fit.final_space: Fit n parameters to observations
In isobxr: Stable Isotope Box Modelling in R

fit.final_space

R Documentation

Fit n parameters to observations

Description

A function to find the combinations of values of n parameters producing final state delta values fitting within confidence intervals of observations.

Usage

fit.final_space(
  workdir,
  obs_file_name,
  sweep_space_digest_folders,
  fit_name = NULL,
  output_dir = NULL,
  delta_reference_box = NaN,
  excluded_boxes = NULL,
  print_correlogram = FALSE,
  print_lda = FALSE,
  print_LS_surfaces = FALSE,
  parameter_subsets = NULL,
  custom_expressions = NULL,
  save_outputs = FALSE,
  export_fit_data = FALSE
)

Arguments

`workdir`	Working directory of *0_ISOBXR_MASTER.xlsx* master file, of the dynamic sweep master file (e.g., *0_EXPLO_DYN_MASTER.xlsx*) and where output files will be stored if saved by user. (character string)
`obs_file_name`	Name of csv file containing observations with csv extension. Stored in workdir. Example: "observations.csv" Should contain the following columns: BOX_ID: BOX ID (e.g., A, OCEAN...) as defined in isobxr master file. delta.def definition of delta value, e.g., d18O delta.ref BOX_ID of reservoir used as a reference. obs.delta average observed delta numerical value obs.CI confidence interval of delta value obs.CI.def definition of confidence interval, e.g., 95 obs.file name of data source file
`sweep_space_digest_folders`	Name of sweep.final_nD digest directory. Should start with "4_FINnD" and end with "_digest"
`fit_name`	Name given to specific fit. If NULL, output are named after date and time of fit.
`output_dir`	Destination directory for fit outputs. If NULL, outputs are stored in sweep_space_digest_folders directory. Default is NULL.
`delta_reference_box`	BOX ID of reference box, used to calculate difference between any box delta and reference box delta. Default is NaN. delta_reference_box should match at least one of the values declared in the delta.ref column of observation csv file.
`excluded_boxes`	list of boxes to exclude from fit. Default is NULL.
`print_correlogram`	If TRUE, includes correlograms to final report when applicable. Default is FALSE.
`print_lda`	If TRUE, includes linear discriminant analysis to final report when applicable. Default is FALSE.
`print_LS_surfaces`	If TRUE, includes surfaces of least squarred residuals to final report when applicable. Default is FALSE.
`parameter_subsets`	List of limits vectors for parameters to subset before fit. For instance: list(swp.A.A_B = c(1, 1.00001)) to subset the swept fractionation factor from box A to B between 1 and 1.00001.
`custom_expressions`	Vector of expressions to add to the list of fitted parameters. For instance: c("m0.A/f.A_B") to add the ratios of mass of A over A to B flux to the list of parameters.
`save_outputs`	If TRUE, saves all run outputs to local working directory (workdir). By default, run outputs are stored in a temporary directory and erased if not saved. Default is FALSE.
`export_fit_data`	If TRUE, exports fitted data as csv and rds files.