In easystats/parameters: Processing of Model Parameters

library(knitr)
options(knitr.kable.NA = "")
options(digits = 2)

knitr::opts_chunk$set(
  echo = TRUE,
  collapse = TRUE,
  warning = FALSE,
  message = FALSE,
  comment = "#>",
  out.width = "100%",
  tidy.opts = list(width.cutoff = 120)
)

pkgs <- c(
  "effectsize", "BayesFactor", "lme4", "metafor", "lavaan", "nFactors", "BH",
  "EGAnet", "brms", "psych", "rstanarm", "glmmTMB", "GLMMadaptive", "FactoMineR"
)

successfully_loaded <- vapply(pkgs, requireNamespace, TRUE, quietly = TRUE)

if (all(successfully_loaded)) {
  library(parameters)
  library(effectsize)
  library(psych)
  library(brms)
  library(GLMMadaptive)
}

set.seed(333)

The model_parameters() function (also accessible via the shortcut parameters()) allows you to extract the parameters and their characteristics from various models in a consistent way. It can be considered as a lightweight alternative to broom::tidy(), with some notable differences:

• The names of the returned data frame are specific to their content. For instance, the column containing the statistic is named following the statistic name, i.e., t, z, etc., instead of a generic name such as statistic (however, you can get standardized (generic) column names using standardize_names()).

• It is able to compute or extract indices not available by default, such as p*-values, CIs, etc.

• It includes feature engineering capabilities, including parameters bootstrapping.

Correlations and t-tests

Frequentist

library(parameters)
cor.test(iris$Sepal.Length, iris$Sepal.Width) |>
  parameters()

t.test(mpg ~ vs, data = mtcars) |>
  parameters()

Bayesian

BayesFactor::correlationBF(iris$Sepal.Length, iris$Sepal.Width) |>
  parameters()

BayesFactor::ttestBF(formula = mpg ~ vs, data = mtcars) |>
  parameters()

ANOVAs

Indices of effect size for ANOVAs, such as partial and non-partial versions of eta_squared(), epsilon_sqared() or omega_squared() are powered by the effectsize-package. However, parameters uses these function to compute such indices for parameters summaries, including confidence intervals

Simple

aov(Sepal.Length ~ Species, data = iris) |>
  parameters(effectsize_type = c("omega", "eta", "epsilon"))

Let's complicate things further with an interaction term:

aov(Sepal.Length ~ Species * Sepal.Width, data = iris) |>
  parameters(
    effectsize_type = c("omega", "eta"),
    ci = 0.8
  )

Repeated measures

parameters() (resp. its alias model_parameters()) also works on repeated measures ANOVAs, whether computed from aov() or from a mixed model.

aov(mpg ~ am + Error(gear), data = mtcars) |>
  parameters()

Regressions (GLMs, Mixed Models, GAMs, ...)

parameters() (resp. its alias model_parameters()) was mainly built with regression models in mind. It works for many types of models and packages, including mixed models and Bayesian models.

GLMs

glm(vs ~ poly(mpg, 2) + cyl, data = mtcars, family = binomial()) |>
  parameters()

# show Odds Ratios and Wald-method for degrees of freedom
glm(vs ~ poly(mpg, 2) + cyl, data = mtcars, family = binomial()) |>
  parameters(exponentiate = TRUE, ci_method = "wald")

# show Odds Ratios and include model summary
glm(vs ~ poly(mpg, 2) + cyl, data = mtcars, family = binomial()) |>
  parameters(exponentiate = TRUE, summary = TRUE)

Mixed Models

library(lme4)

lmer(Sepal.Width ~ Petal.Length + (1 | Species), data = iris) |>
  parameters()

Mixed Models, without Random Effects Variances

lmer(Sepal.Width ~ Petal.Length + (1 | Species), data = iris) |>
  parameters(effects = "fixed")

Mixed Model with Zero-Inflation Model

library(GLMMadaptive)
library(glmmTMB)
data("Salamanders")
model <- mixed_model(
  count ~ spp + mined,
  random = ~ 1 | site,
  zi_fixed = ~ spp + mined,
  family = zi.negative.binomial(),
  data = Salamanders
)
parameters(model)

Mixed Models with Dispersion Model

library(glmmTMB)

sim1 <- function(nfac = 40, nt = 100, facsd = 0.1, tsd = 0.15, mu = 0, residsd = 1) {
  dat <- expand.grid(fac = factor(letters[1:nfac]), t = 1:nt)
  n <- nrow(dat)
  dat$REfac <- rnorm(nfac, sd = facsd)[dat$fac]
  dat$REt <- rnorm(nt, sd = tsd)[dat$t]
  dat$x <- rnorm(n, mean = mu, sd = residsd) + dat$REfac + dat$REt
  dat
}

set.seed(101)
d1 <- sim1(mu = 100, residsd = 10)
d2 <- sim1(mu = 200, residsd = 5)
d1$sd <- "ten"
d2$sd <- "five"
dat <- rbind(d1, d2)
model <- glmmTMB(x ~ sd + (1 | t), dispformula = ~sd, data = dat)

parameters(model)

Bayesian Models

model_parameters() also works with Bayesian models from the rstanarm package:

library(rstanarm)

# if you are unfamiliar with the `refresh` argument here, it just avoids
# printing few messages to the console
stan_glm(mpg ~ wt * cyl, data = mtcars, refresh = 0) |>
  parameters()

Additionally, it also works for models from the brms package.

For more complex models, specific model components can be printed using the arguments effects and component arguments.

library(brms)
data(fish)
set.seed(123)

# fitting a model using `brms`
model <- suppressWarnings(brm(
  bf(
    count ~ persons + child + camper + (1 | persons),
    zi ~ child + camper + (1 | persons)
  ),
  data = fish,
  family = zero_inflated_poisson(),
  refresh = 0
))

parameters(model, component = "conditional", verbose = FALSE)

parameters(model, effects = "all", component = "all", verbose = FALSE)

To include information about the random effect parameters (group levels), set group_level = TRUE:

parameters(
  model,
  effects = "all",
  component = "conditional",
  group_level = TRUE,
  verbose = FALSE
)

Structural Models (PCA, EFA, CFA, SEM...)

The parameters package extends the support to structural models.

Principal Component Analysis (PCA) and Exploratory Factor Analysis (EFA)

psych::pca(mtcars, nfactors = 3) |>
  parameters()

We will avoid displaying a graph while carrying out factor analysis:

FactoMineR::FAMD(iris, ncp = 3, graph = FALSE) |>
  parameters()

Confirmatory Factor Analysis (CFA) and Structural Equation Models (SEM)

Frequentist

library(lavaan)

model <- lavaan::cfa(" visual  =~ x1 + x2 + x3
                       textual =~ x4 + x5 + x6
                       speed   =~ x7 + x8 + x9 ",
  data = HolzingerSwineford1939
)

model_parameters(model)

Bayesian

blavaan to be done.

Meta-Analysis

parameters() also works for rma-objects from the metafor package.

library(metafor)

mydat <<- data.frame(
  effectsize = c(-0.393, 0.675, 0.282, -1.398),
  standarderror = c(0.317, 0.317, 0.13, 0.36)
)

rma(yi = effectsize, sei = standarderror, method = "REML", data = mydat) |>
  model_parameters()

Plotting Model Parameters

There is a plot()-method implemented in the see-package. Several examples are shown in this vignette.

easystats/parameters documentation built on April 12, 2024, 9:33 a.m.