semPaths  R Documentation 
This function creates a path diagram of a SEM model (or general linear model), which is then plotted using qgraph
. Currently many different SEM programs and packages are supported. Please see my website (www.sachaepskamp.com) for more details on which packages are supported and what is supported for each package.
semPaths(object, what = "paths", whatLabels, style, layout = "tree", intercepts = TRUE, residuals = TRUE, thresholds = TRUE, intStyle = "multi", rotation = 1, curve, curvature = 1, nCharNodes = 3, nCharEdges = 3, sizeMan = 5, sizeLat = 8, sizeInt = 2, sizeMan2, sizeLat2, sizeInt2, shapeMan, shapeLat, shapeInt = "triangle", ask, mar, title, title.color = "black", title.adj = 0.1, title.line = 1, title.cex = 0.8, include, combineGroups = FALSE, manifests, latents, groups, color, residScale, gui = FALSE, allVars = FALSE, edge.color, reorder = TRUE, structural = FALSE, ThreshAtSide = FALSE, thresholdColor, thresholdSize = 0.5, fixedStyle = 2, freeStyle = 1, as.expression = character(0), optimizeLatRes = FALSE, inheritColor = TRUE, levels, nodeLabels, edgeLabels, pastel = FALSE, rainbowStart = 0, intAtSide, springLevels = FALSE, nDigits = 2, exoVar, exoCov = TRUE, centerLevels = TRUE, panelGroups = FALSE, layoutSplit = FALSE, measurementLayout = "tree", subScale, subScale2, subRes = 4, subLinks, modelOpts = list(mplusStd = "std"), curveAdjacent = '<>', edge.label.cex = 0.6, cardinal = "none", equalizeManifests = FALSE, covAtResiduals = TRUE, bifactor, optimPoints = 1:8 * (pi/4), ...)
object 
A 
what 
What should the edges indicate in the path diagram? This function uses

whatLabels 
What should the edge labels indicate in the path diagram? This function uses

style 
The style to use. Currently only indicates what the (residual) variances look like. Use 
layout 
A string indicating how the nodes should be placed. Similar to the 'layout' argument in

intercepts 
Logical, should intercepts be included in the path diagram? 
residuals 
Logical, should residuals (and variances) be included in the path diagram? 
thresholds 
Logical, should thresholds be included in the path diagram? 
intStyle 
Style of the intercepts. 
rotation 
An integer indicating the rotation of the layout when "tree" or "tree2" layout is used. 1, 2, 3 and 4 indicate that exogenous variables are placed at the top, left side, bottom and right side respectively. 
curve 
The curvature of the edges. In tree layouts this argument only curves the edges that are between nodes on the same level. e.g., correlations between exogenous manifest variables. 
curvature 
Sets the strength of scaling in curvature for curved edges at the same horizontal level in tree layouts. The curve will be set to 
nCharNodes 
Number of characters to abbreviate node labels to (using 
nCharEdges 
Number of characters to abbreviate edge labels to (using 
sizeMan 
Width of the manifest nodes, sent to the 'vsize' argument in 
sizeLat 
Width of the latent nodes, sent to the 'vsize' argument in 
sizeInt 
Width of the unit vector nodes, sent to the 'vsize' argument in 
sizeMan2 
Height of the manifest nodes, sent to the 'vsize2' argument in 
sizeLat2 
Height of the latent nodes, sent to the 'vsize2' argument in 
sizeInt2 
Height of the unit vector nodes, sent to the 'vsize2' argument in 
shapeMan 
Shape of the manifest nodes, sent to the 'shape' argument in 
shapeLat 
Shape of the latent nodes, sent to the 'shape' argument in 
shapeInt 
Shape of the constant nodes, sent to the 'shape' argument in 
ask 
Specifies the 'ask' parameter in 
mar 
Same as the 'mar' argument in 
title 
Logical, should titles be plotted of the group names above each plot? 
title.color 
Color of the titles. 
