| Title: | Structural Equation Modeling and Confirmatory Network Analysis |
|---|---|
| Description: | Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data <doi:10.31234/osf.io/8ha93>. Allows for confirmatory testing and fit as well as exploratory model search. |
| Authors: | Sacha Epskamp |
| Maintainer: | Sacha Epskamp <[email protected]> |
| License: | GPL-2 |
| Version: | 0.13 |
| Built: | 2024-11-24 07:03:03 UTC |
| Source: | CRAN |
Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data <doi:10.31234/osf.io/8ha93>. Allows for confirmatory testing and fit as well as exploratory model search.
The DESCRIPTION file:
| Package: | psychonetrics |
| Type: | Package |
| Title: | Structural Equation Modeling and Confirmatory Network Analysis |
| Version: | 0.13 |
| Author: | Sacha Epskamp |
| Maintainer: | Sacha Epskamp <[email protected]> |
| Description: | Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data <doi:10.31234/osf.io/8ha93>. Allows for confirmatory testing and fit as well as exploratory model search. |
| License: | GPL-2 |
| LinkingTo: | Rcpp (>= 0.11.3), RcppArmadillo, pbv, roptim |
| Depends: | R (>= 4.3.0) |
| Imports: | methods, qgraph, numDeriv, dplyr, abind, Matrix (>= 1.6-5), lavaan, corpcor, glasso, mgcv, optimx, VCA, pbapply, parallel, magrittr, IsingSampler, tidyr, psych, GA, combinat, rlang |
| Suggests: | psychTools, semPlot, graphicalVAR, metaSEM, mvtnorm, ggplot2 |
| ByteCompile: | true |
| URL: | http://psychonetrics.org/ |
| BugReports: | https://github.com/SachaEpskamp/psychonetrics/issues |
| StagedInstall: | true |
| NeedsCompilation: | yes |
| Packaged: | 2024-06-20 17:09:07 UTC; Sacha |
| Repository: | CRAN |
| Date/Publication: | 2024-06-20 18:00:02 UTC |
| Config/pak/sysreqs: | cmake libglpk-dev make libicu-dev libjpeg-dev libpng-dev libxml2-dev |
Index of help topics:
CIplot Plot Analytic Confidence Intervals
Ising Ising model
Jonas Jonas dataset
MIs Print modification indices
StarWars Star Wars dataset
addMIs Model updating functions
aggregate_bootstraps Aggregate Bootstrapped Models
bifactor Bi-factor models
bootstrap Bootstrap a psychonetrics model
changedata Change the data of a psychonetrics object
checkJacobian Diagnostic functions
compare Model comparison
covML Maximum likelihood covariance estimate
dlvm1 Lag-1 dynamic latent variable model family of
psychonetrics models for panel data
duplicationMatrix Model matrices used in derivatives
emergencystart Reset starting values to simple defaults
esa Ergodic Subspace Analysis
factorscores Compute factor scores
fit Print fit indices
fixpar Parameters modification
fixstart Attempt to Fix Starting Values
generate Generate data from a fitted psychonetrics
object
getVCOV Obtain the asymptotic covariance matrix
getmatrix Extract an estimated matrix
groupequal Group equality constrains
latentgrowth Latnet growth curve model
logbook Retrieve the psychonetrics logbook
lvm Continuous latent variable family of
psychonetrics models
meta_varcov Variance-covariance and GGM meta analysis
ml_lvm Multi-level latent variable model family
ml_tsdlvm1 Multi-level Lag-1 dynamic latent variable model
family of psychonetrics models for time-series
data
modelsearch Stepwise model search
parameters Print parameter estimates
parequal Set equality constrains across parameters
partialprune Partial pruning of multi-group models
prune Stepdown model search by pruning
non-significant parameters.
psychonetrics-class Class '"psychonetrics"'
psychonetrics-package Structural Equation Modeling and Confirmatory
Network Analysis
psychonetrics_bootstrap-class
Class '"psychonetrics_bootstrap"'
psychonetrics_log-class
Class '"psychonetrics"'
runmodel Run a psychonetrics model
setestimator Convenience functions
setverbose Should messages of computation progress be
printed?
simplestructure Generate factor loadings matrix with simple
structure
stepup Stepup model search along modification indices
transmod Transform between model types
tsdlvm1 Lag-1 dynamic latent variable model family of
psychonetrics models for time-series data
unionmodel Unify models across groups
var1 Lag-1 vector autoregression family of
psychonetrics models
varcov Variance-covariance family of psychonetrics
models
This package can be used to perform Structural Equation Modeling and confirmatory network modeling. Current implemented families of models are (1) the variance–covariance matrix (varcov), (2) the latent variable model (lvm), (3) the lag-1 vector autoregression model (var1), and (4) the dynamical lag-1 latent variable model for panel data (dlvm1) and for time-series data (tsdlvm1).
Sacha Epskamp
Maintainer: Sacha Epskamp <[email protected]>
More information: psychonetrics.org
Aggregates bootstrap results into a psychonetrics_bootstrap object
aggregate_bootstraps(sample, bootstraps, remove_problematic = TRUE)aggregate_bootstraps(sample, bootstraps, remove_problematic = TRUE)
sample |
The original |
bootstraps |
A list of bootstrapped |
remove_problematic |
Remove bootstraps that did not converge (sum of absolute gradient > 1) |
After running this function, the helper functions parameters, fit, and CIplot can be used to investigate bootstrap results.
An object of the class psychonetrics_bootstrap
Sacha Epskamp
Wrapper to lvm to specify a bi-factor model.
bifactor(data, lambda, latents, bifactor = "g", ...)bifactor(data, lambda, latents, bifactor = "g", ...)
data |
The data as used by |
lambda |
The factor loadings matrix *without* the bifactor, as used by by |
latents |
A vector of names of the latent variables, as used by |
bifactor |
Name of the bifactor |
... |
Arguments sent to |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
This function will bootstrap the data (once) and return a new unevaluated psychonetrics object. It requres storedata = TRUE to be used when forming a model.
bootstrap(x, replacement = TRUE, proportion = 1, verbose = TRUE, storedata = FALSE, baseline_saturated = TRUE)bootstrap(x, replacement = TRUE, proportion = 1, verbose = TRUE, storedata = FALSE, baseline_saturated = TRUE)
x |
A |
replacement |
Logical, should new samples be drawn with replacement? |
proportion |
Proportion of sample to be drawn. Set to lower than $1$ for subsampling. |
verbose |
Logical, should messages be printed? |
storedata |
Logical, should the bootstrapped data also be stored? |
baseline_saturated |
Logical, should the baseline and saturated models be included? |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
This function can be used to change the data in a psychonetrics object.
changedata(x, data, covs, nobs, means, groups, missing = "listwise")changedata(x, data, covs, nobs, means, groups, missing = "listwise")
x |
A |
data |
A data frame encoding the data used in the analysis. Can be missing if |
covs |
A sample variance–covariance matrix, or a list/array of such matrices for multiple groups. IMPORTANT NOTE: psychonetrics expects the maximum likelihood (ML) covariance matrix, which is NOT obtained from |
nobs |
The number of observations used in |
means |
A vector of sample means, or a list/matrix containing such vectors for multiple groups. |
groups |
An optional string indicating the name of the group variable in |
missing |
How should missingness be handled in computing the sample covariances and number of observations when |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
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)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)
x |
A |
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 |
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 |
prop0 |
Logical only used for results of |
prop0_cex |
Only used for results of |
prop0_alpha |
Only used for results of |
prop0_minAlpha |
Only used for results of |
A single ggplot2 object, or a list of ggplot2 objects for each matrix requested.
Sacha Epskamp
### 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")### 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")
This function will print a table comparing multiple models on chi-square, AIC and BIC.
compare(...) ## S3 method for class 'psychonetrics_compare' print(x, ...)compare(...) ## S3 method for class 'psychonetrics_compare' print(x, ...)
... |
Any number of |
x |
Output of the |
A data frame with chi-square values, degrees of freedoms, RMSEAs, AICs, and BICs.
Sacha Epskamp
These functions complement the base R cov function by simplifying obtaining maximum likelihood (ML) covariance estimates (denominator n) instead of unbiased (UB) covariance estimates (denominator n-1). The function covML can be used to obtain ML estimates, the function covUBtoML transforms from UB to ML estimates, and the function covMLtoUB transforms from UB to ML estimates.
covML(x, ...) covUBtoML(x, n, ...) covMLtoUB(x, n, ...)covML(x, ...) covUBtoML(x, n, ...) covMLtoUB(x, n, ...)
x |
A dataset |
n |
The sample size |
... |
Arguments sent to the |
Sacha Epskamp <[email protected]>
data("StarWars") Y <- StarWars[,1:10] # Unbiased estimate: UB <- cov(Y) # ML Estimate: ML <- covML(Y) # Check: all(abs(UB - covMLtoUB(ML, nrow(Y))) < sqrt(.Machine$double.eps)) all(abs(ML - covUBtoML(UB, nrow(Y))) < sqrt(.Machine$double.eps))data("StarWars") Y <- StarWars[,1:10] # Unbiased estimate: UB <- cov(Y) # ML Estimate: ML <- covML(Y) # Check: all(abs(UB - covMLtoUB(ML, nrow(Y))) < sqrt(.Machine$double.eps)) all(abs(ML - covUBtoML(UB, nrow(Y))) < sqrt(.Machine$double.eps))
The 'checkJacobian' function can be used to check if the analytic gradient / Jacobian is aligned with the numerically approximated gradient / Jacobian, and the 'checkFisher' function can be used to check if the analytic Hessian is aligned with the numerically approximated Hessian.
checkJacobian(x, f = "default", jac = "default", transpose = FALSE, plot = TRUE, perturbStart = FALSE, method = "Richardson") checkFisher(x, f = "default", fis = "default", transpose = FALSE, plot = TRUE, perturbStart = FALSE)checkJacobian(x, f = "default", jac = "default", transpose = FALSE, plot = TRUE, perturbStart = FALSE, method = "Richardson") checkFisher(x, f = "default", fis = "default", transpose = FALSE, plot = TRUE, perturbStart = FALSE)
x |
A 'psychonetrics' object |
f |
A custom fit function or the psychonetrics default fit function (default). |
jac |
A custom Jacobian function or the psychonetrics default Jacobian function (default). |
fis |
A custom Fischer information function or the psychonetrics default Fischer information function (default). |
transpose |
Should the numeric Jacobian be transposed? |
plot |
Should a diagnostic plot be produced? |
perturbStart |
Should start values be perturbed (only used in development) |
method |
Numeric derivative method (default: Richardson) |
Sacha Epskamp
This is the family of models that models a dynamic factor model on panel data. There are four covariance structures that can be modeled in different ways: within_latent, between_latent for the within-person and between-person latent (contemporaneous) models respectively, and within_residual, between_residual for the within-person and between-person residual models respectively. The panelgvar wrapper function sets the lambda to an identity matrix, all residual variances to zero, and models within-person and between-person latent (contemporaneous) models as GGMs. The panelvar wrapper does the same but models contemporaneous relations as a variance-covariance matrix. Finally, the panel_lvgvar wrapper automatically models all latent networks as GGMs.
dlvm1(data, vars, lambda, within_latent = c("cov", "chol", "prec", "ggm"), within_residual = c("cov", "chol", "prec", "ggm"), between_latent = c("cov", "chol", "prec", "ggm"), between_residual = c("cov", "chol", "prec", "ggm"), beta = "full", omega_zeta_within = "full", delta_zeta_within = "diag", kappa_zeta_within = "full", sigma_zeta_within = "full", lowertri_zeta_within = "full", omega_epsilon_within = "zero", delta_epsilon_within = "diag", kappa_epsilon_within = "diag", sigma_epsilon_within = "diag", lowertri_epsilon_within = "diag", omega_zeta_between = "full", delta_zeta_between = "diag", kappa_zeta_between = "full", sigma_zeta_between = "full", lowertri_zeta_between = "full", omega_epsilon_between = "zero", delta_epsilon_between = "diag", kappa_epsilon_between = "diag", sigma_epsilon_between = "diag", lowertri_epsilon_between = "diag", nu, mu_eta, identify = TRUE, identification = c("loadings", "variance"), latents, groups, covs, means, nobs, start = "version2", covtype = c("choose", "ML", "UB"), missing = "listwise", equal = "none", baseline_saturated = TRUE, estimator = "ML", optimizer, storedata = FALSE, verbose = FALSE, sampleStats, baseline = c("stationary_random_intercept", "stationary", "independence", "none"), bootstrap = FALSE, boot_sub, boot_resample) panelgvar(data, vars, within_latent = c("ggm","chol","cov","prec"), between_latent = c("ggm","chol","cov","prec"), ...) panelvar(data, vars, within_latent = c("cov","chol","prec","ggm"), between_latent = c("cov","chol","prec","ggm"), ...) panel_lvgvar(...)dlvm1(data, vars, lambda, within_latent = c("cov", "chol", "prec", "ggm"), within_residual = c("cov", "chol", "prec", "ggm"), between_latent = c("cov", "chol", "prec", "ggm"), between_residual = c("cov", "chol", "prec", "ggm"), beta = "full", omega_zeta_within = "full", delta_zeta_within = "diag", kappa_zeta_within = "full", sigma_zeta_within = "full", lowertri_zeta_within = "full", omega_epsilon_within = "zero", delta_epsilon_within = "diag", kappa_epsilon_within = "diag", sigma_epsilon_within = "diag", lowertri_epsilon_within = "diag", omega_zeta_between = "full", delta_zeta_between = "diag", kappa_zeta_between = "full", sigma_zeta_between = "full", lowertri_zeta_between = "full", omega_epsilon_between = "zero", delta_epsilon_between = "diag", kappa_epsilon_between = "diag", sigma_epsilon_between = "diag", lowertri_epsilon_between = "diag", nu, mu_eta, identify = TRUE, identification = c("loadings", "variance"), latents, groups, covs, means, nobs, start = "version2", covtype = c("choose", "ML", "UB"), missing = "listwise", equal = "none", baseline_saturated = TRUE, estimator = "ML", optimizer, storedata = FALSE, verbose = FALSE, sampleStats, baseline = c("stationary_random_intercept", "stationary", "independence", "none"), bootstrap = FALSE, boot_sub, boot_resample) panelgvar(data, vars, within_latent = c("ggm","chol","cov","prec"), between_latent = c("ggm","chol","cov","prec"), ...) panelvar(data, vars, within_latent = c("cov","chol","prec","ggm"), between_latent = c("cov","chol","prec","ggm"), ...) panel_lvgvar(...)
