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| [[Category:Opasnet]] | | Pages that relate to the [[R]] package [[OpasnetUtils]] (previously called OpasnetBaseUtils). |
| [[Category:R tools]]
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| ==OpasnetUtils features==
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| [[Modelling in Opasnet]] is done using R and the OpasnetUtils package provides most of the actual tools. Most of the package revolves around the [[Ovariable]]-class.
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| Defining and analyzing endpoints of a model can be as easy as Fetching a relevant variable, evaluating it (using EvalOutput) and using some of the available functions (i.e. summary() for ovariables).
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| ...
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| ==List/Glossary of package contents==
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| Find more about each function or method using ?<topic> in the R console or search the [[#Manual]]. Topics are in approximate order of prevalency.
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| ===Ovariable functionalities===
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| *EvalOutput - is the method used to evaluate ovariables.
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| *ComputeDependencies - is automatically run when evaluating ovariables to fetch and evaluate any dependencies they have.
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| *CheckMarginals - is automatically run when evaluating ovariables to check the marginal status of output indices.
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| *CheckInput - is automatically run when evaluating ovariables to incorporate input definitions if available.
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| *CheckCollapse - is automatically run when evaluating ovariables. Uses CollapseMarginal if orders are present.
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| *CheckDecisions - is automatically run when evaluating ovariables. Adds scenarios to output if their definitions are present.
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| *CollapseMarginal - is used to streamline large models by removing indices through summation etc.
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| ===Assessment tools===
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| *DecisionTableParser - parses scenarios used in decision analysis from data.frames.
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| *CollapseTableParser - parses collapse orders from data.frames.
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| *Optimize - finds optimal combination of index values.
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| *Minimize - finds optimal combination of index values so that the resulting value is minimal.
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| ===Custom methods for Opasnet and ovariables===
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| *oprint - prints a data.frame or the output of an ovariable as a html formatted table so it looks nice on the web page.
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| *oapply - uses tapply on ovariable output. Instead of defining INDEX you can define cols as the column names you want to remove.
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| *orbind - uses rbind on the output slots two ovariables. Differing columns are allowed (missing ones are added automatically).
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| *combine - is similar to orbind, but more efficient and combines source columns.
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| *merge - merges ovariable outputs.
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| *summary - provides common statistics about the data using tapply. Defaults to describing the distribution about each ovariable index.
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| *plot - plots ovariable output. Defaults to comparison of data and formula results.
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| *Ops - methods for mathematical operations between ovariables (i.e. X * Y).
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| *Math - methods for single variable mathematical operations (i.e. exp(X)).
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| ===External (serverside) data and objects===
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| *opbase.data - downloads data from the Opasnet database.
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| *opbase.upload - uploads data to the Opasnet database.
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| *opbase.locations - downloads the index information of a particular dataset.
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| *opbase.obj.exists - checks whether object (as identified by page identifier) exists in the database.
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| *opbase.series - downloads list of datasets for a particular object.
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| *opasnet.data - downloads data from any file uploaded to Opasnet as text.
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| *opasnet.csv - downloads data from any .csv file uploaded to Opasnet.
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| *objects.get - downloads saved R objects matching a key.
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| *objects.latest - downloads latest saved R objects matching a code block in Opasnet.
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| *objects.put - uploads R objects. Returns key.
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| *objects.store - uploads public R objects in Opasnet code block.
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| *objects.encode - encrypts R objects.
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| *objects.decode - decrypts R objects.
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| ===General tools===
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| *Ovariable - constructs ovariables. More feature than new("ovariable", ...).
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| *Fetch - downloads saved R objects in batch fashion.
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| *tidy - makes common adjustments to data.frames used for ovariable data slots.
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| *interpret - forms a probability distributions based on regular expressions [[OpasnetUtils/Interpret]].
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| *result - accesses the result column of the output slot of an ovariable. Result(X) <- y -shortcut is possible.
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| *ddata_apply - updates data slot of an ovariable based on a link in the ddata slot. Does not overwrite unless force_ddata = TRUE.
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| *convert.units - is a unit conversion engine.
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| *fillna - looks for empty column values (NA) in specified data.frame columns and replaces them with all other values in the same column.
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| *dropall - cleans factors of unused levels.
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| ===Health impact assessment===
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| *GIS.Exposure - does spatial exposure mapping.
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| *GIS.Concentration.matrix - does spatial concentration mapping based on point emission.
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| ==Installation==
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| OpasnetUtils is available for any platforms capable for running R from the CRAN repository. Use the drop down menu in the RGui or the R command install.packages("OpasnetUtils") to download the most recent official release.
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| ===SVN repository===
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| If you would like to acquire the most recent version, you are welcome to download and compile our source code which is available at https://www.opasnet.org/svn/opasnet_utils/trunk/. For most recent function definitions see [https://www.opasnet.org/svn/opasnet_utils/trunk/R/ the R sub folder]. Compilation on Windows machines requires R tools (See the CRAN homepage for more information).
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| ==Manual==
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| [[File:OpasnetUtils-manual.pdf]]
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OpasnetUtils-manual.pdf ; 160 KB