model_parameters: Model Parameters

Description Usage Arguments Value Confidence intervals and approximation of degrees of freedom Standardization of model coefficients Standardization Methods Labeling the Degrees of Freedom Interpretation of Interaction Terms Note References See Also

View source: R/1_model_parameters.R

Description

Compute and extract model parameters. See the documentation for your object's class:

Usage

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Arguments

model

Statistical Model.

...

Arguments passed to or from other methods. Non-documented arguments are digits, p_digits, ci_digits and footer_digits to set the number of digits for the output. group can also be passed to the print() method. See details in print.parameters_model() and 'Examples' in model_parameters.default().

Value

A data frame of indices related to the model's parameters.

Confidence intervals and approximation of degrees of freedom

There are different ways of approximating the degrees of freedom depending on different assumptions about the nature of the model and its sampling distribution. The ci_method modulates the method for computing degrees of freedom (df) that are used to calculate confidence intervals (CI) and the related p-values. Following options are allowed, depending on the model class:

Classical methods:

Classical inference is generally based on the Wald method. The Wald approach to inference computes a test statistic by dividing the parameter estimate by its standard error (Coefficient / SE), then comparing this statistic against a t- or normal distribution. This approach can be used to compute CIs and p-values.

"wald"

"normal"

"residual"

Methods for mixed models:

Compared to fixed effects (or single-level) models, determining appropriate df for Wald-based inference in mixed models is more difficult. See the R GLMM FAQ for a discussion.

Several approximate methods for computing df are available, but you should also consider instead using profile likelihood ("profile") or bootstrap ("boot") CIs and p-values instead.

"satterthwaite"

"kenward"

"ml1"

"betwithin"

Likelihood-based methods:

Likelihood-based inference is based on comparing the likelihood for the maximum-likelihood estimate to the the likelihood for models with one or more parameter values changed (e.g., set to zero or a range of alternative values). Likelihood ratios for the maximum-likelihood and alternative models are compared to a χ-squared distribution to compute CIs and p-values.

"profile"

"uniroot"

Methods for bootstrapped or Bayesian models:

Bootstrap-based inference is based on resampling and refitting the model to the resampled datasets. The distribution of parameter estimates across resampled datasets is used to approximate the parameter's sampling distribution. Depending on the type of model, several different methods for bootstrapping and constructing CIs and p-values from the bootstrap distribution are available.

For Bayesian models, inference is based on drawing samples from the model posterior distribution.

"quantile"

"eti"

"hdi"

"bci"

"bcai"

"si"

"boot"

For all iteration-based methods other than "boot" ("hdi", "quantile", "ci", "eti", "si", "bci", "bcai"), p-values are based on the probability of direction (bayestestR::p_direction()), which is converted into a p-value using bayestestR::pd_to_p().

Standardization of model coefficients

Standardization is based on effectsize::standardize_parameters(). In case of standardize = "refit", the data used to fit the model will be standardized and the model is completely refitted. In such cases, standard errors and confidence intervals refer to the standardized coefficient. The default, standardize = "refit", never standardizes categorical predictors (i.e. factors), which may be a different behaviour compared to other R packages or other software packages (like SPSS). To mimic behaviour of SPSS or packages such as lm.beta, use standardize = "basic".

Standardization Methods

Labeling the Degrees of Freedom

Throughout the parameters package, we decided to label the residual degrees of freedom df_error. The reason for this is that these degrees of freedom not always refer to the residuals. For certain models, they refer to the estimate error - in a linear model these are the same, but in - for instance - any mixed effects model, this isn't strictly true. Hence, we think that df_error is the most generic label for these degrees of freedom.

Interpretation of Interaction Terms

Note that the interpretation of interaction terms depends on many characteristics of the model. The number of parameters, and overall performance of the model, can differ or not between a * b a : b, and a / b, suggesting that sometimes interaction terms give different parameterizations of the same model, but other times it gives completely different models (depending on a or b being factors of covariates, included as main effects or not, etc.). Their interpretation depends of the full context of the model, which should not be inferred from the parameters table alone - rather, we recommend to use packages that calculate estimated marginal means or marginal effects, such as modelbased, emmeans or ggeffects. To raise awareness for this issue, you may use print(...,show_formula=TRUE) to add the model-specification to the output of the print() method for model_parameters().

Note

The print() method has several arguments to tweak the output. There is also a plot()-method implemented in the see-package, and a dedicated method for use inside rmarkdown files, print_md().

References

See Also

insight::standardize_names() to rename columns into a consistent, standardized naming scheme.


parameters documentation built on Oct. 19, 2021, 1:07 a.m.