ShellChron (version 0.4.0)

wrap_function: Full ShellChron workflow wrapped in a single function

Description

Takes starting parameters and names of input files and directory and runs through all the steps of the ShellChron model. Function includes options for plotting and exporting raw data, which are parsed into underlying formulae.

Usage

wrap_function(
  path = getwd(),
  file_name,
  transfer_function = "KimONeil97",
  t_int = 1,
  T_per = 365,
  d18Ow = 0,
  t_maxtemp = 182.5,
  SCEUApar = c(1, 25, 10000, 5, 0.01, 0.01),
  sinfit = TRUE,
  MC = 1000,
  plot = TRUE,
  plot_export = TRUE,
  export_raw = FALSE,
  export_path = getwd()
)

Arguments

path

String containing the path to the directory that contains the input data.

file_name

Name of the file that contains d18O data

transfer_function

String containing the name of the transfer function. Defaults to Kim and O'Neil, 1997.

t_int

Time interval (in days; default = 1)

T_per

Period of SST sinusoid (in days; default = 365)

d18Ow

Either a single value (constant d18Ow) or a vector of length equal to the period in SST data (365 days by default) containing information about seasonality in d18Ow. Defaults to constant d18Ow of 0 permille VSMOW (the modern mean ocean value)

t_maxtemp

Timing of the warmest day of the year (in julian day; default = 182.5, or May 26th halfway through the year)

SCEUApar

Parameters for SCEUA optimization (iniflg, ngs, maxn, kstop pcento, peps) For details, refer to Duan et al. (1992) in references

sinfit

Apply sinusoidal fitting to guess initial parameters for SCEUA optimization? TRUE/FALSE

MC

Number of Monte Carlo simulations to apply for error propagation. Default = 1000

plot

Should an overview of the results of modeling be plotted? TRUE/FALSE

plot_export

Should the overview plot be exported as a PDF file? TRUE/FALSE

export_raw

Export tables containing all raw model results before being merged into tidy tables? TRUE/FALSE

export_path

Path where result files are exported

Value

CSV tables of model results in the current working directory, optional plots in PDF format and list object of model results for further processing in the R workspace.

References

function dependencies: data_import, run_model, cumulative_day, export_results

Examples

# NOT RUN {
# find attached dummy data
# }
# NOT RUN {
example <- wrap_function(path = getwd(),
    file_name = system.file("extdata", "Virtual_shell.csv",
    package = "ShellChron"),
    transfer_function = "KimONeil97",
    t_int = 1,
    T_per = 365,
    d18Ow = 0,
    t_maxtemp = 182.5,
    SCEUApar = c(1, 25, 10000, 5, 0.01, 0.01),
    sinfit = TRUE,
    MC = 1000,
    plot = FALSE,
    plot_export = FALSE,
    export_raw = FALSE,
    export_path = tempdir())
# }
# NOT RUN {
 # Run function
# }