3. Model Definition¶

To define the model, we have to describe the different entities, their fields, the way they interact (links) and how they behave over time (processes). This is done in one file. We use the YAML-markup language. This format uses the level of indentation to specify objects and sub objects.

In a LIAM2 model file, all text following a # is considered to be comments, and is therefore ignored.

A LIAM2 model has the following structure:

# imports are optional (this section can be entirely omitted)
import:
    ...

# globals are optional (this section can be entirely omitted)
globals:
    ...

entities:
    ...

simulation:
    ...

3.1. import¶

A model file can (optionally) import (an)other model file(s). This can be used to simply split a large model file into smaller files, or (more interestingly) to create simulation variants without having to duplicate the common parts.

For details, see the Importing other models section.

3.2. globals¶

globals are variables (aka. parameters) that do not relate to any particular entity defined in the model. They can be used in expressions in any entity.

LIAM2 currently supports two kinds of globals: tables and multi-dimensional arrays. Both kinds need to be declared in the simulation file, as follow:

globals:
    mytable:
        fields:
            - MYINTFIELD: int
            - MYFLOATFIELD: float

    MYARRAY:
        type: float

Please see the globals usage section for how to use them in you expressions.

Globals can be loaded from either .csv files during the simulation, or from the HDF5 input file, along with the entities data. In the later case, they need to be imported (as explained in the Importing data section) before they can be used. If globals need to be loaded from .csv files during the simulation, the path to the files need to be given like

globals:
    mytable:
        path: mytable.csv
        fields:
            - MYINTFIELD: int
            - MYFLOATFIELD: float

    MYARRAY:
        path: path\to\myarray.csv
        type: float

If no path is specified, the globals are assumed to be in the HDF5 file.

There are globals with a special status: periodic globals. Those globals have a different value for each period. periodic is thus a reserved word and is always a table, so the “fields” keyword can be omitted for that table.

For example, the retirement age for women in Belgium has been gradually increasing from 61 in 1997 to 65 in 2009. A global variable WEMRA has therefore been included.

globals:
    periodic:
        # PERIOD is an implicit column of the periodic table
        - WEMRA: float

3.3. entities¶

Each entity has a unique identifier and a set of attributes (fields). You can use different entities in one model. You can define the interaction between members of the same entity (eg. between partners) or among different entities (eg. a person and its household) using links.

The processes section describe how the entities behave. The order in which they are declared is not important. In the simulation block you define if and when they have to be executed, this allows to simulate processes of different entities in the order you want.

LIAM2 declares the entities as follows:

entities:
    entity-name1:
        fields:
            fields definition

        links:
            links definition

        macros:
            macros definition

        processes:
            processes definition

    entity-name2:
        ...

As we use YAML as the description language, indentation and the use of ”:” are important.

3.3.1. fields¶

The fields hold the information of each member in the entity. That information is global in a run of the model. Every process defined in that entity can use and change the value.

LIAM2 handles three types of fields:

bool: boolean (True or False)
int: integer
float: real number

There are two implicit fields that do not have to be defined:

id: the unique identifier of the item
period: the current period in the run of the program

example

entities:
    person:
        fields:
            # period and id are implicit
            - age:        int
            - dead:       bool
            - gender:     bool
            # 1: single, 2: married, 3: cohabitant, 4: divorced, 5: widowed
            - civilstate: int
            - partner_id: int
            - earnings:   float

This example defines the entity person. Each person has an age, gender, is dead or not, has a civil state, possibly a partner. We use the field civilstate to store the marital status as a switch of values.

By default, all declared fields are supposed to be present in the input file (because they are observed or computed elsewhere and their value can be found in the supplied data set). The value for all declared fields will also be stored for each period in the output file.

However, in practice, there are often some fields which are not present in the input file. They will need to be calculated later by the model, and you need to tell LIAM2 that the field is missing, by using “initialdata: false” in the definition for that field (see the agegroup variable in the example below).

example

entities:
    person:
        fields:
            - age:      int
            - agegroup: {type: int, initialdata: false}

Field names must be unique per entity (i.e. several entities may have a field with the same name).

