NLL_dynamic_contrast: Function for fitting the GVRDM and Aksnes and Utne model
In sean-rohan-NOAA/GVRDM: Generalized visual reaction distance model

Generalized visual reaction distance model and Aksnes and Utne model

NLL_dynamic_contrast(
  rr,
  cc,
  Ap = NA,
  C0 = NA,
  Eprime = NA,
  prey.types = NA,
  prey = NA,
  prey.size = NA,
  tt = NA,
  tt1 = NA,
  tt2 = NA,
  tt3 = NA,
  tt4 = NA,
  Ke,
  Ke.trans = FALSE,
  Eb,
  angle = NA,
  kd = NA,
  kd.mult = NA,
  beta = NA,
  kk = NA,
  delta = NA,
  alpha = 1,
  sigma = NA,
  rr.log = TRUE,
  NVrd = NA,
  NVthreshold = 0,
  NVsigma = NA,
  fit.model = TRUE,
  fit.obs = TRUE,
  ccoffset = NA,
  silent = F,
  ...
)

`rr`	Reaction distance
`cc`	Effective attenuation coefficient or beam attenuation coefficient
`Ap`	Prey area. If Ap and C0 are not provided, tt will be estimated.
`C0`	Prey inherent contrast. If Ap and C0 are not provided, tt will be estimated.
`Eprime`	Composite saturation parameter.
`prey.types`	A vector specifying unique prey name categories that are passed to 'prey.' Used if parameters are simultaneously estimated for multiple prey types.
`prey`	Vector of prey names for each observation.
`prey.size`	Vector of prey size
`tt`	T parameter for prey type 0. Default = NA
`tt1`	T parameter for prey type 1. Default = NA
`tt2`	T parameter for prey type 2. Default = NA
`tt3`	T parameter for prey type 3. Default = NA
`tt4`	T parameter for prey type 4. Default = NA
`Ke`	Half-saturation constant
`Ke.trans`	Should Ke be transformed in the model?
`Eb`	# Light level
`angle`	Nadir viewing angle in degrees
`kd`	Diffuse attenuation coefficient of downwelling irradiance
`kd.mult`	Multiplier to convert beam attenuation
`beta`	Dynamic scaling function intercept parameter
`delta`	Dynamic scaling function shape parameter
`alpha`	Naka-Rushton exponent. Default = 1
`sigma`	Standard deviation of visual reaction distance
`rr.log`	Are visual errors lognormal distribution? Default = TRUE
`NVrd`	Non-visual reaction distance. Default = NA (only fit visual component of the model)
`NVthreshold`	Light threshold for non-visual reaction. Default = NA(only fit visual component of the model)
`NVsigma`	Standard deviation of non-visual reaction distance. Default = NA(only fit visual component of the model)
`fit.model`	Logical.Should the model be fitted? If FALSE, produces model diagnostics and predictions based on provided parameters.
`fit.obs`	Logical. Should observations be used to calculate a likelihood?
`ccoffset`	Shift kappa or beam attenuation? Default = NA results in no shift.
`silent`	Logical. Should diagnostic plots be produced?
`hh`	Dynamic scaling function rate parameter
`return`	If fit.model is TRUE, returns the negative log likelihood. If fit is FALSE, returns model diagnostics and predictions using parameters that are passed to the model.