data |
A data frame encoding the data used in the analysis. Can be missing if |
vars |
Required argument. Different from in other psychonetrics models, this must be a *matrix* with each row indicating a variable and each column indicating a measurement. The matrix must be filled with names of the variables in the dataset corresponding to variable i at wave j. NAs can be used to indicate missing waves. The rownames of this matrix will be used as variable names. |
lambda |
Required argument. A model matrix encoding the factor loading structure. Each row indicates an indicator and each column a latent. A 0 encodes a fixed to zero element, a 1 encoding a free to estimate element, and higher integers encoding equality constrains. For multiple groups, this argument can be a list or array with each element/slice encoding such a matrix. |
within_latent |
The type of within-person latent contemporaneous model to be used. |
within_residual |
The type of within-person residual model to be used. |
between_latent |
The type of between-person latent model to be used. |
between_residual |
The type of between-person residual model to be used. |
beta |
A model matrix encoding the temporal relationships (transpose of temporal network). A 0 encodes a fixed to zero element, a 1 encoding a free to estimate element, and higher integers encoding equality constrains. For multiple groups, this argument can be a list or array with each element/slice encoding such a matrix. Can also be |
omega_zeta_within |
Only used when |
delta_zeta_within |
Only used when |
kappa_zeta_within |
Only used when |
sigma_zeta_within |
Only used when |
lowertri_zeta_within |
Only used when |
omega_epsilon_within |
Only used when |
delta_epsilon_within |
Only used when |
kappa_epsilon_within |
Only used when |
sigma_epsilon_within |
Only used when |
lowertri_epsilon_within |
Only used when |
omega_zeta_between |
Only used when |
delta_zeta_between |
Only used when |
kappa_zeta_between |
Only used when |
sigma_zeta_between |
Only used when |
lowertri_zeta_between |
Only used when |
omega_epsilon_between |
Only used when |
delta_epsilon_between |
Only used when |
kappa_epsilon_between |
Only used when |
sigma_epsilon_between |
Only used when |
lowertri_epsilon_between |
Only used when |
nu |
Optional vector encoding the intercepts of the observed variables. Set elements to 0 to indicate fixed to zero constrains, 1 to indicate free intercepts, and higher integers to indicate equality constrains. For multiple groups, this argument can be a list or array with each element/column encoding such a vector. |
mu_eta |
Optional vector encoding the means of the latent variables. Set elements to 0 to indicate fixed to zero constrains, 1 to indicate free intercepts, and higher integers to indicate equality constrains. For multiple groups, this argument can be a list or array with each element/column encoding such a vector. |
identify |
Logical, should the model be automatically identified? |
identification |
Type of identification used. |
latents |
An optional character vector with names of the latent variables. |
groups |
An optional string indicating the name of the group variable in |
covs |
A sample variance–covariance matrix, or a list/array of such matrices for multiple groups. IMPORTANT NOTE: psychonetrics expects the maximum likelihood (ML) covariance matrix, which is NOT obtained from |
means |
A vector of sample means, or a list/matrix containing such vectors for multiple groups. |
nobs |
The number of observations used in |
start |
Start value specification. Can be either a string or a psychonetrics model. If it is a string, |
missing |
How should missingness be handled in computing the sample covariances and number of observations when |
equal |
A character vector indicating which matrices should be constrained equal across groups. |
baseline_saturated |
A logical indicating if the baseline and saturated model should be included. Mostly used internally and NOT Recommended to be used manually. |
estimator |
The estimator to be used. Currently implemented are |
optimizer |
The optimizer to be used. Can be one of |
storedata |
Logical, should the raw data be stored? Needed for bootstrapping (see |
verbose |
Logical, should progress be printed to the console? |
sampleStats |
An optional sample statistics object. Mostly used internally. |
covtype |
If 'covs' is used, this is the type of covariance (maximum likelihood or unbiased) the input covariance matrix represents. Set to |
baseline |
What baseline model should be used? |
bootstrap |
Should the data be bootstrapped? If |
boot_sub |
Proportion of cases to be subsampled ( |
boot_resample |
Logical, should the bootstrap be with replacement ( |
... |
Arguments sent to |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
library("dplyr") # Smoke data cov matrix, based on LISS data panel https://www.dataarchive.lissdata.nl smoke <- structure(c(47.2361758611759, 43.5366809116809, 41.0057465682466, 43.5366809116809, 57.9789886039886, 47.6992521367521, 41.0057465682466, 47.6992521367521, 53.0669434731935), .Dim = c(3L, 3L), .Dimnames = list( c("smoke2008", "smoke2009", "smoke2010"), c("smoke2008", "smoke2009", "smoke2010"))) # Design matrix: design <- matrix(rownames(smoke),1,3) # Form model: mod <- panelvar(vars = design, covs = smoke, nobs = 352 ) # Run model: mod <- mod %>% runmodel # Evaluate fit: mod %>% fitlibrary("dplyr") # Smoke data cov matrix, based on LISS data panel https://www.dataarchive.lissdata.nl smoke <- structure(c(47.2361758611759, 43.5366809116809, 41.0057465682466, 43.5366809116809, 57.9789886039886, 47.6992521367521, 41.0057465682466, 47.6992521367521, 53.0669434731935), .Dim = c(3L, 3L), .Dimnames = list( c("smoke2008", "smoke2009", "smoke2010"), c("smoke2008", "smoke2009", "smoke2010"))) # Design matrix: design <- matrix(rownames(smoke),1,3) # Form model: mod <- panelvar(vars = design, covs = smoke, nobs = 352 ) # Run model: mod <- mod %>% runmodel # Evaluate fit: mod %>% fit
These matrices are used in the analytic gradients
duplicationMatrix(n, diag = TRUE) eliminationMatrix(n, diag = TRUE) diagonalizationMatrix(n)duplicationMatrix(n, diag = TRUE) eliminationMatrix(n, diag = TRUE) diagonalizationMatrix(n)
n |
Number of rows and columns in the original matrix |
diag |
Logical indicating if the diagonal should be included (set to FALSE for derivative of vech(x)) |
A sparse matrix
Sacha Epskamp
# Duplication matrix for 10 variables: duplicationMatrix(10) # Elimination matrix for 10 variables: eliminationMatrix(10) # Diagonailzation matrix for 10 variables: diagonalizationMatrix(10)# Duplication matrix for 10 variables: duplicationMatrix(10) # Elimination matrix for 10 variables: eliminationMatrix(10) # Diagonailzation matrix for 10 variables: diagonalizationMatrix(10)
This function overwrites the starting values to simple defaults. This can help in cases where optimization fails.
emergencystart(x)emergencystart(x)
x |
A |
A psychonetrics model.
Sacha Epskamp
These functions implement Ergodic Subspace Analysis by von Oertzen, Schmiedek and Voelkle (2020). The functions can be used on the output of a dlvm1 model, or manually by supplying a within persons and between persons variance-covariance matrix.
esa(x, cutoff = 0.1, between = c("crosssection", "between")) esa_manual(sigma_wp, sigma_bp, cutoff = 0.1) ## S3 method for class 'esa' print(x, printref = TRUE, ...) ## S3 method for class 'esa_manual' print(x, printref = TRUE, ...) ## S3 method for class 'esa' plot(x, plot = c("observed", "latent"), ...) ## S3 method for class 'esa_manual' plot(x, ...)esa(x, cutoff = 0.1, between = c("crosssection", "between")) esa_manual(sigma_wp, sigma_bp, cutoff = 0.1) ## S3 method for class 'esa' print(x, printref = TRUE, ...) ## S3 method for class 'esa_manual' print(x, printref = TRUE, ...) ## S3 method for class 'esa' plot(x, plot = c("observed", "latent"), ...) ## S3 method for class 'esa_manual' plot(x, ...)
x |
Output of a |
sigma_wp |
Manual within-person variance-covariance matrix |
sigma_bp |
Manual between-person variance-covariance matrix |
cutoff |
Cutoff used to determine ergodicity |
printref |
Logical, should the reference be printed? |
plot |
Should ergodicity of observed or latent variables be plotted? |
between |
Should the between-persons variance-covariance matrix be based on exected cross-sectional or between-person relations |
... |
Not used |
For each group a esa_manual object with the following elements:
ergodicity |
Ergodicity values of each component |
Q_esa |
Component loadings |
V_bp |
Between persons subspace |
V_ergodic |
Ergodic subspace |
V_wp |
Within person subspace |
cutoff |
Cutoff value used |
Sacha Epskamp <[email protected]>
von Oertzen, T., Schmiedek, F., and Voelkle, M. C. (2020). Ergodic Subspace Analysis. Journal of Intelligence, 8(1), 3.
Currently, only the lvm framework with single group and no missing data is supported.
factorscores(data, model, method = c("bartlett", "regression"))factorscores(data, model, method = c("bartlett", "regression"))
data |
Dataset to compute factor scores for |
model |
A psychonetrics model |
method |
The method to use: |
Sacha Epskamp <[email protected]>
This function will print all fit indices of the model/
fit(x)fit(x)
x |
A |
Invisibly returns a data frame with fit measure estimates.
Sacha Epskamp
# 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, omega = "zero") # Run model: mod0 <- mod0 %>% runmodel # Inspect fit: mod0 %>% fit # Pretty bad fit...# 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, omega = "zero") # Run model: mod0 <- mod0 %>% runmodel # Inspect fit: mod0 %>% fit # Pretty bad fit...
The fixpar function can be used to fix a parameter to some value (Typically zero), and the freepar function can be used to free a parameter from being fixed to a value.
fixpar(x, matrix, row, col, value = 0, group, verbose, log = TRUE, runmodel = FALSE, ...) freepar(x, matrix, row, col, start, group, verbose, log = TRUE, runmodel = FALSE, startEPC = TRUE, ...)fixpar(x, matrix, row, col, value = 0, group, verbose, log = TRUE, runmodel = FALSE, ...) freepar(x, matrix, row, col, start, group, verbose, log = TRUE, runmodel = FALSE, startEPC = TRUE, ...)
x |
A |
matrix |
String indicating the matrix of the parameter |
row |
Integer or string indicating the row of the matrix of the parameter |
col |
Integer or string indicating the column of the matrix of the parameter |
value |
Used in |
start |
Used in |
group |
Integer indicating the group of the parameter to be constrained |
verbose |
Logical, should messages be printed? |
log |
Logical, should the log be updated? |
runmodel |
Logical, should the model be updated? |
startEPC |
Logical, should the starting value be set at the expected parameter change? |
... |
Arguments sent to |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
This function attempts to fix starting values by comparing the analytic gradient to a numerically approximated gradient. Parameters with a difference between the analytic and numeric gradient that exceeds 'maxdiff' will be reduced by a factor of 'reduce' in each iteration until the average absolute difference between analytic and numeric gradients is lower than 'tol'. Only off-diagonal elements in omega, sigma, kappa, lowertri or rho matrices or any element in beta matrices are adjusted.
fixstart(x, reduce = 0.5, maxdiff = 0.1, tol = 0.01, maxtry = 25)fixstart(x, reduce = 0.5, maxdiff = 0.1, tol = 0.01, maxtry = 25)
x |
A 'psychonetrics' model |
reduce |
The factor with which problematic parameters are reduced in each iteration. |
maxdiff |
Maximum difference between analytic and numeric gradient to be considered problematic. |
tol |
Average absolute difference between analytic and numeric gradient that is considered acceptable. |
maxtry |
Maximum number of iterations to attempt to fix starting values. |
Sacha Epskamp
This function will generate new data from the estimated mean and variance-covariance structure of a psychonetrics model.
generate(x, n = 500)generate(x, n = 500)
x |
A |
n |
Number of cases to sample per group. |
A data frame with simulated data
Sacha Epskamp
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.
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)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)
x |
A |
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 |
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. |
A matrix of parameter estimates, of a list of such matrices for multiple group models.
Sacha Epskamp
# 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")# 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")
This function can be used to obtain the estimated asymptotic covariance matrix from a psychonetrics object.
getVCOV(model, approximate_SEs = FALSE)getVCOV(model, approximate_SEs = FALSE)
model |
A |
approximate_SEs |
Logical, should standard errors be approximated? If true, an approximate matrix inverse of the Fischer information is used to obtain the standard errors. |
This function returns a matrix.
Sacha Epskamp
The groupequal function constrains parameters equal across groups, and the groupfree function frees equality constrains across groups.
groupequal(x, matrix, row, col, verbose, log = TRUE, runmodel = FALSE, identify = TRUE, ...) groupfree(x, matrix, row, col, verbose, log = TRUE, runmodel = FALSE, identify = TRUE, ...)groupequal(x, matrix, row, col, verbose, log = TRUE, runmodel = FALSE, identify = TRUE, ...) groupfree(x, matrix, row, col, verbose, log = TRUE, runmodel = FALSE, identify = TRUE, ...)
x |
A |
matrix |
String indicating the matrix of the parameter |
row |
Integer or string indicating the row of the matrix of the parameter |
col |
Integer or string indicating the column of the matrix of the parameter |
verbose |
Logical, should messages be printed? |
log |
Logical, should the log be updated? |
runmodel |
Logical, should the model be updated? |
identify |
Logical, should the model be identified? |
... |
Arguments sent to |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
This is the family of Ising models fit to dichotomous datasets. Note that the input matters (see also https://arxiv.org/abs/1811.02916) in this model! Models based on a dataset that is encoded with -1 and 1 are not entirely equivalent to models based on datasets encoded with 0 and 1 (non-equivalences occur in multi-group settings with equality constrains).
Ising(data, omega = "full", tau, beta, vars, groups, covs, means, nobs, covtype = c("choose", "ML", "UB"), responses, missing = "listwise", equal = "none", baseline_saturated = TRUE, estimator = "default", optimizer, storedata = FALSE, WLS.W, sampleStats, identify = TRUE, verbose = FALSE, maxNodes = 20, min_sum = -Inf, bootstrap = FALSE, boot_sub, boot_resample)Ising(data, omega = "full", tau, beta, vars, groups, covs, means, nobs, covtype = c("choose", "ML", "UB"), responses, missing = "listwise", equal = "none", baseline_saturated = TRUE, estimator = "default", optimizer, storedata = FALSE, WLS.W, sampleStats, identify = TRUE, verbose = FALSE, maxNodes = 20, min_sum = -Inf, bootstrap = FALSE, boot_sub, boot_resample)
data |
A data frame encoding the data used in the analysis. Can be missing if |
omega |
The network structure. Either |
tau |
Optional vector encoding the threshold/intercept structure. Set elements to 0 to indicate fixed to zero constrains, 1 to indicate free intercepts, and higher integers to indicate equality constrains. For multiple groups, this argument can be a list or array with each element/column encoding such a vector. |
beta |
Optional scalar encoding the inverse temperature. 1 indicate free beta parameters, and higher integers to indicate equality constrains. For multiple groups, this argument can be a list or array with each element/column encoding such scalers. |
vars |
An optional character vector encoding the variables used in the analyis. Must equal names of the dataset in |
groups |
An optional character vector encoding the variables used in the analyis. Must equal names of the dataset in |
covs |
A sample variance–covariance matrix, or a list/array of such matrices for multiple groups. Make sure |
means |
A vector of sample means, or a list/matrix containing such vectors for multiple groups. |
nobs |
The number of observations used in |
covtype |
If 'covs' is used, this is the type of covariance (maximum likelihood or unbiased) the input covariance matrix represents. Set to |
responses |
A vector of dichotemous responses used (e.g., |
missing |
How should missingness be handled in computing the sample covariances and number of observations when |
equal |
A character vector indicating which matrices should be constrained equal across groups. |
baseline_saturated |
A logical indicating if the baseline and saturated model should be included. Mostly used internally and NOT Recommended to be used manually. |
estimator |
The estimator to be used. Currently implemented are |
optimizer |
The optimizer to be used. Can be one of |
storedata |
Logical, should the raw data be stored? Needed for bootstrapping (see |
WLS.W |
Optional WLS weights matrix. CURRENTLY NOT USED. |
sampleStats |
An optional sample statistics object. Mostly used internally. |
identify |
Logical, should the model be identified? |
verbose |
Logical, should messages be printed? |
maxNodes |
The maximum number of nodes allowed in the analysis. This function will stop with an error if more nodes are used (it is not recommended to set this higher). |
min_sum |
The minimum sum score that is artifically possible in the dataset. Defaults to -Inf. Set this only if you know a lower sum score is not possible in the data, for example due to selection bias. |
bootstrap |
Should the data be bootstrapped? If |
boot_sub |
Proportion of cases to be subsampled ( |
boot_resample |
Logical, should the bootstrap be with replacement ( |
The Ising Model takes the following form:
With Hamiltonian:
And Z representing the partition function or normalizing constant.
