Plot path diagram for SEM models.

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Description

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.

Usage

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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(), curveAdjacent = '<->', 
  edge.label.cex = 0.6,  cardinal = "none", equalizeManifests = FALSE, 
  covAtResiduals = TRUE, bifactor, optimPoints = 1:8 * (pi/4), ...)

Arguments

object

A "semPlotModel" object or any of the input types that can be used in semPlotModel directly.

what

What should the edges indicate in the path diagram? This function uses grepl to allow fuzzy matching and is not case sensitive. E.g., par will also match Parameters.

path, diagram or mod

This will display the model as an unweighted network (gray edges by default).

est or par

This will display the parameter estimates as weighted edges.

stand or std

This will display the standardized parameter estimates, if available, as weighted edges.

eq or cons

This is the same graph as path. except that parameters with equality constraints are now colored. Parameters with the same color are constrained to be equal.

col

This will create an unweighted graph of the path diagram, where edges are colored with a mix of the colors of connected nodes.

whatLabels

What should the edge labels indicate in the path diagram? This function uses grepl to allow fuzzy matching and is not case sensitive. E.g., par will also match Parameters. Default depends on the what argument, defaulting to the respective elements in the list below for values of what in the list above.

name, label, path or diagram

This will display the edge names as labels.

est or par

This will display the parameter estimate in edge labels.

stand or std

This will display the standardized parameter estimate in edge labels.

eq or cons

This will display the parameter number in edge labels. 0 indicates the parameter is fixed, parameters with the same parameter number are constrained to be equal.

no, omit, hide or invisible

Hides edge labels.

style

The style to use. Currently only indicates what the (residual) variances look like. Use "ram", "mx" or "OpenMx" for double headed selfloops and "lisrel" for single headed edges with no node as origin. Defaults to "ram" unless the input is a lisrel model.

layout

A string indicating how the nodes should be placed. Similar to the 'layout' argument in qgraph. Can be one of the following strings.

tree

The integrated tree-like layout. Places exogenous variables at the top and endogenous variables at the bottom. See 'details' for more details.

circle

The same layout as "tree", except that afterwards the horizontal levels of the layout are placed in circles. Especially useful for models with a large number of manifest variables and a relatively small number of latent variables.

spring

Calls the "spring" layout in qgraph, which uses the Fruchterman-reingold algorithm (Fruchterman & Reingold, 1991).

tree2

Calls the layout.reingold.tilford function from the igraph package (Csardi & Nepusz, 2006), which uses the Reingold-Tilford algorithm (Reingold & Tilford, 1981). Before calling the algorithm roots are chosen and a slightly modified version of the graph is used to produce consistent results. See 'details'.

circle2

The same layout as "tree2", except that afterwards the horizontal levels of the layout are placed in circles.

Other options

If the assigned value is not in this list it is sent to qgraph. This allows for manual specification of the layout as well as using functions found in the 'igraph; library.

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. "multi" plots a separate unit vector node for each intercept and "single" plots a single unit vector node. Currently, "single" is not well supported and might lead to unexpected results.

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 curve + curvature * n / max(n), where n is the number of nodes in between the two connected nodes.

nCharNodes

Number of characters to abbreviate node labels to (using abbreviate). Set to 0 to omit abbreviation.

nCharEdges

Number of characters to abbreviate edge labels to (using abbreviate). Set to 0 to omit abbreviation.

sizeMan

Width of the manifest nodes, sent to the 'vsize' argument in qgraph.

sizeLat

Width of the latent nodes, sent to the 'vsize' argument in qgraph.

sizeInt

Width of the unit vector nodes, sent to the 'vsize' argument in qgraph.

sizeMan2

Height of the manifest nodes, sent to the 'vsize2' argument in qgraph.

sizeLat2

Height of the latent nodes, sent to the 'vsize2' argument in qgraph.

sizeInt2

Height of the unit vector nodes, sent to the 'vsize2' argument in qgraph.

shapeMan

Shape of the manifest nodes, sent to the 'shape' argument in qgraph. Defaults to "square" or "rectangle" if width and height differ.

shapeLat

Shape of the latent nodes, sent to the 'shape' argument in qgraph. Defaults to "circle" or "ellipse" if width and height differ.

shapeInt

Shape of the constant nodes, sent to the 'shape' argument in qgraph. Defaults to "triangle".

ask

Specifies the 'ask' parameter in par. Defaults to TRUE if multiple groups are in the model.

mar

Same as the 'mar' argument in qgraph. By default this argument is based on the values of 'rotation', 'style' and 'title'.

