model.bso.customize {barrks}R Documentation

Customize BSO

Description

This page describes the parameters that can be used to customize BSO. The model was developed by Jakoby et al. (2019). 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.

dd_onset_threshold

Degree days that are required before the individuals start regeneration feeding in slot_dia of the maturation stage. When the regeneration feeding has finished, the onset is triggered.

slot_dia

Maturation feeding slot where the individuals start regeneration feeding after diapause.

k

Factor for the calculation of the phloem temperature.

alpha, tlo, tup

Parameters used to calculate the transition probabilities for each stage (except preflight) in the following order: development, maturation feeding, reproduction.

tfly_min, tfly_max, pfly_max, beta

Parameters used to calculate the transition probabilities for the preflight stage.

num_slots

Named vector that defines the number of slots for each stage. The development stage is subdivided into the stages egg, larva and pupa.

psis

Probability that a sister brood will be established.

slot_sis

Maturation feeding slot where the individuals start regeneration feeding before they establish a sister brood.

model_end_date

Date when the model ends (no further development will be modeled).

diapause_first

The day of year when the diapause could start at the earliest.

diapause_last

The day of year when the diapause could start at the latest.

tdia_min

The diapause will be initiated when the average daily temperature falls below that value.

Details

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

model("bso",

      # ==== onset ====

      dd_onset_start_date = '01-01',
      dd_onset_base = 5.124198,
      dd_onset_threshold = 100,
      slot_dia = 6,

      # ==== onset + development ====

      k = 2.853738e-02,
      alpha = c(2.549060e-05, 0.0000789, 1.009450e-05),
      tlo = c(-1.297644e+01, 4.760089e+00, -4.424628e+00),
      tup = c(3.600070e+01, 4.002483e+01, 3.999390e+01),
      tfly_min = 16.1064,
      tfly_max = 31.2901,
      pfly_max = 9.863263e-03,
      beta = 1.363763,

      num_slots = c(
        'reproduction' = 11,
        'egg' = 18,
        'larva' = 45,
        'pupa' = 8,
        'maturation' = 8,
        'preflight' = 1
      ),

      # ==== development ====

      psis = 2.994450e-01,
      slot_sis = 4,

      model_end_date = '12-30',

      # ==== diapause ====

      diapause_first = 210,
      diapause_last = 232,
      tdia_min = 1.645209e+01
)

References

Jakoby O, Lischke H, Wermelinger B (2019). “Climate change alters elevational phenology patterns of the European spruce bark beetle (Ips typographus).” Global Change Biology, 25(12), 4048-4063. doi:10.1111/gcb.14766.

See Also

model(), phenology(), model.bso.apply

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


[Package barrks version 1.1.1 Index]