An object of the class psychonetrics
Sacha Epskamp <[email protected]>
Epskamp, S., Maris, G., Waldorp, L. J., & Borsboom, D. (2018). Network Psychometrics. In: Irwing, P., Hughes, D., & Booth, T. (Eds.), The Wiley Handbook of Psychometric Testing, 2 Volume Set: A Multidisciplinary Reference on Survey, Scale and Test Development. New York: Wiley.
library("dplyr") data("Jonas") # Variables to use: vars <- names(Jonas)[1:10] # Arranged groups to put unfamiliar group first (beta constrained to 1): Jonas <- Jonas[order(Jonas$group),] # Form saturated model: model1 <- Ising(Jonas, vars = vars, groups = "group") # Run model: model1 <- model1 %>% runmodel(approximate_SEs = TRUE) # We approximate the SEs because there are zeroes in the crosstables # of people that know Jonas. This leads to uninterpretable edge # estimates, but as can be seen below only in the model with # non-equal estimates across groups. # Prune-stepup to find a sparse model: model1b <- model1 %>% prune(alpha = 0.05) %>% stepup(alpha = 0.05) # Equal networks: suppressWarnings( model2 <- model1 %>% groupequal("omega") %>% runmodel ) # Prune-stepup to find a sparse model: model2b <- model2 %>% prune(alpha = 0.05) %>% stepup(mi = "mi_equal", alpha = 0.05) # Equal thresholds: model3 <- model2 %>% groupequal("tau") %>% runmodel # Prune-stepup to find a sparse model: model3b <- model3 %>% prune(alpha = 0.05) %>% stepup(mi = "mi_equal", alpha = 0.05) # Equal beta: model4 <- model3 %>% groupequal("beta") %>% runmodel # Prune-stepup to find a sparse model: model4b <- model4 %>% prune(alpha = 0.05) %>% stepup(mi = "mi_equal", alpha = 0.05) # Compare all models: compare( `1. all parameters free (dense)` = model1, `2. all parameters free (sparse)` = model1b, `3. equal networks (dense)` = model2, `4. equal networks (sparse)` = model2b, `5. equal networks and thresholds (dense)` = model3, `6. equal networks and thresholds (sparse)` = model3b, `7. all parameters equal (dense)` = model4, `8. all parameters equal (sparse)` = model4b ) %>% arrange(BIC)library("dplyr") data("Jonas") # Variables to use: vars <- names(Jonas)[1:10] # Arranged groups to put unfamiliar group first (beta constrained to 1): Jonas <- Jonas[order(Jonas$group),] # Form saturated model: model1 <- Ising(Jonas, vars = vars, groups = "group") # Run model: model1 <- model1 %>% runmodel(approximate_SEs = TRUE) # We approximate the SEs because there are zeroes in the crosstables # of people that know Jonas. This leads to uninterpretable edge # estimates, but as can be seen below only in the model with # non-equal estimates across groups. # Prune-stepup to find a sparse model: model1b <- model1 %>% prune(alpha = 0.05) %>% stepup(alpha = 0.05) # Equal networks: suppressWarnings( model2 <- model1 %>% groupequal("omega") %>% runmodel ) # Prune-stepup to find a sparse model: model2b <- model2 %>% prune(alpha = 0.05) %>% stepup(mi = "mi_equal", alpha = 0.05) # Equal thresholds: model3 <- model2 %>% groupequal("tau") %>% runmodel # Prune-stepup to find a sparse model: model3b <- model3 %>% prune(alpha = 0.05) %>% stepup(mi = "mi_equal", alpha = 0.05) # Equal beta: model4 <- model3 %>% groupequal("beta") %>% runmodel # Prune-stepup to find a sparse model: model4b <- model4 %>% prune(alpha = 0.05) %>% stepup(mi = "mi_equal", alpha = 0.05) # Compare all models: compare( `1. all parameters free (dense)` = model1, `2. all parameters free (sparse)` = model1b, `3. equal networks (dense)` = model2, `4. equal networks (sparse)` = model2b, `5. equal networks and thresholds (dense)` = model3, `6. equal networks and thresholds (sparse)` = model3b, `7. all parameters equal (dense)` = model4, `8. all parameters equal (sparse)` = model4b ) %>% arrange(BIC)
Responses of 10 attitude items towards a researcher named Jonas. Participants were shown three photos of Jonas with the text: "This is Jonas, a researcher from Germany who is now becoming a PhD in Psychology". Subsequently, the participants had to answer 10 yes / no questions starting with "I believe that Jonas...", as well as rate their familliarity with Jonas. The sample consists of people familiar with Jonas and not familiar with Jonas, and allows for testing Attitudinal Entropy Framework <doi:10.1080/1047840X.2018.1537246>.
data("Jonas")data("Jonas")
A data frame with 215 observations on the following 12 variables.
scientist... is a good scientist
jeans... Is a person that wears beautiful jeans
cares... really cares about people like you
economics... would solve our economic problems
hardworking... is hardworking
honest... is honest
intouch... is in touch with ordinary people
knowledgeable... is knowledgeable
makeupmind... can't make up his mind
getsthingsdone... gets things done
familiarAnswers to the question "How familiar are you with Jonas?" (three responses possible)
groupThe question 'familiar' categorized in two groups ("Knows Jonas" and "Doesn't Know Jonas")
data(Jonas)data(Jonas)
Wrapper to lvm to specify a latent growth curve model.
latentgrowth(vars, time = seq_len(ncol(vars)) - 1, covariates = character(0), covariates_as = c("regression", "covariance"), ...)latentgrowth(vars, time = seq_len(ncol(vars)) - 1, covariates = character(0), covariates_as = c("regression", "covariance"), ...)
vars |
Different from in other psychonetrics models, this must be a *matrix* with each row indicating a variable and each column indicating a measurement. The matrix must be filled with names of the variables in the dataset corresponding to variable i at wave j. NAs can be used to indicate missing waves. The rownames of this matrix will be used as variable names. |
time |
A vector with the encoding of each measurement (e.g., 0, 1, 2, 3). |
covariates |
A vector with strings indicating names of between-person covariate variables in the data |
covariates_as |
Should covariates be included as regressions or actual covariates? |
... |
Arguments sent to |
See https://github.com/SachaEpskamp/SEM-code-examples/tree/master/Latent_growth_examples/psychonetrics for examples
An object of the class psychonetrics (psychonetrics-class). See for an example https://github.com/SachaEpskamp/SEM-code-examples/tree/master/Latent_growth_examples/psychonetrics.
Sacha Epskamp
library("dplyr") # Smoke data cov matrix, based on LISS data panel https://www.dataarchive.lissdata.nl smoke <- structure(c(47.2361758611759, 43.5366809116809, 41.0057465682466, 43.5366809116809, 57.9789886039886, 47.6992521367521, 41.0057465682466, 47.6992521367521, 53.0669434731935), .Dim = c(3L, 3L), .Dimnames = list( c("smoke2008", "smoke2009", "smoke2010"), c("smoke2008", "smoke2009", "smoke2010"))) # Design matrix: design <- matrix(rownames(smoke),1,3) # Form model: mod <- latentgrowth(vars = design, covs = smoke, nobs = 352 ) ## Not run: # Run model: mod <- mod %>% runmodel # Evaluate fit: mod %>% fit # Look at parameters: mod %>% parameters ## End(Not run)library("dplyr") # Smoke data cov matrix, based on LISS data panel https://www.dataarchive.lissdata.nl smoke <- structure(c(47.2361758611759, 43.5366809116809, 41.0057465682466, 43.5366809116809, 57.9789886039886, 47.6992521367521, 41.0057465682466, 47.6992521367521, 53.0669434731935), .Dim = c(3L, 3L), .Dimnames = list( c("smoke2008", "smoke2009", "smoke2010"), c("smoke2008", "smoke2009", "smoke2010"))) # Design matrix: design <- matrix(rownames(smoke),1,3) # Form model: mod <- latentgrowth(vars = design, covs = smoke, nobs = 352 ) ## Not run: # Run model: mod <- mod %>% runmodel # Evaluate fit: mod %>% fit # Look at parameters: mod %>% parameters ## End(Not run)
This function can be used to retrieve the logbook of a 'psychonetrics' object.
logbook(x, log = TRUE)logbook(x, log = TRUE)
x |
A 'psychonetrics' object. |
log |
Logical, should the entry that the logbook is accessed be added? |
Sacha Epskamp
This is the family of models that models the data as a structural equation model (SEM), allowing the latent and residual variance-covariance matrices to be further modeled as networks. The latent and residual arguments can be used to define what latent and residual models are used respectively: "cov" (default) models a variance-covariance matrix directly, "chol" models a Cholesky decomposition, "prec" models a precision matrix, and "ggm" models a Gaussian graphical model (Epskamp, Rhemtulla and Borsboom, 2017). The wrapper lnm() sets latent = "ggm" for the latent network model (LNM), the wrapper rnm() sets residual = "ggm" for the residual network model (RNM), and the wrapper lrnm() combines the LNM and RNM.
lvm(data, lambda, latent = c("cov", "chol", "prec", "ggm"), residual = c("cov", "chol", "prec", "ggm"), sigma_zeta = "full", kappa_zeta = "full", omega_zeta = "full", lowertri_zeta = "full", delta_zeta = "full", sigma_epsilon = "diag", kappa_epsilon = "diag", omega_epsilon = "zero", lowertri_epsilon = "diag", delta_epsilon = "diag", beta = "zero", nu, nu_eta, identify = TRUE, identification = c("loadings", "variance"), vars, latents, groups, covs, means, nobs, missing = "listwise", equal = "none", baseline_saturated = TRUE, estimator = "ML", optimizer, storedata = FALSE, WLS.W, covtype = c("choose", "ML", "UB"), standardize = c("none", "z", "quantile"), sampleStats, verbose = FALSE, simplelambdastart = FALSE, bootstrap = FALSE, boot_sub, boot_resample) lnm(...) rnm(...) lrnm(...)lvm(data, lambda, latent = c("cov", "chol", "prec", "ggm"), residual = c("cov", "chol", "prec", "ggm"), sigma_zeta = "full", kappa_zeta = "full", omega_zeta = "full", lowertri_zeta = "full", delta_zeta = "full", sigma_epsilon = "diag", kappa_epsilon = "diag", omega_epsilon = "zero", lowertri_epsilon = "diag", delta_epsilon = "diag", beta = "zero", nu, nu_eta, identify = TRUE, identification = c("loadings", "variance"), vars, latents, groups, covs, means, nobs, missing = "listwise", equal = "none", baseline_saturated = TRUE, estimator = "ML", optimizer, storedata = FALSE, WLS.W, covtype = c("choose", "ML", "UB"), standardize = c("none", "z", "quantile"), sampleStats, verbose = FALSE, simplelambdastart = FALSE, bootstrap = FALSE, boot_sub, boot_resample) lnm(...) rnm(...) lrnm(...)
data |
A data frame encoding the data used in the analysis. Can be missing if |
lambda |
A model matrix encoding the factor loading structure. Each row indicates an indicator and each column a latent. A 0 encodes a fixed to zero element, a 1 encoding a free to estimate element, and higher integers encoding equality constrains. For multiple groups, this argument can be a list or array with each element/slice encoding such a matrix. |
latent |
The type of latent model used. See description. |
residual |
The type of residual model used. See description. |
sigma_zeta |
Only used when |
kappa_zeta |
Only used when |
omega_zeta |
Only used when |
lowertri_zeta |
Only used when |
delta_zeta |
Only used when |
sigma_epsilon |
Only used when |
kappa_epsilon |
Only used when |
omega_epsilon |
Only used when |
lowertri_epsilon |
Only used when |
delta_epsilon |
Only used when |
beta |
A model matrix encoding the structural relations between latent variables. A 0 encodes a fixed to zero element, a 1 encoding a free to estimate element, and higher integers encoding equality constrains. For multiple groups, this argument can be a list or array with each element/slice encoding such a matrix. |
nu |
Optional vector encoding the intercepts of the observed variables. Set elements to 0 to indicate fixed to zero constrains, 1 to indicate free intercepts, and higher integers to indicate equality constrains. For multiple groups, this argument can be a list or array with each element/column encoding such a vector. |
nu_eta |
Optional vector encoding the intercepts of the latent variables. Set elements to 0 to indicate fixed to zero constrains, 1 to indicate free intercepts, and higher integers to indicate equality constrains. For multiple groups, this argument can be a list or array with each element/column encoding such a vector. |
identify |
Logical, should the model be automatically identified? |
identification |
Type of identification used. |
vars |
An optional character vector encoding the variables used in the analysis. Must equal names of the dataset in |
latents |
An optional character vector with names of the latent variables. |
groups |
An optional string indicating the name of the group variable in |
covs |
A sample variance–covariance matrix, or a list/array of such matrices for multiple groups. Make sure |
means |
A vector of sample means, or a list/matrix containing such vectors for multiple groups. |
nobs |
The number of observations used in |
missing |
How should missingness be handled in computing the sample covariances and number of observations when |
equal |
A character vector indicating which matrices should be constrained equal across groups. |
baseline_saturated |
A logical indicating if the baseline and saturated model should be included. Mostly used internally and NOT Recommended to be used manually. |
estimator |
The estimator to be used. Currently implemented are |
optimizer |
The optimizer to be used. Can be one of |
storedata |
Logical, should the raw data be stored? Needed for bootstrapping (see |
verbose |
Logical, should progress be printed to the console? |
WLS.W |
The weights matrix used in WLS estimation (experimental) |
sampleStats |
An optional sample statistics object. Mostly used internally. |
covtype |
If 'covs' is used, this is the type of covariance (maximum likelihood or unbiased) the input covariance matrix represents. Set to |
standardize |
Which standardization method should be used? |
simplelambdastart |
Logical, should simple start values be used for lambda? Setting this to TRUE can avoid some estimation problems. |
bootstrap |
Should the data be bootstrapped? If |
boot_sub |
Proportion of cases to be subsampled ( |
boot_resample |
Logical, should the bootstrap be with replacement ( |
... |
Arguments sent to |
The model used in this family is:
in which the latent covariance matrix can further be modeled in three ways. With latent = "chol" as Cholesky decomposition:
,
with latent = "prec" as Precision matrix:
,
and finally with latent = "ggm" as Gaussian graphical model:
.
Likewise, the residual covariance matrix can also further be modeled in three ways. With residual = "chol" as Cholesky decomposition:
,
with latent = "prec" as Precision matrix:
,
and finally with latent = "ggm" as Gaussian graphical model:
.
