psychonetrics (version 0.13)

getmatrix: Extract an estimated matrix

Description

This function will extract an estimated matrix, and will either return a single matrix for single group models or a list of such matrices for multiple group models.

Usage

getmatrix(x, matrix, group, threshold = FALSE, alpha = 0.01,
           adjust = c("none", "holm", "hochberg", "hommel",
           "bonferroni", "BH", "BY", "fdr"), mode = c("tested",
           "all"), diag = TRUE)

Value

A matrix of parameter estimates, of a list of such matrices for multiple group models.

Arguments

x

A psychonetrics model.

matrix

String indicating the matrix to be extracted.

group

Integer indicating the group for the matrix to be extracted.

threshold

Logical. Should the matrix be thresholded (non-significant values set to zero? Can also be a value with an absolute threshold below wich parameters are set to zero.)

alpha

Significance level to use.

adjust

p-value adjustment method to use. See p.adjust.

mode

Mode for adjusting for multiple comparisons. Should all parameters be considered as the total number of tests or only the tested parameters (parameters of interest)?

diag

Set to FALSE to set diagonal elements to zero.

Author

Sacha Epskamp

Examples

# 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 a full GGM:
mod <- ggm(ConsData, vars = vars, omega = "full")

# Run model:
mod <- mod %>% runmodel

# Obtain network:
mod %>% getmatrix("omega")