% 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}