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
Epskamp, S., Rhemtulla, M., & Borsboom, D. (2017). Generalized network psychometrics: Combining network and latent variable models. Psychometrika, 82(4), 904-927.
library("dplyr") ### Confirmatory Factor Analysis ### # Example also shown in https://youtu.be/Hdu5z-fwuk8 # Load data: data(StarWars) # Originals only: Lambda <- matrix(1,4) # Model: mod0 <- lvm(StarWars, lambda = Lambda, vars = c("Q1","Q5","Q6","Q7"), identification = "variance", latents = "Originals") # Run model: mod0 <- mod0 %>% runmodel # Evaluate fit: mod0 %>% fit # Full analysis # Factor loadings matrix: Lambda <- matrix(0, 10, 3) Lambda[1:4,1] <- 1 Lambda[c(1,5:7),2] <- 1 Lambda[c(1,8:10),3] <- 1 # Observed variables: obsvars <- paste0("Q",1:10) # Latents: latents <- c("Prequels","Original","Sequels") # Make model: mod1 <- lvm(StarWars, lambda = Lambda, vars = obsvars, identification = "variance", latents = latents) # Run model: mod1 <- mod1 %>% runmodel # Look at fit: mod1 # Look at parameter estimates: mod1 %>% parameters # Look at modification indices: mod1 %>% MIs # Add and refit: mod2 <- mod1 %>% freepar("sigma_epsilon","Q10","Q4") %>% runmodel # Compare: compare(original = mod1, adjusted = mod2) # Fit measures: mod2 %>% fit ### Path diagrams ### # semPlot is not (yet) supported by default, but can be used as follows: # Load packages: library("semPlot") # Estimates: lambdaEst <- getmatrix(mod2, "lambda") psiEst <- getmatrix(mod2, "sigma_zeta") thetaEst <- getmatrix(mod2, "sigma_epsilon") # LISREL Model: LY = Lambda (lambda-y), TE = Theta (theta-epsilon), PS = Psi mod <- lisrelModel(LY = lambdaEst, PS = psiEst, TE = thetaEst) # Plot with semPlot: semPaths(mod, "std", "est", as.expression = "nodes") # We can make this nicer (set whatLabels = "none" to hide labels): semPaths(mod, # this argument controls what the color of edges represent. In this case, # standardized parameters: what = "std", # This argument controls what the edge labels represent. In this case, parameter # estimates: whatLabels = "est", # This argument draws the node and edge labels as mathematical exprssions: as.expression = "nodes", # This will plot residuals as arrows, closer to what we use in class: style = "lisrel", # This makes the residuals larger: residScale = 10, # qgraph colorblind friendly theme: theme = "colorblind", # tree layout options are "tree", "tree2", and "tree3": layout = "tree2", # This makes the latent covariances connect at a cardinal center point: cardinal = "lat cov", # Changes curve into rounded straight lines: curvePivot = TRUE, # Size of manifest variables: sizeMan = 4, # Size of latent varibales: sizeLat = 10, # Size of edge labels: edge.label.cex = 1, # Sets the margins: mar = c(9,1,8,1), # Prevents re-ordering of ovbserved variables: reorder = FALSE, # Width of the plot: width = 8, # Height of plot: height = 5, # Colors according to latents: groups = "latents", # Pastel colors: pastel = TRUE, # Disable borders: borders = FALSE ) # Use arguments filetype = "pdf" and filename = "semPlotExample1" to store PDF ### Latent Network Modeling ### # Latent network model: lnm <- lvm(StarWars, lambda = Lambda, vars = obsvars, latents = latents, identification = "variance", latent = "ggm") # Run model: lnm <- lnm %>% runmodel # Look at parameters: lnm %>% parameters # Remove non-sig latent edge: lnm <- lnm %>% prune(alpha = 0.05) # Compare to the original CFA model: compare(cfa = mod1, lnm = lnm) # Plot network: library("qgraph") qgraph(lnm@modelmatrices[[1]]$omega_zeta, labels = latents, theme = "colorblind", vsize = 10) # A wrapper for the latent network model is the lnm function: lnm2 <- lnm(StarWars, lambda = Lambda, vars = obsvars, latents = latents, identification = "variance") lnm2 <- lnm2 %>% runmodel %>% prune(alpha = 0.05) compare(lnm, lnm2) # Is the same as the model before. # I could also estimate a "residual network model", which adds partial correlations to # the residual level: # This can be done using lvm(..., residal = "ggm") or with rnm(...) rnm <- rnm(StarWars, lambda = Lambda, vars = obsvars, latents = latents, identification = "variance") # Stepup search: rnm <- rnm %>% stepup # It will estimate the same model (with link Q10 - Q4) as above. In the case of only one # partial correlation, There is no difference between residual covariances (SEM) or # residual partial correlations (RNM). # For more information on latent and residual network models, see: # Epskamp, S., Rhemtulla, M.T., & Borsboom, D. Generalized Network Psychometrics: # Combining Network and Latent Variable Models # (2017). Psychometrika. doi:10.1007/s11336-017-9557-x ### Gaussian graphical models ### # All psychonetrics functions (e.g., lvm, lnm, rnm...) allow input via a covariance # matrix, with the "covs" and "nobs" arguments. # The following fits a baseline GGM network with no edges: S <- (nrow(StarWars) - 1)/ (nrow(StarWars)) * cov(StarWars[,1:10]) ggmmod <- ggm(covs = S, nobs = nrow(StarWars)) # Run model with stepup search and pruning: ggmmod <- ggmmod%>% prune %>% modelsearch # Fit measures: ggmmod %>% fit # Plot network: nodeNames <- c( "I am a huge Star Wars\nfan! (star what?)", "I would trust this person\nwith my democracy.", "I enjoyed the story of\nAnakin's early life.", "The special effects in\nthis scene are awful (Battle of\nGeonosis).", "I would trust this person\nwith my life.", "I found Darth Vader's big\nreveal in 'Empire' one of the greatest moments in movie history.", "The special effects in\nthis scene are amazing (Death Star\nExplosion).", "If possible, I would\ndefinitely buy this\ndroid.", "The story in the Star\nWars sequels is an improvement to\nthe previous movies.", "The special effects in\nthis scene are marvellous (Starkiller\nBase Firing)." ) library("qgraph") qgraph(as.matrix(ggmmod@modelmatrices[[1]]$omega), nodeNames = nodeNames, legend.cex = 0.25, theme = "colorblind", layout = "spring") # We can actually compare this model statistically (note they are not nested) to the # latent variable model: compare(original_cfa = mod1, adjusted_cfa = mod2, exploratory_ggm = ggmmod) ### Meausrement invariance ### # Let's say we are interested in seeing if people >= 30 like the original trilogy better # than people < 30. # First we can make a grouping variable: StarWars$agegroup <- ifelse(StarWars$Q12 < 30, "young", "less young") # Let's look at the distribution: table(StarWars$agegroup) # Pretty even... # Observed variables: obsvars <- paste0("Q",1:10) # Let's look at the mean scores: StarWars %>% group_by(agegroup) %>% summarize_each_(funs(mean),vars = obsvars) # Less young people seem to score higher on prequel questions and lower on other # questions # Factor loadings matrix: Lambda <- matrix(0, 10, 3) Lambda[1:4,1] <- 1 Lambda[c(1,5:7),2] <- 1 Lambda[c(1,8:10),3] <- 1 # Residual covariances: Theta <- diag(1, 10) Theta[4,10] <- Theta[10,4] <- 1 # Latents: latents <- c("Prequels","Original","Sequels") # Make model: mod_configural <- lvm(StarWars, lambda = Lambda, vars = obsvars, latents = latents, sigma_epsilon = Theta, identification = "variance", groups = "agegroup") # Run model: mod_configural <- mod_configural %>% runmodel # Look at fit: mod_configural mod_configural %>% fit # Looks good, let's try weak invariance: mod_weak <- mod_configural %>% groupequal("lambda") %>% runmodel # Compare models: compare(configural = mod_configural, weak = mod_weak) # weak invariance can be accepted, let's try strong: mod_strong <- mod_weak %>% groupequal("nu") %>% runmodel # Means are automatically identified # Compare models: compare(configural = mod_configural, weak = mod_weak, strong = mod_strong) # Questionable p-value and AIC difference, but ok BIC difference. This is quite good, but # let's take a look. I have not yet implemented LM tests for equality constrains, but we # can look at something called "equality-free" MIs: mod_strong %>% MIs(matrices = "nu", type = "free") # Indicates that Q10 would improve fit. We can also look at residuals: residuals(mod_strong) # Let's try freeing intercept 10: mod_strong_partial <- mod_strong %>% groupfree("nu",10) %>% runmodel # Compare all models: compare(configural = mod_configural, weak = mod_weak, strong = mod_strong, strong_partial = mod_strong_partial) # This seems worth it and lead to an acceptable model! It seems that older people find # the latest special effects more marvellous! mod_strong_partial %>% getmatrix("nu") # Now let's investigate strict invariance: mod_strict <- mod_strong_partial %>% groupequal("sigma_epsilon") %>% runmodel # Compare all models: compare(configural = mod_configural, weak = mod_weak, strong_partial = mod_strong_partial, strict = mod_strict) # Strict invariance can be accepted! # Now we can test for homogeneity! # Are the latent variances equal? mod_eqvar <- mod_strict %>% groupequal("sigma_zeta") %>% runmodel # Compare: compare(strict = mod_strict, eqvar = mod_eqvar) # This is acceptable. What about the means? (alpha = nu_eta) mod_eqmeans <- mod_eqvar %>% groupequal("nu_eta") %>% runmodel # Compare: compare(eqvar = mod_eqvar, eqmeans = mod_eqmeans) # Rejected! We could look at MIs again: mod_eqmeans %>% MIs(matrices = "nu_eta", type = "free") # Indicates the strongest effect for prequels. Let's see what happens: eqmeans2 <- mod_eqvar %>% groupequal("nu_eta",row = c("Original","Sequels")) %>% runmodel # Compare: compare(eqvar = mod_eqvar, eqmeans = eqmeans2) # Questionable, what about the sequels as well? eqmeans3 <- mod_eqvar %>% groupequal("nu_eta", row = "Original") %>% runmodel # Compare: compare(eqvar = mod_eqvar, eqmeans = eqmeans3) # Still questionable.. Let's look at the mean differences: mod_eqvar %>% getmatrix("nu_eta") # Looks like people over 30 like the prequels better and the other two trilogies less!library("dplyr") ### Confirmatory Factor Analysis ### # Example also shown in https://youtu.be/Hdu5z-fwuk8 # Load data: data(StarWars) # Originals only: Lambda <- matrix(1,4) # Model: mod0 <- lvm(StarWars, lambda = Lambda, vars = c("Q1","Q5","Q6","Q7"), identification = "variance", latents = "Originals") # Run model: mod0 <- mod0 %>% runmodel # Evaluate fit: mod0 %>% fit # Full analysis # Factor loadings matrix: Lambda <- matrix(0, 10, 3) Lambda[1:4,1] <- 1 Lambda[c(1,5:7),2] <- 1 Lambda[c(1,8:10),3] <- 1 # Observed variables: obsvars <- paste0("Q",1:10) # Latents: latents <- c("Prequels","Original","Sequels") # Make model: mod1 <- lvm(StarWars, lambda = Lambda, vars = obsvars, identification = "variance", latents = latents) # Run model: mod1 <- mod1 %>% runmodel # Look at fit: mod1 # Look at parameter estimates: mod1 %>% parameters # Look at modification indices: mod1 %>% MIs # Add and refit: mod2 <- mod1 %>% freepar("sigma_epsilon","Q10","Q4") %>% runmodel # Compare: compare(original = mod1, adjusted = mod2) # Fit measures: mod2 %>% fit ### Path diagrams ### # semPlot is not (yet) supported by default, but can be used as follows: # Load packages: library("semPlot") # Estimates: lambdaEst <- getmatrix(mod2, "lambda") psiEst <- getmatrix(mod2, "sigma_zeta") thetaEst <- getmatrix(mod2, "sigma_epsilon") # LISREL Model: LY = Lambda (lambda-y), TE = Theta (theta-epsilon), PS = Psi mod <- lisrelModel(LY = lambdaEst, PS = psiEst, TE = thetaEst) # Plot with semPlot: semPaths(mod, "std", "est", as.expression = "nodes") # We can make this nicer (set whatLabels = "none" to hide labels): semPaths(mod, # this argument controls what the color of edges represent. In this case, # standardized parameters: what = "std", # This argument controls what the edge labels represent. In this case, parameter # estimates: whatLabels = "est", # This argument draws the node and edge labels as mathematical exprssions: as.expression = "nodes", # This will plot residuals as arrows, closer to what we use in class: style = "lisrel", # This makes the residuals larger: residScale = 10, # qgraph colorblind friendly theme: theme = "colorblind", # tree layout options are "tree", "tree2", and "tree3": layout = "tree2", # This makes the latent covariances connect at a cardinal center point: cardinal = "lat cov", # Changes curve into rounded straight lines: curvePivot = TRUE, # Size of manifest variables: sizeMan = 4, # Size of latent varibales: sizeLat = 10, # Size of edge labels: edge.label.cex = 1, # Sets the margins: mar = c(9,1,8,1), # Prevents re-ordering of ovbserved variables: reorder = FALSE, # Width of the plot: width = 8, # Height of plot: height = 5, # Colors according to latents: groups = "latents", # Pastel colors: pastel = TRUE, # Disable borders: borders = FALSE ) # Use arguments filetype = "pdf" and filename = "semPlotExample1" to store PDF ### Latent Network Modeling ### # Latent network model: lnm <- lvm(StarWars, lambda = Lambda, vars = obsvars, latents = latents, identification = "variance", latent = "ggm") # Run model: lnm <- lnm %>% runmodel # Look at parameters: lnm %>% parameters # Remove non-sig latent edge: lnm <- lnm %>% prune(alpha = 0.05) # Compare to the original CFA model: compare(cfa = mod1, lnm = lnm) # Plot network: library("qgraph") qgraph(lnm@modelmatrices[[1]]$omega_zeta, labels = latents, theme = "colorblind", vsize = 10) # A wrapper for the latent network model is the lnm function: lnm2 <- lnm(StarWars, lambda = Lambda, vars = obsvars, latents = latents, identification = "variance") lnm2 <- lnm2 %>% runmodel %>% prune(alpha = 0.05) compare(lnm, lnm2) # Is the same as the model before. # I could also estimate a "residual network model", which adds partial correlations to # the residual level: # This can be done using lvm(..., residal = "ggm") or with rnm(...) rnm <- rnm(StarWars, lambda = Lambda, vars = obsvars, latents = latents, identification = "variance") # Stepup search: rnm <- rnm %>% stepup # It will estimate the same model (with link Q10 - Q4) as above. In the case of only one # partial correlation, There is no difference between residual covariances (SEM) or # residual partial correlations (RNM). # For more information on latent and residual network models, see: # Epskamp, S., Rhemtulla, M.T., & Borsboom, D. Generalized Network Psychometrics: # Combining Network and Latent Variable Models # (2017). Psychometrika. doi:10.1007/s11336-017-9557-x ### Gaussian graphical models ### # All psychonetrics functions (e.g., lvm, lnm, rnm...) allow input via a covariance # matrix, with the "covs" and "nobs" arguments. # The following fits a baseline GGM network with no edges: S <- (nrow(StarWars) - 1)/ (nrow(StarWars)) * cov(StarWars[,1:10]) ggmmod <- ggm(covs = S, nobs = nrow(StarWars)) # Run model with stepup search and pruning: ggmmod <- ggmmod%>% prune %>% modelsearch # Fit measures: ggmmod %>% fit # Plot network: nodeNames <- c( "I am a huge Star Wars\nfan! (star what?)", "I would trust this person\nwith my democracy.", "I enjoyed the story of\nAnakin's early life.", "The special effects in\nthis scene are awful (Battle of\nGeonosis).", "I would trust this person\nwith my life.", "I found Darth Vader's big\nreveal in 'Empire' one of the greatest moments in movie history.", "The special effects in\nthis scene are amazing (Death Star\nExplosion).", "If possible, I would\ndefinitely buy this\ndroid.", "The story in the Star\nWars sequels is an improvement to\nthe previous movies.", "The special effects in\nthis scene are marvellous (Starkiller\nBase Firing)." ) library("qgraph") qgraph(as.matrix(ggmmod@modelmatrices[[1]]$omega), nodeNames = nodeNames, legend.cex = 0.25, theme = "colorblind", layout = "spring") # We can actually compare this model statistically (note they are not nested) to the # latent variable