| Subset an ont | [.ontology |
| Modify an ontology | [[<-.ontology |
| Modify an ontology | [<-.ontology |
| Modify an ontology | $<-.ontology |
| Add Sub Version to Specification | add.sub.version |
| Anchor Intervention Effect's Location and Version | anchor.intervention.effect.location.and.version |
| Apply an Ontology Mapping to Data | apply.ontology.mapping |
| Check if Simulations Have Been Saved | are.simulations.present |
| Functions for subsetting an array when the number and order of dimensions is not known at the point of coding. The array.access function performs error checking on the arguments; fast.array.access is optimized for speed but does not check arguments | array.access fast.array.access |
| Convert an ontology back to a plain list | as.list.ontology |
| Convert a named list to an ontology | as.ontology |
| Assemble an MCMC From a Calibration | assemble.mcmc.from.calibration |
| Assemble Simulations From A Calibration | assemble.simulations.from.calibration |
| Assemble Transmuted Simulations | assemble.transmuted.simulations |
| Burn Simulations From a Simulation Set | burn.simset |
| Cache A Summary of an MCMC | cache.mcmc.summary |
| Assess Whether Simulations from one Version/Specification can be Transmuted to Another Version | can.transmute.versions |
| Clear JHEEM Version, Calibration, Intervention, and Ontology Mappings | clear.all.managers |
| Clear a Calibration Cache | clear.calibration.cache |
| Clear JHEEM Calibrations | clear.calibrations |
| Clear JHEEM Interventions | clear.interventions |
| Clear Ontology Error Debug Info | clear.ontology.error.debug.info |
| Clear All Registered Ontology Mappings | clear.ontology.mappings |
| Clear a Calibration Cache | clear.transmute.calibration.cache |
| Clear JHEEM Versions | clear.versions |
| Collapse an Array According to Indices | collapse.array.according.to.indices |
| Combine multiple ontology mappings into a single mapping | combine.ontology.mappings |
| Compare Two Simsets | compare.sims |
| Compute Likelihood | compute.likelihood |
| Compute Joint Likelihood Piecewise | compute.likelihood.piecewise |
| Copy Calibration Info to a New Code | copy.calibration.info |
| Create a copy of a JHEEM Data Manager | copy.data.manager |
| Make a copy of a Simulation Set | copy.simulation.set |
| Create JHEEM Basic Likelihood Instructions | create.basic.likelihood.instructions |
| Create JHEEM Basic Likelihood Instructions With Included Multiplier | create.basic.likelihood.instructions.with.included.multiplier |
| Create JHEEM Basic Likelihood Instructions With Specified Outcome | create.basic.likelihood.instructions.with.specified.outcome |
| Create Basic Ratio Likelihood Instructions | create.basic.ratio.likelihood.instructions |
| Create Bernoulli Likelihood Instructions | create.bernoulli.likelihood.instructions |
| Create Custom Likelihood Instructions | create.custom.likelihood.instructions |
| Create a data binding | create.data.binding |
| Create a JHEEM Data Manager | create.data.manager |
| Make a variable an alias for a bound data manager | create.data.manager.alias |
| Create If-Else Likelihood Instructions | create.ifelse.likelihood.instructions |
| Create an Intervention | create.intervention |
| Create an Effect for an Intervention to Have on a Model Quantity | create.intervention.effect |
| Create an Engine to Run JHEEM Simulations | create.jheem.engine |
| Create a Model Specification for Running the JHEEM | create.jheem.specification |
| Create a Transmuter | create.jheem.transmuter |
| Create Weights to Be Applied in Calculating a JHEEM Likelihood | create.likelihood.weights |
| Create an Functional Form that is Linear (possibly on a transformed scale) | create.linear.functional.form |
| Create a Linear Spline Functional Form | create.linear.spline.functional.form |
| Create Location Based If-Else Likelihood Instructions | create.location.based.ifelse.likelihood.instructions |
| Create a Functional Form that is Linear on the Log Scale | create.log.linear.functional.form |
| Create a Functional Form that is Linear on the Logistic Scale | create.logistic.linear.functional.form |
| Create a Logistic Spline Functional Form | create.logistic.spline.functional.form |
| Create a "Logistic Tail" Functional Form | create.logistic.tail.functional.form |
| Create a Model Foreground Object | create.model.foreground |
| Create a "Guess-and-Check" Intervention that Must Satisfy Some Criteria by Varying Parameters | create.monotonic.criteria.based.intervention |
| Create a criterion for monotonic parameter, criteria-based interventions | create.monotonic.criterion |
| Create a Natural Spline Functional Form | create.natural.spline.functional.form |
