![[Experimental]](figures/lifecycle-experimental.svg)
A tidier for models generated with VGAM::vglm() or VGAM::vgam().
Term names will be updated to be consistent with generic models. The original
term names are preserved in an "original_term" column. Depending on the
model, additional column "group", "component" and/or "y.level" may be
added to the results.
Arguments
- x
(
vglmorvgam)
AVGAM::vglm()or aVGAM::vgam()model.- conf.int
(
logical)
Whether or not to include a confidence interval in the tidied output.- conf.level
(
numeric)
The confidence level to use for the confidence interval (between0ans1).- ...
Additional parameters passed to
parameters::model_parameters().
See also
Other custom_tieders:
tidy_broom(),
tidy_multgee(),
tidy_parameters(),
tidy_with_broom_or_parameters(),
tidy_zeroinfl()
Examples
# \donttest{
library(VGAM)
#> Loading required package: stats4
#> Loading required package: splines
mod <- vglm(
Species ~ Sepal.Length + Sepal.Width,
family = multinomial(),
data = iris
)
#> Warning: 5 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
#> Warning: 15 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
#> Warning: 45 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
#> Warning: 68 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: 72 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: 75 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: 75 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: 75 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: 75 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: 75 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: 75 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted values close to 0 or 1
#> Warning: some quantities such as z, residuals, SEs may be inaccurate due to convergence at a half-step
mod |> tidy_vgam(exponentiate = TRUE)
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> Warning: fitted probabilities numerically 0 or 1 occurred
#> original_term term group estimate std.error conf.level
#> 1 (Intercept):1 (Intercept) 1 1.145503e+40 8.898639e+41 0.95
#> 2 (Intercept):2 (Intercept) 2 4.632101e+05 1.435034e+06 0.95
#> 3 Sepal.Length:1 Sepal.Length 1 4.850629e-15 1.314042e-13 0.95
#> 4 Sepal.Length:2 Sepal.Length 2 1.492052e-01 7.712864e-02 0.95
#> 5 Sepal.Width:1 Sepal.Width 1 8.789873e+11 2.197615e+13 0.95
#> 6 Sepal.Width:2 Sepal.Width 2 6.673158e-01 5.756157e-01 0.95
#> conf.low conf.high statistic df.error p.value
#> 1 8.607659e-27 1.524429e+106 1.1873761 Inf 2.350793e-01
#> 2 1.068411e+03 2.008250e+08 4.2110557 Inf 2.541801e-05
#> 3 4.232840e-38 5.558586e+08 -1.2166667 Inf 2.237310e-01
#> 4 5.417171e-02 4.109562e-01 -3.6802527 Inf 2.330030e-04
#> 5 4.597519e-10 1.680512e+33 1.1000080 Inf 2.713286e-01
#> 6 1.230549e-01 3.618794e+00 -0.4689306 Inf 6.391192e-01
#> component y.level
#> 1 log(mu[,1]/mu[,3]) setosa
#> 2 log(mu[,2]/mu[,3]) versicolor
#> 3 log(mu[,1]/mu[,3]) setosa
#> 4 log(mu[,2]/mu[,3]) versicolor
#> 5 log(mu[,1]/mu[,3]) setosa
#> 6 log(mu[,2]/mu[,3]) versicolor
mod <- vglm(
Species ~ Sepal.Length + Sepal.Width,
family = multinomial(parallel = TRUE),
data = iris
)
mod |> tidy_vgam(exponentiate = TRUE)
#> original_term term group estimate std.error conf.level
#> 1 (Intercept) (Intercept) 7.224907e+05 2.252168e+06 0.95
#> 2 Sepal.Length Sepal.Length 7.408586e-02 3.264124e-02 0.95
#> 3 Sepal.Width Sepal.Width 2.108096e+00 1.351928e+00 0.95
#> conf.low conf.high statistic df.error p.value component y.level
#> 1 1.604882e+03 3.252532e+08 4.327710 Inf 1.506675e-05 parallel parallel
#> 2 3.123973e-02 1.756966e-01 -5.906966 Inf 3.484646e-09 parallel parallel
#> 3 5.998083e-01 7.409148e+00 1.162922 Inf 2.448611e-01 parallel parallel
# }