Parallel Episodic Processing (PEP) Model
Version 2.1.0


MULTITHREADING NOTES

The PEP model takes advantage of multiprocessor system capabilities by using
multithreading. This aids in simulation times with modern computers with multiple
cores. The number of threads can be set in the maxThreads variable in the Main
method. This number shouldn't exceed the number of processors (or processors x 2
with hyper-threading processors like Intel i7), less at least one for other system
processes. The simulation times for multiple threads do seem to be limited by memory
bandwidth. Thus, gains from increasing the number of threads will tend to diminish
with each added thread. From my experience, little is gained after 3 or 4 threads.


SOURCE FILES

Source files are formatted with four tab-delimited columns of integers (0 to n-1).
These columns, in order, represent:
(1) correct response - technically, this should always be exactly the same as the
     value in the targets column, unless other changes have been made to the
     model to allow for something other than 1-to-1 target-response mappings
(2) targets
(3) distracters - muliple distracting columns possible
(4) condition - multiple condition columns possible (congruency is automatically
     the first if congruency is manipulated)


MAIN.JAVA VARIABLES

To lesion the attentional wandering device see the "Attenional Wandering" section
of Attention.java. To lesion temporal learning, see the monitorTemp() method in
RunTime.java. For running previous simulations, see the instructions file of the
corresponding version. To simulate other paradigms, the following variables can
be adjusted in the "VARIABLES" section of Main.java. These are:

---Basic Experiment Information-------------------------------------------------
source (String) - Filename where condition information is saved
     (these are included with the download)
nSubjects (integer) - Number of "subjects" to run (default = 500)
maxThreads (integer) - Number of concurrent threads to run (default = 3)
---Structure of Task------------------------------------------------------------
isReplace (boolean) - "true" = random with replacement, "false" = without
nBlocks (integer array) - Number of blocks per subject, multiple sets possible
nSamples (integer) - Number of trials (only for with replacement)
twoTasks (boolean) - "true" = two alternating tasks
isPaired (boolean) - "true" = trial pairs in fixed sequence
---Stimulus Characteristics-----------------------------------------------------
nResponses (integer) - Number of responses (normally the same as nTargets)
nTargets (integer) - Number of targets (e.g., colours)
nDistracters (integer array) - Number of distracters, multiple sets possible
nConflicting (integer) - Number of distracters that can conflict
     (distracters above this limit are neutral)
isConflict (boolean) - Determines whether distracters conflict (true) or not
nPerVar (integer array) - Number of conditions (multiple variables possible)
---Stimulus Inputs (Only Useful for Degraded Stimuli)----------------------------
tBias, tSignal, dBias, & dSignal - fixed input variables (do not change)
tDegrade - Sets input signal for degraded stimuli (default = .65)
isDegrade - Determines whether stimuli are degraded
---Trial Timing Information (Normally Only Adjusted with Prime-Probe)------------
tOnset, tOffset, dOnset, & dOffset (integers) - Stimulus onset and offset of the
     target (t) and distracter (d)
dMask (integer) - Distracter mask (e.g., by the target)
trialLength - Number of cycles before "no response" is made (default = 2000),
     longer times appropriate for paradigms where target onset is delayed
     (e.g., prime-probe) or to match original study design
isi (integer) - The number of blank cycles between trials (default = 300)
---------------------------------------------------------------------------------

The values used for each simulation are included in the parameters.txt file.
These can simply be copy-pasted into the Main.java "VARIABLES" section. Note that
most variables in the VARIABLES section can be ignored. Some of these are default
parameters that shouldn't be changed. Others are for coding for unrelated effects
in different paradigms. Questions about any other parameters can be addressed to
me via email at: james.schmidt@ugent.be.


RUNNING A SIMULATION

After setting your variables in Main.java, you can run the main project. You should
be using a software development kit (SDK), such as the Java Development Kit (JDK),
and an integrated development environment (IDE), such as NetBeans. It is important
that your source file is with your java class files so that the compiler can find
the trials that it will present to the model. Running the project will cause the
model to simulate all participants with a different random trial order. The model
will also create a tab-delimited text file called Means.txt that will contain the
mean response time and percentage error for each "participant" in each condition.
This is created by DataAnalysis.java and can be run independently of the rest of
the model. The model also produces a large Dataset.txt file with full datasets of
all participants concatenated together. This method also codes for previous RT and
previous accuracy. Note that any simulation results that you want to keep should be
removed from your source folder before starting a new simulation run, as new
datafiles will overwrite old ones.

To analyse congruency sequence (Gratton) effects, see the "Sequence Analysis
Variables" in DataAnalysis.java. Specifically:

isCheckSeq (boolean) - set to "true" to analyses previous congruency
isTrimmed (boolean) - set to "true" to delete feature repetitions
isAllSeq (boolean) - set to "true" to separately assess each kind of feature
     repetition