CIplot function

Plot Analytic Confidence Intervals

Function to plot analytic confidence intervals (CI) of matrix elements estimated in psychonetrics.

CIplot(x, matrices, alpha_ci = 0.05, alpha_color = c(0.05,
                   0.01, 0.001, 1e-04), labels, labels2, labelstart,
                   print = TRUE, major_break = 0.2, minor_break = 0.1,
                   split0, prop0, prop0_cex = 1, prop0_alpha = 0.95,
                   prop0_minAlpha = 0.25)

Arguments

• x: A psychonetrics model.
• matrices: Vector of strings indicating the matrices to plot CIs for
• alpha_ci: The alpha level used for the CIs
• alpha_color: A vector of alphas used for coloring the CIs
• labels: The labels for the variables associated with the rows of a matrix.
• labels2: The labels for the variables associated with the columns of a matrix. Defaults to the value of labels for square matrices.
• labelstart: The value to determine if labels are printed to the right or to the left of the CI
• print: Logical, should the plots also be printed? Only works when one matrix is used in 'matrices'
• major_break: Numeric indicating the step size between major breaks
• minor_break: Numeric indicating the step size between minor breaks
• split0: Logical only used for results of aggregate_bootstraps. When set to TRUE, the displayed intervals are based on occasions when the parameter was not estimated to be zero, and an extra box is added indicating the number of times a parameter is estimated to be zero. Defaults to TRUE when model selection is used and FALSE otherwise.
• prop0: Logical only used for results of aggregate_bootstraps, should boxes indicating the proportion of times parameters were estimated to be zero be added to the plot? Defaults to the value of split0.
• prop0_cex: Only used for results of aggregate_bootstraps. Size of the boxes indicating number of times a parameter was set to zero.
• prop0_alpha: Only used for results of aggregate_bootstraps. Transparency of the boxes indicating number of times a parameter was set to zero.
• prop0_minAlpha: Only used for results of aggregate_bootstraps. Minimal transparency of the lines of plotted intervals as the proportion of times an edge was not included goes to 0.

Returns

A single ggplot2 object, or a list of ggplot2 objects for each matrix requested.

Author(s)

Sacha Epskamp

Examples

### Example from ?ggm ###
# Load bfi data from psych package:
library("psychTools")
data(bfi)

# Also load dplyr for the pipe operator:
library("dplyr")

# Let's take the agreeableness items, and gender:
ConsData <- bfi %>% 
  select(A1:A5, gender) %>% 
  na.omit # Let's remove missingness (otherwise use Estimator = "FIML)

# Define variables:
vars <- names(ConsData)[1:5]

# Let's fit an empty GGM:
mod0 <- ggm(ConsData, vars = vars)

# Run the model:
mod0 <- mod0 %>% runmodel

# Labels:
labels <- c(
  "indifferent to the feelings of others",
  "inquire about others' well-being",
  "comfort others",
  "love children",
  "make people feel at ease")

# Plot the CIs:
CIplot(mod0,  "omega", labels = labels, labelstart = 0.2)

### Example from ?gvar ###
library("dplyr")
library("graphicalVAR")

beta <- matrix(c(
  0,0.5,
  0.5,0
),2,2,byrow=TRUE)
kappa <- diag(2)
simData <- graphicalVARsim(50, beta, kappa)

# Form model:
model <- gvar(simData)

# Evaluate model:
model <- model %>% runmodel

# Plot the CIs:
CIplot(model,  "beta")