title.adj 
Adjustment of title as used by 
title.line 
Line of title as used by 
title.cex 
Size of title as used by 
include 
Integer vector indicating which groups should be included in the output. e.g., to only plot a diagram for the first group use 
combineGroups 
Logical. If TRUE all groups are combined in the same path diagram. 
manifests 
A character vector in which every element is the name of a manifest variable in the model. This argument can be used to overwrite the order in which nodes are plotted in the graph if 
latents 
A character vector in which every element is the name of a latent variable in the model. This argument can be used to overwrite the order in which nodes are plotted in the graph if 
groups 
Groups nodes that should be colored the same, similar to the 'groups' argument in In addition, this argument can be assigned a single character: "manifests", "latents" or "both" to make a single group for each manifest, latent or both manifest and latent variables. e.g., 
color 
Controls the color of nodes. Similar to 'color' in

residScale 
The size of residual edges if 
gui 
Not yet implemented. 
allVars 
Logical. If TRUE all variables are plotted in the path diagrams for each group. If FALSE only variables are plotted that are used in the group. 
edge.color 
A value indicating the color of all edges or a vector indicating the color of each edge. Useful for manually overwriting edge colors. 
reorder 
Logical. Should manifest variables be reordered to be near latent factors they are most connected to in the "tree" layout? If FALSE manifest variables are placed in the order they appear in the Pars. 
structural 
Logical. Set this to TRUE to only show the structural model (omit all manifest variables.) 
ThreshAtSide 
Logical. If TRUE, thresholds are plotted as small lines at the side of manifest nodes, otherwise they are plotted as lines inside the nodes. 
thresholdColor 
Color of the threshold lines. Defaults to "black" 
thresholdSize 
Size of threshold bars relative to the size of the node. 
fixedStyle 
A vector of length one or two specifying the color and line type (same as 'lty' in For example, 
freeStyle 
Same as 'fixedStyle' but for free parameters instead. 
as.expression 
A character vector indicating which labels should be treated as an 
optimizeLatRes 
Logical. If this is TRUE, the angle of the incoming residuals on latent variables is attempted to be optimally chosen so its position conflicts with the least amount of connected edges. 
inheritColor 
Logical, should uncolored nodes obtain a mix of connected colored nodes? Defaults to 
levels 
A numeric vector usually of length 4. Controls the relative vertical position of variable levels (exogenous and endogenous latents and manifests) under default rotation in tree and circle layouts. This can be used to control the spacing between these levels. e.g., 
nodeLabels 
A vector or list to manually overwrite the node labels. Can include expressions. 
edgeLabels 
A vector or list to manually overwrite the edge labels. Can include expressions. 
pastel 
Logical, should default colors (for groups or edge equality constraints) be chosen from pastel colors? If TRUE then 
rainbowStart 
A number between 0 and 1 indicating the offset used in rainbow functions for default node coloring. 
exoVar 
Should variances of truely exogenous variables (no incomming directed edge) be plotted? Defaults to 
intAtSide 
Logical to control if intercepts should be plotted to the side of manifest nodes or at the bottom/top. Defaults only to FALSE if 'residuals=FALSE'. 
springLevels 
Logical indicating if the placement on horizontal levels with 
nDigits 
Number of digits to round numeric values to. 
exoCov 
Should covariances between truely exogenous variables (no incomming directed edge) be plotted? Defaults to 
centerLevels 
Only used if 
panelGroups 
Logical to automatically create a panel plot of multiple group models. Defaults to FALSE. 
layoutSplit 
Logical that can be used to split computing of layout between structural and measurment models. This is very useful in more complicated models where the structural part is best shown by using a spring layout. 
measurementLayout 
Logical indicating the layout algorithm to use for measurement models if 
subScale 
Width of submodels (measurment models) if 
subScale2 
Height of submodels (measurment models) if 
subRes 
Integer indicating the resolution of which measurment models can be rotated around their corresponding latent variable. The default, 4, indicates that they can be placed only to polar coordinates. Set to 360 to allow every angle of rotation. 
