Upgrade a MizerParams object for therMizer

Add therMizer-specific thermal parameters, temperature forcing, optional plankton forcing, and realm structure to a standard MizerParams object.

Usage

upgradeTherParams(
  params,
  temp_min = NULL,
  temp_max = NULL,
  ocean_temp_array = NULL,
  n_pp_array = NULL,
  vertical_migration_array = NULL,
  exposure_array = NULL,
  aerobic_effect = TRUE,
  metabolism_effect = TRUE
)

Arguments

params

A MizerParams object to augment.

temp_min

Numeric vector giving the lower thermal limit of each species, in degrees C. Its length must match the number of species in params.

temp_max

Numeric vector giving the upper thermal limit of each species, in degrees C. Its length must match the number of species in params.

ocean_temp_array

Numeric scalar, vector, matrix, or array of temperatures. The first dimension is interpreted as time. If a second dimension is present it is interpreted as realms. Character time labels in %Y, %Y-%m, or %Y-%m-%d format are converted to numeric years.

n_pp_array

Optional vector, matrix, or array of plankton forcing with dimensions time x size. The time dimension must match ocean_temp_array, and the size dimension must match params@w_full. Values are interpreted on the log10 scale used by plankton_forcing().

vertical_migration_array

Optional array of dimensions realm x species x size giving the fraction of time each species spends in each realm at each size. Values must be non-negative and sum to 1 across realms for every species-size combination.

exposure_array

Optional array of dimensions realm x species with values between 0 and 1 describing how strongly each species is exposed to temperature in each realm.

aerobic_effect

Logical. If TRUE, replace mizer's default encounter and predation-rate functions with therMizer's temperature-scaled versions. Default is TRUE.

metabolism_effect

Logical. If TRUE, replace mizer's default energy-for-growth-and-reproduction function with therMizer's temperature-scaled version. Default is TRUE.

Value

The modified params object, ready to use with therMizer.

Details

If vertical_migration_array is omitted, a default realm allocation is constructed from the available temperature data. If n_pp_array is supplied, the resource dynamics function is set to plankton_forcing(). The returned object also stores a time offset in other_params(params)$t_idx so therMizer can align mizer's simulation time with the supplied forcing series.

See also

setVerticality(), setEncounterPredScale(), setMetabTher(), and plankton_forcing().

Examples

# \donttest{
params <- suppressMessages(
  mizer::newMultispeciesParams(
    data.frame(species = c("sp1", "sp2"), w_inf = c(100, 1000),
               k_vb = c(0.3, 0.2), w_mat = c(10, 100),
               beta = c(100, 100), sigma = c(2, 2)),
    no_w = 16))
#> Warning: The species parameter data frame is missing a `w_max` column. I am copying over the values from the `w_inf` column. But note that `w_max` should be the maximum size of the largest individual, not the asymptotic size of an average indivdidual.
#> Warning: The species parameter data frame is missing a `w_max` column. I am copying over the values from the `w_inf` column. But note that `w_max` should be the maximum size of the largest individual, not the asymptotic size of an average indivdidual.

# Minimal usage: constant temperature, one realm per species
params <- suppressWarnings(suppressMessages(
  upgradeTherParams(params,
    temp_min = c(-2, 5), temp_max = c(12, 18),
    ocean_temp_array = c("2000" = 5, "2001" = 6, "2002" = 7))))

# Project for 2 years starting from the first temperature time step
sim <- project(params, t_start = 2000, t_max = 2, dt = 1)

# Two realms: sp1 lives at the surface, sp2 in the deep
ocean_temp <- array(
  c(4, 8, 5, 9, 6, 10),
  dim = c(3, 2),
  dimnames = list(time = c("2000", "2001", "2002"),
                  realm = c("surface", "deep")))
vm <- array(0,
  dim = c(2, 2, length(params@w)),
  dimnames = list(realm = c("surface", "deep"),
                  sp = c("sp1", "sp2"), w = params@w))
vm["surface", "sp1", ] <- 1
vm["deep",    "sp2", ] <- 1
params2 <- suppressWarnings(suppressMessages(
  upgradeTherParams(params,
    temp_min = c(-2, 5), temp_max = c(12, 18),
    ocean_temp_array = ocean_temp,
    vertical_migration_array = vm)))
sim2 <- project(params2, t_start = 2000, t_max = 2, dt = 1)
# }