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 'adj' in par.

title.line

Line of title as used by 'line' in title.

title.cex

Size of title as used by 'cex.main' in par.

include

Integer vector indicating which groups should be included in the output. e.g., to only plot a diagram for the first group use include = 1.

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 reorder = FALSE

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 reorder = FALSE

groups

Groups nodes that should be colored the same, similar to the 'groups' argument in qgraph with a few exceptions. Should be a list containing in each element the names (instead of numbers as in qgraph) of nodes that belong together. Nodes that are indicated to belong to a group will be assigned the same color, as given by the 'color' argument. Nodes not belonging to a group will be assigned the color "", which indicates that they will inherit a mix of the colors of connected nodes (or white, if no connected nodes are colored.)

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., groups = "latents" will color each latent variable uniquely, and color all manifest variables a mixture of the colors of latents they load on.

color

Controls the color of nodes. Similar to 'color' in qgraph. A color vector indicating the color for each group, a single color character indicating the color for all nodes or a color vector indicating the color for each node separately. Can also be a list contaning one or more of the following elements (using fuzzy matching):

man

The colors for manifest nodes

lat

The colors for latent nodes

int

The color for intercepts

residScale

The size of residual edges if style = "lisrel". Defaults to two times the value of 'sizeMan'.

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 FALSE 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 par) of fixed parameters. Can be both character and numeric. If one of the elements encodes a color it is used to overwrite the color of fixed edges, and if an element can be coerced to a numeric it is used to encode the line type.

For example, fixedStyle = c("red",3) specifies that all fixed parameters should be visualized with a red edge with lty=3

freeStyle

Same as 'fixedStyle' but for free parameters instead.

as.expression

A character vector indicating which labels should be treated as an expression, so that mathematical notation and Greek letters can be used in the path diagram. If this vector contains "nodes" all node labels are converted to expressions, and if this vector contains "edges" all node labels are converted to expressions. Defaults to "edges" only if the input is a Lisrel model.

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 TRUE.

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., c(1,5,6,7) will create more space between endogenous manifests and latents.

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 rainbow_hcl is used.

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 TRUE unless style = "lisrel".

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 tree3 layout should be determined by a force embedded algorithm.

nDigits

Number of digits to round numeric values to.

exoCov

Should covariances between truely exogenous variables (no incomming directed edge) be plotted? Defaults to TRUE.

centerLevels

Only used if layout is set to "tree2", should each level be centered? Defaults to TRUE

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 layoutSplit = TRUE (the structural model will obtain a layout given by the layout argument).

subScale

Width of submodels (measurment models) if layoutSplit = TRUE.

subScale2

Height of submodels (measurment models) if layoutSplit = TRUE.

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 semPlotModel in case the input is not of class semPlotModel.

curveAdjacent

What edges between adjacent horizontal nodes be curved? Can be '<->' or 'cov' to indicate bidirectional covariances, '->' or 'reg' for directed regressions or a vector containing both.

edge.label.cex

Controls the font size of the edge labels. Same as in qgraph except that the default is now 0.8.

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 TRUE or "all" to enamble this behavior for all edges and FALSE or "none" to disable this behavior for all edges. Alternatively a vector with strings can be specified in which each string specifies a certain group of edges. Fuzzy matching is used on the strings "exo" for edges with the first node being exogenous (or indicator of exogenous latent), endo for edges with first node being endogeonous, manifest for edges connected to any manifest node, latent for edges connected to any latent node, cov for covariances, reg for regressions, load for factor-loadings, source for only the start of an edge and end for only the end of a node. These strings can be combined at will. For example, cardinal = c("exo cov","load end") (the default) or equivelantly cardinal = c("exogenous covariances","source of loadings") will only cardenalize the edges that repressent exogenous covariances or the end of factor loadings.

equalizeManifests

Logical. Should the distances between manifest nodes in the tree1 layout be equalized? Defaults to TRUE

covAtResiduals

Logical, should covariances be drawn at the start of residuals when style="lisrel" is used? Defaults to TRUE.

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 optimizeLatRes = TRUE

...

