Structural Equation Modeling (SEM) using R-Project-based Lavaan, and Online calculator (R-Project-Shiny-based)
This online calculator has been developed using R-Project (4.4.1), RStudio 2025.05.0 Build 496. It is made using packages, including lavaan 0.6-19; Shiny; semPlot; shinethemes, and DT
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Structural Equation Modeling (SEM)
Structural Equation Modeling (SEM)
Structural Equation Modeling (SEM)
The SEM is a statistical technique that can help in looking at different variables and their relationship at the same time, rather than spending time on these variables and their relationship one by one
The SEM is a statistical technique that can help in looking a...
The SEM is a statistical technique that can help in looking at different variables and their relationship at the same time, rather than spending time on these variables and their relationship one by one
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Moreover, SEM can help in working on different types of equations, which can be considered important in assessing the relationship of variables, at the same time.
Moreover, SEM can help in working on different types of equat...
Moreover, SEM can help in working on different types of equations, which can be considered important in assessing the relationship of variables, at the same time.
This technique can also help in assessing different types of relationships, such as the effect of a single variable on another variable or the combined effect of more than one variable/s on some other variable/s
This technique can also help in assessing different types of ...
This technique can also help in assessing different types of relationships, such as the effect of a single variable on another variable or the combined effect of more than one variable/s on some other variable/s
Structural Equation Modeling (SEM).1047
Structural Equation Modeling (SEM)
Structural Equation Modeling (SEM)
ML – Maximum Likelihood
ML – Maximum Likelihood GLS - Generalized Least Squares WLS -...
· ML – Maximum Likelihood · GLS - Generalized Least Squares · WLS - Weighted Least Squares · ULS - Unweighted Least Squares · DWLS - Diagonally Weighted Least Squares
Different estimation methods to find the best-fitting parameters for a model
Different estimation methods to find the best-fitting paramet...
Different estimation methods to find the best -fitting parameters for a model
Estimators include
Estimators include
Estimators include
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ML - Maximum Likelihood
ML - Maximum Likelihood
ML - Maximum Likelihood
Multivariate normality of observed variables
Multivariate normality of observed variables
Multivariate normality of observed variables
Each option is suited for different types of data and assumptions about the distribution.
Each option is suited for different types of data and assumpt...
Each option is suited for different types of data and assumptions about the distribution.
Continuous variables with approximately normal distribution
Continuous variables with approximately normal distribution
Continuous variables with approximately normal distribution
Most common estimator
Most common estimator
Most common estimator
Assumes 1
Assumes
Assumes
Best for 1
Best for
Best for
Properties 1
Properties
Properties
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Cohen's d.1077
GLS - Generalized Least Squares
GLS - Generalized Least Squares
Multivariate normality
Multivariate normality
Multivariate normality
When error structure is known or can be modeled more accurately than ML
When error structure is known or can be modeled more accurate...
When error structure is known or can be modeled more accurately than ML
Similar to ML but uses a different weight matrix.
Similar to ML but uses a different weight matrix. Less robust...
Similar to ML but uses a different weight matrix. Less robust to violations of assumptions than ML.
Assumes 2
Assumes
Assumes
Best for 2
Best for
Best for
Properties 2
Properties
Properties
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WLS - Weighted Least Squares
WLS - Weighted Least Squares
WLS - Weighted Least Squares
Large sample size
Large sample size
Large sample size
Ordinal/categorical data (though rarely used now due to DWLS)
Ordinal/categorical data (though rarely used now due to DWLS)
Ordinal/categorical data (though rarely used now due to DWLS)
Uses full weight matrix (inverse of asymptotic covariance matrix of sample statistics).
Uses full weight matrix (inverse of asymptotic covariance mat...
Uses full weight matrix (inverse of asymptotic covariance matrix of sample statistics). Requires large samples; may fail or be unstable in small samples.
Assumes 3
Assumes
Assumes
Best for 3
Best for
Best for
Properties 3
Properties
Properties
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ULS - Unweighted Least Squares
ULS - Unweighted Least Squares
ULS - Unweighted Least Squares
No distributional assumptions (distribution-free)
No distributional assumptions (distribution-free)
No distributional assumptions (distribution -free)
Exploratory purposes or when robustness is desired
Exploratory purposes or when robustness is desired
Exploratory purposes or when robustness is desired
Doesn't use a weight matrix.
