model.phenips_clim.customize: Customize PHENIPS-Clim

In barrks: Calculate Bark Beetle Phenology Using Different Models

Customize PHENIPS-Clim

Description

In barrks, model() is used to customize a model. Here, the parameters are described that can be used to customize PHENIPS-Clim. The model is currently unpublished. This manual will be updated as soon as a publication is available. Look here to find out how to apply the model.

Arguments

dd_onset_start_date	The date, when the degree days start to sum up ('MM-DD').
dd_onset_base	Base temperature to calculate degree days to trigger the onset.
onset_func	Function with the SpatRasters tmax (maximum temperature) and dd_tmax (degree days of maximum temperature) as parameters. The function should return TRUE when the base onset is triggered. See onset_add_dd for the actual onset of infestation.
dd_onset_alt_start_date, dd_onset_alt_base, onset_alt_func	Alternative way to calculate the diapause (see dd_onset_start_date, dd_onset_base and onset_func). The first of both onset variants will be used. Set onset_alt_func = NULL to disable the alternative onset calculation.
onset_add_dd	Vector of options to calculate the actual onset of infestation. The vector should be named after the share of beetles that already started breeding when the onset is triggered (choose an option via ⁠phenology(..., onset_mode = [option])⁠ when applying the model). The values specify the degree days that are required starting at the first positive return value of onset_func.
tfly	Minimum temperature that beetles need to fly.
dd_total_dev	Degree days that are required for a generation to fully develop
dev_oviposition	Named numeric vector of shares in the total development when the oviposition is finished. The vector should be named after the share of beetles that should be taken into account (choose an option via ⁠phenology(..., oviposition_mode = [option])⁠ when applying the model).
dev_end	Share in total development when the juvenile beetle's development ends. Usable if the development above this threshold should account for mating, oviposition etc.
dev_sister_brood	Share in the total development, when a sister brood will be established.
dev_mortal_min, dev_mortal_max	The beetles are considered to be in white stages (egg, larva, pupa) if their development exceeds dev_mortal_min and subceeds dev_mortal_max. During these stages, the beetles could die due to a mortality event. NULL means that no lower/upper threshold is defined.
topt	Temperature for optimal development.
func_btmean, func_btmax, func_btdiff	Functions to calculate the bark temperatures (see \insertCiteBaier2007;nobracketsbarrks, equations A.3 to A.5). Each parameter will be passed as SpatRaster: tmean: mean air temperature tmax: maximum air temperature rad: radiation btmax: maximum bark temperature
dev_rates	Data frame that specifies the development rates per day depending on the mean temperature and the temperature amplitude. Column names are the mean temperatures and row names the temperature amplitudes both with one decimal place. base onset (see onset_func) to trigger the actual onset.
model_end_date	Date when the model ends (no further development will be modeled).
first_diapause_date	Date before which an initiation of the diapause is impossible ('MM-DD').
diapause_thermal_func	Function to calculate the initiation of the diapause if the model was applied using phenology(..., diapause_mode = 'thermal'). The diapause will be initiated the last time when the function returns TRUE.
daylength_dia	When the daylength falls below this threshold, diapause will be initiated if the model was applied using phenology(..., diapause_mode = 'photoperiodic').
tlethal	Temperature threshold below which white stages will die.

Details

In barrks, model() is used to customize a model. The following code illustrates which parameters are available for PHENIPS-Clim and specifies their default values.

model("phenips-clim",

      # ==== onset ====

      dd_onset_start_date = '03-01',
      dd_onset_base = 12,
      onset_func = \(tmax, dd_tmax) {
        0.564071 * tmax + 0.006434 * dd_tmax - 12.37046 > 0
      },

      dd_onset_alt_start_date = '04-01',
      dd_onset_alt_base = 8.3,
      onset_alt_func = \(tmax, dd_tmax) dd_tmax >= 140,

      onset_add_dd = c('0.1' = 0, '0.5' = 90, '0.9' = 190),

      # ==== development ====

      tfly = 16.5,

      dd_total_dev = 557,

      dev_oviposition = c('0.1' = 0.1,
                          '0.5' = 0.15,
                          '0.9' = 0.26),
      dev_end = 1,
      dev_sister_brood = 0.3,

      dev_mortal_min = NULL,
      dev_mortal_max = 0.6,

      topt = 30.4,

      func_btmean = function(tmean, rad) {
        -0.173 + 0.0008518 * rad + 1.054 * tmean
      },
      func_btmax = function(tmax, rad) {
        1.656 + 0.002955 * rad + 0.534 * tmax + 0.01884 * tmax ^ 2
      },
      func_btdiff = function(tmax) {
        (-310.667 + 9.603 * tmax) / 24
      },

      # dev_rates too large to show here, type `params('phenips-clim')$dev_rates`
      # to get the dev_rates that are used by default
      # dev_rates = matrix(...),

      model_end_date = '12-31',

      # ==== diapause ====

      first_diapause_date = '08-12',
      diapause_thermal_func = function(daylength, tmax) {
        0.8619156 * daylength + 0.5081128 * tmax - 23.63691 > 0
      },
      daylength_dia = 14.5,

      # ==== mortality ====

      tlethal = -5
)

References

\insertAllCited

See Also

model(), phenology(), model.phenips_clim.apply

Other model customizations: model.bso.customize, model.chapy.customize, model.joensson.customize, model.lange.customize, model.phenips.customize, model.rity.customize

barrks documentation built on April 3, 2025, 9:47 p.m.