model: compare(original_cfa = mod1, adjusted_cfa = mod2, exploratory_ggm = ggmmod) ### Meausrement invariance ### # Let's say we are interested in seeing if people >= 30 like the original trilogy better # than people < 30. # First we can make a grouping variable: StarWars$agegroup <- ifelse(StarWars$Q12 < 30, "young", "less young") # Let's look at the distribution: table(StarWars$agegroup) # Pretty even... # Observed variables: obsvars <- paste0("Q",1:10) # Let's look at the mean scores: StarWars %>% group_by(agegroup) %>% summarize_each_(funs(mean),vars = obsvars) # Less young people seem to score higher on prequel questions and lower on other # questions # Factor loadings matrix: Lambda <- matrix(0, 10, 3) Lambda[1:4,1] <- 1 Lambda[c(1,5:7),2] <- 1 Lambda[c(1,8:10),3] <- 1 # Residual covariances: Theta <- diag(1, 10) Theta[4,10] <- Theta[10,4] <- 1 # Latents: latents <- c("Prequels","Original","Sequels") # Make model: mod_configural <- lvm(StarWars, lambda = Lambda, vars = obsvars, latents = latents, sigma_epsilon = Theta, identification = "variance", groups = "agegroup") # Run model: mod_configural <- mod_configural %>% runmodel # Look at fit: mod_configural mod_configural %>% fit # Looks good, let's try weak invariance: mod_weak <- mod_configural %>% groupequal("lambda") %>% runmodel # Compare models: compare(configural = mod_configural, weak = mod_weak) # weak invariance can be accepted, let's try strong: mod_strong <- mod_weak %>% groupequal("nu") %>% runmodel # Means are automatically identified # Compare models: compare(configural = mod_configural, weak = mod_weak, strong = mod_strong) # Questionable p-value and AIC difference, but ok BIC difference. This is quite good, but # let's take a look. I have not yet implemented LM tests for equality constrains, but we # can look at something called "equality-free" MIs: mod_strong %>% MIs(matrices = "nu", type = "free") # Indicates that Q10 would improve fit. We can also look at residuals: residuals(mod_strong) # Let's try freeing intercept 10: mod_strong_partial <- mod_strong %>% groupfree("nu",10) %>% runmodel # Compare all models: compare(configural = mod_configural, weak = mod_weak, strong = mod_strong, strong_partial = mod_strong_partial) # This seems worth it and lead to an acceptable model! It seems that older people find # the latest special effects more marvellous! mod_strong_partial %>% getmatrix("nu") # Now let's investigate strict invariance: mod_strict <- mod_strong_partial %>% groupequal("sigma_epsilon") %>% runmodel # Compare all models: compare(configural = mod_configural, weak = mod_weak, strong_partial = mod_strong_partial, strict = mod_strict) # Strict invariance can be accepted! # Now we can test for homogeneity! # Are the latent variances equal? mod_eqvar <- mod_strict %>% groupequal("sigma_zeta") %>% runmodel # Compare: compare(strict = mod_strict, eqvar = mod_eqvar) # This is acceptable. What about the means? (alpha = nu_eta) mod_eqmeans <- mod_eqvar %>% groupequal("nu_eta") %>% runmodel # Compare: compare(eqvar = mod_eqvar, eqmeans = mod_eqmeans) # Rejected! We could look at MIs again: mod_eqmeans %>% MIs(matrices = "nu_eta", type = "free") # Indicates the strongest effect for prequels. Let's see what happens: eqmeans2 <- mod_eqvar %>% groupequal("nu_eta",row = c("Original","Sequels")) %>% runmodel # Compare: compare(eqvar = mod_eqvar, eqmeans = eqmeans2) # Questionable, what about the sequels as well? eqmeans3 <- mod_eqvar %>% groupequal("nu_eta", row = "Original") %>% runmodel # Compare: compare(eqvar = mod_eqvar, eqmeans = eqmeans3) # Still questionable.. Let's look at the mean differences: mod_eqvar %>% getmatrix("nu_eta") # Looks like people over 30 like the prequels better and the other two trilogies less!
Meta analysis of correlation matrices to fit a homogenous correlation matrix or Gaussian graphical model. Based on meta-analytic SEM (Jak and Cheung, 2019).
meta_varcov(cors, nobs, Vmats, Vmethod = c("individual", "pooled", "metaSEM_individual", "metaSEM_weighted"), Vestimation = c("averaged", "per_study"), type = c("cor", "ggm"), sigma_y = "full", kappa_y = "full", omega_y = "full", lowertri_y = "full", delta_y = "full", rho_y = "full", SD_y = "full", randomEffects = c("chol", "cov", "prec", "ggm", "cor"), sigma_randomEffects = "full", kappa_randomEffects = "full", omega_randomEffects = "full", lowertri_randomEffects = "full", delta_randomEffects = "full", rho_randomEffects = "full", SD_randomEffects = "full", vars, baseline_saturated = TRUE, optimizer, estimator = c("FIML", "ML"), sampleStats, verbose = FALSE, bootstrap = FALSE, boot_sub, boot_resample) meta_ggm(...)meta_varcov(cors, nobs, Vmats, Vmethod = c("individual", "pooled", "metaSEM_individual", "metaSEM_weighted"), Vestimation = c("averaged", "per_study"), type = c("cor", "ggm"), sigma_y = "full", kappa_y = "full", omega_y = "full", lowertri_y = "full", delta_y = "full", rho_y = "full", SD_y = "full", randomEffects = c("chol", "cov", "prec", "ggm", "cor"), sigma_randomEffects = "full", kappa_randomEffects = "full", omega_randomEffects = "full", lowertri_randomEffects = "full", delta_randomEffects = "full", rho_randomEffects = "full", SD_randomEffects = "full", vars, baseline_saturated = TRUE, optimizer, estimator = c("FIML", "ML"), sampleStats, verbose = FALSE, bootstrap = FALSE, boot_sub, boot_resample) meta_ggm(...)
cors |
A list of correlation matrices. Must contain rows and columns with |
nobs |
A vector with the number of observations per study. |
Vmats |
Optional list with 'V' matrices (sampling error variance approximations). |
Vmethod |
Which method should be used to apprixomate the sampling error variance? |
Vestimation |
How should the sampling error estimates be evaluated? |
type |
What to model? Currently only |
sigma_y |
Only used when |
kappa_y |
Only used when |
omega_y |
Only used when |
lowertri_y |
Only used when |
delta_y |
Only used when |
rho_y |
Only used when |
SD_y |
Only used when |
randomEffects |
What to model for the random effects? |
sigma_randomEffects |
Only used when |
kappa_randomEffects |
Only used when |
omega_randomEffects |
Only used when |
lowertri_randomEffects |
Only used when |
delta_randomEffects |
Only used when |
rho_randomEffects |
Only used when |
SD_randomEffects |
Only used when |
vars |
Variables to be included. |
baseline_saturated |
A logical indicating if the baseline and saturated model should be included. Mostly used internally and NOT Recommended to be used manually. |
optimizer |
The optimizer to be used. Can be one of |
estimator |
The estimator to be used. Currently implemented are |
sampleStats |
An optional sample statistics object. Mostly used internally. |
verbose |
Logical, should progress be printed to the console? |
bootstrap |
Should the data be bootstrapped? If |
boot_sub |
Proportion of cases to be subsampled ( |
boot_resample |
Logical, should the bootstrap be with replacement ( |
... |
Arguments sent to |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp <[email protected]>
Jak, S., and Cheung, M. W. L. (2019). Meta-analytic structural equation modeling with moderating effects on SEM parameters. Psychological methods.
This function prints a list of modification indices (MIs)
MIs(x, all = FALSE, matrices, type = c("normal", "equal", "free"), top = 10, verbose = TRUE, nonZero = FALSE)MIs(x, all = FALSE, matrices, type = c("normal", "equal", "free"), top = 10, verbose = TRUE, nonZero = FALSE)
x |
A |
all |
Logical, should all MIs be printed or only the highest? |
matrices |
Optional vector of matrices to include in the output. |
type |
String indicating which kind of modification index should be printed. ( |
top |
Number of MIs to include in output if |
verbose |
Logical, should messages be printed? |
nonZero |
Logical, should only MIs be printed of non-zero parameters? Useful to explore violations of group equality. |
Invisibly returns a relevant subset of the data frame containing all information on the parameters, or a list of such data frames if multiple types of MIs are requested.
Sacha Epskamp
# 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 = "zero") # Run model: mod <- mod %>% runmodel # Modification indices: mod %>% MIs# 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 = "zero") # Run model: mod <- mod %>% runmodel # Modification indices: mod %>% MIs
This family is the two-level random intercept variant of the lvm model family. It is mostly a special case of the dlvm1 family, with the addition of structural effects rather than temporal effects in the beta matrix.
ml_lnm(...) ml_rnm(...) ml_lrnm(...) ml_lvm(data, lambda, clusters, within_latent = c("cov", "chol", "prec", "ggm"), within_residual = c("cov", "chol", "prec", "ggm"), between_latent = c("cov", "chol", "prec", "ggm"), between_residual = c("cov", "chol", "prec", "ggm"), beta_within = "zero", beta_between = "zero", omega_zeta_within = "full", delta_zeta_within = "full", kappa_zeta_within = "full", sigma_zeta_within = "full", lowertri_zeta_within = "full", omega_epsilon_within = "zero", delta_epsilon_within = "diag", kappa_epsilon_within = "diag", sigma_epsilon_within = "diag", lowertri_epsilon_within = "diag", omega_zeta_between = "full", delta_zeta_between = "full", kappa_zeta_between = "full", sigma_zeta_between = "full", lowertri_zeta_between = "full", omega_epsilon_between = "zero", delta_epsilon_between = "diag", kappa_epsilon_between = "diag", sigma_epsilon_between = "diag", lowertri_epsilon_between = "diag", nu, nu_eta, identify = TRUE, identification = c("loadings", "variance"), vars, latents, groups, equal = "none", baseline_saturated = TRUE, estimator = c("FIML", "MUML"), optimizer, storedata = FALSE, verbose = FALSE, standardize = c("none", "z", "quantile"), sampleStats, bootstrap = FALSE, boot_sub, boot_resample)ml_lnm(...) ml_rnm(...) ml_lrnm(...) ml_lvm(data, lambda, clusters, within_latent = c("cov", "chol", "prec", "ggm"), within_residual = c("cov", "chol", "prec", "ggm"), between_latent = c("cov", "chol", "prec", "ggm"), between_residual = c("cov", "chol", "prec", "ggm"), beta_within = "zero", beta_between = "zero", omega_zeta_within = "full", delta_zeta_within = "full", kappa_zeta_within = "full", sigma_zeta_within = "full", lowertri_zeta_within = "full", omega_epsilon_within = "zero", delta_epsilon_within = "diag", kappa_epsilon_within = "diag", sigma_epsilon_within = "diag", lowertri_epsilon_within = "diag", omega_zeta_between = "full", delta_zeta_between = "full", kappa_zeta_between = "full", sigma_zeta_between = "full", lowertri_zeta_between = "full", omega_epsilon_between = "zero", delta_epsilon_between = "diag", kappa_epsilon_between = "diag", sigma_epsilon_between = "diag", lowertri_epsilon_between = "diag", nu, nu_eta, identify = TRUE, identification = c("loadings", "variance"), vars, latents, groups, equal = "none", baseline_saturated = TRUE, estimator = c("FIML", "MUML"), optimizer, storedata = FALSE, verbose = FALSE, standardize = c("none", "z", "quantile"), sampleStats, bootstrap = FALSE, boot_sub, boot_resample)
data |
A data frame encoding the data used in the analysis. Must be a raw dataset. |
lambda |
A model matrix encoding the factor loading structure. Each row indicates an indicator and each column a latent. A 0 encodes a fixed to zero element, a 1 encoding a free to estimate element, and higher integers encoding equality constrains. For multiple groups, this argument can be a list or array with each element/slice encoding such a matrix. Could also be the result of |
clusters |
A string indicating the variable in the dataset that describes group membership. |
within_latent |
The type of within-person latent contemporaneous model to be used. |
within_residual |
The type of within-person residual model to be used. |
between_latent |
The type of between-person latent model to be used. |
between_residual |
The type of between-person residual model to be used. |
beta_within |
A model matrix encoding the within-cluster structural. A 0 encodes a fixed to zero element, a 1 encoding a free to estimate element, and higher integers encoding equality constrains. For multiple groups, this argument can be a list or array with each element/slice encoding such a matrix. Defaults to |
beta_between |
A model matrix encoding the between-cluster structural. A 0 encodes a fixed to zero element, a 1 encoding a free to estimate element, and higher integers encoding equality constrains. For multiple groups, this argument can be a list or array with each element/slice encoding such a matrix. Defaults to |
omega_zeta_within |
Only used when |
delta_zeta_within |
Only used when |
kappa_zeta_within |
Only used when |
sigma_zeta_within |
Only used when |
lowertri_zeta_within |
Only used when |
omega_epsilon_within |
Only used when |
delta_epsilon_within |
Only used when |
kappa_epsilon_within |
Only used when |
sigma_epsilon_within |
Only used when |
lowertri_epsilon_within |
Only used when |
omega_zeta_between |
Only used when |
delta_zeta_between |
Only used when |
kappa_zeta_between |
Only used when |
sigma_zeta_between |
Only used when |
lowertri_zeta_between |
Only used when |
omega_epsilon_between |
Only used when |
delta_epsilon_between |
Only used when |
kappa_epsilon_between |
Only used when |
sigma_epsilon_between |
Only used when |
lowertri_epsilon_between |
Only used when |
nu |
Optional vector encoding the intercepts of the observed variables. Set elements to 0 to indicate fixed to zero constrains, 1 to indicate free intercepts, and higher integers to indicate equality constrains. For multiple groups, this argument can be a list or array with each element/column encoding such a vector. |
nu_eta |
Optional vector encoding the intercepts of the latent variables. Set elements to 0 to indicate fixed to zero constrains, 1 to indicate free intercepts, and higher integers to indicate equality constrains. For multiple groups, this argument can be a list or array with each element/column encoding such a vector. |
identify |
Logical, should the model be automatically identified? |
identification |
Type of identification used. |
vars |
An optional character vector with names of the variables used. |
latents |
An optional character vector with names of the latent variables. |
groups |
An optional string indicating the name of the group variable in |
equal |
A character vector indicating which matrices should be constrained equal across groups. |
baseline_saturated |
A logical indicating if the baseline and saturated model should be included. Mostly used internally and NOT Recommended to be used manually. |
estimator |
Estimator used. Currently only |
optimizer |
The optimizer to be used. Usually either |
storedata |
Logical, should the raw data be stored? Needed for bootstrapping (see |
verbose |
Logical, should progress be printed to the console? |
standardize |
Which standardization method should be used? |
sampleStats |
An optional sample statistics object. Mostly used internally. |
bootstrap |
Should the data be bootstrapped? If |
boot_sub |
Proportion of cases to be subsampled ( |
boot_resample |
Logical, should the bootstrap be with replacement ( |
... |
Arguments sent to 'ml_lvm' |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp <[email protected]>
This function is a wrapper around dlvm1 that allows for specifying the model using a long format data and similar input as the mlVAR package. The ml_ts_lvgvar simply sets within_latent = "ggm" and between_latent = "ggm" by default. The ml_gvar and ml_var are simple wrappers with different named defaults for contemporaneous and between-person effects.