subLinks 
Vector of variables to link to. Currently not well supported so avoid using this argument. 
modelOpts 
A lists containing arguments sent to 
curveAdjacent 
What edges between adjacent horizontal nodes be curved? Can be 
edge.label.cex 
Controls the font size of the edge labels. Same as in 
cardinal 
Should edges in a tree layout connect to the four cardinal points of one of the borders of the node rather than point to the center of the node? Can be set to 
equalizeManifests 
Logical. Should the distances between manifest nodes in the 
covAtResiduals 
Logical, should covariances be drawn at the start of residuals when 
bifactor 
A string vector containing the name(s) of the general bifactor(s). This will automatically create a bifactor plot. 
optimPoints 
A vector of radians residuals can optimize to if 
... 
Arguments sent to the

The default "tree"
layout under default rotation places the nodes in one of four horizontal levels. At the top the exogenous manifest variables, under that the exogenous latent variables, under that the endogenous latent variables and at the bottom the endogenous manifest variables. If one of these kinds of variables does not exist its level is omitted. Afterwards, the rotation
argument will rotate the graph and the "circle"
layout will make the layout circular using these levels as nested circles.
If not manually set (see semPlotModeledit
), semPath
will automatically try to set the endogenous and exogenous variables, such that the resulting layout looks good. A latent variable is identified as exogenous if it is not on the right hand side of a directed edge (>
or ~>
) with another latent variable as node of origin. A manifest variable is set as exogenous if it is only connected, in any way, to exogenous latent variables and if it is not the right hand side (dependent variable) of a regression edge (~>
). If all variables are set to exogenous this way, they are all set to endogenous for consistency in the layouts. Afterwards, manifest variables only used in formative measurement models (only outgoing directed edges to latents) are set to exogenous again so that MIMIC models are displayed properly.
Intercepts are placed on the same level as the variable, either on the left or right side of the node (pointing outward from the center). Residuals for manifest variables are placed at the top or bottom (for exogenous and endogenous manifests respectively). Residuals of latents are placed at the bottom or top respectively for exogenous and endogenous variables, but is switched if the latent is not connected to a manifest. Residuals for the leftmost and rightmost latent are placed at the left and right side respectively, or diagonal if the latent is connected to an intercept.
The "tree2"
and "circle2"
layouts call the layout.reingold.tilford
function from the igraph
package. As roots are used the first available variables of the following list:
Intercepts of exogenous manifests
Exogenous manifest
Intercepts of exogenous latents
Exogenous latents
Interceots of endogenous latents
Endogenous latents
Intercepts of endogenous manifests
The endogenous manifest with the most outgoing edges (this should not be possible by default, but can be manually set)
The most connected endogenous manigest.
To compute an optimal layout layout.reingold.tilford
is run on a slightly altered version of the path diagram. In this version, the direction of edges from all intercepts that are not roots is reversed, the direction of all edges leading to exogenous manifests is reversed and all bidirectional edges are removed.
A "qgraph"
object as returned by qgraph
. This object can be used to alter the graph (such as manually redefining the layout) and to plot the graph again with different arguments.
If there are multiple groups a list is returned with a "qgraph" object for each path diagram that has been produced.
Sacha Epskamp <mail@sachaepskamp.com>
Fruchterman, T. & Reingold, E. (1991). Graph drawing by forcedirected placement. Software  Pract. Exp. 21, 11291164.
Reingold, E and Tilford, J (1981). Tidier drawing of trees. IEEE Trans. on Softw. Eng., SE7(2):223228.
