\section{Glossary}

\textbf{Variable} is used to refer to a variable that is updated during the course of the program or to a variable that has a fixed value from a data file.

\textbf{Parameter}: When considering models (e.g. doesn't apply to command-line parameters), refers to a variable that is updated during the program run. 

\textbf{Variable/parameter group}: When a variable/parameter is inside an entity in the model, there are multiple instances of the variable; one for each instance of the entity. An example: Let's consider a model model that has an entity `bird' with a data file of 50 lines. This entity has a variable called weight. So the variable group weight has variables $weight_1, ..., weight_{50}$.

\textbf{Spatial expressions}: The models of the language used in PIANOS differ a little from common bayesian models. In PIANOS, it is possible to define `a = SUM(\&x)' which means that `a' gets the value of all neighbouring entities' variable x's values summed up. We can also define `a = COUNT(\&x)' where `a' gets the number of neighbouring entities as its value. These two expressions are called \textit{spatial expressions}. Neighbours are defined in an \textit{adjacency matrix} (below).

\textbf{Entity}: A repetitive structure (indexing structure, parent group) of variables. Represented in the example model diagrams by a large box that contains some variables. In this document, entity is also used to refer to an intersection of two entities as a special intersection entity. An entity is in the models an object with some properties that the variables contained in it represent. See \ref{def_entities}

\textbf{Adjacency matrix}: A text file with 0:s and 1:s in a matrix form, each 1 meaning that the corresponding indices are neighbours. An adjacency matrix has as many lines and columns as there are spatial entities (e.g. squares or counties, the data file's number of lines) in the model. If we have, for example, 4 squares, and squares 1 and 3 are neighbours, the matrix would look like this:
\begin{verbatim}
0 0 1 0
0 0 0 0
1 0 0 0
0 0 0 0
\end{verbatim}

\textbf{Generator}: Used to refer to the modules of the software that write out the specific executable Program that carries out the simulation for a given simulation model.

\textbf{Program}: The program that is run to simulate the problem model. Synonym: generated program.

\textbf{Model file}: A text file that contains the names, distributions and equations of variables and entities for a PIANOS model. See \ref{inputs_model}

\textbf{Iterations}: The number of rounds a simulation will last. Note that \textit{burn-in} counts towards the iterations. See \ref{updatestrategy}

\textbf{Burn-in}: The number of iterations or variable updates that a simulation will run before any output is printed. See \ref{simulationfile}

\textbf{Thinning}: The period after which output is printed. If this is set to 1, output is printed every iteration round or variable update, if it is set to 100, for example, output is printed every 100th iteration. See \ref{simulationfile} for defining thinning, and \ref{outputsfortran} for output.

\textbf{Proposal strategy file}: The proposal strategies and distributions file (also called proposal file) is used for just that: it defines proposal strategies and proposal distributions for variables. See below for proposal strategies and distributions, See \ref{proposalfile} for the format of the file. 

\textbf{Initial values file}: a text file that contains the starting values for simulated parameters in a model. See \ref{initialvalues}

\textbf{Missing values}: `holes' in the data file, marked with `*'. These are simulated as parameters. See \ref{data}

\textbf{Frequency function}: A density or frequency function that is used to gauge the `goodness' of variables' values.

\textbf{Proposal distribution}: A distribution that is used for calculating a new value to be proposed for a variable. This value is then accepted or rejected using the Metropolis-Hastings algorithm.

\textbf{Proposal strategy}: The way new values are proposed for a parameter. PIANOS has two proposal strategies to choose from: \textit{fixed} and \textit{random walk} (RW). A \textit{fixed} proposal strategy means that the new value from the proposal distribution is proposed `as is'. \textit{Random walk} means that  the proposed value is the variable's current value added to the value from the proposal distribution, e.g. $x' = x + uniform(-1, 1)$

\textbf{Symbols used in the diagrams}:

\begin{figure}[ht]
%\begin{center}
\epsfig{file=content/diagrams/legend.ps,width=10cm,height=8cm}
%\end{center}
\caption{Symbols used in diagrams.}
\end{figure}