Doesn't use a weight matrix. Often leads to underestimation o...
Doesn't use a weight matrix. Often leads to underestimatio n of standard errors.
Assumes 4
Assumes
Assumes
Best for 4
Best for
Best for
Properties 4
Properties
Properties
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NORM.DIST Function.1129
DWLS - Diagonally Weighted Least Squares
DWLS - Diagonally Weighted Least Squares
DWLS - Diagonally Weighted Least Squares
Suitable for ordinal/categorical data
Suitable for ordinal/categorical data
Suitable for ordinal/ categorical data
Ordinal variables or non-normal continuous data
Ordinal variables or non-normal continuous data
Ordinal variables or non -normal continuous data
Uses only diagonal elements of the weight matrix (simpler, more stable than WLS).
Uses only diagonal elements of the weight matrix (simpler, mo...
Uses only diagonal elements of the weight matrix (simpler, more stable than WLS). Recommended in lavaan for ordinal data (e.g., Likert scales). Also returns robust standard errors and a mean - and variance -adjusted test statistic.
Assumes
Assumes
Assumes
Best for
Best for
Best for
Properties
Properties
Properties
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The model syntax
The model syntax
The model syntax
It is the main area of how you define measurement models (like CFA) and structural models (like SEM).
It is the main area of how you define measurement models (lik...
It is the main area of how you define measurement models (like CFA) and structural models (like SEM).
Latent variables (also called factors)
Latent variables (also called factors) Regression paths Covar...
· Latent variables (also called factors) · Regression paths · Covariances · Intercepts or means · (Optional) Constraints
Helps in specifying
Helps in specifying
Helps in specifying
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=~
=~
=~
Latent variable definition (factor loading)
Latent variable definition (factor loading)
Latent variable definition (factor loading)
F1 =~ x1 + x2 + x3
F1 =~ x1 + x2 + x3
F1 =~ x1 + x2 + x3
Operator
Operator
Operator
Meaning
Meaning
Meaning
Example
Example
Example
~
~
~
Regression (dependent ~ independent)
Regression (dependent ~ independent)
Regression (dependent ~ independent)
y ~ x1 + x2
y ~ x1 + x2
y ~ x1 + x2
~~
~~
~~
Covariance or variance
Covariance or variance
Covariance or variance
x1 ~~ x2 or
x1 ~~ x2 or x1 ~~ x1
x1 ~~ x2 or x1 ~~ x1
~1
~1
~1
Intercept or mean
Intercept or mean
Intercept or mean
x1 ~ 1
x1 ~ 1
x1 ~ 1
==
==
==
Constraint
Constraint
Constraint
x1 ~~ x2 == 0
x1 ~~ x2 == 0
x1 ~~ x2 == 0
*
*
*
Fix or label a parameter
Fix or label a parameter
Fix or label a parameter
F1 =~ 1*x1 or
F1 =~ 1*x1 or F1 =~ a*x2
F1 =~ 1*x1 or F1 =~ a*x2
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ability =~ item1 + item2 + item3 + item4
ability =~ item1 + item2 + item3 + item4
ability =~ item1 + item2 + item3 + item4
Confirmatory Factor Analysis (CFA)
Confirmatory Factor Analysis (CFA)
Confirmatory Factor Analysis (CFA)
syntax example
syntax example
syntax example
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One-factor model
One-factor model
One-factor model
Multiple Factors.1212
verbal =~ v1 + v2 + v3 math =~ m1 + m2 + m3
verbal =~ v1 + v2 + v3math =~ m1 + m2 + m3
Multiple Latent Variables
Multiple Latent Variables
Multiple Latent Variables
syntax example 2
syntax example
syntax example
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Multiple Factors
Multiple Factors
Multiple Factors
stress =~ s1 + s2 + s3
stress =~ s1 + s2 + s3 anxiety =~ a1 + a2 + a3
stress =~ s1 + s2 + s3anxiety =~ a1 + a2 + a3
Structural Equation Model (SEM)
Structural Equation Model (SEM)
Structural Equation Model (SEM)
syntax example 4
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Measurement model
Measurement model
Measurement model
