Visualisation Recipe for 'modelbased' Objects

Usage

# S3 method for estimate_grouplevel
visualisation_recipe(
  x,
  hline = NULL,
  pointrange = NULL,
  facet_wrap = NULL,
  labs = NULL,
  ...
)

# S3 method for estimate_means
visualisation_recipe(
  x,
  show_data = "jitter",
  point = NULL,
  jitter = point,
  boxplot = NULL,
  violin = NULL,
  line = NULL,
  pointrange = NULL,
  labs = NULL,
  ...
)

# S3 method for estimate_predicted
visualisation_recipe(
  x,
  show_data = "points",
  point = NULL,
  density_2d = NULL,
  line = NULL,
  ribbon = NULL,
  labs = NULL,
  ...
)

# S3 method for estimate_slopes
visualisation_recipe(
  x,
  hline = NULL,
  line = NULL,
  pointrange = NULL,
  ribbon = NULL,
  labs = NULL,
  facet_wrap = NULL,
  ...
)

Arguments

x: A modelbased object.
...: Other arguments passed to other functions.
show_data: Display the "raw" data as a background to the model-based estimation. Can be set to "none" to remove it. When input is the result of estimate_means, show_data can be "points" (the jittered observation points), "boxplot", "violin" a combination of them (see examples). When input is the result of estimate_response or estimate_relation, show_data can be "points" (the points of the original data corresponding to the x and y axes), "density_2d", "density_2d_filled", "density_2d_polygon" or "density_2d_raster".
point, jitter, boxplot, violin, pointrange, density_2d, line, hline, ribbon, labs, facet_wrap: Additional aesthetics and parameters for the geoms (see customization example).

Examples

# ==============================================
# estimate_grouplevel
# ==============================================
if (require("see") && require("lme4")) {
  data <- lme4::sleepstudy
  data <- rbind(data, data)
  data$Newfactor <- rep(c("A", "B", "C", "D"))

  # 1 random intercept
  model <- lmer(Reaction ~ Days + (1 | Subject), data = data)
  x <- estimate_grouplevel(model)
  layers <- visualisation_recipe(x)
  layers
  plot(layers)
}

# \donttest{
if (require("see") && require("lme4")) {
  # 2 random intercepts
  model <- lmer(Reaction ~ Days + (1 | Subject) + (1 | Newfactor), data = data)
  x <- estimate_grouplevel(model)
  plot(visualisation_recipe(x))


  model <- lmer(Reaction ~ Days + (1 + Days | Subject) + (1 | Newfactor), data = data)
  x <- estimate_grouplevel(model)
  plot(visualisation_recipe(x))
}

# }
# Simple Model ---------------
x <- estimate_means(lm(Sepal.Width ~ Species, data = iris))
#> We selected `at = c("Species")`.
layers <- visualisation_recipe(x)
layers
#> Layer 1
#> --------
#> Geom type: jitter
#> data = [150 x 2]
#> aes_string(
#>   x = 'Species'
#>   y = 'Sepal.Width'
#> )
#> stroke = 0
#> shape = 16
#> width = 0.1
#> height = 0
#> 
#> Layer 2
#> --------
#> Geom type: line
#> data = [3 x 5]
#> aes_string(
#>   y = 'Mean'
#>   x = 'Species'
#>   group = 1
#> )
#> 
#> Layer 3
#> --------
#> Geom type: pointrange
#> data = [3 x 5]
#> aes_string(
#>   y = 'Mean'
#>   x = 'Species'
#>   ymin = 'CI_low'
#>   ymax = 'CI_high'
#> )
#> 
#> Layer 4
#> --------
#> Geom type: labs
#> x = 'Species'
#> y = 'Sepal.Width'
#> title = 'Estimated Means (Sepal.Width ~ Species)'
#> 
plot(layers)