ml_tsdlvm1(data, beepvar, idvar, vars, groups, estimator = "FIML", standardize = c("none", "z", "quantile"), ...) ml_ts_lvgvar(...) ml_gvar(..., contemporaneous = c("ggm", "cov", "chol", "prec"), between = c("ggm", "cov", "chol", "prec")) ml_var(..., contemporaneous = c("cov", "chol", "prec", "ggm"), between = c("cov", "chol", "prec", "ggm"))ml_tsdlvm1(data, beepvar, idvar, vars, groups, estimator = "FIML", standardize = c("none", "z", "quantile"), ...) ml_ts_lvgvar(...) ml_gvar(..., contemporaneous = c("ggm", "cov", "chol", "prec"), between = c("ggm", "cov", "chol", "prec")) ml_var(..., contemporaneous = c("cov", "chol", "prec", "ggm"), between = c("cov", "chol", "prec", "ggm"))
data |
The data to be used. Must be raw data in long format (each row indicates one person at one time point). |
beepvar |
Optional string indicating assessment beep per day. Adding this argument will cause non-consecutive beeps to be treated as missing! |
idvar |
String indicating the subject ID |
vars |
Vectors of variables to include in the analysis |
groups |
An optional string indicating the name of the group variable in |
estimator |
Estimator to be used. Must be |
standardize |
Which standardization method should be used? |
contemporaneous |
The type of within-person latent contemporaneous model to be used. |
between |
The type of between-person latent model to be used. |
... |
Arguments sent to |
Sacha Epskamp <[email protected]>
This function peforms stepwise model search to find an optimal model that (locally) minimzes some criterion (by default, the BIC).
modelsearch(x, criterion = "bic", matrices, prunealpha = 0.01, addalpha = 0.01, verbose, ...)modelsearch(x, criterion = "bic", matrices, prunealpha = 0.01, addalpha = 0.01, verbose, ...)
x |
A |
criterion |
String indicating the criterion to minimize. Any criterion from |
matrices |
Vector of strings indicating which matrices should be searched. Will default to network structures and factor loadings. |
prunealpha |
Minimal alpha used to consider edges to be removed |
addalpha |
Maximum alpha used to consider edges to be added |
verbose |
Logical, should messages be printed? |
... |
Arguments sent to |
The full algorithm is as follows:
1. Evaluate all models in which an edge is removed that has p > prunealpha, or an edge is added that has a modification index with p < addalpha
2. If none of these models improve the criterion, return the previous model and stop the algorithm
3. Update the model to the model that improved the criterion the most
4. Evaluate all other considered models that improved the criterion
5. If none of these models improve the criterion, go to 1, else go to 3
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
# 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) # Run model: mod <- mod %>% runmodel # Model search mod <- mod %>% prune(alpha= 0.01) %>% modelsearch# 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) # Run model: mod <- mod %>% runmodel # Model search mod <- mod %>% prune(alpha= 0.01) %>% modelsearch
This function will print a list of parameters of the model
parameters(x)parameters(x)
x |
A |
Invisibly returns a data frame containing information on all parameters.
Sacha Epskamp
# 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 = "zero") # Run model: mod <- mod %>% runmodel # Parameter estimates: mod %>% parameters# 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 = "zero") # Run model: mod <- mod %>% runmodel # Parameter estimates: mod %>% parameters
This function can be used to set parameters equal
parequal(x, ..., inds = integer(0), verbose, log = TRUE, runmodel = FALSE)parequal(x, ..., inds = integer(0), verbose, log = TRUE, runmodel = FALSE)
x |
A |
... |
Arguments sent to |
inds |
Parameter indices of parameters to be constrained equal |
verbose |
Logical, should messages be printed? |
log |
Logical, should the log be updated? |
runmodel |
Logical, should the model be updated? |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
This function will search for a multi-group model with equality constrains on some but not all parameters. This is called partial pruning (Epskamp, Isvoranu, & Cheung, 2020; Haslbeck, 2020). The algorithm is as follows: 1. remove all parameters not significant at alpha in all groups (without equality constrains), 2. create a union model with all parameters included in any group included in all groups and constrained equal. 3. Stepwise free equality constrains of the parameter that features the largest sum of modification indices until BIC can no longer be improved. 4. Select and return (by default) the best model according to BIC (original model, pruned model, union model and partially pruned model).
partialprune(x, alpha = 0.01, matrices, verbose, combinefun = unionmodel, return = c("best","partialprune","union_equal","prune"), criterion = "bic", best = c("lowest","highest"), ...)partialprune(x, alpha = 0.01, matrices, verbose, combinefun = unionmodel, return = c("best","partialprune","union_equal","prune"), criterion = "bic", best = c("lowest","highest"), ...)
x |
A |
alpha |
Significance level to use. |
matrices |
Vector of strings indicating which matrices should be pruned. Will default to network structures. |
verbose |
Logical, should messages be printed? |
combinefun |
Function used to combine models of different groups. |
return |
What model to retur? |
best |
Should the lowest or the highest index of |
criterion |
What criterion to use for the model selection in the last step? Defaults to |
... |
Arguments sent to |
Sacha Epskamp <[email protected]>
Epskamp, S., Isvoranu, A. M., & Cheung, M. (2020). Meta-analytic gaussian network aggregation. PsyArXiv preprint. DOI:10.31234/osf.io/236w8.
Haslbeck, J. (2020). Estimating Group Differences in Network Models using Moderation Analysis. PsyArXiv preprint. DOI:10.31234/osf.io/926pv.
This function will (recursively) remove parameters that are not significant and refit the model.
prune(x, alpha = 0.01, adjust = c("none", "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr"), matrices, runmodel = TRUE, recursive = FALSE, verbose, log = TRUE, identify = TRUE, startreduce = 1, limit = Inf, mode = c("tested","all"), ...)prune(x, alpha = 0.01, adjust = c("none", "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr"), matrices, runmodel = TRUE, recursive = FALSE, verbose, log = TRUE, identify = TRUE, startreduce = 1, limit = Inf, mode = c("tested","all"), ...)
x |
A |
alpha |
Significance level to use. |
adjust |
p-value adjustment method to use. See |
matrices |
Vector of strings indicating which matrices should be pruned. Will default to network structures. |
runmodel |
Logical, should the model be evaluated after pruning? |
recursive |
Logical, should the pruning process be repeated? |
verbose |
Logical, should messages be printed? |
log |
Logical, should the log be updated? |
identify |
Logical, should models be identified automatically? |
startreduce |
A numeric value indicating a factor with which the starting values should be reduced. Can be useful when encountering numeric problems. |
limit |
The maximum number of parameters to be pruned. |
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)? |
... |
Arguments sent to |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
# 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 # Prune model: mod <- mod %>% prune(adjust = "fdr", recursive = FALSE)# 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 # Prune model: mod <- mod %>% prune(adjust = "fdr", recursive = FALSE)
"psychonetrics_bootstrap"
Class for aggregated bootstrap results.
Objects can be created by calls of the form new("psychonetrics_bootstrap", ...).
model:Object of class "character" ~~
submodel:Object of class "character" ~~
parameters:Object of class "data.frame" ~~
models:Object of class "list" ~~
matrices:Object of class "data.frame" ~~
fitmeasures:Object of class "data.frame" ~~
distribution:Object of class "character" ~~
verbose:Object of class "logical" ~~
boot_sub:Object of class "numeric" ~~
boot_resample:Object of class "logical" ~~
n_fail:Object of class "numeric" ~~
n_success:Object of class "numeric" ~~
types:Object of class "list" ~~
signature(object = "psychonetrics_bootstrap"): ...
Sacha Epskamp
showClass("psychonetrics_bootstrap")showClass("psychonetrics_bootstrap")
"psychonetrics"
A logbook entry in the psychonetrics logbook
Objects can be created by calls of the form new("psychonetrics_log", ...).
event:Object of class "character" ~~
time:Object of class "POSIXct" ~~
sessionInfo:Object of class "sessionInfo" ~~
signature(object = "psychonetrics_log"): ...
Sacha Epskamp
showClass("psychonetrics_log")showClass("psychonetrics_log")
These functions update a psychonetrics model. Typically they are not required.
addMIs(x, matrices = "all", type = c("normal", "free", "equal"), verbose, analyticFisher = TRUE) addSEs(x, verbose, approximate_SEs = FALSE) addfit(x, verbose) identify(x)addMIs(x, matrices = "all", type = c("normal", "free", "equal"), verbose, analyticFisher = TRUE) addSEs(x, verbose, approximate_SEs = FALSE) addfit(x, verbose) identify(x)
x |
A |
matrices |
Optional vector of matrices to include in MIs. |
type |
String indicating which modification indices should be updated. |
verbose |
Logical, should messages be printed? |
analyticFisher |
Logical indicating if an analytic Fisher information matrix should be used. |
approximate_SEs |
Logical, should standard errors be approximated? If true, an approximate matrix inverse of the Fischer information is used to obtain the standard errors. |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
"psychonetrics"
Main class for psychonetrics results.
Objects can be created by calls of the form new("psychonetrics", ...).
model:Object of class "character" ~~
submodel:Object of class "character" ~~
parameters:Object of class "data.frame" ~~
matrices:Object of class "data.frame" ~~
meanstructure:Object of class "logical" ~~
computed:Object of class "logical" ~~
sample:Object of class "psychonetrics_samplestats" ~~
modelmatrices:Object of class "list" ~~
log:Object of class "psychonetrics_log" ~~
optim:Object of class "list" ~~
fitmeasures:Object of class "list" ~~
baseline_saturated:Object of class "list" ~~
equal:Object of class "character" ~~
objective:Object of class "numeric" ~~
information:Object of class "matrix" ~~
identification:Object of class "character" ~~
optimizer:Object of class "character" ~~
optim.args:Object of class "list" ~~
estimator:Object of class "character" ~~
distribution:Object of class "character" ~~
extramatrices:Object of class "list" ~~
rawts:Object of class "logical" ~~
Drawts:Object of class "list" ~~
types:Object of class "list" ~~
cpp:Object of class "logical" ~~
verbose:Object of class "logical" ~~
signature(object = "psychonetrics"): ...
signature(object = "psychonetrics"): ...
signature(object = "psychonetrics"): ...
Sacha Epskamp
showClass("psychonetrics")showClass("psychonetrics")
This is the main function used to run a psychonetrics model.
runmodel(x, level = c("gradient", "fitfunction"), addfit = TRUE, addMIs = TRUE, addSEs = TRUE, addInformation = TRUE, log = TRUE, verbose, optim.control, analyticFisher = TRUE, warn_improper = FALSE, warn_gradient = TRUE, warn_bounds = TRUE, return_improper = TRUE, bounded = TRUE, approximate_SEs = FALSE)runmodel(x, level = c("gradient", "fitfunction"), addfit = TRUE, addMIs = TRUE, addSEs = TRUE, addInformation = TRUE, log = TRUE, verbose, optim.control, analyticFisher = TRUE, warn_improper = FALSE, warn_gradient = TRUE, warn_bounds = TRUE, return_improper = TRUE, bounded = TRUE, approximate_SEs = FALSE)
x |
A |
level |
Level at which the model should be estimated. Defaults to |
addfit |
Logical, should fit measures be added? |
addMIs |
Logical, should modification indices be added? |
addSEs |
Logical, should standard errors be added? |
addInformation |
Logical, should the Fisher information be added? |
log |
Logical, should the log be updated? |
verbose |
Logical, should messages be printed? |
optim.control |
A list with options for |
analyticFisher |
Logical, should the analytic Fisher information be used? If |
return_improper |
Should a result in which improper computation was used be return? Improper computation can mean that a pseudoinverse of small spectral shift was used in computing the inverse of a matrix. |
warn_improper |
Logical. Should a warning be given when at some point in the estimation a pseudoinverse was used? |
warn_gradient |
Logical. Should a warning be given when the average absolute gradient is > 1? |
bounded |
Logical. Should bounded estimation be used (e.g., variances should be positive)? |
approximate_SEs |
Logical, should standard errors be approximated? If true, an approximate matrix inverse of the Fischer information is used to obtain the standard errors. |
warn_bounds |
Should a warning be given when a parameter is estimated near its bounds? |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
# 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# 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
These functions can be used to change some estimator options.
setestimator(x, estimator) setoptimizer(x, optimizer = c("default", "nlminb", "ucminf", "cpp_L-BFGS-B", "cpp_BFGS", "cpp_CG", "cpp_SANN", "cpp_Nelder-Mead"), optim.args) usecpp(x, use = TRUE)setestimator(x, estimator) setoptimizer(x, optimizer = c("default", "nlminb", "ucminf", "cpp_L-BFGS-B", "cpp_BFGS", "cpp_CG", "cpp_SANN", "cpp_Nelder-Mead"), optim.args) usecpp(x, use = TRUE)
x |
A |
estimator |
A string indicating the estimator to be used |
optimizer |
The optimizer to be used. Can be one of |
use |
Logical indicating if C++ should be used (currently only used in FIML) |
optim.args |
List of arguments to sent to the optimizer. |
The default optimizer is nlminb with the following arguments:
eval.max=20000L
iter.max=10000L
trace=0L
abs.tol=sqrt(.Machine$double.eps)
rel.tol=sqrt(.Machine$double.eps)
step.min=1.0
step.max=1.0
x.tol=1.5e-8
xf.tol=2.2e-14
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
This function controls if messages should be printed for a psychonetrics model.
setverbose(x, verbose = TRUE)setverbose(x, verbose = TRUE)
x |
A |
verbose |
Logical indicating if verbose should be enabled |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
This function generates the input for lambda arguments in latent variable models using a simple structure. The input is a vector with an element for each variable indicating the factor the variable loads on.
simplestructure(x)simplestructure(x)
x |
A vector indicating which factor each indicator loads on. |
Sacha Epskamp <[email protected]>
This questionaire was constructed by Carolin Katzera, Charlotte Tanis, Esther Niehoff, Myrthe Veenman, and Jason Nak as part of an assignment for a course on confirmatory factor analysis (http://sachaepskamp.com/SEM2018). They also collected the data among fellow psychology students as well as through social media.
data("StarWars")data("StarWars")
A data frame with 271 observations on the following 13 variables.
