Structural equation modeling (SEM) has a long history of representing models graphically as path diagrams. This article presents the freely available semPlot package for R, which fills the gap ...between advanced, but time-consuming, graphical software and the limited graphics produced automatically by SEM software. In addition, semPlot offers more functionality than drawing path diagrams: It can act as a common ground for importing SEM results into R. Any result usable as input to semPlot can also be represented in any of the 3 popular SEM frameworks, as well as translated to input syntax for the R packages sem (Fox, Nie, & Byrnes, 2013) and lavaan (Rosseel, 2012). Special considerations are made in the package for the automatic placement of variables, using 3 novel algorithms that extend the earlier work of Boker, McArdle, and Neale (2002). The article concludes with detailed instructions on these node-placement algorithms.
The estimation of the correct number of dimensions is a long-standing problem in psychometrics. Several methods have been proposed, such as parallel analysis (PA), Kaiser-Guttman's ...eigenvalue-greater-than-one rule, multiple average partial procedure (MAP), the maximum-likelihood approaches that use fit indexes as BIC and EBIC and the less used and studied approach called very simple structure (VSS). In the present paper a new approach to estimate the number of dimensions will be introduced and compared via simulation to the traditional techniques pointed above. The approach proposed in the current paper is called exploratory graph analysis (EGA), since it is based on the graphical lasso with the regularization parameter specified using EBIC. The number of dimensions is verified using the walktrap, a random walk algorithm used to identify communities in networks. In total, 32,000 data sets were simulated to fit known factor structures, with the data sets varying across different criteria: number of factors (2 and 4), number of items (5 and 10), sample size (100, 500, 1000 and 5000) and correlation between factors (orthogonal, .20, .50 and .70), resulting in 64 different conditions. For each condition, 500 data sets were simulated using lavaan. The result shows that the EGA performs comparable to parallel analysis, EBIC, eBIC and to Kaiser-Guttman rule in a number of situations, especially when the number of factors was two. However, EGA was the only technique able to correctly estimate the number of dimensions in the four-factor structure when the correlation between factors were .7, showing an accuracy of 100% for a sample size of 5,000 observations. Finally, the EGA was used to estimate the number of factors in a real dataset, in order to compare its performance with the other six techniques tested in the simulation study.
We introduce the network model as a formal psychometric model, conceptualizing the covariance between psychometric indicators as resulting from pairwise interactions between observable variables in a ...network structure. This contrasts with standard psychometric models, in which the covariance between test items arises from the influence of one or more common latent variables. Here, we present two generalizations of the network model that encompass latent variable structures, establishing network modeling as parts of the more general framework of structural equation modeling (SEM). In the first generalization, we model the covariance structure of latent variables as a network. We term this framework latent network modeling (LNM) and show that, with LNM, a unique structure of conditional independence relationships between latent variables can be obtained in an explorative manner. In the second generalization, the residual variance–covariance structure of indicators is modeled as a network. We term this generalization residual network modeling (RNM) and show that, within this framework, identifiable models can be obtained in which local independence is structurally violated. These generalizations allow for a general modeling framework that can be used to fit, and compare, SEM models, network models, and the RNM and LNM generalizations. This methodology has been implemented in the free-to-use software package
lvnet
, which contains confirmatory model testing as well as two exploratory search algorithms: stepwise search algorithms for low-dimensional datasets and penalized maximum likelihood estimation for larger datasets. We show in simulation studies that these search algorithms perform adequately in identifying the structure of the relevant residual or latent networks. We further demonstrate the utility of these generalizations in an empirical example on a personality inventory dataset.
Methodological developments and software implementations are progressing at an increasingly fast pace. The introduction and widespread acceptance of preprint archived reports and open-source software ...have made state-of-the-art statistical methods readily accessible to researchers. At the same time, researchers are increasingly concerned that their results should be reproducible (i.e., the same analysis should yield the same numeric results at a later time), which is a basic requirement for assessing the results’ replicability (i.e., whether results at a later time support the same conclusions). Although this age of fast-paced methodology greatly facilitates reproducibility and replicability, it also undermines them in ways not often realized by researchers. This article draws researchers’ attention to these threats and proposes guidelines to help minimize their impact. Reproducibility may be influenced by software development and change over time, a problem that is greatly compounded by the rising dependency between software packages. Replicability is affected by rapidly changing standards, researcher degrees of freedom, and possible bugs or errors in code, whether introduced by software developers or empirical researchers implementing an analysis. This article concludes with a list of recommendations to improve the reproducibility and replicability of results.
Network models, in which psychopathological disorders are conceptualized as a complex interplay of psychological and biological components, have become increasingly popular in the recent ...psychopathological literature (Borsboom, et. al., 2011). These network models often contain significant numbers of unknown parameters, yet the sample sizes available in psychological research are limited. As such, general assumptions about the true network are introduced to reduce the number of free parameters. Incorporating these assumptions, however, means that the resulting network will lead to reflect the particular structure assumed by the estimation method-a crucial and often ignored aspect of psychopathological networks. For example, observing a sparse structure and simultaneously assuming a sparse structure does not imply that the true model is, in fact, sparse. To illustrate this point, we discuss recent literature and show the effect of the assumption of sparsity in three simulation studies.