# \donttest{
# Customize aesthetics
layers <- visualisation_recipe(x,
  jitter = list(width = 0.03, color = "red"),
  line = list(linetype = "dashed")
)
plot(layers)


# Customize raw data
plot(visualisation_recipe(x, show_data = c("violin", "boxplot", "jitter")))


# Two levels ---------------
data <- mtcars
data$cyl <- as.factor(data$cyl)
data$new_factor <- as.factor(rep(c("A", "B"), length.out = nrow(mtcars)))

model <- lm(mpg ~ new_factor * cyl * wt, data = data)
x <- estimate_means(model, at = c("new_factor", "cyl"))
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> NOTE: Results may be misleading due to involvement in interactions
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
plot(visualisation_recipe(x))
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.


# Modulations --------------
x <- estimate_means(model, at = c("new_factor", "wt"))
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> NOTE: Results may be misleading due to involvement in interactions
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
plot(visualisation_recipe(x))
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.


x <- estimate_means(model, at = c("new_factor", "cyl", "wt"))
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
plot(visualisation_recipe(x))
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> Error in geom_from_list(x[[i]]): Problem while computing aesthetics.
#> ℹ Error occurred in the 2nd layer.
#> Caused by error in `FUN()`:
#> ! object 'interaction(wt, cyl)' not found

#'   # GLMs ---------------------
data <- data.frame(vs = mtcars$vs, cyl = as.factor(mtcars$cyl))
x <- estimate_means(glm(vs ~ cyl, data = data, family = "binomial"))
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> We selected `at = c("cyl")`.
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
plot(visualisation_recipe(x))
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.

# }
# ==============================================
# estimate_relation, estimate_response, ...
# ==============================================
if (require("ggplot2")) {
  # Simple Model ---------------
  x <- estimate_relation(lm(mpg ~ wt, data = mtcars))
  layers <- visualisation_recipe(x)
  layers
  plot(layers)
}

# \donttest{
if (require("ggplot2")) {
  # Customize aesthetics ----------

  layers <- visualisation_recipe(x,
    point = list(color = "red", alpha = 0.6, size = 3),
    line = list(color = "blue", size = 3),
    ribbon = list(fill = "green", alpha = 0.7),
    labs = list(subtitle = "Oh yeah!")
  )
  layers
  plot(layers)

  # Customize raw data -------------

  plot(visualisation_recipe(x, show_data = "none"))
  plot(visualisation_recipe(x, show_data = c("density_2d", "points")))
  plot(visualisation_recipe(x, show_data = "density_2d_filled"))
  plot(visualisation_recipe(x, show_data = "density_2d_polygon"))
  plot(visualisation_recipe(x, show_data = "density_2d_raster")) +
    scale_x_continuous(expand = c(0, 0)) +
    scale_y_continuous(expand = c(0, 0))

  # Single predictors examples -----------

  plot(estimate_relation(lm(Sepal.Length ~ Sepal.Width, data = iris)))
  plot(estimate_relation(lm(Sepal.Length ~ Species, data = iris)))

  # 2-ways interaction ------------

  # Numeric * numeric
  x <- estimate_relation(lm(mpg ~ wt * qsec, data = mtcars))
  layers <- visualisation_recipe(x)
  plot(layers)

  # Numeric * factor
  x <- estimate_relation(lm(Sepal.Width ~ Sepal.Length * Species, data = iris))
  layers <- visualisation_recipe(x)
  plot(layers)

  # Factor * numeric
  x <- estimate_relation(lm(Sepal.Width ~ Species * Sepal.Length, data = iris))
  layers <- visualisation_recipe(x)
  plot(layers)

  # 3-ways interaction ------------

  data <- mtcars
  data$vs <- as.factor(data$vs)
  data$cyl <- as.factor(data$cyl)
  data$new_factor <- as.factor(rep(c("A", "B"), length.out = nrow(mtcars)))

