Plot Functions for a List of Models

Various plot functions for the output of eq_models(), eq_df_models(), and similar functions.

Usage

partables_plots(
  object,
  ...,
  partables = NULL,
  original_model = NULL,
  auto_node_color = TRUE,
  par_diff_settings = list(color = "blue", width = 2),
  fix_pars_fixed_zero = TRUE,
  par_fixed_zero_settings = list(color = "white", width = 0),
  exclude_original_model = FALSE,
  curve_cov = TRUE,
  curve_cov_settings = list(base_curve = 1.5)
)

# S3 method for class 'partables_plots'
plot(
  x,
  ...,
  title_mode = c("digest", "name", "none"),
  title_adj = 1.4,
  title_args = list(),
  ncol = 1,
  nrow = 1,
  scale_plots = c("auto", "always"),
  scale = NULL,
  elements_to_scale = c("Nodes:width", "Nodes:height", "Edges:width", "Edges:asize"),
  original_model_mode = c("include", "exclude", "side_by_side")
)

# S3 method for class 'partables_plots'
print(x, ...)

lhs %p>% rhs

Arguments

object: If it is a list of models (parameter tables), such as the output of eq_models(), it will be used as the value for partables. If it is a partables_plots object (i.e., an output of partables_plots(), then it will be updated with any new values for other arguments.
...: For plot.partables_plots(), these are optional arguments to be passed to semPlot::semPaths(). For print.partables_plots(), they are not used.
partables: It should be a list of models in the form of parameter tables, such as the output of eq_models() or eq_df_models().
original_model: The model to which models in partables will be compared to. If NULL, then the plots will be generated without checking for differences between a model and original_model. Model comparison is conducted by model_diff().
auto_node_color: If TRUE, and the number of nodes is 12 or less, they will be automatically set to different colors. Ignored if color of nodes is in ....
par_diff_settings: A named list of settings to configure the change of a parameter from original_model to a model in partables. For now, two settings are supported: color for the color and width for the width of an edge (arrow/path).
fix_pars_fixed_zero: If TRUE, parameters fixed to zero will be modified based on par_fixed_zero_settings.
par_fixed_zero_settings: A named settings to configure edges (arrows) fixed to zero. For now, two settings are supported: color for the color and width for the width of an edge (arrow/path). Setting the width to zero, the default, effectively hides an arrow/path.
exclude_original_model: If TRUE and original_model is set, the output will not include the plot of the original model, though this plot will be stored in the attribute "original_model", as a one-element list.
curve_cov: If TRUE, lines denoting covariances will be automatically curve. Implemented by calling auto_curve_covariance().
curve_cov_settings: A named list of arguments to be passed to auto_curve_covariance(). Used only if curve_cov is TRUE.
x: The output of partables_plots(), a partables_plots object.
title_mode: What will be used as the title. If "digest", then the digest value of a model, generated by digest_partable(), will be used as its title. If "name", then its name in x will be used, which may also be the digest value. If "none", then no title will be drawn with the plot.
title_adj: Adjust the position of the title. Increase this value if the plot is too close to the title, and decrease this value if the space between the plot and its title is too large.
title_args: A named list of arguments to be passed to title() when printing the title.
ncol, nrow: The number of columns and rows when drawing the models. Used by mfrow in par().
scale_plots: How the models will be scaled. If "auto", then the models will be scaled based on ncol and nrow, using scale as a reference. If "always", then scale will always be used to scale the models, even if they are drawn one by one.
scale: How the model will be further scaled when drawn. If this value is greater than one, then elements in elements_to_scale will be increased by this ratio. If this value is less than one, then elements in elements_to_scale will be decreased by this ratio.
elements_to_scale: Elements in the qgraph object that will be scaled based on the values of scale_plots and scale.
original_model_mode: How original model, if present, will be handled when drawing the models. If "exclude", then the original model will not be drawn. If "include", the original model will be drawn as the first model, along with other models. If "side_by_side", then the number of columns is always two and the number of rows is always one. In each plot, the original model will be drawn on the left and the other model will be drawn on the right.
lhs: A partables_plots object.
rhs: A function call to be applied to all stored plots. Each plot will be inserted as the first argument.

Value

The function partables_plots() returns a list of qgraph objects generated from semPlot::semPaths(), of the class partables_plots.

The plot method of the output of partables_plots() returns x invisibly. Called for its side effect.

The print method of the output of partables_plots() returns x invisibly. Called for its side effect.

The %p>% operator returns a partables_plots object, processed by the right-hand side function.

Details

The functions provide different ways to visualize the models. Basic knowledge of semPlot::semPaths() from the package semPlot is required to customize the plots.

Examples

library(lavaan)

# Model 1

mod1 <-
"
fx =~ x1 + x2 + x3
fm =~ m1 + m2 + m3
fy =~ y1 + y2 + y3
fm ~ fx
fy ~ fm + fx
"
fit1 <- sem(
          model = mod1,
          data = data_test_3_factor_3_item
        )
fit1_1_more <- drop_k(fit1)
fit1_1_more_1_less <- lapply(
  fit1_1_more,
  add_k
)

partables1 <- combine_partables(fit1_1_more_1_less)
eq_out_1 <- eq_models(
          partables1,
          original_model = fit1,
          parallel = FALSE
        )

eq_out_1 <- eq_models(
          partables1,
          original_model = fit1,
          parallel = FALSE
        )

layout_i <- matrix(c(  NA, "fm",  NA,
                     "fx",   NA, "fy"),
                   ncol = 3,
                   nrow = 2,
                   byrow = TRUE)
layout_i
#>      [,1] [,2] [,3]
#> [1,] NA   "fm" NA  
#> [2,] "fx" NA   "fy"
p <- partables_plots(
  eq_out_1,
  original_model = fit1,
  layout = layout_i,
  label.cex = 1.5,
  sizeLat = 15,
  edge.width = 5,
  asize = 5,
  structural = TRUE,
  par_diff_settings = list(
            color = "blue",
            width = 10
          )
)
plot(p)

Usage

Arguments

Value

Details

See also

Examples