Q1I am a huge Star Wars fan! (star what?)
Q2I would trust this person with my democracy <picture of Jar Jar Binks>
Q3I enjoyed the story of Anakin's early life
Q4The special effects in this scene are awful <video of the Battle of Geonosis>
Q5I would trust this person with my life <picture of Han Solo>
Q6I found Darth Vader'ss big reveal in "Empire" one of the greatest moments in movie history
Q7The special effects in this scene are amazing <video of the Death Star explosion>
Q8If possible, I would definitely buy this droid <picture of BB-8>
Q9The story in the Star Wars sequels is an improvement to the previous movies
Q10The special effects in this scene are marvellous <video of the Starkiller Base firing>
Q11What is your gender?
Q12How old are you?
Q13Have you seen any of the Star Wars movies?
The questionaire is online at https://github.com/SachaEpskamp/SEM-code-examples/blob/master/CFA_fit_examples/StarWars_questionaire.pdf. The authors of the questionaire defined a measurement model before collecting data: Q2 - Q4 are expected to load on a "prequel" factor, Q5 - Q7 are expected to load in a "originals" factor, and Q8 - Q10 are expected to load on a "sequal" factor. Finally, Q1 is expected to load on all three.
https://github.com/SachaEpskamp/SEM-code-examples/blob/master/CFA_fit_examples
data(StarWars)data(StarWars)
This function automatically peforms step-up search by adding the parameter with the largest modification index until some criterion is reached or no modification indices are significant at alpha.
stepup(x, alpha = 0.01, criterion = "bic", matrices, mi = c("mi", "mi_free", "mi_equal"), greedyadjust = c("bonferroni", "none", "holm", "hochberg", "hommel", "fdr", "BH", "BY"), stopif, greedy = FALSE, verbose, checkinformation = TRUE, singularinformation = c("tryfix", "skip", "continue", "stop"), startEPC = TRUE, ...)stepup(x, alpha = 0.01, criterion = "bic", matrices, mi = c("mi", "mi_free", "mi_equal"), greedyadjust = c("bonferroni", "none", "holm", "hochberg", "hommel", "fdr", "BH", "BY"), stopif, greedy = FALSE, verbose, checkinformation = TRUE, singularinformation = c("tryfix", "skip", "continue", "stop"), startEPC = TRUE, ...)
x |
A |
alpha |
Significance level to use. |
criterion |
String indicating the criterion to minimize. Any criterion from |
matrices |
Vector of strings indicating which matrices should be searched. Will default to network structures and factor loadings. |
mi |
String indicating which kind of modification index should be used ( |
greedyadjust |
String indicating which p-value adjustment should be used in greedy start. Any method from |
stopif |
An R expression, using objects from |
greedy |
Logical, should a greedy start be used? If |
verbose |
Logical, should messages be printed? |
checkinformation |
Logical, should the Fisher information be checked for potentially non-identified models? |
singularinformation |
String indicating how to proceed if the information matrix is singular. |
startEPC |
Logical, should the starting value be set at the expected parameter change? |
... |
Arguments sent to |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
# 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 %>%prune(alpha = 0.05) # Remove an edge (example): mod <- mod %>%fixpar("omega",1,2) %>%runmodel # Stepup search mod <- mod %>%stepup(alpha = 0.05)# 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 %>%prune(alpha = 0.05) # Remove an edge (example): mod <- mod %>%fixpar("omega",1,2) %>%runmodel # Stepup search mod <- mod %>%stepup(alpha = 0.05)
This function allows to transform a model variance–covariance structure from one type to another. Its main uses are to (1) use a Cholesky decomposition to estimate a saturated covariance matrix or GGM, and (2) to transform between conditional (ggm) and marginal associations (cov).
transmod(x, ..., verbose, keep_computed = FALSE, log = TRUE, identify = TRUE)transmod(x, ..., verbose, keep_computed = FALSE, log = TRUE, identify = TRUE)
x |
A psychonetrics model |
... |
Named arguments with the new types to use (e.g., |
verbose |
Logical, should messages be printed? |
keep_computed |
Logical, should the model be stated to be uncomputed adter the transformation? In general, a model does not need to be re-computed as transformed parameters should be at the maximum likelihood estimate. |
log |
Logical, should a logbook entry be made? |
identify |
Logical, should the model be identified after transforming? |
Transformations are only possible if the model is diagonal (e.g., no partial correlations) or saturated (e.g., all covariances included).
Sacha Epskamp
# 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] # Model with Cholesky decompositon: mod <- varcov(ConsData, vars = vars, type = "chol") # Run model: mod <- mod %>% runmodel # Transform to GGM: mod_trans <- transmod(mod, type = "ggm") %>% runmodel # Note: runmodel often not needed # Obtain thresholded GGM: getmatrix(mod_trans, "omega", threshold = TRUE)# 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] # Model with Cholesky decompositon: mod <- varcov(ConsData, vars = vars, type = "chol") # Run model: mod <- mod %>% runmodel # Transform to GGM: mod_trans <- transmod(mod, type = "ggm") %>% runmodel # Note: runmodel often not needed # Obtain thresholded GGM: getmatrix(mod_trans, "omega", threshold = TRUE)
This is the family of models that models a dynamic factor model on time-series. There are two covariance structures that can be modeled in different ways: contemporaneous for the contemporaneous model and residual for the residual model. These can be set to "cov" for covariances, "prec" for a precision matrix, "ggm" for a Gaussian graphical model and "chol" for a Cholesky decomposition. The ts_lvgvar wrapper function sets contemporaneous = "ggm" for the graphical VAR model.
tsdlvm1(data, lambda, contemporaneous = c("cov", "chol", "prec", "ggm"), residual = c("cov", "chol", "prec", "ggm"), beta = "full", omega_zeta = "full", delta_zeta = "diag", kappa_zeta = "full", sigma_zeta = "full", lowertri_zeta = "full", omega_epsilon = "zero", delta_epsilon = "diag", kappa_epsilon = "diag", sigma_epsilon = "diag", lowertri_epsilon = "diag", nu, mu_eta, identify = TRUE, identification = c("loadings", "variance"), latents, beepvar, dayvar, idvar, vars, groups, covs, means, nobs, missing = "listwise", equal = "none", baseline_saturated = TRUE, estimator = "ML", optimizer, storedata = FALSE, sampleStats, covtype = c("choose", "ML", "UB"), centerWithin = FALSE, standardize = c("none", "z", "quantile"), verbose = FALSE, bootstrap = FALSE, boot_sub, boot_resample) ts_lvgvar(...)tsdlvm1(data, lambda, contemporaneous = c("cov", "chol", "prec", "ggm"), residual = c("cov", "chol", "prec", "ggm"), beta = "full", omega_zeta = "full", delta_zeta = "diag", kappa_zeta = "full", sigma_zeta = "full", lowertri_zeta = "full", omega_epsilon = "zero", delta_epsilon = "diag", kappa_epsilon = "diag", sigma_epsilon = "diag", lowertri_epsilon = "diag", nu, mu_eta, identify = TRUE, identification = c("loadings", "variance"), latents, beepvar, dayvar, idvar, vars, groups, covs, means, nobs, missing = "listwise", equal = "none", baseline_saturated = TRUE, estimator = "ML", optimizer, storedata = FALSE, sampleStats, covtype = c("choose", "ML", "UB"), centerWithin = FALSE, standardize = c("none", "z", "quantile"), verbose = FALSE, bootstrap = FALSE, boot_sub, boot_resample) ts_lvgvar(...)
data |
A data frame encoding the data used in the analysis. Can be missing if |
lambda |
A model matrix encoding the factor loading structure. Each row indicates an indicator and each column a latent. A 0 encodes a fixed to zero element, a 1 encoding a free to estimate element, and higher integers encoding equality constrains. For multiple groups, this argument can be a list or array with each element/slice encoding such a matrix. |
contemporaneous |
The type of contemporaneous model used. See description. |
residual |
The type of residual model used. See description. |
beta |
A model matrix encoding the temporal relationships (transpose of temporal network) between latent variables. A 0 encodes a fixed to zero element, a 1 encoding a free to estimate element, and higher integers encoding equality constrains. For multiple groups, this argument can be a list or array with each element/slice encoding such a matrix. Can also be |
omega_zeta |
Only used when |
delta_zeta |
Only used when |
kappa_zeta |
Only used when |
sigma_zeta |
Only used when |
lowertri_zeta |
Only used when |
omega_epsilon |
Only used when |
delta_epsilon |
Only used when |
kappa_epsilon |
Only used when |
sigma_epsilon |
Only used when |
lowertri_epsilon |
Only used when |
nu |
Optional vector encoding the intercepts of the observed variables. Set elements to 0 to indicate fixed to zero constrains, 1 to indicate free intercepts, and higher integers to indicate equality constrains. For multiple groups, this argument can be a list or array with each element/column encoding such a vector. |
mu_eta |
Optional vector encoding the means of the latent variables. Set elements to 0 to indicate fixed to zero constrains, 1 to indicate free intercepts, and higher integers to indicate equality constrains. For multiple groups, this argument can be a list or array with each element/column encoding such a vector. |
identify |
Logical, should the model be automatically identified? |
identification |
Type of identification used. |
latents |
An optional character vector with names of the latent variables. |
beepvar |
Optional string indicating assessment beep per day. Adding this argument will cause non-consecutive beeps to be treated as missing! |
dayvar |
Optional string indicating assessment day. Adding this argument makes sure that the first measurement of a day is not regressed on the last measurement of the previous day. IMPORTANT: only add this if the data has multiple observations per day. |
idvar |
Optional string indicating the subject ID |
vars |
An optional character vector encoding the variables used in the analyis. Must equal names of the dataset in |
groups |
An optional string indicating the name of the group variable in |
covs |
A sample variance–covariance matrix, or a list/array of such matrices for multiple groups. Make sure |
means |
A vector of sample means, or a list/matrix containing such vectors for multiple groups. |
nobs |
The number of observations used in |
missing |
How should missingness be handled in computing the sample covariances and number of observations when |
equal |
A character vector indicating which matrices should be constrained equal across groups. |
baseline_saturated |
A logical indicating if the baseline and saturated model should be included. Mostly used internally and NOT Recommended to be used manually. |
estimator |
The estimator to be used. Currently implemented are |
optimizer |
The optimizer to be used. Can be one of |
storedata |
Logical, should the raw data be stored? Needed for bootstrapping (see |
standardize |
Which standardization method should be used? |
sampleStats |
An optional sample statistics object. Mostly used internally. |
centerWithin |
Logical, should data be within-person centered? |
covtype |
If 'covs' is used, this is the type of covariance (maximum likelihood or unbiased) the input covariance matrix represents. Set to |
verbose |
Logical, should messages be printed? |
bootstrap |
Should the data be bootstrapped? If |
boot_sub |
Proportion of cases to be subsampled ( |
boot_resample |
Logical, should the bootstrap be with replacement ( |
... |
Arguments sent to |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
# Note: this example is wrapped in a dontrun environment because the data is not # available locally. ## Not run: # Obtain the data from: # # Epskamp, S., van Borkulo, C. D., van der Veen, D. C., Servaas, M. N., Isvoranu, A. M., # Riese, H., & Cramer, A. O. (2018). Personalized network modeling in psychopathology: # The importance of contemporaneous and temporal connections. Clinical Psychological # Science, 6(3), 416-427. # # Available here: https://osf.io/c8wjz/ tsdata <- read.csv("Supplementary2_data.csv") # Encode time variable in a way R understands: tsdata$time <- as.POSIXct(tsdata$time, tz = "Europe/Amsterdam") # Extract days: tsdata$Day <- as.Date(tsdata$time, tz = "Europe/Amsterdam") # Variables to use: vars <- c("relaxed", "sad", "nervous", "concentration", "tired", "rumination", "bodily.discomfort") # Create lambda matrix (in this case: one factor): Lambda <- matrix(1,7,1) # Estimate dynamical factor model: model <- tsdlvm1( tsdata, lambda = Lambda, vars = vars, dayvar = "Day", estimator = "FIML" ) # Run model: model <- model %>% runmodel # Look at fit: model %>% print model %>% fit # Pretty bad fit ## End(Not run)# Note: this example is wrapped in a dontrun environment because the data is not # available locally. ## Not run: # Obtain the data from: # # Epskamp, S., van Borkulo, C. D., van der Veen, D. C., Servaas, M. N., Isvoranu, A. M., # Riese, H., & Cramer, A. O. (2018). Personalized network modeling in psychopathology: # The importance of contemporaneous and temporal connections. Clinical Psychological # Science, 6(3), 416-427. # # Available here: https://osf.io/c8wjz/ tsdata <- read.csv("Supplementary2_data.csv") # Encode time variable in a way R understands: tsdata$time <- as.POSIXct(tsdata$time, tz = "Europe/Amsterdam") # Extract days: tsdata$Day <- as.Date(tsdata$time, tz = "Europe/Amsterdam") # Variables to use: vars <- c("relaxed", "sad", "nervous", "concentration", "tired", "rumination", "bodily.discomfort") # Create lambda matrix (in this case: one factor): Lambda <- matrix(1,7,1) # Estimate dynamical factor model: model <- tsdlvm1( tsdata, lambda = Lambda, vars = vars, dayvar = "Day", estimator = "FIML" ) # Run model: model <- model %>% runmodel # Look at fit: model %>% print model %>% fit # Pretty bad fit ## End(Not run)
The unionmodel will add all parameters to all groups that are free in at least one group, and the intersectionmodel will constrain all parameters across groups to zero unless they are free to estimate in all groups.
unionmodel(x, runmodel = FALSE, verbose, log = TRUE, identify = TRUE, matrices, ...) intersectionmodel(x, runmodel = FALSE, verbose, log = TRUE, identify = TRUE, matrices, ...)unionmodel(x, runmodel = FALSE, verbose, log = TRUE, identify = TRUE, matrices, ...) intersectionmodel(x, runmodel = FALSE, verbose, log = TRUE, identify = TRUE, matrices, ...)
x |
A |
runmodel |
Logical, should the model be updated? |
verbose |
Logical, should messages be printed? |
log |
Logical, should the log be updated? |
identify |
Logical, should the model be identified? |
matrices |
Which matrices should be used to form the union/intersection model? |
... |
Arguments sent to |
An object of the class psychonetrics (psychonetrics-class)
Sacha Epskamp
This is the family of models that models time-series data using a lag-1 vector autoregressive model (VAR; Epskamp,Waldorp, Mottus, Borsboom, 2018). The model is fitted to the Toeplitz matrix, but unlike typical SEM software the block of covariances of the lagged variables is not used in estimating the temporal and contemporaneous relationships (the block is modeled completely separately using a cholesky decomposition, and does not enter the model elsewise). The contemporaneous argument can be used to define what contemporaneous model is used: contemporaneous = "cov" (default) models a variance-covariance matrix, contemporaneous = "chol" models a Cholesky decomposition, contemporaneous = "prec" models a precision matrix, and contemporaneous = "ggm" (alias: gvar()) models a Gaussian graphical model, also then known as a graphical VAR model.
