# Supplementary materials to "DstarM: an R package for analyzing two choice reaction time data with the D*M method"
This project contains the supplementary files for the manuscript "DstarM: an R package for analyzing two choice reaction time data with the D*M method." In the root of the project folder, the example analysis used in the manuscript can be found.
## Simulation study
Simulated datasets were analyzed on a cluster. Hence, each analysis was called from the command line using: `Rscript.exe $filename $param1 $param2 $param3 ...`. To replicate this, the script `replicatedSimulation` can be used. All relevant files can be found in folders prefixed with simulation. Their contents are:
- simulationDatasets: the simulated datasets
- simulationResults: DstarM output after analyzing the datasets
- simulationScripts: R code for simulating and analyzing the data
**WARNING**: The reason we used a cluster is because the duration of the simulation would exceed a month on a single core machine. Adjust your expectations accordingly when replicating the results.
#### simulationScripts
`simulateData.R` simulates first parameter configurations (saved in `parameterConfigurations.txt`) and subsequently simulates the datasets. The file `simulatedDataProperties.R` examines properties of the data (e.g., median, sd).
`analysisDstarM.R` and `analysisTraditional.R` analyze the datasets inside `simulationDatasets` using respectively the DstarM and the standard DDM method. `Expconfig.R` contains the setup for analyzing the datasets, its result is stored in `Expconfig.txt`.
`processResultsDstarM.R` and `processResultsTraditional.R` postprocess the analyzed datasets and create `resultsDstarM.RData` and `resultsTraditional.RData` respectively. These files also create some output, although more output is created in `processResults.R`.
`multiplot.R` contains a function for aligning multiple ggplots (obtained from http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_(ggplot2)/).
## Analysis of `speed_acc` dataset
All materials are stored in the folder `speed_acc`. `Analysis.R` contains the script to do the analyses; the results of which are stored in `resultsSpeedAcc.RData`. `postAnalysis` postprocesses the result and creates tables and figures. `Data.Rdata` contains the cleaned `speed_acc` dataset. `exampleAnalysis.R` contains the entire script discussed in the manuscript.