Temporary variables are not considered as a fields and do not have to be declared.

3.3.2. links¶

Individuals can be linked with each other or with individuals of other entities, for example, mothers are linked to their children, partners are linked to each other and persons belong to households.

For details, see the Links section.

3.3.3. macros¶

Macros are a way to make the code easier to read and maintain. They are defined on the entity level. Macros are re-evaluated wherever they appear. Use capital letters to define macros.

example

entities:
    person:
        fields:
            - age: int

        macros:
            ISCHILD: age < 18

        processes:
            test_macros:
                - ischild: age < 18
                - before1: if(ischild, 1, 2)
                - before2: if(ISCHILD, 1, 2)  # before1 == before2
                - age: age + 1
                - after1: if(ischild, 1, 2)
                - after2: if(ISCHILD, 1, 2)   # after1 != after2

simulation:
    processes:
        - person: [test_macros]

The above example does

ischild: creates a temporary variable ischild and sets it to True if the age of the person is under 18 and to False if not
before1: creates a temporary variable before1 and sets it to 1 if the value of the temporary variable ischild is True and to 2 if not.
before2: creates a temporary variable before2 and sets it to 1 if the value age < 18 is True and to 2 if not
age: the age is changed
after1: creates a temporary variable after1 and sets it to 1 if the value of the temporary variable ischild is True and to 2 is not.
after2: creates a temporary variable after2 and sets it to 1 if the value age < 18 is True and to 2 if not.

It is clear that after1 != after2 since the age has been changed and ischild has not been updated since.

3.3.4. processes¶

Here you define the processes you will need in the model.

For details, see the Processes section.

3.4. simulation¶

The simulation block includes the location of the datasets (input, output), the number of periods and the start period. It sets what processes defined in the entities block are simulated (since some can be omitted), and the order in which this is done.

Please note that even though in all our examples periods correspond to years, the interpretation of the period is up to the modeller and can thus be an integer number representing anything (a day, a month, a quarter or anything you can think of). This is an important choice as it will impact the whole model.

Suppose that we have a model that starts in 2002 and has to simulate for 10 periods. Furthermore, suppose that we have two entities: individuals and households. The model starts by some initial processes (defined in the init section) that precede the actual prospective simulation of the model, and that only apply to the observed dataset in 2001 (or before). These initial simulations can pertain to the level of the individual or the household. Use the init block to calculate variables for the starting period.

The prospective part of the model starts by a number of sub-processes setting the household size and composition. Next, two processes apply on the level of the individual, changing the age and agegroup. Finally, mortality and fertility are simulated. Seeing that this changes the numbers of individuals in households, the process establishing the household size and composition is again used.

example

simulation:
    init:                   # optional
        - household: [household_composition]
        - person: [agegroup]

    processes:
        - household: [household_composition]
        - person: [
               age, agegroup,
               dead_procedure, birth
           ]
        - household: [household_composition]

    input:
        path: liam2         # optional
        file: base.h5
    output:
        path: liam2         # optional
        file: simulation.h5
    start_period: 2002
    periods: 10
    skip_shows: False       # optional
    random_seed: 5235       # optional
    assertions: warn        # optional
    default_entity: person  # optional
    logging:                # optional
        timings: True       # optional
        level: procedures   # optional
    autodump: False         # optional
    autodiff: False         # optional

3.4.1. processes¶

This block defines which processes are executed and in what order. They will be executed for each period starting from start_period for periods times. Since processes are defined on a specific entities (they change the values of items of that entity), you have to specify the entity before each list of process. Note that you can execute the same process more than once during a simulation and that you can alternate between entities in the simulation of a period.

In the example you see that after dead_procedure and birth, the household_composition procedure is re-executed.

3.4.2. init¶

Every process specified here is only executed in the last period before start period (start_period - 1). You can use it to calculate (initialise) variables derived from observed data. This section is optional (it can be entirely omitted).

3.4.3. input¶

The initial (observed) data is read from the file specified in the input entry.

