spreadr

The notion of spreading activation is a prevalent metaphor in the cognitive sciences. This package provides the tools for cognitive scientists and psychologists to conduct computer simulations that implement spreading activation in a network representation. The algorithmic method implemented in spreadr subroutines follows the approach described in Vitevitch, Ercal, and Adagarla (2011, Frontiers), who viewed activation as a fixed cognitive resource that could spread among nodes that were connected to each other via edges or connections (i.e., a network). See Vitevitch, M. S., Ercal, G., & Adagarla, B. (2011).

Installation

You can install the stable version via

> install.packages("spreadr")

or the latest version (on the GitHub master branch)

> remotes::install_github("csqsiew/spreadr")
> # alternatively
> # devtools::install_github("csqsiew/spreadr")

If you encounter which looks like

Error: (converted from warning) package 'Rcpp' was built under R version x.y.z

try setting Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true") first [1].

Development Notes

Install developer dependencies

There are some additional packages that need to be installed for the spreadr developer, e.g. those used in the unit tests. To install these developer dependencies, use

> devtools::install_dev_deps()

Testing with the semantic priming simulation

By default, running the test suite will replicate most of the simulations in the article describing spreadr [2] except for the last, "Simulation Study 3: Semantic priming". That simulation requires 800 iterations each taking a few minutes, making it impractical for testing.

However, there is an option to include the replication of the first iteration of that simulation, with retention = 0.8. Simply set the environment variable TEST_SEMANTIC_PRIMING to any non-empty string. For example, within an interactive R session:

> Sys.setenv(TEST_SEMANTIC_PRIMING="true")
> devtools::test()

Or, through R CMD:

$ cd ..
$ R CMD build spreadr
$ TEST_SEMANTIC_PRIMING=true R CMD check spreadr_x.y.z.tar.gz

replacing x.y.z with the version string.

Testing with animated GIFs

There are some snapshot tests checking for the generation the animated GIFs. By default, these tests are not run. This is because (i) we expect GIF generation to differ trivially with development environments (so that the tests fail, but not in meaningful ways), and (ii) the spreadr results underlying the GIF is always tested before the GIF generation.

However, the GIF generation snapshot tests are still available for use. Simply set the environment variable TEST_ANIMATED_GIF to any non-empty string, just as with the semantic priming simulation tests. These tests can be useful for you to visualise the spreadr results.

Invalid ELF header

If you encounter an "invalid ELF header" error, as in

> devtools::load_all()
Loading spreadr
Error in dyn.load(dllfile) :
  unable to load shared object '/home/ning/github/spreadr/src/spreadr.so':
  /home/ning/github/spreadr/src/spreadr.so: invalid ELF header

Try calling devtools::clean_dll first [3].

[1]	r-lib/remotes#403 (comment)

[2]	https://doi.org/10.3758/s13428-018-1186-5

[3]	r-lib/devtools#2027 (comment)