We discuss the Gaussian graphical model (GGM; an undirected network of partial correlation coefficients) and detail its utility as an exploratory data analysis tool. The GGM shows which variables ...predict one-another, allows for sparse modeling of covariance structures, and may highlight potential causal relationships between observed variables. We describe the utility in three kinds of psychological data sets: data sets in which consecutive cases are assumed independent (e.g., cross-sectional data), temporally ordered data sets (e.g., n = 1 time series), and a mixture of the 2 (e.g., n > 1 time series). In time-series analysis, the GGM can be used to model the residual structure of a vector-autoregression analysis (VAR), also termed graphical VAR. Two network models can then be obtained: a temporal network and a contemporaneous network. When analyzing data from multiple subjects, a GGM can also be formed on the covariance structure of stationary means-the between-subjects network. We discuss the interpretation of these models and propose estimation methods to obtain these networks, which we implement in the R packages graphicalVAR and mlVAR. The methods are showcased in two empirical examples, and simulation studies on these methods are included in the supplementary materials.
Abstract Background The symptoms for Major Depression (MD) defined in the DSM-5 differ markedly from symptoms assessed in common rating scales, and the empirical question about core depression ...symptoms is unresolved. Here we conceptualize depression as a complex dynamic system of interacting symptoms to examine what symptoms are most central to driving depressive processes. Methods We constructed a network of 28 depression symptoms assessed via the Inventory of Depressive Symptomatology (IDS-30) in 3,463 depressed outpatients from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. We estimated the centrality of all IDS-30 symptoms, and compared the centrality of DSM and non-DSM symptoms; centrality reflects the connectedness of each symptom with all other symptoms. Results A network with 28 intertwined symptoms emerged, and symptoms differed substantially in their centrality values. Both DSM symptoms (e.g., sad mood) and non-DSM symptoms (e.g., anxiety) were among the most central symptoms, and DSM criteria were not more central than non-DSM symptoms. Limitations Many subjects enrolled in STAR*D reported comorbid medical and psychiatric conditions which may have affected symptom presentation. Conclusion The network perspective neither supports the standard psychometric notion that depression symptoms are equivalent indicators of MD, nor the common assumption that DSM symptoms of depression are of higher clinical relevance than non-DSM depression symptoms. The findings suggest the value of research focusing on especially central symptoms to increase the accuracy of predicting outcomes such as the course of illness, probability of relapse, and treatment response.
A growing number of publications focus on estimating Gaussian graphical models (GGM, networks of partial correlation coefficients). At the same time, generalizibility and replicability of these ...highly parameterized models are debated, and sample sizes typically found in datasets may not be sufficient for estimating the underlying network structure. In addition, while recent work emerged that aims to compare networks based on different samples, these studies do not take potential cross-study heterogeneity into account. To this end, this paper introduces methods for estimating GGMs by aggregating over multiple datasets. We first introduce a general maximum likelihood estimation modeling framework in which all discussed models are embedded. This modeling framework is subsequently used to introduce meta-analytic Gaussian network aggregation (MAGNA). We discuss two variants: fixed-effects MAGNA, in which heterogeneity across studies is not taken into account, and random-effects MAGNA, which models sample correlations and takes heterogeneity into account. We assess the performance of MAGNA in large-scale simulation studies. Finally, we exemplify the method using four datasets of post-traumatic stress disorder (PTSD) symptoms, and summarize findings from a larger meta-analysis of PTSD symptom.
Bayesian parameter estimation and Bayesian hypothesis testing present attractive alternatives to classical inference using confidence intervals and
p
values. In part I of this series we outline ten ...prominent advantages of the Bayesian approach. Many of these advantages translate to concrete opportunities for pragmatic researchers. For instance, Bayesian hypothesis testing allows researchers to quantify evidence and monitor its progression as data come in, without needing to know the intention with which the data were collected. We end by countering several objections to Bayesian hypothesis testing. Part II of this series discusses JASP, a free and open source software program that makes it easy to conduct Bayesian estimation and testing for a range of popular statistical scenarios (Wagenmakers et al.
this issue
).
•Network analysis can foster novel insights in personality psychology.•We provide an overview of network analysis.•We show how R can be used to analyze personality networks.•We show how to simulate ...personality networks in R.
Network analysis represents a novel theoretical approach to personality. Network approaches motivate alternative ways of analyzing data, and suggest new ways of modeling and simulating personality processes. In the present paper, we provide an overview of network analysis strategies as they apply to personality data. We discuss different ways to construct networks from typical personality data, show how to compute and interpret important measures of centrality and clustering, and illustrate how one can simulate on networks to mimic personality processes. All analyses are illustrated using a data set on the commonly used HEXACO questionnaire using elementary R-code that readers may easily adapt to apply to their own data.
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