anxiety ~ stress
anxiety ~ stress
anxiety ~ stress
syntax example 3
syntax example
syntax example
Structural model
Structural model
Structural model
y ~ x1 + x2.1247
y ~ x1 + x2
y ~ x1 + x2
Regression between Observed Variables
Regression between Observed Variables
Regression between Observed Variables
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syntax example 5
syntax example
syntax example
x1 ~~ x2
x1 ~~ x2
x1 ~~ x2
Covariances between Variables
Covariances between Variables
Covariances between Variables
syntax example 6
syntax example
syntax example
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Covariance between x1 and x2
Covariance between x1 and x2
Covariance between x1 and x2
x1 ~~ x1
x1 ~~ x1
x1 ~~ x1
syntax example 7
syntax example
syntax example
Variance of x1
Variance of x1
Variance of x1
factor1 ~~ factor2
factor1 ~~ factor2
factor1 ~~ factor2
Covariance between latent variables
Covariance between latent variables
Covariance between latent variables
syntax example 8
syntax example
syntax example
F1 =~ 1*x1 + x2 + x3
F1 =~ 1*x1 + x2 + x3
F1 =~ 1*x1 + x2 + x3
Fix a Loading or Set Equality Constraints
Fix a Loading or Set Equality Constraints
Fix a Loading or Set Equality Constraints
syntax example 9
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Fix loading of x1 to 1 (often done for scale)
Fix loading of x1 to 1 (often done for scale)
Fix loading of x1 to 1 (often done for scale)
F1 =~ a*x2 + a*x3
F1 =~ a*x2 + a*x3
F1 =~ a*x2 + a*x3
syntax example 10
syntax example
syntax example
Equal loading constraint (labeled 'a')
Equal loading constraint (labeled 'a')
Equal loading constraint (labeled 'a')
x1 ~ 1.1290
x1 ~ 1
x1 ~ 1
Means/Intercepts of Observed Variables
Means/Intercepts of Observed Variables
Means/Intercepts of Observed Variables
syntax example 11
syntax example
syntax example
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Estimate intercept/mean of x1
Estimate intercept/mean of x1
Estimate intercept/mean of x1
y ~ x1 + x2.1300
y ~ x1 + x2 x1 ~~ x2
y ~ x1 + x2x1 ~~ x2
Path Model with Observed Variables Only
Path Model with Observed Variables Only
Path Model with Observed Variables Only
syntax example 12
syntax example
syntax example
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F1 =~ x1 + x2 + x3.1310
F1 =~ x1 + x2 + x3
F1 =~ x1 + x2 + x3
Constraints on Parameters
Constraints on Parameters
Constraints on Parameters
syntax example 13
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x1 ~~ x2 == 0.1320
x1 ~~ x2 == 0
x1 ~~ x2 == 0
syntax example 14
syntax example
syntax example
Force zero covariance
Force zero covariance
Force zero covariance
Test statistic: 85.306 | Degrees of freedom = 24 | P-value (Chi-square) = 0.000
Test statistic: 85.306 | Degrees of freedom = 24 | P-value (C...
Test statistic: 85.306 | Degrees of freedom = 24 | P -value (Chi-square) = 0.000
Chi-square Test of Model Fit – User Model
Chi-square Test of Model Fit – User Model
Chi-square Test of Model Fit – User Model
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This test checks if the model-implied covariance = sample covariance.
This test checks if the model-implied covariance = sample cov...
This test checks if the model -implied covariance = sample covariance.
Significant p-value (p < 0.001) means poor fit if taken strictly, but Chi-square is sensitive to large sample sizes.
Significant p-value (p < 0.001) means poor fit if taken stric...
Significant p-value (p < 0.001) means poor fit if taken strictly, but Chi -square is sensitive to large sample sizes.
Don't rely on this alone — look at other fit indices.
Don't rely on this alone — look at other fit indices.
Don't rely on this alone — look at other fit indices.
Test statistic: 918.852 | Degrees of freedom = 36 | P-value (Chi-square) = 0.000
Test statistic: 918.852 | Degrees of freedom = 36 | P-value (...