Specifying the path is optional. If it is omitted, it defaults to the directory where the simulation file is located.

The hdf5-file format can be browsed with vitables (http://vitables.berlios.de/) or another hdf5-browser available on the net.

3.4.4. output¶

The simulation result is stored in the file specified in the output entry. Only the variables defined at the entity level are stored. Temporary (local) variables are not saved. The output file contains values for each period and each field and each item.

Specifying the path is optional. If it is omitted, it defaults to the directory where the simulation file is located.

3.4.5. start_period¶

Defines the first period (integer) to be simulated. It should be consistent (use the same scale/time unit) with the “period” column in the input data.

3.4.6. periods¶

Defines the number of periods (integer) to be simulated.

3.4.7. random_seed¶

Defines the starting point (integer) of the pseudo-random generator. This section is optional. This can be useful if you want to have several runs of a simulation use the same random numbers.

3.4.8. skip_shows¶

If set to True, makes all show() functions do nothing. This can speed up simulations which include many shows (usually for debugging). Defaults to False.

3.4.9. assertions¶

This option can take any of the following values:

raise: interrupt the simulation if an assertion fails (this is the default).
warn: display a warning message.
skip: do not run the assertions at all.

3.4.10. default_entity¶

If set to the name of an entity, the interactive console will start in that entity.

3.4.11. logging¶

3.4.11.1. level¶

Sets logging level. If set, it should be one of the three following values (by increasing level of verbosity):

periods: show only periods.
procedures: show periods and procedures (this is the default).
processes: show periods, procedures and individual processes.

3.4.11.2. timings¶

If set to False, hide all timings from the simulation log, so that two simulation log files are more easily comparable (for example with “diff” tools like WinMerge). Defaults to True.

3.4.12. autodump¶

If this option is used, at the end of each procedure, all (non-scalar) variables changed during the procedure (including temporaries) will be dumped in an hdf5 file (named “autodump.h5” by default). This option can be used alone for debugging, or in combination with autodiff (in a later run). This option can take either a filename or a boolean (in which case “autodump.h5” is used as the filename). Defaults to False.

3.4.13. autodiff¶

If this option is used, at the end of each procedure, all (non-scalar) variables changed during the procedure (including temporaries) will be compared with the values stored previously by autodump in another run of the model (or a variant of it). This can be used to precisely compare two versions/variants of a model and see exactly where they start to differ. This option can take either a filename or a boolean (in which case “autodump.h5” is used as the filename). Defaults to False.

4. Running a model/simulation¶

If you are using the bundled editor, simply open the simulation file and press F6.

If you are using the command line, use:

[BUNDLEPATH]\liam2\main run <path_to_simulation_file>

3. Model Definition¶

3.1. import¶

3.2. globals¶

3.3. entities¶

3.3.1. fields¶

3.3.2. links¶

3.3.3. macros¶

3.3.4. processes¶

3.4. simulation¶

3.4.1. processes¶

3.4.2. init¶

3.4.3. input¶

3.4.4. output¶

3.4.5. start_period¶

3.4.6. periods¶

3.4.7. random_seed¶

3.4.8. skip_shows¶

3.4.9. assertions¶

3.4.10. default_entity¶

3.4.11. logging¶

3.4.11.1. level¶

3.4.11.2. timings¶

3.4.12. autodump¶

3.4.13. autodiff¶

4. Running a model/simulation¶

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3. Model Definition¶

3.1. import¶

3.2. globals¶

3.3. entities¶

3.3.1. fields¶

3.3.2. links¶

3.3.3. macros¶

3.3.4. processes¶

3.4. simulation¶

3.4.1. processes¶

3.4.2. init¶

3.4.3. input¶

3.4.4. output¶

3.4.5. start_period¶

3.4.6. periods¶

3.4.7. random_seed¶

3.4.8. skip_shows¶

3.4.9. assertions¶

3.4.10. default_entity¶

3.4.11. logging¶

3.4.11.1. level¶

3.4.11.2. timings¶

3.4.12. autodump¶

3.4.13. autodiff¶

4. Running a model/simulation¶

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