| Create Nested Proportion Likelihood Instructions | create.nested.proportion.likelihood.instructions |
| Create Nested Proportion Likelihood Instructions With Included Multiplier | create.nested.proportion.likelihood.instructions.with.included.multiplier |
| Create a mapping that allows transformations of arrays | create.ontology.mapping |
| Create an ontology mapping that lumps otherwise unspecified categories into an "other" category | create.other.catchall.ontology.mapping |
| Create Outcome Location Mapping | create.outcome.location.mapping |
| Create a metadata object for tracked quantities or tracked transitions | create.outcome.metadata |
| Create a Collection of JHEEM Simulation-Sets | create.simset.collection |
| Create Solver Metadata | create.solver.metadata |
| Create an Static (Time-Invariant) Functional Form | create.static.functional.form |
| Create A Style Manager | create.style.manager |
| Create a Target Population to Which Interventions May be Applied | create.target.population |
| Create JHEEM Basic Likelihood Instructions | create.time.lagged.comparison.likelihood.instructions |
| Create JHEEM Basic Likelihood Instructions | create.time.lagged.comparison.likelihood.instructions.with.included.multiplier |
| Create Time Lagged Comparison Nested Proportion Likelihood Instructions | create.time.lagged.comparison.nested.proportion.likelihood.instructions |
| Declare the data managers a specification uses | declare.data.managers |
| Create a Target Population that is the DIFFERENCE between two other Target Populations | diff.target.populations |
| Disable JHEEM Solver Tracking | disable.jheem.solver.tracking |
| Distribute dimension values | distribute.dimension.values |
| Enable JHEEM Solver Tracking | enable.jheem.solver.tracking |
| Identify any Reasons for a Failure to Get Mappings to Align Ontologies | examine.get.mappings.to.align.ontologies |
| Identify any Reasons for a Failure to Map Ontologies | examine.get.ontology.mapping |
| Get Detailed Information on a Recent Failed Attempt to Map Ontologies | examine.recent.failed.ontology.mapping |
| Execute Plotly Plot A utility that performs the plot-rendering half of the plot simulations in plotly operation for applications like webtools that need the step to be separate. | execute.plotly.plot |
| Execute Simplot A utility that performs the plot-rendering half of the simplot operation for applications like webtools that need the step to be separate. | execute.simplot |
| Expand an Array to Greater Dimensions | expand.array |
| Extract the Last Simulation From A Calibration | extract.last.simulation.from.calibration |
| Find Ontology Mapping | find.ontology.mapping |
| Get Calibration Progress | get.calibration.progress |
| Get a Set of Indices to Collapse One Array into Another | get.collapse.array.indices |
| Get a function that projects a smoothed cumulative count up to a given age | get.cumulative.age.counts.smoother |
| Get the active data binding | get.data.binding |
| Get the identity of a data binding | get.data.binding.identity |
| Get the data inputs recorded for an artifact | get.data.inputs |
| Get a data manager by name | get.data.manager |
| Get the provenance of a data manager | get.data.manager.provenance |
| Get pretty names for outcomes | get.data.outcome.descriptions get.data.outcome.labels get.data.outcome.pretty.names |
| Get full names for data sources | get.data.source.full.names get.data.source.short.names |
| Get the default data manager | get.default.data.manager |
| Get the Default Style Manager | get.default.style.manager |
| Get the Array Indices Under Expanded Dim-names | get.expand.array.indices |
| Get a Set of Indices to Collapse One Array into Another, expanding the first array if needed to add dimensions | get.expand.then.collapse.array.indices |
| Get an "Identity" Ontology Mapping (that does not change data structure when applied) | get.identity.ontology.mapping |
| Get JHEEM Root Directory #' @description Gets the directory that calibration directories and files will be written into, if it has been set with "set.jheem.root.directory" | get.jheem.root.directory |
| Get JHEEM Solver Tracked Info | get.jheem.solver.tracked.info |
| Get locations with data for an outcome | get.locations.with.data |
| Get a Pair of Ontology Mappings that Aligns two Data Elements | get.mappings.to.align.ontologies |
| Get MCMC Mixing Statistic | get.mcmc.mixing.statistic |
| Get Ontology Error Debug Info | get.ontology.error.debug.info |
| Get an Ontology Mapping to Transform Data | get.ontology.mapping |
| Get a Matrix that Applies an Ontology Mapping | get.ontology.mapping.matrix |
| Get P Bias Estimates | get.p.bias.estimates |
| Get Prior JHEEM Model Versions | get.prior.versions |
