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 1m^{2} 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 fixedfactor 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. 
5m radius 
10m radius 
15m radius 
20m 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, 5m 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 oneyear old seedlings through the second year. See Methods for a description of the generalized estimating equation model; the 5m 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 (10m 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 oneyear 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 1m^{2} 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 fixedfactor 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: 5m 
Adults:10m 
Adults: 5m 
Adults:10m 

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).