Conspecific seedling density |
1.000 |
1.000 |
1.001 |
1.001 |
Height × Heterospecific seedling density |
1.001 |
1.001 |
1.001 |
1.001 |
Height × Seedling diversity |
1.038 |
1.040 |
1.036 |
1.037 |
Recruit Year = 2004 2 |
0.250 |
0.237 |
0.269 |
0.256 |
Recruit Year = 2005 2 |
0.190 |
0.183 |
0.208 |
0.202 |
Recruit Year = 2006 2 |
0.143 |
0.137 |
0.165 |
0.162 |
Recruit Year = 2007 2 |
0.141 |
0.136 |
0.159 |
0.156 |
ROC |
0.791 |
0.797 |
0.724 |
0.719 |
1 Phylogenetic distance measured as an effect size with values >0 indicating phylogenetic clustering (neighborhood is more closely related than expected by null model) and values <0 indicating phylogenetic dispersion (neighborhood is more distantly related than expected from null model). Positive effects (odds ratios >1) indicate better survival with increased phylogenetic clustering; negative effects (odds ratios <1) indicate survival is decreased when neighbors are more closely related.
2 Change in intercept relative to baseline cohort (recruit year = 2003).