Test statistic: 918.852 | Degrees of freedom = 36 | P -value (Chi-square) = 0.000
Model Test - Baseline Model
Model Test - Baseline Model
Model Test - Baseline Model
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The baseline model assumes no correlations between variables.
The baseline model assumes no correlations between variables.
The baseline model assumes no correlations between variables.
This model is much better than the baseline (918 vs. 85).
This model is much better than the baseline (918 vs. 85).
This model is much better than the baseline (918 vs. 85).
Comparative Fit Index (CFI)= 0.931 | Tucker-Lewis Index (TLI) = 0.896
Comparative Fit Index (CFI)= 0.931 | Tucker-Lewis Index (TLI)...
Comparative Fit Index (CFI)= 0.931 | Tucker -Lewis Index (TLI) = 0.896
Incremental Fit Indices
Incremental Fit Indices
Incremental Fit Indices
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CFI and TLI > 0.90 is good fit, > 0.95 is excellent fit.
CFI and TLI > 0.90 is good fit, > 0.95 is excellent fit.
CFI and TLI > 0.90 is good fit, > 0.95 is excellent fit.
CFI is good to excellent, TLI slightly below good.
CFI is good to excellent, TLI slightly below good.
CFI is good to excellent, TLI slightly below good.
It is a method to measure how well a statistical model fits the data.
It is a method to measure how well a statistical model fits t...
It is a method to measure how well a statistical model fits the data.
RMSEA = 0.092 | 90% CI: [0.071, 0.114]
RMSEA = 0.092 | 90% CI: [0.071, 0.114] P(RMSEA ≤ 0.05) = 0.00...
RMSEA = 0.092 | 90% CI: [0.071, 0.114] P(RMSEA ≤ 0.05) = 0.001 | P(RMSEA ≥ 0.08) = 0.840
Root Mean Square Error of Approximation (RMSEA)
Root Mean Square Error of Approximation (RMSEA)
Root Mean Square Error of Approximation (RMSEA)
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RMSEA as 0 = Perfect fit, ≤ 0.05 = Close fit, 0.05 - 0.08 = Reasonable fit, and ≥ 0.10 = Poor fit
RMSEA as 0 = Perfect fit, ≤ 0.05 = Close fit, 0.05 - 0.08 = R...
RMSEA as 0 = Perfect fit, ≤ 0.05 = Close fit, 0.05 - 0.08 = Reasonable fit, and ≥ 0.10 = Poor fit
RMSEA = 0.092 is high, so the fit is not great
RMSEA = 0.092 is high, so the fit is not great
RMSEA = 0.092 is high, so the fit is not great
A goodness-of-fit measure/test in SEM that is used to determine how well a model fits the population data
A goodness-of-fit measure/test in SEM that is used to determi...
A goodness-of-fit measure/test in SEM that is used to determine how well a model fits the population data
SRMR = 0.065
SRMR = 0.065
SRMR = 0.065
Standardized Root Mean Squared Residual (SRMR)
Standardized Root Mean Squared Residual (SRMR)
Standardized Root Mean Squared Residual (SRMR)
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SRMR as 0 = Perfect fit, < 0.08 = Good fit
SRMR as 0 = Perfect fit, < 0.08 = Good fit
SRMR as 0 = Perfect fit, < 0.08 = Good fit
SRMR is acceptable
SRMR is acceptable
SRMR is acceptable
The SRMR is also used to show how well a model fits the data. It is also considered a “badness of fit” measure.
The SRMR is also used to show how well a model fits the data....
The SRMR is also used to show how well a model fits the data. It is also considered a “ badness of fit” measure.
Loglikelihood user model (H0): -3737.745 | Akaike (AIC): 7517.49 | Bayesian (BIC): 7595.34
Loglikelihood user model (H0): -3737.745 | Akaike (AIC): 7517...
Loglikelihood user model (H0): -3737.745 | Akaike (AIC): 7517.49 | Bayesian (BIC): 7595.34
Loglikelihood and Information Criteria
Loglikelihood and Information Criteria
Loglikelihood and Information Criteria
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Lower AIC/BIC = better model (used for comparing different models).
