Deprecated alias for fit_model_set. Retained because
fit.model.set is the function name cited in Fisher et al.
(2018, Ecology and Evolution) and is used by existing downstream code.
New code should call fit_model_set directly.
Arguments
- ...
Arguments passed on to
fit_model_set.
Value
See fit_model_set.
Examples
library(mgcv)
data(case_study1)
use.dat <- case_study1
use.dat$site <- as.factor(use.dat$site)
test.fit <- gam(Herbivore.abundance ~ s(depth, k = 3, bs = "cr") + s(site, bs = "re"),
family = tw(), data = use.dat)
model.set <- generate_model_set(
use.dat = use.dat,
test.fit = test.fit,
pred.vars.cont = c("complexity", "depth"),
pred.vars.fact = "ZONE",
null.terms = "s(site,bs='re')",
max.predictors = 2,
k = 3
)
fit.model.set(model.set, parallel = FALSE)
#> Warning: 'fit.model.set' is deprecated.
#> Use 'fit_model_set' instead.
#> See help("Deprecated")
#>
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#> $mod.data.out
#> modname
#> null null
#> complexity complexity
#> depth depth
#> ZONE ZONE
#> ZONE+complexity ZONE+complexity
#> ZONE+depth ZONE+depth
#> ZONE+complexity.by.ZONE ZONE+complexity.by.ZONE
#> ZONE+depth.by.ZONE ZONE+depth.by.ZONE
#> formula
#> null s(site, bs = "re")
#> complexity s(complexity, k = 3, bs = "cr") + s(site, bs = "re")
#> depth s(depth, k = 3, bs = "cr") + s(site, bs = "re")
#> ZONE ZONE + s(site, bs = "re")
#> ZONE+complexity s(complexity, k = 3, bs = "cr") + ZONE + s(site, bs = "re")
#> ZONE+depth s(depth, k = 3, bs = "cr") + ZONE + s(site, bs = "re")
#> ZONE+complexity.by.ZONE s(complexity, by = ZONE, k = 3, bs = "cr") + ZONE + s(site, bs = "re")
#> ZONE+depth.by.ZONE s(depth, by = ZONE, k = 3, bs = "cr") + ZONE + s(site, bs = "re")
#> AICc BIC r2.vals r2.vals.unique edf
#> null 601.8165 613.9550 0.13574 NA 2.93
#> complexity 530.3521 546.5630 0.55313 NA 5.15
#> depth 604.2478 620.2653 0.17579 NA 4.98
#> ZONE 603.0187 616.7110 0.13529 NA 4.02
#> ZONE+complexity 531.1829 548.2208 0.55773 NA 5.94
#> ZONE+depth 604.7738 621.8040 0.17570 NA 5.94
#> ZONE+complexity.by.ZONE 531.6302 549.9272 0.53534 NA 6.83
#> ZONE+depth.by.ZONE 600.4762 619.5704 0.23486 NA 7.56
#> edf.less.1 delta.AICc delta.BIC wi.AICc wi.BIC
#> null 0 71.464 67.392 0.000 0.000
#> complexity 0 0.000 0.000 0.457 0.616
#> depth 0 73.896 73.702 0.000 0.000
#> ZONE 0 72.667 70.148 0.000 0.000
#> ZONE+complexity 0 0.831 1.658 0.302 0.269
#> ZONE+depth 0 74.422 75.241 0.000 0.000
#> ZONE+complexity.by.ZONE 0 1.278 3.364 0.241 0.115
#> ZONE+depth.by.ZONE 0 70.124 73.007 0.000 0.000
#> complexity depth ZONE
#> null 0 0 0
#> complexity 1 0 0
#> depth 0 1 0
#> ZONE 0 0 1
#> ZONE+complexity 1 0 1
#> ZONE+depth 0 1 1
#> ZONE+complexity.by.ZONE 1 0 1
#> ZONE+depth.by.ZONE 0 1 1
#>
#> $failed.models
#> named list()
#>
#> $success.models
#> $success.models$null
#>
#> Family: Tweedie(p=1.469)
#> Link function: log
#>
#> Formula:
#> Herbivore.abundance ~ s(site, bs = "re")
#>
#> Estimated degrees of freedom:
#> 1.93 total = 2.93
#>
#> REML score: 297.6204
#>
#> $success.models$complexity
#>
#> Family: Tweedie(p=1.265)
#> Link function: log
#>
#> Formula:
#> Herbivore.abundance ~ s(complexity, k = 3, bs = "cr") + s(site,
#> bs = "re")
#>
#> Estimated degrees of freedom:
#> 1.73 2.42 total = 5.15
#>
#> REML score: 261.5252
#>
#> $success.models$depth
#>
#> Family: Tweedie(p=1.465)
#> Link function: log
#>
#> Formula:
#> Herbivore.abundance ~ s(depth, k = 3, bs = "cr") + s(site, bs = "re")
#>
#> Estimated degrees of freedom:
#> 1.42 2.57 total = 4.98
#>
#> REML score: 297.5266
#>
#> $success.models$ZONE
#>
#> Family: Tweedie(p=1.469)
#> Link function: log
#>
#> Formula:
#> Herbivore.abundance ~ ZONE + s(site, bs = "re")
#>
#> Estimated degrees of freedom:
#> 2.02 total = 4.02
#>
#> REML score: 297.9798
#>
#> $success.models$`ZONE+complexity`
#>
#> Family: Tweedie(p=1.267)
#> Link function: log
#>
#> Formula:
#> Herbivore.abundance ~ s(complexity, k = 3, bs = "cr") + ZONE +
#> s(site, bs = "re")
#>
#> Estimated degrees of freedom:
#> 1.71 2.23 total = 5.94
#>
#> REML score: 262.176
#>
#> $success.models$`ZONE+depth`
#>
#> Family: Tweedie(p=1.465)
#> Link function: log
#>
#> Formula:
#> Herbivore.abundance ~ s(depth, k = 3, bs = "cr") + ZONE + s(site,
#> bs = "re")
#>
#> Estimated degrees of freedom:
#> 1.47 2.47 total = 5.94
#>
#> REML score: 297.7074
#>
#> $success.models$`ZONE+complexity.by.ZONE`
#>
#> Family: Tweedie(p=1.262)
#> Link function: log
#>
#> Formula:
#> Herbivore.abundance ~ s(complexity, by = ZONE, k = 3, bs = "cr") +
#> ZONE + s(site, bs = "re")
#>
#> Estimated degrees of freedom:
#> 1.78 1.00 2.05 total = 6.83
#>
#> REML score: 261.0315
#>
#> $success.models$`ZONE+depth.by.ZONE`
#>
#> Family: Tweedie(p=1.45)
#> Link function: log
#>
#> Formula:
#> Herbivore.abundance ~ s(depth, by = ZONE, k = 3, bs = "cr") +
#> ZONE + s(site, bs = "re")
#>
#> Estimated degrees of freedom:
#> 1.71 1.00 2.85 total = 7.56
#>
#> REML score: 294.4957
#>
#>
#> $variable.importance
#> $variable.importance$aic
#> $variable.importance$aic$variable.weights.raw
#> complexity depth ZONE
#> 1.000 0.000 0.543
#>
#>
#> $variable.importance$bic
#> $variable.importance$bic$variable.weights.raw
#> complexity depth ZONE
#> 1.000 0.000 0.384
#>
#>
#>