Arguments sent to the qgraph function. These arguments can further control the output of the graph. Some usefull arguments in drawing path diagrams are:

edge.width

Scales the edge width and arrow size of the plot. These can also be manually set using 'esize' and 'asize'.

node.width

Scales the width of nodes and also the height if shapes circle and square are used. Can also be a vector with scalar for each node.

node.height

Scales the height of nodes. Can also be a vector with scalar for each node. Not used with circle and square shapes.

esize

Size of the largest edge (or what it would be if there was an edge with weight maximum). Defaults to: max((-1/72)*(nNodes)+5.35,1) for weighted graphs and 2 for unweighted graphs. In directed graphs these values are halved.

asize

Size of the arrowhead. Defaults to 2 for graphs with more than 10 nodes and 2 to smaller graphs.

minimum

Edges with absolute weights under this value are omitted. Defaults to 0 for graphs with less than 50 nodes or 0.1 for larger graphs.

maximum

qgraph regards the highest of the maximum or highest absolute edge weight as the highest weight to scale the edge widths too. To compare several graphs, set this argument to a higher value than any edge weight in the graphs (typically 1 for correlations).

cut

In weighted graphs, this argument can be used to cut the scaling of edges in width and color saturation. Edges with absolute weights over this value will have the strongest color intensity and become wider the stronger they are, and edges with absolute weights under this value will have the smallest width and become vaguer the weaker the weight. If this is set to NULL, no cutoff is used and all edges vary in width and color. Defaults to NULL for graphs with less then 50 nodes and 0.3 to larger graphs.

details

Logical indicating if minimum, maximum and cutoff score should be printed under the graph. Defaults to FALSE.

mar

A vector of the form c(bottom, left, top, right) which gives the margins. Works similar to the argument in par(). Defaults to c(3,3,3,3)

filetype

A character containing the file type to save the output in. "R" outputs in a new R window, "pdf" creates a pdf file. "svg" creates a svg file (requires RSVGTipsDevice). "tex" creates LaTeX code for the graph (requires tikzDevice). 'jpg', 'tiff' and 'png' can also be used. If this is given any other string (e.g. filetype="") no device is opened. Defaults to 'R' if the current device is the NULL-device or no new device if there already is an open device. A function such as x11 can also be used

filename

Name of the file without extension

width

Width of the plot, in inches

height

Height of the plot, in inches

normalize

Logical, should the plot be normalized to the plot size. If TRUE (default) border width, vertex size, edge width and arrow sizes are adjusted to look the same for all sizes of the plot, corresponding to what they would look in a 7 by 7 inches plot if normalize is FALSE.

DoNotPlot

Runs qgraph but does not plot. Useful for saving the output (i.e. layout) without plotting

plot

Logical. Should a new plot be made? Defaults to TRUE. Set to FALSE to add the graph to the existing plot.

rescale

Logical. Defines if the layout should be rescaled to fit the -1 to 1 x and y area. Defaults to TRUE. Can best be used in combination with plot=FALSE.

label.cex

Scalar on the label size.

label.color

Character containing the color of the labels, defaults to "black"

borders

Logical indicating if borders should be plotted, defaults to TRUE.

border.color

Color vector indicating colors of the borders. Is repeated if length is equal to 1. Defaults to "black"

border.width

Controls the width of the border. Defaults to 2 and is comparable to 'lwd' argument in 'points'.

polygonList

A list contaning named lists for each element to include polygons to lookup in the shape arguments. Each element must be named as they are used in shape and contain a list with elements x and y contaning the coordinates of the polygon. By default ellipse and heart are added to this list. These polygons are scaled according to vsize and vsize2

vTrans

Transparency of the nodes, must be an integer between 0 and 255, 255 indicating no transparency. Defaults to 255

label.prop

Controls the proportion of the width of the node that the label rescales to. Defaults to 0. 9.

label.norm

A single string that is used to normalize label size. If the width of the label is lower than the width of the hypothetical label given by this argument the width of label given by this argument is used instead. Defaults to "OOO" so that every label up to three characters has the same fontsize.

label.scale

Logical indicating if labels should be scaled to fit the node. Defaults to TRUE.

label.font

Integer specifying the label font of nodes. Can be a vector with value for each node

posCol

Color of positive edges. Can be a vector of two to indicate color of edges under 'cut' value and color of edges over 'cut' value. If 'fade is set to TRUE the first color will be faded the weaker the edge weight is. If this is only one element this color will also be used for edges stronger than the 'cut' value. Defaults to c("#009900","darkgreen")

negCol

Color of negative edges. Can be a vector of two to indicate color of edges under 'cut' value and color of edges over 'cut' value. If 'fade is set to TRUE the first color will be faded the weaker the edge weight is. If this is only one element this color will also be used for edges stronger than the 'cut' value. Defaults to c("#BF0000","red")

unCol

Color to indicate the default edge color of unweighted graphs. Defaults to "#808080".

colFactor

Exponent of transformation in color intensity of relative strength. Defaults to 1 for linear behavior.

