| % Generated by roxygen2: do not edit by hand |
| % Please edit documentation in R/task_parameterestimation.R |
| \name{defineExperiments} |
| \alias{defineExperiments} |
| \title{Define a parameter estimation experiment} |
| \usage{ |
| defineExperiments( |
| experiment_type = c("time_course", "steady_state"), |
| data = NULL, |
| types = NULL, |
| mappings = NULL, |
| weights = NULL, |
| weight_method = NULL, |
| normalize_weights_per_experiment = FALSE, |
| filename = NULL |
| ) |
| } |
| \arguments{ |
| \item{experiment_type}{string} |
|
|
| \item{data}{list of tidy data frames} |
|
|
| \item{types}{data column types as character vector |
|
|
| Allowed types of columns are: 'time', 'independent', 'dependent', 'ignore'. |
|
|
| Type 'time' is only allowed for time course experiments. |
|
|
| Can be a named vector to only specify for a subset of data columns.} |
|
|
| \item{mappings}{data column mappings as character vector |
|
|
| Expects value references. |
|
|
| If no mappings are given, column names can serve as mappings. |
|
|
| Can be a named vector to only specify for a subset of data columns.} |
|
|
| \item{weights}{data column weights as numeric vector |
|
|
| `NaN` corresponds to automatic weight. |
|
|
| Can be a named vector to only specify for a subset of data columns.} |
|
|
| \item{weight_method}{string |
|
|
| Allowed methods: 'mean', 'mean_square', 'sd', 'value_scaling'.} |
|
|
| \item{normalize_weights_per_experiment}{flag} |
|
|
| \item{filename}{optional string |
|
|
| When adding the experiments to a COPASI model, this filename will be used. |
| In use cases, where experiments are only used temporarily, the filename is ignored.} |
| } |
| \value{ |
| copasi_exp object for input into related functions |
| } |
| \description{ |
| \code{defineExperiments} defines a set of experiments given as tidy data frame to the given model. |
| } |
| \details{ |
| CoRC uses it's own methodology for defining experimental data for use with a COPASI model. |
| To this end it is required that experimental data be imported to R by the user and transformed to tidy data. |
| For help on data import and tidying see: \code{vignette("tidy-data", "tidyr")}. |
| This function adds required metadata to experimental data for use with CoRC. |
| } |
| \seealso{ |
| \code{\link{addExperiments}} \code{\link{clearExperiments}} |
| |
| Other parameter estimation: |
| \code{\link{addExperiments}()}, |
| \code{\link{addParameterEstimationParameter}()}, |
| \code{\link{clearExperiments}()}, |
| \code{\link{clearParameterEstimationParameters}()}, |
| \code{\link{clearValidations}()}, |
| \code{\link{getParameterEstimationSettings}()}, |
| \code{\link{runParameterEstimation}()}, |
| \code{\link{setParameterEstimationSettings}()} |
| } |
| \concept{parameter estimation} |
| |