Lower AIC/BIC = better model (used for comparing different mo...
Lower AIC/BIC = better model (used for comparing different models).
Not interpretable alone, but useful when comparing alternative models
Not interpretable alone, but useful when comparing alternativ...
Not interpretable alone, but useful when comparing alternative models
Akaike’s Information Criterion (AIC) and Bayesian Information Criterion (BIC) are the methods to choose the best statistical model
Akaike’s Information Criterion (AIC) and Bayesian Information...
Akaike’s Information Criterion (AIC) and Bayesian Information Criterion (BIC) are the methods to choose the best statistical model
visual =~ x1 (1.000), x2 (0.554), x3 (0.729)
visual =~ x1 (1.000), x2 (0.554), x3 (0.729)
visual =~ x1 (1.000), x2 (0.554), x3 (0.729)
Latent Variables (Factor Loadings)
Latent Variables (Factor Loadings)
Latent Variables (Factor Loadings)
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These tell how much each observed variable loads on its latent factor.
These tell how much each observed variable loads on its laten...
These tell how much each observed variable loads on its latent factor.
=~ means factor loading
=~ means factor loading
=~ means factor loading
x1 loads on visual with standardized loading of 0.772 → strong,
x1 loads on visual with standardized loading of 0.772 → stron...
x1 loads on visual with standardized loading of 0.772 → strong,x2 with 0.424 → moderate.All loadings are statistically significant (p < 0.001).
Std.all column = standardized loadings (like correlations)
Std.all column = standardized loadings (like correlations)
Std.all column = standardized loadings (like correlations)
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visual ~~ txt = 0.408 (Std.all = 0.459)
visual ~~ txt = 0.408 (Std.all = 0.459)
visual ~~ txt = 0.408 (Std.all = 0.459)
Covariances between Latent Variables
Covariances between Latent Variables
Covariances between Latent Variables
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These tell how much each observed variable loads on its latent factor.1432
These tell how much each observed variable loads on its laten...
These tell how much each observed variable loads on its latent factor.
Positive, significant covariances → latent traits are related
Positive, significant covariances → latent traits are related...
Positive, significant covariances → latent traits are related visual, txt, and speed are positively correlated.
Following results are from the Holzinger-Swineford example (data related to HolzingerSwineford1939) containing 301 observations...
Following results are from the Holzinger-Swineford example (d...
Following results are from the Holzinger-Swineford example (data related to HolzingerSwineford1939) containing 301 observations...
.x1 = 0.549 (Std.all = 0.404)
.x1 = 0.549 (Std.all = 0.404)
.x1 = 0.549 (Std.all = 0.404)
Variances of Observed Variables and Latents
Variances of Observed Variables and Latents
Variances of Observed Variables and Latents
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. before x1 means residual variance of x1.
. before x1 means residual variance of x1. Standardized resid...
. before x1 means residual variance of x1. Standardized residual of 0.404 = remaining unexplained variance (after accounting for latent factor).
visual = 0.809 (Std.all = 1.000)
visual = 0.809 (Std.all = 1.000)
visual = 0.809 (Std.all = 1.000)
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Variance of latent variable is fixed at 1 when standardized.
Variance of latent variable is fixed at 1 when standardized.
Variance of latent variable is fixed at 1 when standardized.
SEM Path Diagram
SEM Path Diagram
SEM Path Diagram
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SEM Path Diagram image
→
→
→
Single-headed arrow
Single-headed arrow
Single-headed arrow
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A directional relationship, such as:
A directional relationship, such as: Factor loading
A directional relationship, such as: Factor loading
(M1-M2)/SDpooled.1485
Circles (e.g., vsl, txt, spd)
Circles (e.g., vsl, txt, spd)
Overall Structure
Overall Structure
Overall Structure
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Latent variables (unobserved constructs):
Latent variables (unobserved constructs): vsl = Visual txt = ...