| param ontology.name The name of an ontology (must be registered in the data manager) | get.registered.ontology |
| Get Simulation Data | get.simset.data |
| Get Simset Filename | get.simset.filename |
| Get Simset Filename and Directory | get.simset.filename.and.dir |
| Get Simulation Set Paramater Values | get.simset.params |
| Get a Simulation Metadata Object | get.simulation.metadata |
| Get a JHEEM Specification Object | get.specification.for.version |
| Get a Specification Metadata Object | get.specification.metadata |
| Get year bounds for outcome | get.year.bounds.for.outcome |
| Import data from another JHEEM Data Manager | import.data |
| Get an ontology's incomplete dimensions | incomplete.dimensions |
| Get an ontology's incomplete dimensions | incomplete.dimensions.ontology |
| Inspect marginal sums between stratifications | inspect.marginals |
| Instantiate Likelihood | instantiate.likelihood |
| Interpolate Values | interpolate |
| Create a Target Population that is the INTERSECTION of Other Target Populations | intersect.target.populations |
| Get indicators of which dimensions in an ontology are complete | is.complete is_complete |
| Get indicators of which dimensions in an ontology are complete | is_complete.ontology |
| Test if an object is of type 'ontology' | is.ontology |
| Still need to flesh out this interface | JHEEM |
| jheem2: A package for setting up and running simulations using the JHEEM Engine #' | jheem2-package jheem2 |
| JHEEM Calibration Parameters | jheem2-calibration-params |
| JHEEM Data Manager Parameters | jheem2-data-manager-params |
| JHEEM Likelihood Parameters | jheem2-likelihood-params |
| JHEEM Parameters | jheem2-params |
| JHEEM Simulation Set Parameters | jheem2-simset-params |
| Join Multiple Interventions into a Single Intervention | join.interventions |
| Make a single (joint) set of likelihood instructions out of two or more likelihood instructions objects | join.likelihood.instructions |
| Join Outcome Location Mappings | join.outcome.location.mappings |
| Join multiple simulation sets into a single set | join.simulation.sets |
| List registered data managers | list.data.managers |
| Load a cached data manager | load.data.manager |
| Load a Simulation Set | load.simulation.set |
| Make Names for a Set of Age Strata | make.age.strata.names |
| Map Value's Ontology | map.value.ontology |
| Create Traceplot of MCMC | mcmc.traceplot |
| Modify an Ontology's Names | names<-.ontology |
| Create an ontology object | ontology |
| The Constructor | ONTOLOGY.MAPPING |
| Join multiple dim.names lists | outer.join.dim.names |
| Convert Age Strata Names into Lower and Upper Bounds for Each Stratum | parse.age.strata.names |
| Parse Simset Filename | parse.simset.filename |
| Parse Year Names | parse.year.names |
| Get Percentage of Run Cache Completed | percentage.cache.complete |
| Cleaning and verifying the plotting data so it can be properly plotted | plot.data.validation |
| Plot Simulations With Plotly | plot.simulations |
| Prepare Plot Data A utility that performs the data-pulling half of the simplot operation for applications like webtools that need the step to be separate. | prepare.plot |
| Print an ontology | print.ontology |
| Pull data from a data manager | pull.data |
| Put data into a data manager | put.data |
| Put long-form data into a data manager #'@inheritParams distribute.dimension.values | put.data.long.form |
| Rebuild the data binding an artifact was built under | rebuild.data.binding |
| Register Information about Aging for a Model Specification | register.aging |
| Register Parameters to Be Used in Calibrating a JHEEM Version | register.calibrated.parameters.for.version |
| Register Calibration Info | register.calibration.info |
| Register a data manager under a name | register.data.manager |
| Register a metadata field to a data manager | register.data.metadata.field |
| Register a new data ontology to a data manager before putting data to it | register.data.ontology |
| Register an outcome to a data manager before putting data for that outcome | register.data.outcome |
| Register a data source to a data manager before putting data from that source | register.data.source |
| Register Default Parameter Values | register.default.parameter.values |
| Set Whether to Fix Strata Sizes During a Time Period | register.fixed.model.strata |
| Set The Initial Model Population | register.initial.population |
| Register a Model Element | register.model.element |
| A convenience function to streamline registering multiple model.elements for which we only need to specify a value | register.model.element.values |
| Register a Foreground for a Model Specification | register.model.foreground |