  # Numeric * numeric * numeric
  x <- estimate_relation(lm(mpg ~ wt * qsec * hp, data = data), length = c(5, 3, 20))
  layers <- visualisation_recipe(x)
  plot(layers)

  # Numeric * numeric * factor
  x <- estimate_relation(lm(mpg ~ wt * am * vs, data = data))
  layers <- visualisation_recipe(x)
  plot(layers)

  # Numeric * factor * factor
  x <- estimate_relation(lm(mpg ~ wt * cyl * new_factor, data = data))
  layers <- visualisation_recipe(x)
  plot(layers)

  # Factor * numeric * numeric
  x <- estimate_relation(lm(mpg ~ cyl * qsec * hp, data = data))
  layers <- visualisation_recipe(x)
  plot(layers) +
    scale_size_continuous(range = c(0.2, 1))

  # GLMs ---------------------
  x <- estimate_relation(glm(vs ~ mpg, data = mtcars, family = "binomial"))
  plot(visualisation_recipe(x))
  plot(visualisation_recipe(x, show_data = "jitter", point = list(height = 0.03)))

  # Multiple CIs ---------------------
  plot(estimate_relation(lm(mpg ~ disp, data = mtcars),
    ci = c(.50, .80, .95)
  ))
  plot(estimate_relation(lm(Sepal.Length ~ Species, data = iris),
    ci = c(0.5, 0.7, 0.95)
  ))
}
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.


# Bayesian models ---------------------
if (require("ggplot2") && require("rstanarm")) {
  model <- rstanarm::stan_glm(mpg ~ wt, data = mtcars, refresh = 0)

  # Plot individual draws instead of regular ribbon
  x <- estimate_relation(model, keep_iterations = 100)
  layers <- visualisation_recipe(x, ribbon = list(color = "red"))
  plot(layers)

  model <- rstanarm::stan_glm(Sepal.Width ~ Species * Sepal.Length, data = iris, refresh = 0)
  plot(estimate_relation(model, keep_iterations = 100))
}

# }
# ==============================================
# estimate_slopes
# ==============================================
if (require("ggplot2")) {
  model <- lm(Sepal.Width ~ Species * Petal.Length, data = iris)
  x <- estimate_slopes(model, trend = "Petal.Length", at = "Species")

  layers <- visualisation_recipe(x)
  layers
  plot(layers)

  model <- lm(Petal.Length ~ poly(Sepal.Width, 4), data = iris)
  x <- estimate_slopes(model, at = "Sepal.Width", length = 20)
  plot(visualisation_recipe(x))

  model <- lm(Petal.Length ~ Species * poly(Sepal.Width, 3), data = iris)
  x <- estimate_slopes(model, at = c("Sepal.Width", "Species"))
  plot(visualisation_recipe(x))
}
#> No numeric variable was specified for slope estimation. Selecting `trend = "Sepal.Width"`.
#> No numeric variable was specified for slope estimation. Selecting `trend = "Sepal.Width"`.
#> Warning: Using alpha for a discrete variable is not advised.

# \dontrun{
# TODO: fails with latest emmeans (1.8.0)
if (require("mgcv")) {
  data <- iris
  data$Petal.Length <- data$Petal.Length^2

  model <- mgcv::gam(Sepal.Width ~ t2(Petal.Width, Petal.Length), data = data)
  x <- estimate_slopes(model, at = c("Petal.Width", "Petal.Length"), length = 20)
  plot(visualisation_recipe(x))

  model <- mgcv::gam(Sepal.Width ~ t2(Petal.Width, Petal.Length, by = Species), data = data)
  x <- estimate_slopes(model, at = c("Petal.Width", "Petal.Length", "Species"), length = 10)
  plot(visualisation_recipe(x))
}
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> No numeric variable was specified for slope estimation. Selecting `trend = "Petal.Width"`.
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.
#> No numeric variable was specified for slope estimation. Selecting `trend = "Petal.Width"`.
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.

# }