var1(data, contemporaneous = c("cov", "chol", "prec", "ggm"), beta = "full", omega_zeta = "full", delta_zeta = "full", kappa_zeta = "full", sigma_zeta = "full", lowertri_zeta = "full", mu, beepvar, dayvar, idvar, vars, groups, covs, means, nobs, missing = "listwise", equal = "none", baseline_saturated = TRUE, estimator = "ML", optimizer, storedata = FALSE, covtype = c("choose", "ML", "UB"), standardize = c("none", "z", "quantile"), sampleStats, verbose = FALSE, bootstrap = FALSE, boot_sub, boot_resample) gvar(...)var1(data, contemporaneous = c("cov", "chol", "prec", "ggm"), beta = "full", omega_zeta = "full", delta_zeta = "full", kappa_zeta = "full", sigma_zeta = "full", lowertri_zeta = "full", mu, beepvar, dayvar, idvar, vars, groups, covs, means, nobs, missing = "listwise", equal = "none", baseline_saturated = TRUE, estimator = "ML", optimizer, storedata = FALSE, covtype = c("choose", "ML", "UB"), standardize = c("none", "z", "quantile"), sampleStats, verbose = FALSE, bootstrap = FALSE, boot_sub, boot_resample) gvar(...)
data |
A data frame encoding the data used in the analysis. Can be missing if |
contemporaneous |
The type of contemporaneous model used. See description. |
beta |
A model matrix encoding the temporal relationships (transpose of temporal network). A 0 encodes a fixed to zero element, a 1 encoding a free to estimate element, and higher integers encoding equality constrains. For multiple groups, this argument can be a list or array with each element/slice encoding such a matrix. Can also be |
omega_zeta |
Only used when |
delta_zeta |
Only used when |
kappa_zeta |
Only used when |
sigma_zeta |
Only used when |
lowertri_zeta |
Only used when |
mu |
Optional vector encoding the mean structure. Set elements to 0 to indicate fixed to zero constrains, 1 to indicate free means, and higher integers to indicate equality constrains. For multiple groups, this argument can be a list or array with each element/column encoding such a vector. |
beepvar |
Optional string indicating assessment beep per day. Adding this argument will cause non-consecutive beeps to be treated as missing! |
dayvar |
Optional string indicating assessment day. Adding this argument makes sure that the first measurement of a day is not regressed on the last measurement of the previous day. IMPORTANT: only add this if the data has multiple observations per day. |
idvar |
Optional string indicating the subject ID |
vars |
An optional character vector encoding the variables used in the analyis. Must equal names of the dataset in |
groups |
An optional string indicating the name of the group variable in |
covs |
A sample variance–covariance matrix, or a list/array of such matrices for multiple groups. Make sure |
means |
A vector of sample means, or a list/matrix containing such vectors for multiple groups. |
nobs |
The number of observations used in |
missing |
How should missingness be handled in computing the sample covariances and number of observations when |
equal |
A character vector indicating which matrices should be constrained equal across groups. |
baseline_saturated |
A logical indicating if the baseline and saturated model should be included. Mostly used internally and NOT Recommended to be used manually. |
estimator |
The estimator to be used. Currently implemented are |
optimizer |
The optimizer to be used. Can be one of |
storedata |
Logical, should the raw data be stored? Needed for bootstrapping (see |
standardize |
Which standardization method should be used? |
sampleStats |
An optional sample statistics object. Mostly used internally. |
covtype |
If 'covs' is used, this is the type of covariance (maximum likelihood or unbiased) the input covariance matrix represents. Set to |
verbose |
Logical, should messages be printed? |
bootstrap |
Should the data be bootstrapped? If |
boot_sub |
Proportion of cases to be subsampled ( |
boot_resample |
Logical, should the bootstrap be with replacement ( |
... |
Arguments sent to |
This will be updated in a later version.
An object of the class psychonetrics
Sacha Epskamp
Epskamp, S., Waldorp, L. J., Mottus, R., & Borsboom, D. (2018). The Gaussian graphical model in cross-sectional and time-series data. Multivariate Behavioral Research, 53(4), 453-480.
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 # Parameter estimates: model %>% parameters # Plot the CIs: CIplot(model, "beta") # Note: this example is wrapped in a dontrun environment because the data is not # available locally. ## Not run: # Longer example: # # Obtain the data from: # # Epskamp, S., van Borkulo, C. D., van der Veen, D. C., Servaas, M. N., Isvoranu, A. M., # Riese, H., & Cramer, A. O. (2018). Personalized network modeling in psychopathology: # The importance of contemporaneous and temporal connections. Clinical Psychological # Science, 6(3), 416-427. # # Available here: https://osf.io/c8wjz/ tsdata <- read.csv("Supplementary2_data.csv") # Encode time variable in a way R understands: tsdata$time <- as.POSIXct(tsdata$time, tz = "Europe/Amsterdam") # Extract days: tsdata$Day <- as.Date(tsdata$time, tz = "Europe/Amsterdam") # Variables to use: vars <- c("relaxed", "sad", "nervous", "concentration", "tired", "rumination", "bodily.discomfort") # Estimate, prune with FDR, and perform stepup search: model_FDRprune <- gvar( tsdata, vars = vars, dayvar = "Day", estimator = "FIML" ) %>% runmodel %>% prune(adjust = "fdr", recursive = FALSE) %>% stepup(criterion = "bic") # Estimate with greedy stepup search: model_stepup <- gvar( tsdata, vars = vars, dayvar = "Day", estimator = "FIML", omega_zeta = "zero", beta = "zero" ) %>% runmodel %>% stepup(greedy = TRUE, greedyadjust = "bonferroni", criterion = "bic") # Compare models: compare( FDRprune = model_FDRprune, stepup = model_stepup ) # Very similar but not identical. Stepup is prefered here according to AIC and BIC # Stepup results: temporal <- getmatrix(model_stepup, "PDC") # PDC = Partial Directed Correlations contemporaneous <- getmatrix(model_stepup, "omega_zeta") # Average layout: library("qgraph") L <- averageLayout(temporal, contemporaneous) # Labels: labs <- gsub("\\.","\n",vars) # Plot: layout(t(1:2)) qgraph(temporal, layout = L, theme = "colorblind", directed=TRUE, diag=TRUE, title = "Temporal", vsize = 12, mar = rep(6,4), asize = 5, labels = labs) qgraph(contemporaneous, layout = L, theme = "colorblind", title = "Contemporaneous", vsize = 12, mar = rep(6,4), asize = 5, labels = labs) ## End(Not run)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 # Parameter estimates: model %>% parameters # Plot the CIs: CIplot(model, "beta") # Note: this example is wrapped in a dontrun environment because the data is not # available locally. ## Not run: # Longer example: # # Obtain the data from: # # Epskamp, S., van Borkulo, C. D., van der Veen, D. C., Servaas, M. N., Isvoranu, A. M., # Riese, H., & Cramer, A. O. (2018). Personalized network modeling in psychopathology: # The importance of contemporaneous and temporal connections. Clinical Psychological # Science, 6(3), 416-427. # # Available here: https://osf.io/c8wjz/ tsdata <- read.csv("Supplementary2_data.csv") # Encode time variable in a way R understands: tsdata$time <- as.POSIXct(tsdata$time, tz = "Europe/Amsterdam") # Extract days: tsdata$Day <- as.Date(tsdata$time, tz = "Europe/Amsterdam") # Variables to use: vars <- c("relaxed", "sad", "nervous", "concentration", "tired", "rumination", "bodily.discomfort") # Estimate, prune with FDR, and perform stepup search: model_FDRprune <- gvar( tsdata, vars = vars, dayvar = "Day", estimator = "FIML" ) %>% runmodel %>% prune(adjust = "fdr", recursive = FALSE) %>% stepup(criterion = "bic") # Estimate with greedy stepup search: model_stepup <- gvar( tsdata, vars = vars, dayvar = "Day", estimator = "FIML", omega_zeta = "zero", beta = "zero" ) %>% runmodel %>% stepup(greedy = TRUE, greedyadjust = "bonferroni", criterion = "bic") # Compare models: compare( FDRprune = model_FDRprune, stepup = model_stepup ) # Very similar but not identical. Stepup is prefered here according to AIC and BIC # Stepup results: temporal <- getmatrix(model_stepup, "PDC") # PDC = Partial Directed Correlations contemporaneous <- getmatrix(model_stepup, "omega_zeta") # Average layout: library("qgraph") L <- averageLayout(temporal, contemporaneous) # Labels: labs <- gsub("\\.","\n",vars) # Plot: layout(t(1:2)) qgraph(temporal, layout = L, theme = "colorblind", directed=TRUE, diag=TRUE, title = "Temporal", vsize = 12, mar = rep(6,4), asize = 5, labels = labs) qgraph(contemporaneous, layout = L, theme = "colorblind", title = "Contemporaneous", vsize = 12, mar = rep(6,4), asize = 5, labels = labs) ## End(Not run)
This is the family of models that models only a variance-covariance matrix with mean structure. The type argument can be used to define what model is used: type = "cov" (default) models a variance-covariance matrix directly, type = "chol" (alias: cholesky()) models a Cholesky decomposition, type = "prec" (alias: precision()) models a precision matrix, type = "ggm" (alias: ggm()) models a Gaussian graphical model (Epskamp, Rhemtulla and Borsboom, 2017), and type = "cor" (alias: corr()) models a correlation matrix.
varcov(data, type = c("cov", "chol", "prec", "ggm", "cor"), sigma = "full", kappa = "full", omega = "full", lowertri = "full", delta = "diag", rho = "full", SD = "full", mu, tau, vars, ordered = character(0), groups, covs, means, nobs, missing = "listwise", equal = "none", baseline_saturated = TRUE, estimator = "default", optimizer, storedata = FALSE, WLS.W, sampleStats, meanstructure, corinput, verbose = FALSE, covtype = c("choose", "ML", "UB"), standardize = c("none", "z", "quantile"), fullFIML = FALSE, bootstrap = FALSE, boot_sub, boot_resample) cholesky(...) precision(...) prec(...) ggm(...) corr(...)varcov(data, type = c("cov", "chol", "prec", "ggm", "cor"), sigma = "full", kappa = "full", omega = "full", lowertri = "full", delta = "diag", rho = "full", SD = "full", mu, tau, vars, ordered = character(0), groups, covs, means, nobs, missing = "listwise", equal = "none", baseline_saturated = TRUE, estimator = "default", optimizer, storedata = FALSE, WLS.W, sampleStats, meanstructure, corinput, verbose = FALSE, covtype = c("choose", "ML", "UB"), standardize = c("none", "z", "quantile"), fullFIML = FALSE, bootstrap = FALSE, boot_sub, boot_resample) cholesky(...) precision(...) prec(...) ggm(...) corr(...)
data |
A data frame encoding the data used in the analysis. Can be missing if |
type |
The type of model used. See description. |
sigma |
Only used when |
kappa |
Only used when |
omega |
Only used when |
lowertri |
Only used when |
delta |
Only used when |
rho |
Only used when |
SD |
Only used when |
mu |
Optional vector encoding the mean structure. Set elements to 0 to indicate fixed to zero constrains, 1 to indicate free means, and higher integers to indicate equality constrains. For multiple groups, this argument can be a list or array with each element/column encoding such a vector. |
tau |
Optional list encoding the thresholds per variable. |
vars |
An optional character vector encoding the variables used in the analyis. Must equal names of the dataset in |
groups |
An optional string indicating the name of the group variable in |
covs |
A sample variance–covariance matrix, or a list/array of such matrices for multiple groups. Make sure |
means |
A vector of sample means, or a list/matrix containing such vectors for multiple groups. |
nobs |
The number of observations used in |
covtype |
If 'covs' is used, this is the type of covariance (maximum likelihood or unbiased) the input covariance matrix represents. Set to |
missing |
How should missingness be handled in computing the sample covariances and number of observations when |
equal |
A character vector indicating which matrices should be constrained equal across groups. |
baseline_saturated |
A logical indicating if the baseline and saturated model should be included. Mostly used internally and NOT Recommended to be used manually. |
estimator |
The estimator to be used. Currently implemented are |
optimizer |
The optimizer to be used. Can be one of |
storedata |
Logical, should the raw data be stored? Needed for bootstrapping (see |
standardize |
Which standardization method should be used? |
WLS.W |
Optional WLS weights matrix. |
sampleStats |
An optional sample statistics object. Mostly used internally. |
verbose |
Logical, should progress be printed to the console? |
ordered |
A vector with strings indicating the variables that are ordered catagorical, or set to |
meanstructure |
Logical, should the meanstructure be modeled explicitly? |
corinput |
Logical, is the input a correlation matrix? |
fullFIML |
Logical, should row-wise FIML be used? Not recommended! |
bootstrap |
Should the data be bootstrapped? If |
boot_sub |
Proportion of cases to be subsampled ( |
boot_resample |
Logical, should the bootstrap be with replacement ( |
... |
Arguments sent to |
The model used in this family is:
in which the covariance matrix can further be modeled in three ways. With type = "chol" as Cholesky decomposition:
,
with type = "prec" as Precision matrix:
,
and finally with type = "ggm" as Gaussian graphical model:
.
An object of the class psychonetrics
Sacha Epskamp
Epskamp, S., Rhemtulla, M., & Borsboom, D. (2017). Generalized network psychometrics: Combining network and latent variable models. Psychometrika, 82(4), 904-927.
# 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] # Saturated estimation: mod_saturated <- ggm(ConsData, vars = vars) # Run the model: mod_saturated <- mod_saturated %>% runmodel # We can look at the parameters: mod_saturated %>% parameters # Labels: labels <- c( "indifferent to the feelings of others", "inquire about others' well-being", "comfort others", "love children", "make people feel at ease") # Plot CIs: CIplot(mod_saturated, "omega", labels = labels, labelstart = 0.2) # We can also fit an empty network: mod0 <- ggm(ConsData, vars = vars, omega = "zero") # Run the model: mod0 <- mod0 %>% runmodel # We can look at the modification indices: mod0 %>% MIs # To automatically add along modification indices, we can use stepup: mod1 <- mod0 %>% stepup # Let's also prune all non-significant edges to finish: mod1 <- mod1 %>% prune # Look at the fit: mod1 %>% fit # Compare to original (baseline) model: compare(baseline = mod0, adjusted = mod1) # We can also look at the parameters: mod1 %>% parameters # Or obtain the network as follows: getmatrix(mod1, "omega")# 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] # Saturated estimation: mod_saturated <- ggm(ConsData, vars = vars) # Run the model: mod_saturated <- mod_saturated %>% runmodel # We can look at the parameters: mod_saturated %>% parameters # Labels: labels <- c( "indifferent to the feelings of others", "inquire about others' well-being", "comfort others", "love children", "make people feel at ease") # Plot CIs: CIplot(mod_saturated, "omega", labels = labels, labelstart = 0.2) # We can also fit an empty network: mod0 <- ggm(ConsData, vars = vars, omega = "zero") # Run the model: mod0 <- mod0 %>% runmodel # We can look at the modification indices: mod0 %>% MIs # To automatically add along modification indices, we can use stepup: mod1 <- mod0 %>% stepup # Let's also prune all non-significant edges to finish: mod1 <- mod1 %>% prune # Look at the fit: mod1 %>% fit # Compare to original (baseline) model: compare(baseline = mod0, adjusted = mod1) # We can also look at the parameters: mod1 %>% parameters # Or obtain the network as follows: getmatrix(mod1, "omega")