10_model-selection
Nikki Moore
29/07/2021
Trait model selection and averaging
First, look for multicolinearity among our variables:
Cold:
| GVIF | Df | GVIF^(1/(2*Df)) | |
|---|---|---|---|
| abs_lat_mp | 1.696322 | 1 | 1.302429 |
| log_range_area_km2 | 1.623753 | 1 | 1.274266 |
| realm | 167.689290 | 2 | 3.598540 |
| dispersal_ability_category | 422.337173 | 7 | 1.540094 |
| dispersal_distance_continuous | 3.456143 | 1 | 1.859071 |
| log_maximum_body_size | 1.679799 | 1 | 1.296071 |
| hot_season_dormancy_ | 1.123206 | 1 | 1.059814 |
| cold_season_dormancy_ | 1.708868 | 1 | 1.307237 |
| Trophic_position | 3.458725 | 3 | 1.229757 |
| metric | 2.074655 | 1 | 1.440366 |
Warm:
| GVIF | Df | GVIF^(1/(2*Df)) | |
|---|---|---|---|
| abs_lat_mp | 1.653388 | 1 | 1.285841 |
| log_range_area_km2 | 1.367756 | 1 | 1.169511 |
| realm | 126.941905 | 2 | 3.356613 |
| dispersal_ability_category | 275.732412 | 9 | 1.366415 |
| dispersal_distance_continuous | 2.253621 | 1 | 1.501207 |
| log_maximum_body_size | 1.670321 | 1 | 1.292409 |
| hot_season_dormancy_ | 1.069713 | 1 | 1.034269 |
| cold_season_dormancy_ | 1.678150 | 1 | 1.295434 |
| Trophic_position | 2.662762 | 4 | 1.130229 |
| metric | 2.266053 | 1 | 1.505342 |
Dispersal ability category and realm are highly colinear, so let’s leave dispersal ability category out of our models from now on.
Behind the scenes, here is where I:
- Normalize all continuous variables (absolute latitudinal midpoint of realized range, log maximum body size, log range area, dispersal distance) so that all have mean = 0 and sd = 1
- Get only complete cases
Now, run the full models and check out the residuals:
Cold:
filling_value ~ abs_lat_mp*realm + log_range_area_km2 + dispersal_distance_continuous + log_maximum_body_size + cold_season_dormancy_ + Trophic_position + metric
random = ~1|Class/Order/Family/Genus
Warm:
filling_value ~ abs_lat_mp*realm + log_range_area_km2 + dispersal_distance_continuous + log_maximum_body_size + hot_season_dormancy_ + Trophic_position + metric
random = ~1|Class/Order/Family/Genus 
Now, fit all the models using dredge, select the confidence set and average the models:
Cold:
## Fixed term is "(Intercept)"##
## Call:
## model.avg(object = confset.95p_cold)
##
## Component model call:
## lme.formula(fixed = filling_value ~ <11 unique rhs>, data = cold,
## random = ~1 | Class/Order/Family/Genus)
##
## Component models:
## df logLik AICc delta weight
## 1256789 17 -713.35 1463.63 0.00 0.28
## 12456789 18 -712.73 1464.76 1.13 0.16
## 12356789 18 -712.92 1465.14 1.51 0.13
## 125789 16 -715.40 1465.39 1.77 0.12
## 123456789 19 -712.31 1466.29 2.66 0.07
## 1245789 17 -714.78 1466.50 2.87 0.07
## 1235789 17 -714.98 1466.89 3.27 0.05
## 125679 14 -718.75 1467.49 3.86 0.04
## 12345789 18 -714.36 1468.01 4.39 0.03
## 1245679 15 -718.21 1468.69 5.07 0.02
## 1235679 15 -718.33 1468.93 5.30 0.02
##
## Term codes:
## abs_lat_mp cold_season_dormancy_
## 1 2
## dispersal_distance_continuous log_maximum_body_size
## 3 4
## log_range_area_km2 metric
## 5 6
## realm Trophic_position
## 7 8
## abs_lat_mp:realm
## 9
##
## Model-averaged coefficients:
## (full average)
## Estimate Std. Error Adjusted SE z value
## (Intercept) 8.476895 3.640332 3.680593 2.303
## abs_lat_mp 3.489329 0.631288 0.638329 5.466
## cold_season_dormancy_Yes -5.453496 1.173895 1.187003 4.594
## log_range_area_km2 5.950262 0.532155 0.538087 11.058
## metriclt -0.946134 2.499538 2.555925 0.370
## realmIntertidal -4.088253 6.032696 7.529122 0.543
## realmMarine -10.494283 7.063595 8.817312 1.190
## Trophic_positionomnivore -2.262152 1.751150 1.767805 1.280
## Trophic_positioninsectivore -1.099164 2.059210 2.081670 0.528
## Trophic_positioncarnivore -1.473983 2.263272 2.287640 0.644
## abs_lat_mp:realmIntertidal 3.713646 2.207027 2.231671 1.664
## abs_lat_mp:realmMarine -2.952854 1.536047 1.571923 1.878
## log_maximum_body_size -0.003709 0.439773 0.444711 0.008
## dispersal_distance_continuous 0.031127 0.340140 0.343894 0.091
## Pr(>|z|)
## (Intercept) 0.0213 *
## abs_lat_mp < 2e-16 ***
## cold_season_dormancy_Yes 4.3e-06 ***
## log_range_area_km2 < 2e-16 ***
## metriclt 0.7113
## realmIntertidal 0.5871
## realmMarine 0.2340
## Trophic_positionomnivore 0.2007
## Trophic_positioninsectivore 0.5975
## Trophic_positioncarnivore 0.5194
## abs_lat_mp:realmIntertidal 0.0961 .
## abs_lat_mp:realmMarine 0.0603 .
## log_maximum_body_size 0.9933
## dispersal_distance_continuous 0.9279
##
## (conditional average)
## Estimate Std. Error Adjusted SE z value
## (Intercept) 8.47690 3.64033 3.68059 2.303
## abs_lat_mp 3.48933 0.63129 0.63833 5.466
## cold_season_dormancy_Yes -5.45350 1.17389 1.18700 4.594
## log_range_area_km2 5.95026 0.53216 0.53809 11.058
## metriclt -1.29518 2.84614 2.91389 0.444
## realmIntertidal -4.08825 6.03270 7.52912 0.543
## realmMarine -10.49428 7.06359 8.81731 1.190
## Trophic_positionomnivore -2.46685 1.68495 1.70381 1.448
## Trophic_positioninsectivore -1.19863 2.12246 2.14622 0.558
## Trophic_positioncarnivore -1.60736 2.31766 2.34360 0.686
## abs_lat_mp:realmIntertidal 3.71365 2.20703 2.23167 1.664
## abs_lat_mp:realmMarine -2.95285 1.53605 1.57192 1.878
## log_maximum_body_size -0.01045 0.73822 0.74651 0.014
## dispersal_distance_continuous 0.09955 0.60265 0.60943 0.163
## Pr(>|z|)
## (Intercept) 0.0213 *
## abs_lat_mp < 2e-16 ***
## cold_season_dormancy_Yes 4.3e-06 ***
## log_range_area_km2 < 2e-16 ***
## metriclt 0.6567
## realmIntertidal 0.5871
## realmMarine 0.2340
## Trophic_positionomnivore 0.1477
## Trophic_positioninsectivore 0.5765
## Trophic_positioncarnivore 0.4928
## abs_lat_mp:realmIntertidal 0.0961 .
## abs_lat_mp:realmMarine 0.0603 .
## log_maximum_body_size 0.9888
## dispersal_distance_continuous 0.8702
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Warm:
## Fixed term is "(Intercept)"##
## Call:
## model.avg(object = confset.95p_warm)
##
## Component model call:
## lme.formula(fixed = filling_value ~ <17 unique rhs>, data = warm,
## random = ~1 | Class/Order/Family/Genus)
##
## Component models:
## df logLik AICc delta weight
## 1356789 18 -1101.57 2241.03 0.00 0.27
## 12356789 19 -1101.07 2242.24 1.21 0.15
## 13456789 19 -1101.33 2242.77 1.74 0.11
## 135789 17 -1103.60 2242.89 1.86 0.11
## 123456789 20 -1100.83 2243.99 2.97 0.06
## 135679 14 -1107.75 2244.65 3.62 0.04
## 1345789 18 -1103.45 2244.79 3.76 0.04
## 1235789 18 -1103.56 2245.00 3.97 0.04
## 156789 17 -1104.75 2245.17 4.15 0.03
## 13579 13 -1109.52 2246.03 5.00 0.02
## 1235679 15 -1107.38 2246.08 5.05 0.02
## 1256789 18 -1104.23 2246.34 5.31 0.02
## 1345679 15 -1107.61 2246.53 5.50 0.02
## 1456789 18 -1104.47 2246.82 5.80 0.02
## 12345789 19 -1103.40 2246.89 5.87 0.01
## 15789 16 -1106.82 2247.12 6.10 0.01
## 12345679 16 -1107.24 2247.97 6.94 0.01
##
## Term codes:
## abs_lat_mp dispersal_distance_continuous
## 1 2
## hot_season_dormancy_ log_maximum_body_size
## 3 4
## log_range_area_km2 metric
## 5 6
## realm Trophic_position
## 7 8
## abs_lat_mp:realm
## 9
##
## Model-averaged coefficients:
## (full average)
## Estimate Std. Error Adjusted SE z value
## (Intercept) -3.65901 2.74429 2.76358 1.324
## abs_lat_mp -2.04354 0.38656 0.38929 5.249
## hot_season_dormancy_Yes -2.69991 1.67661 1.68575 1.602
## log_range_area_km2 2.02962 0.29464 0.29672 6.840
## metriclt -1.74855 1.67036 1.67812 1.042
## realmIntertidal 0.29575 4.02193 4.04989 0.073
## realmMarine -0.99581 3.34385 3.36704 0.296
## Trophic_positionomnivore 1.21663 1.35137 1.35979 0.895
## Trophic_positionfungivore -0.57577 4.32178 4.37197 0.132
## Trophic_positioninsectivore 0.61652 1.49476 1.50498 0.410
## Trophic_positioncarnivore 0.50887 1.54839 1.55910 0.326
## abs_lat_mp:realmIntertidal 0.55950 1.60622 1.61753 0.346
## abs_lat_mp:realmMarine 2.77211 0.69450 0.69936 3.964
## dispersal_distance_continuous 0.11829 0.25517 0.25612 0.462
## log_maximum_body_size 0.05116 0.25269 0.25428 0.201
## Pr(>|z|)
## (Intercept) 0.186
## abs_lat_mp 2.00e-07 ***
## hot_season_dormancy_Yes 0.109
## log_range_area_km2 < 2e-16 ***
## metriclt 0.297
## realmIntertidal 0.942
## realmMarine 0.767
## Trophic_positionomnivore 0.371
## Trophic_positionfungivore 0.895
## Trophic_positioninsectivore 0.682
## Trophic_positioncarnivore 0.744
## abs_lat_mp:realmIntertidal 0.729
## abs_lat_mp:realmMarine 7.38e-05 ***
## dispersal_distance_continuous 0.644
## log_maximum_body_size 0.841
##
## (conditional average)
## Estimate Std. Error Adjusted SE z value
## (Intercept) -3.6590 2.7443 2.7636 1.324
## abs_lat_mp -2.0435 0.3866 0.3893 5.249
## hot_season_dormancy_Yes -2.9406 1.5342 1.5451 1.903
## log_range_area_km2 2.0296 0.2946 0.2967 6.840
## metriclt -2.2932 1.5525 1.5634 1.467
## realmIntertidal 0.2957 4.0219 4.0499 0.073
## realmMarine -0.9958 3.3438 3.3670 0.296
## Trophic_positionomnivore 1.3752 1.3587 1.3682 1.005
## Trophic_positionfungivore -0.6508 4.5896 4.6430 0.140
## Trophic_positioninsectivore 0.6969 1.5715 1.5825 0.440
## Trophic_positioncarnivore 0.5752 1.6346 1.6461 0.349
## abs_lat_mp:realmIntertidal 0.5595 1.6062 1.6175 0.346
## abs_lat_mp:realmMarine 2.7721 0.6945 0.6994 3.964
## dispersal_distance_continuous 0.3770 0.3316 0.3340 1.129
## log_maximum_body_size 0.1864 0.4554 0.4586 0.406
## Pr(>|z|)
## (Intercept) 0.186
## abs_lat_mp 2.00e-07 ***
## hot_season_dormancy_Yes 0.057 .
## log_range_area_km2 < 2e-16 ***
## metriclt 0.142
## realmIntertidal 0.942
## realmMarine 0.767
## Trophic_positionomnivore 0.315
## Trophic_positionfungivore 0.889
## Trophic_positioninsectivore 0.660
## Trophic_positioncarnivore 0.727
## abs_lat_mp:realmIntertidal 0.729
## abs_lat_mp:realmMarine 7.38e-05 ***
## dispersal_distance_continuous 0.259
## log_maximum_body_size 0.684
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Model selection for sensitivity analysis