Collecting, Outputting &

Inputting Data in AnyLogic

Nathaniel Osgood
MIT 15.879

April 4, 2012
 Recording of Results
• A frequent modeler need is to record some
components of model state over time
– State variables (e.g. stocks)
– States of agents
– Summaries of model state
– We informally term this a “trajectory file”
• Trajectory recording is only supported by AnyLogic
Professional
• AnyLogic does allow for
– Definition of DataSets that record recent values of
parameters
– Statistics summarizing model state
– Reporting on values of data sets as a graph or table
 Techniques for Outputting Data
• Ad-Hoc Exports from variables
• Manual copies from visible datasets
• Export to files
• Writing to console
• Export to databases
• [AnyLogic Professional] Dataset archiving
• Capturing images of graphs
 Cross-Method Output Tips
• A convenient mechanism is to periodically output
data using events (e.g. every time unit)
• Beyond output, be sure to save information on
context of run
– Model version (Use unique id that increment whenever
change model)
– Parameter assumptions
– Intention
• Think carefully about whether want to save away
intermediate data
 Hands on Model Use Ahead

Load Sample Model:

SIR Agent Based Calibration
(Via “Sample Models” under “Help” Menu)
 Techniques for Collecting & Outputting
Data
• Ad-Hoc Exports from variables
• Pre-Prepared methods
– Statistics
– Charts
– Manual copies from visible datasets
– Export to files
– Writing to console
– Export to databases
– [AnyLogic Professional] Dataset archiving
– Capturing images of graphs
Add an Experiment
Add an Experiment
Save the Resulting Model (To Avoid
Overwriting the Other Model)
Run the Experiment (To Verify
Functionality)
Click on Variable “nInfectious”
Graph of Variable
Right-Click to Copy the Numeric Data
Pasting Into Excel
Press Red “Stop” Button to Terminate
Execution
 Techniques for Collecting & Outputting
Data
• Ad-Hoc Exports from variables
• Pre-Prepared methods
– Statistics
– Charts
– Manual copies from visible datasets
– Export to files
– Writing to console
– Export to databases
– [AnyLogic Professional] Dataset archiving
– Capturing images of graphs
 Statistics & Charts
• A population of agents can have associated statistics
that calculate values
• Examples of things that can be computed with using
AnyLogic’s statistics
– Count of agents in the population for which certain
condition (“predicate”) evaluates to true
– Function of the values of some expression over the
population
• Maximum value
• Minimum value
• Average value
• Sum (total) over population
– Statistics can be defined as properties of the population
Select “People”, and Choose “Statistics”
Also, Expand “Statechart” Under “Person”
Click “Add Statistics”
Fill in the “Condition” (Predicate) on Person
Continue Typing
 Full Expression

Expression: item.statechart.isStateActive(Person.Susceptible)
Example Statistics
The population in which the statistics
are to be calculated

What statistics we wish to calculate

Name the Statistic “countSusceptible”
Run the Model, and Click on “people”
The Statistic should be Visible

Close the Model after you’re done

Drag a “Time Plot” from the Palette to
the “Main” Canvas
Enlarge the Chart
Click “Add Data Item”
Put in “people.” and Press Ctrl-Space
Choose “Count Susceptible”
Now Run the Model