Csardi G, Nepusz T (2006). The igraph software package for complex network research, InterJournal, Complex Systems 1695. http://igraph.sf.net
qgraph
semPlotModel
semPlotModelclass
semCors
lisrelModel
semSyntax
# Regression analysis with interaction effects  # A silly dataset: X < rnorm(100) Y < rnorm(100) Z < rnorm(1)*X + rnorm(1)*Y + rnorm(1)*X*Y DF < data.frame(X,Y,Z) # Regression including interaction: res < lm(Z ~ X*Y, data = DF) # Path diagram: semPaths(res, intAtSide=TRUE) # Standardized estimates: semPaths(res,"std","hide", intAtSide=TRUE) # Simple CFA  library("lavaan") example(cfa) semPaths(fit, 'std', 'est', curveAdjacent = TRUE, style = "lisrel") # MIMIC model  ## Lavaan ## Not run: library("lavaan") # Example 5.8 from mplus user guide: Data < read.table("http://www.statmodel.com/usersguide/chap5/ex5.8.dat") names(Data) < c(paste("y", 1:6, sep=""), paste("x", 1:3, sep="")) # Model: model.Lavaan < 'f1 =~ y1 + y2 + y3 f2 =~ y4 + y5 + y6 f1 + f2 ~ x1 + x2 + x3 ' # Run Lavaan: library("lavaan") fit < lavaan:::cfa(model.Lavaan, data=Data, std.lv=TRUE) # Plot path diagram: semPaths(fit,title=FALSE) # Omit exogenous covariances: semPaths(fit,title=FALSE, exoVar = FALSE, exoCov = FALSE) # Standardized parameters: semPaths(fit,"std", edge.label.cex = 0.5, exoVar = FALSE, exoCov = FALSE) ## Mplus # Same model, now using mplus output: outfile < tempfile(fileext=".out") download.file("http://www.statmodel.com/usersguide/chap5/ex5.8.html",outfile) # Plot model: semPaths(outfile,intercepts=FALSE) # Note that mplus did not report the fixed variances of the exogenous variables. # Thresholds  ## Lavaan # Example 5.8 from mplus user guide: Data < read.table("http://www.statmodel.com/usersguide/chap5/ex5.2.dat") names(Data) < c("u1","u2","u3","u4","u5","u6") Data < as.data.frame(lapply(Data, ordered)) # Lavaan model: model < ' f1 =~ u1 + u2 + u3; f2 =~ u4 + u5 + u6 ' # Run Lavaan: fit < lavaan::cfa(model, data=Data) # Plot path diagram: semPaths(fit,intercepts=FALSE) ## Mplus # Same model, now using mplus output: outfile < tempfile(fileext=".out") download.file("http://www.statmodel.com/usersguide/chap5/ex5.2.html",outfile) # Plot model: semPaths(outfile) # OpenMx  # To install OpenMx see: # http://openmx.psyc.virginia.edu/ library("OpenMx") # Example from mxRun help page: # Create and run the 1factor CFA on the openmx.psyc.virginia.edu front page data(demoOneFactor) # load the demoOneFactor dataframe manifests < names(demoOneFactor) # set the manifest to the 5 demo variables latents < c("G") # define 1 latent variable model < mxModel("One Factor", type="RAM", manifestVars = manifests, latentVars = latents, mxPath(from=latents , to=manifests), mxPath(from=manifests, arrows=2), mxPath(from=latents , arrows=2, free=FALSE, values=1.0), mxData(cov(demoOneFactor), type="cov", numObs=500) ) model < mxRun(model) #run model, returning the result # Plot with colors from OpenMx front page: semPaths(model, color = list( lat = rgb(245, 253, 118, maxColorValue = 255), man = rgb(155, 253, 175, maxColorValue = 255)), mar = c(10, 5, 10, 5)) ## Factor Analysis: source("http://openmx.ssri.psu.edu/docs/OpenMx/latest/_static/demo/TwoFactorModel_PathCov.R") semPaths(twoFactorFit, layout = "tree2") # Multigroup analysis  ## LISREL: # Download measurment invariance example: modFile < tempfile(fileext=".OUT") download.file("http://sachaepskamp.com/files/mi1.OUT",modFile) layout(t(1:2)) semPaths(modFile,"eq",ask=FALSE, intAtSide = TRUE, mar = c(8, 1, 5, 1)) # Color indicates equality constraints. ## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.