run_model: Function that optimizes sinusoid parameters to fit d18O data
In ShellChron: Builds Chronologies from Oxygen Isotope Profiles in Shells

Description Usage Arguments Value References See Also Examples

The second core function of the ShellChron growth model. Loops through all data windows and uses the growth_model function to create d18O series that match the input data. This step is iterated and optimized (minimizing the Sum of Squared Residuals) through the SCEUA algorithm (by Duan et al., 1992) which finds the optimal input parameters to the growth rate and Sea Surface Temperature (SST) sinusoids to simulate d18O data.

run_model(
  dat,
  dynwindow,
  transfer_function = "KimONeil97",
  d18Ow = 0,
  T_per = 365,
  G_per = 365,
  t_int = 1,
  t_maxtemp = 182.5,
  SCEUApar = c(1, 25, 10000, 5, 0.01, 0.01),
  sinfit = TRUE,
  MC = 1000,
  plot = FALSE
)

`dat`	Matrix containing the input data
`dynwindow`	Information on the position and length of modeling windows
`transfer_function`	Transfer function used to convert d18Oc to temperature data.
`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_per`	Period of SST sinusoid (in days; default = 365)
`G_per`	Period of growth rate sinusoid (in days; default = 365)
`t_int`	Time interval (in days; default = 1)
`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 results of modeling be plotted? `TRUE/FALSE`

A list containing the resultarray which contains the full result of all simulations on each data window and the parmat listing all optimized growth rate and SST parameters used to model d18O in each data window

package dependencies: ggplot2 3.2.1; rtop 0.5.14 Function dependencies: sinreg, d18O_model, growth_model

doi: 10.1029/91WR02985

Duan, Qingyun, Soroosh Sorooshian, and Vijai Gupta. "Effective and efficient global optimization for conceptual rainfall runoff models." Water resources research 28.4 (1992): 1015-1031. https://doi.org/10.1029/91WR02985

# Create dummy input data column by column
dat <- as.data.frame(seq(1000, 40000, 1000))
colnames(dat) <- "D"
dat$d18Oc <- sin((2 * pi * (seq(1, 40, 1) - 8 + 7 / 4)) / 7)
dat$YEARMARKER <- c(0, rep(c(0, 0, 0, 0, 0, 0, 1), 5), 0, 0, 0, 0)
dat$D_err <- rep(100, 40)
dat$d18Oc_err <- rep(0.1, 40)
# Create dummy dynwindow data
dynwindow <- as.data.frame(seq(1, 29, 2))
colnames(dynwindow) <- "x"
dynwindow$y <- rep(12, 15)
# Run model function
resultlist <- run_model(dat = dat,
    dynwindow = dynwindow,
    transfer_function = "KimONeil97",
    d18Ow = 0,
    T_per = 365,
    G_per = 365,
    t_int = 1,
    t_maxtemp = 182.5,
    SCEUApar = c(1, 25, 10000, 5, 0.01, 0.01),
    sinfit = TRUE,
    MC = 1000,
    plot = FALSE)