Notice that this only goes back to time 100

Stop the Simulation, and Click on the Plot.
Change Time Window & Display Size to 200
This Captures the Full Time Range
 Techniques for Collecting & Outputting
Data
• Ad-Hoc Exports from variables
• Pre-Prepared methods
– Statistics
– Charts
– Manual copies from visible datasets
– Export to files
– Writing to console
– Export to databases
– [AnyLogic Professional] Dataset archiving
– Capturing images of graphs
 Datasets
• Datasets store recent values of some
quantities from the model
• Datasets can be exported easily using custom
code
– This can simply call the dataset’s toString method
Output: Datasets
Run the Experiment & Click on
“Infectious DS”
Click on “InfectiousDS” to See Data in
Dataset
Right Click and Select “Copy”
Call Up Excel and Paste into It
Dataset Properties
Chart Use of Datasets
Ad-hoc Export
Begins as a Small Chart
Copying Data
Data Exported from Ad-Hoc Chart
 Techniques for Outputting Data
• Ad-Hoc Exports from variables
• Manual copies from visible datasets
• Capturing images of graphs
• Export to files
• Writing to console
• [AnyLogic Professional] Dataset archiving
• Export to databases
Manual Output from Datasets
Right Clicking Gives Context Menu
Copied Data Can be Pasted into Excel
Declaratively Specifying Datasets
 Supported Dataset Types
• Simple
– holds values only -- no timestamps
• Timed
– holds values and timestamps
• Phase
– holds pairs of values but no timestamps
• Histogram
– can define bins for data set
– data set will record # falling in each bin
 Techniques for Outputting Data
• Ad-Hoc Exports from variables
• Manual copies from visible datasets
• Capturing images of graphs
• Output to console
• Export to files
• [AnyLogic Professional] Dataset archiving
• Export to databases
 Output to Console
• Pros
– Easy to program
• ActiveObject.traceln(String str) outputs string to console
• System.out.println(String str) (Black)
• System.err.println(String str) (Red)
– Readily visible
– Copy & Paste to another document
• Cons
– May be mixed with other output (easy to miss other
output)
– Limited length
– Depends on memory to copy
– Less structured
 Techniques for Outputting Data
• Ad-Hoc Exports from variables
• Manual copies from visible datasets
• Capturing images of graphs
• Writing to console
• Export to files
• [AnyLogic Professional] Dataset archiving
• Export to databases
 Data Output to File
• Pros
– Simple to perform
– Relatively easy to import into e.g. Excel, R, etc.
– Files can be readily archived
• Cons
– Awkward to draw combine from multiple files
– Denormalization: Requires either
• Duplication of scenario-wide information (e.g. parameter
values) on each row
• Separate header section & later section
 Outputting a Dataset to a File
Requires 2 Steps
• “Importing” (specifying how to find) the
necessary Java code
• Defining the code
Step 1: Importing the Necessary Java Libraries
 Step 2: Code to Export Dataset to File
try Substitute whatever file name you wish to use
{ You may wish to put a “path” in front of this
FileOutputStream fos = new
FileOutputStream("Filename.tab");
PrintStream p = new PrintStream(fos);
p.println(datasetName.toString()); // outputs
tab delimited values
}
catch (Exception e)
Substitute the name of the dataset
{ You wish to output
traceln("Could not write to file.");
}
Suggestion: For greater versatility, place this in a function that
takes the file name as a parameter.
Where to Put the Code to Output the Dataset
Option 1: In “Destroy Code” for Main
 Where to Put the Code to Output the Dataset
Option 2: In “Action” for an Event Triggered at times
 Techniques for Outputting Data
• Ad-Hoc Exports from variables
• Manual copies from visible datasets
• Capturing images of graphs
• Writing to console
• Export to files
• [AnyLogic Professional] Dataset archiving
• Export to databases
 Output to Databases: Tradeoffs
• Pros
– More flexible than string output to file
– Can query from diverse tools (e.g. excel, R, SPSS, SAS,
etc.)
– Can easily clean up
– For larger databases
• Transactional (either writes entirely or not at all)
• Can query from remote machines
• Cons
– More programming
– Need to set up a database
 Output to Databases: Steps
• One Time:
– Install database on computer
– Add reference to database libraries
• Each time during simulation
– Open database connection at start of model
– Optionally, “insert” model version & parameter
information into the database
– Periodically during simulation
• “insert” values into databases
– At end of model execution, close database connection
 Relevant Databases
• Databases most oriented • Databases oriented
towards single users & towards multiple users &
single computers multiple computers
– MS Access – Oracle
– H2 – DB2
– These databases less robust – MS SQL Server
=> risk of corruption – Open source
– These are often quite fast • Postgres
• Derby
• MySQL
• More robust
• Support remote access
Database Dependencies (MySQL database)
 Options for Database Access
• AnyLogic Professional: Built-in visual database
classes
– Simplify the composition of database operations
• Direct calling of database operations in Java’s “Java
DataBase Connectivity” (JDBC) Library
– Note ODBC “bridge” for windows database driver
support
• Custom database classes
– We would be happy to share our simple interface
– More refined interfaces possible
 Example Simple
Database Class
for SQL Relational
Database
Systems
A Method is
associated with
each of
Execute
Query
Insert
Example: Execute Query
Setup for Database Class
 Example Database Output Code
A database query language (SQL) statement

Requesting that the database class execute the SQL statemen

Checking to make sure that the insert worked properly

 Database Output: Suggestions
• Maintain metadata
– Purpose of run
– Parameter settings
– Model version (& possibly .alp file)
• Be mindful of performance & space burdens
– Try to batch up data inserts
– Be selective in what data to store, balancing pros & cons
of storing more material
• Pros: Analytic flexibility, greater understanding, less risk of
having to re-run simulation
• Cons: Mammoth database size, Impaired performance
– Use a local database if possible
 Database Input
• Database input can be desirable when “feeding in”
certain data to model
– Connection choreography
– Agent movement patterns
– Count of incident cases of a condition
– Count of vaccinations over time
• Frequently this data is “quantized” into time units
– In those cases, Dynamic Events can be helpful