trans

In weighted graphs: logical indicating if the edges should fade to white (FALSE) or become more transparent (TRUE; use this only if you use a background). In directed graphs this is a value between 0 and 1 indicating the level of transparency. (also used as 'transparency')

fade

if TRUE (default) and if 'edge.color' is assigned, transparency will be added to edges that are not transparent (or for which no transparency has been assigned) relative to the edge strength, similar if 'trans' is set to TRUE.

loop

This can be used to scale the size of the loop. defaults to 1.

curvePivot

Quantile to pivot curves on. This can be used to, rather than round edges, make straight edges as curves with "knicks" in them. Can be logical or numeric. FALSE (default) indicates no pivoting in the curved edges, a number indicates the quantile (and one minus this value as quantile) on which to pivot curved edges and TRUE indicates a value of 0.1.

curvePivotShape

The shape of the curve around the pivots, as used in xspline. Defaults to 0.25.

edge.label.bg

Either a logical or character vector/matrix. Indicates the background behind edge labels. If TRUE (default) a white background is plotted behind each edge label. If FALSE no background is plotted behind edge labels. Can also be a single color character, a vector or matrix of color vectors for each edge.

edge.label.position

Vetor of numbers between 0 and 1 controlling the relative position of each edge label. Defaults to 0.5 for placing edge labels at the middle of the edge.

edge.label.font

Integer specifying the label font of edges. Can be a vector or matrix with value for each node

layout.par

A list of arguments passed to qgraph.layout.fruchtermanreingold when layout="spring" or to an igraph function when such a function is assigned to 'layout'

bg

If this is TRUE, a background is plotted in which node colors cast a light of that color on a black background. Can also be a character containing the color of the background Defaults to FALSE

bgcontrol

The higher this is, the less light each node gives if bg=TRUE. Defaults to 6.

bgres

square root of the number of pixels used in bg=TRUE, defaults to 100.

pty

See 'par'

font

Integer specifying the default font for node and edge labels

arrows

A logical indicating if arrows should be drawn, or a number indicating how much arrows should be drawn on each edge. If this is TRUE, a simple arrow is plotted, if this is a number, arrows are put in the middle of the edges.

arrowAngle

Angle of the arrowhead, in radians. Defaults to pi/8 for unweighted graphs and pi/4 for weighted graphs.

asize

Size of the arrowhead. Defaults to 2 for graphs with more than 10 nodes and 2 to smaller graphs.

open

Logical indicating if open (TRUE) or closed (FALSE) arrowheads should be drawn.

weighted

Logical that can be used to force either a weighted graph (TRUE) or an unweighted graph(FALSE).

XKCD

If set to TRUE the graph is plotted in XKCD style based on http://stackoverflow.com/a/12680841/567015.

Details

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 semPlotModel-edit), 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.

Value

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.

Author(s)

Sacha Epskamp <mail@sachaepskamp.com>

References

Fruchterman, T. & Reingold, E. (1991). Graph drawing by force-directed placement. Software - Pract. Exp. 21, 1129-1164.

Reingold, E and Tilford, J (1981). Tidier drawing of trees. IEEE Trans. on Softw. Eng., SE-7(2):223-228.

Csardi G, Nepusz T (2006). The igraph software package for complex network research, InterJournal, Complex Systems 1695. http://igraph.sf.net

See Also

qgraph semPlotModel semPlotModel-class semCors lisrelModel semSyntax

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 # 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)


## End(Not run)
## Mplus

# Same model, now using mplus output:
outfile <- tempfile(fileext=".out")
download.file("http://www.statmodel.com/usersguide/chap5/ex5.8.out",outfile)

# Plot model:
semPaths(outfile,intercepts=FALSE)
# Note that mplus did not report the fixed variances of the exogenous variables.




# Thresholds  -----------------------------------------------------
## Not run: 
## 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)

## End(Not run)

## Mplus

# Same model, now using mplus output:
outfile <- tempfile(fileext=".out")
download.file("http://www.statmodel.com/usersguide/chap5/ex5.2.out",outfile)

# Plot model:
semPaths(outfile)




# OpenMx ----------------------------------------------------------
## Not run: 
# To isntall OpenMx see:
# http://openmx.psyc.virginia.edu/

library("OpenMx")

# Example from mxRun help page:
# Create and run the 1-factor 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.psyc.virginia.edu/svn/trunk/demo/TwoFactorModel_PathCov.R")
semPaths(twoFactorFit, layout = "tree2")





# Multi-group 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)