pubSEM: Publication-Ready Path Diagrams in R

pubSEM is a tool designed for the easy creation of publication-ready path diagrams. The tool is functional but still in its early stages. See the roadmap below for future plans.

Installing

Important

pubSEM requires a recent version of Go for compilation. Go can be installed here: https://go.dev/doc/install

To install the package in R, run the following line:

remotes::install_github("dylanwglenn/pubSEM")

Usage

Note

pubSEM is designed only for plotting the output of lavaan models. If you want to interactively create lavaan models by visually connecting nodes, try the wonderful lavaangui.

To use pubSEM, first create a diagram layout from a fitted lavaan model using the GUI.

pubSEM::sem_gui(fit = lavaan_fit, layout_name = "my-layout", standardized = FALSE) 

When you first see your model it will be laid out essentially at random. Click and drag the nodes to arrange the diagram as you would like. Be sure to press "ctrl/cmd-S" to save your layout!

Once the layout is saved, feel free to add/remove variables from your lavaan model, or change the model structure altogether. As long as you use the same layout, all your node positions will be remembered.

To export your diagram to a PDF, use the export_diagram function.

pubSEM::export_diagram(layout_name = "my-layout", filename = "my-awsome-path-diagram")

Examples

Motivation

Existing tools for the creation of path diagrams are either programmatic or interactive.

Programmatic solutions, such as semPlot and tidySEM, have the benefit of producing diagrams that are easily reproducible, meaning that once a layout of nodes is defined, the output automatically adapts to new data and can be exported within the script (i.e. without having to export from an external editor). The downsides of these solutions include the unintuitive programmatic creation of layouts and difficulty in maintaining legibility for complex diagrams.

Interactive solutions, including lavaangui, have the benefit of being interactive and intuitive. With these tools, users can easily layout and customize a path diagram; however, existing solutions in this category lack the exactness and reproducibility of programmatic solutions. After you manually positions nodes and connections (often with some slight misalignment), the layout is not remembered. If you want redo the model with new data or add another variable, all your previous work in laying out the model must be redone.

The pubSEM solution

pubSEM seeks to offer the intuitiveness of interactive plotting solutions along with the precision and reproducibility of programmatic solutions. The tool features an interactive editor that can be used to precisely position nodes. The positions of these nodes are then remembered — once a layout is defined and saved with thesem_gui() function, export_diagram() can be used to export a path diagram according to the layout previously defined without opening the GUI.

Why is it not on CRAN?

The pubSEM GUI is a standalone Go executable compiled from source. As Go is not within the CRAN standard toolchain and CRAN understandably makes it difficult to distribute pre-built executables as part of an R package, this package will live only on GitHub for the foreseeable future.

Roadmap

• Support for intercepts
• Proper toolbar
• Multiple node selection
• Editing the visual names of variables
• Adjusting color and weight of elements
• Option to show confidence interval
• Adjusting the height of nodes
• Multi-line variable names
• Option to use serif or sans-serif fonts
• Per-node text sizing
• Option to grey out insignificant paths
• support for blavaan models
• support for multiple groups
• support for multi-level models