Latent variables (unobserved constructs): vsl = Visual txt = Textual spd = Speed
Squares (e.g., x1, x2, ..., x9)
Squares (e.g., x1, x2, ..., x9)
Squares (e.g., x1, x2, ..., x9)
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Observed variables (measured items)
Observed variables (measured items)
Observed variables (measured items)
Straight arrows (→) from latent to observed
Straight arrows (→) from latent to observed
Straight arrows (→) from latent to observed
Arrows
Arrows
Arrows
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Example: From vsl → x1, x2, x3
Example: From vsl → x1, x2, x3 Numbers near these arrows = St...
Example: From vsl → x1, x2, x3Numbers near these arrows = Standardized loadings (e.g., 0.77, 0.42, 0.58 for x1, x2, x3) Higher values (closer to 1) mean a stronger relationship between the factor and item.
These are factor loadings, showing how strongly a latent variable explains the observed variable.
These are factor loadings, showing how strongly a latent vari...
These are factor loadings, showing how strongly a latent variable explains the observed variable.
Curved arrows (↔) between latent variables
Curved arrows (↔) between latent variables
Curved arrows (↔) between latent variables
Arrows.1518
Arrows
Arrows
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Example: vsl ↔ txt = 0.46
Example: vsl ↔ txt = 0.46 txt ↔ spd = 0.28 vsl ↔ spd = 0.47 T...
Example: vsl ↔ txt = 0.46txt ↔ spd = 0.28vsl ↔ spd = 0.47 These values tell how much the factors are correlated. Values closer to 1 = strong positive relationship.
These represent covariances between latent variables
These represent covariances between latent variables
These represent covariances between latent variables
Curved arrows looping back to the same circle (e.g., vsl ↔ vsl)
Curved arrows looping back to the same circle (e.g., vsl ↔ vsl)
Curved arrows looping back to the same circle (e.g., vsl ↔ vsl)
Arrows.1531
Arrows
Arrows
Arrow 35
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Typically fixed to 1.00 for model identification in standardized solutions.
Typically fixed to 1.00 for model identification in standardi...
Typically fixed to 1.00 for model identification in standardized solutions.
These indicate the variance of the latent variable
These indicate the variance of the latent variable
These indicate the variance of the latent variable
Dotted arrows
Dotted arrows
Dotted arrows
Arrows.1544
Arrows
Arrows
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Low values = most of the variable is explained by the factor.
Low values = most of the variable is explained by the factor....
Low values = most of the variable is explained by the factor. High values = large portion unexplained.
These show residual variances (errors) — the part of the observed variable not explained by the latent variable.
These show residual variances (errors) — the part of the obse...
These show residual variances (errors) — the part of the observed variable not explained by the latent variable.
0.77, 0.42, etc
0.77, 0.42, etc
0.77, 0.42, etc
Number Type
Number Type
Number Type
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They represent Standardized factor loadings
They represent Standardized factor loadings
They represent Standardized factor loadings
On straight arrows from latent to observed
On straight arrows from latent to observed
On straight arrows from latent to observed
0.46, 0.28, etc
0.46, 0.28, etc
0.46, 0.28, etc
Number Type.1570
Number Type
Number Type
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They represent covariances/correlations between latent factors
They represent covariances/correlations between latent factors
They represent covariances/correlations between latent factors
On curved arrows between latent variables
On curved arrows between latent variables
On curved arrows between latent variables
0.40, 0.82, etc
0.40, 0.82, etc
0.40, 0.82, etc
Number Type.1583
Number Type
Number Type
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They represent residual variances/errors of observed variables
They represent residual variances/errors of observed variables
They represent residual variances/errors of observed variables
Near arrows looping to observed vars
Near arrows looping to observed vars
Near arrows looping to observed vars
1.00
1.00
1.00
Number Type.1596
Number Type
Number Type
Arrow 40
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Fixed latent variances for model identification
Fixed latent variances for model identification
Fixed latent variances for model identification
On looping arrows at latent vars
On looping arrows at latent vars
On looping arrows at latent vars
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Example data - Holzinger-Swineford example
The model syntax used...
The model syntax used...
The model syntax used...
visual =~ x1 + x2 + x3
visual =~ x1 + x2 + x3 txt =~ x4 + x5 + x6 speed =~ x7 + x8 +...
visual =~ x1 + x2 + x3txt =~ x4 + x5 + x6 speed =~ x7 + x8 + x9
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Lavaan model syntax area
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