| Register Information about Disease Transmission for a Model Specification | register.model.mechanism |
| Register a Model Quantity | register.model.quantity |
| Register a Value to a Subset of a Model Quantity or Transition | register.model.quantity.subset |
| Register a JHEEM Model Specification | register.model.specification |
| Register Information about Mortality for a Model Specification | register.mortality |
| Register Information about Natality (Births) for a Model Specification | register.natality |
| Create and register a mapping that allows transformations of arrays | register.ontology.mapping |
| Register a parent data source to a data manager | register.parent.data.source |
| Register Information about Remission from Infection for a Model Specification | register.remission |
| Register Parameters to Be Sampled Prior to Making Projections from a JHEEM Version | register.sampled.parameters.for.version |
| Register Parameters to Be Set for Running a Simulation | register.set.parameters.for.version |
| Register Information about Disease Transmission for a Model Specification | register.transition |
| Register Information about Disease Transmission for a Model Specification | register.transmission |
| Register Transmute Calibration Info | register.transmute.calibration.info |
| Remove Data From Data Manager | remove.data |
| Rerun a Simulation Set | rerun.simulations |
| #@export | resolve.intervention.effect |
| Resolve dimension.values into a set of dimnames for an ontology | resolve.ontology.dimension.values |
| Re-distribute counts according to one set of age brackets into a different set of age brackets | restratify.age.counts |
| Retrieve a Saved Simulation Set | retrieve.simulation.set |
| Run A Calibration | run.calibration |
| Run a Simulations from a Set of Parameters | run.simulations.from.parameters |
| Run Transmute Calibration | run.transmute.calibration |
| Save a JHEEM Simulation Set | save.simulation.set |
| Set the session's data binding | set.data.binding |
| Set the function that loads a data manager release | set.data.release.resolver |
| Set the default data manager | set.default.data.manager |
| Set the Default Style Manager | set.default.style.manager |
| Set multiple functional form main effect alphas from parameters | set.element.functional.form.alphas.from.parameters |
| Set the Times From and To Which the Functional Form Determines a Model Element's Value | set.element.functional.form.from.time set.element.functional.form.to.time |
| Set a "Future Slope" and the time after which it applies, for a model element | set.element.functional.form.future.slope set.element.functional.form.future.slope.after.time |
| Set Interaction Alpha Values for a Functional Form for a Model Element | set.element.functional.form.interaction.alphas |
| Set Main Effect Alpha Values for a Functional Form for a Model Element | set.element.functional.form.main.effect.alphas |
| Set a ramp or taper (times and values) for a model element | set.element.ramp.times set.element.ramp.values set.element.taper.times set.element.taper.values |
| Set the Value of a Model Element | set.element.value |
| Set JHEEM Root Directory | set.jheem.root.directory |
| Set Up Calibration | set.up.calibration |
| Set Up Transmute Calibration | set.up.transmute.calibration |
| Plot Simulations And Data | simplot |
| Simplot Data Only | simplot.data.only |
| Convert Age Strata Names to a Standard Form | standardize.age.strata.names |
| Create an Static (Time-Invariant) Functional Form | STATIC.FUNCTIONAL.FORM |
| Subset a JHEEM Data Manager | subset_data |
| Subset a Simulation Set | subset.simset |
| Thin A Simulation Set | thin.simset |
| Track a Combination of Cumulative Outcomes | track.cumulative.outcome |
| Track an Outcome Formed by Integrating a Time-Varying Rate into a Proportion | track.cumulative.proportion.from.rate |
| Mark a Transition for Tracking | track.dynamic.outcome |
| Mark an Outcome to Be Integrated and Tracked | track.integrated.outcome |
| Track a Combination of "Point" (Non-Cumulative) Outcomes | track.point.outcome |
| Track Sub Version Outcomes for a Specification | track.sub.version.outcomes |
| Mark a Transition for Tracking | track.transition |
| Get the union of dimension values sets | union.dimension.values |
| Create a Target Population that is the UNION Other Target Populations | union.target.populations |
| Change the keep.dimensions of an outcome registered to an ancestor specification | update.outcome.keep.dimensions |
| Evaluate an expression under a data binding | using.data.binding |
| Check Whether a JHEEM Model Specification has been Registered for a Version | version.has.been.registered |
