Object-oriented programming in Opasnet
From Testiwiki
This page is a method.
The page identifier is Op_en5529 |
|---|
| Moderator:Jouni (see all) |
| This page is a stub. You may improve it into a full page, and then a rating bar will appear here. |
| Upload data
|
Object-oriented programming is an approach where programs (or, in Opasnet, typically assessment models) have a modular structure in such a way that each part is considered as a separate object that has specific properties and interacts with other objects in standard ways.
Contents
Question
How should object-oriented programming be utilised in Opasnet in such a way that
- it has seamless connections to R-tools,
- it is easy to understand by non-expert users and contributors,
- it uses the variable structure and other information structures (e.g. universal object) used in open assessment, and
- it enables standards for typical processes in environmental health assessments (such as distribution modelling, life tables, decision optimising, etc.).
Answer
Structure of objects
Objects have two different implementations: wiki page in Opasnet, and S4 class object called oavar in R-tools. The wiki page is the user-friendly interface for users, and oavar is the versatile format for efficient, standardised modelling.
| Attribute | What it contains | How implemented in the wiki | How implemented in the R-tools as a S4 class object oavar |
|---|---|---|---|
| question | A research question that defines the topic of the object | First main heading | Slot question = "character". Contains the question as text. |
| answer | The current best answer to the question, shown as text, data table, or distribution. | Second main heading; contains a single data table. NOTE! The data table is actually under ratonale/data but often it is the same as answer. The actual answer is precisely described by distribution and sample (see below). | Only sub-attributes are implemented. |
| index | List of indices that are used to specify the answer. | Index columns in the data table | Slot index = "data.frame". A data frame where the first column is a factor with all indices used, and the second column is a factor with the index type (text, real, date) where text is a discrete index type. |
| observation | An identifier of an individual when the answer consists of a group of individuals. | Obs column (usually implicit because the default is that each row is an observation) in the data table | Slot observation = "vector". A vector from 1..o where o is the number of observations. |
| iteration | An identifier of a probabilistic run or iteration. Sometimes it is also called a possible world or realisation. | Iter column in the data table (data usually not shown probabilistically) | Slot iteration = "vector". A vector from 1..n where n is the number of iterations. Default n = 10000. |
| distribution | A joint probability distribution (with indices as dimensions) describing the answer mathematically. | Not shown | Slot distribution = "distribution?". A distribution created with e.g. dnorm(0,1). We don't know yet how to actually implement this and how the indices are included. |
| sample | A random sample from the distribution (default is 10000 iterations). | Not shown | Slot sample = "data.frame". The data frame must contain columns Iter, one column for each index, and at least one result column. There may also be a column Obs. |
| rationale | Any information that is needed to convince a critical reader that the answer is good. | Third main heading | Only sub-attributes are implemented. |
| data | Observations, expert judgement, discussions, and other pieces of information. | Subheading under Rationale | Slot data = "data.frame". The data frame must contain at least one index column, and at least one result column. If column Obs is omitted, it is assumed that each row is a separate observation. |
| unit | The measurement unit(s) that are used in the answer to measure the topic. | Subheading under Rationale with plain text. Also mentioned in the data table with parameter unit. | Slot unit = "character". The format used is kg m^2 /s^2 where a space implies a multiplication. |
| dependencies | List of upstream objects that are causally related to this object. | Subheading under Rationale with a list of links to upstream (and sometimes downstream) wiki pages. | Slot dependencies = "factor". The format is Op_fi:Vaativuusluokkien keskipalkat. If the wiki identifier is omitted, the default is op_en. |
| formula | A computer code or algorithm to derive the answer from rationale and objects listed in dependencies. The formula may assume a deterministic dependency (e.g. y = k*x + b), a conditional probability structure (y ~ dnorm(x, sd), or a rank correlation matrix. | Subheading under Rationale, often using <rcode> tags. | Slot formula = "list". There may be several competing algorithms. Each of them is described (as a function?) as one entry in the list. When implementing the formula, the algorithm that is implemented is randomly selected for each iteration with equal probability unless otherwise specified in formula.prob. |
| formula.prob | A list of probabilities assigned to the competing algorithms in formula. The default is that each has an equal probability. | A detail in <rcode> code. | Slot formula.prob = "vector". Should have the same size as formula. |
Coding
R code should be developed in such a way that there are object-specific implementations of critical functions. The user should see straightforward content, and all messy indexing etc should happen behind scenes.
Rationale
See also
References
Related files
<mfanonymousfilelist></mfanonymousfilelist>
