R/datadoc.R

In spartan: Simulation Parameter Analysis R Toolkit ApplicatioN: 'spartan'

#' Latin-hypercube value set use to demonstrate emulated sensitivity analysis
#'
#' A dataset containing values for the six parameters that control the
#' simulation detailed in the case study section of the vignette. These
#' parameters are defined the accompanying publications referred to in
#' the vignette
#'
#' \itemize{
#'   \item stableBindProbability. Parameter values between 0 and 100
#'   \item chemokineExpressionThreshold. Parameter values between 0 and 1
#'   \item initialChemokineExpressionValue. Parameter values between 0.1 and 0.5
#'   \item maxChemokineExpressionValue. Parameter values between 0.015 and 0.08
#'   \item maxProbabilityOfAdhesion. Parameter values between 0 and 1
#'   \item adhesionFactorExpressionSlope. Parameter values between 0.25 and 5
#' }
#'
#' @docType data
#' @keywords datasets
#' @name emulated_lhc_values
#' @usage data(emulated_lhc_values)
#' @format A list with 500 rows (one per parameter set) and six columns
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#' Set of parameter and response pairs for training an emulator of a simulation
#'
#' This dataset contains 500 sets of parameter values and the responses that
#' were observed under those conditions when run through the simulator. This
#' is used as a dataset to show how one could use a set of simulation results
#' to train emulators, that in turn could be combined to form an ensemble.
#'
#' \itemize{
#'   \item stableBindProbability. Parameter values between 0 and 100
#'   \item chemokineExpressionThreshold. Parameter values between 0 and 1
#'   \item initialChemokineExpressionValue. Parameter values between 0.1 and 0.5
#'   \item maxChemokineExpressionValue. Parameter values between 0.015 and 0.08
#'   \item maxProbabilityOfAdhesion. Parameter values between 0 and 1
#'   \item adhesionFactorExpressionSlope. Parameter values between 0.25 and 5
#'   \item Velocity. Simulation response measure for cell speed
#'   \item Displacement. Simulation response measure for cell displacement
#'   \item PatchArea. Simulation response measure for size of formed clusters
#' }
#'
#' @docType data
#' @keywords datasets
#' @name sim_data_for_emulation
#' @usage data(sim_data_for_emulation)
#' @format A list with 500 rows (one per parameter set) and nine columns
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#' Example dataset showing the structure for consistency analysis data
#'
#' This dataset contains exemplar results from a consistency analysis, that
#' shown in the tutorial. This data can be read in and processed using the
#' functions detailed in the vignette. The important thing to obtain from this
#' object is the structure the data is expected to be in
#'
#' \itemize{
#'   \item SampleSize. Number of simulation executions in each subset
#'   \item Set. The number of the subset this result belongs to
#'   \item Velocity. The median velocity observed in simulation executions in
#'   this set
#'   \item Displacement. The median displacement observed in simulation
#'   executions in this set
#' }
#'
#' @docType data
#' @keywords datasets
#' @name tutorial_consistency_set
#' @usage data(tutorial_consistency_set)
#' @format A list with 9060 rows and four columns
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#' Analysed results from tutorial_consistency_set: a-test scores when sets compared
#'
#' This dataset contains the results of the analysis aa_getATestResults when
#' applied to the tutorial_consistency_dataset. Used in testing
#'
#' \itemize{
#'   \item Sample.Size Sample size being analysed
#'   \item Sample The number of the subset of this sample size
#'   \item ATestVelocity A-Test score for the velocity measure
#'   \item ATestVelocityNorm Normalised A-Test score for the velocity measure
#'   \item ATestDisplacement A-Test score for the displacement measure
#'   \item ATestDisplacementNorm Normalised A-Test score for the displacement measure
#' }
#'
#' @docType data
#' @keywords datasets
#' @name a_test_results
#' @usage data(a_test_results)
#' @format A list with 95 rows and 6 columns
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#' Example of a dataset output from an agent-based simulation, used in package testing
#'
#' This dataset contains exemplar results from an agent-based simulation, the
#' case study shown in the tutorial. This is used in unit testing of the spartan
#' package.
#'
#' \itemize{
#'   \item Cell.Type. The type of cell
#'   \item Time.Span Amount of minutes this cell was tracked for
#'   \item Cell.State Current state of this agent
#'   \item Cell.Speed Cell speed, assigned at start of sim
#'   \item Cell.Start.Position.X Start point X
#'   \item Cell.Start.Position.Y Start point Y
#'   \item Cell.End.Position.X End point X
#'   \item Cell.End.Position.Y End point Y
#'   \item Length Distance covered from start to end point
#'   \item Velocity Calculated velocity over this period
#'   \item Displacement The displacement of this agent
#'   \item Displacement.Rate Displacement rate of this agent
#'   \item Meandering.Index Meandering index of the agent
#'   \item Nearest.LTo.Cell..microns. Distance to nearest LTo cell
#' }
#'
#' @docType data
#' @keywords datasets
#' @name exemplar_sim_output
#' @usage data(exemplar_sim_output)
#' @format A list with 136 rows and 14 columns
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