model.chapy.customize {barrks}R Documentation

Customize CHAPY

Description

This page describes the parameters that can be used to customize CHAPY. The model was developed by Ogris et al. (2020). 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 to trigger the onset of infestation. Additionally, the maximum temperature must exceed tfly.

tfly

Minimum temperature that beetles need to fly.

dd_development_base

Base temperature to calculate degree days for development.

dd_total_dev

Degree days that are required for a generation to fully develop

dev_start, dev_end

Share in total development when the egg development starts and the juvenile beetle's development ends respectively. Usable if the development below/above these thresholds 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.

func_ftmin, func_ftmean, func_ftmax

Functions to caclulate the air temperature in forest stands (see Ogris et al. 2019, equations 1 - 3). Each parameter will be passed as SpatRaster:

  • tmin: min air temperature

  • tmean: mean air temperature

  • tmax: maximum air temperature

func_btmin, func_btmean, func_btmax

Functions to caclulate the bark temperature (see Ogris et al. 2019, equations 4 - 6). Each parameter will be passed as SpatRaster:

  • ftmin: min air temperature in forest stands

  • ftmean: mean air temperature in forest stands

  • ftmax: maximum air temperature in forest stands

dt_low, dt_up, topt, tmax, alpha, beta, gamma

Parameters to calculate the effective bark temperature (see Ogris et al. 2020, equations A.7 - A.9).

model_end_date

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

daylength_dia

When the daylength falls below this threshold, diapause will be initiated.

mortality_date

Date when all white stages (egg, larva, pupa) die.

Details

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

model("chapy",

      # ==== onset ====

      dd_onset_start_date = '03-09',
      dd_onset_base = 7.4,
      dd_onset_threshold = 216.5,

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

      tfly = 15.6,

      # ==== development ====

      dd_development_base = 7.4,
      dd_total_dev = 635.4,
      dev_start = 0,
      dev_end = 1,
      dev_sister_brood = 0.5,
      dev_mortal_min = NULL,
      dev_mortal_max = 0.8,

      func_ftmin = function(tmin) { 1.44 + 0.82 * tmin },
      func_ftmean = function(tmean) { 0.50 + 0.81 * tmean },
      func_ftmax = function(tmax) { 1.03 + 0.86 * tmax },

      func_btmin = function(atmin) { 0.56 + 0.99 * atmin },
      func_btmean = function(atmean) { -0.48 + 1.03 * atmean },
      func_btmax = function(atmax) { 0.03 + 0.99 * atmax },

      dt_low = 7.4,
      dt_up = 39.4,
      topt = 30,
      tmax = 41.97,
      alpha = 0.031,
      beta = 5.3,
      gamma = 1.25,

      model_end_date = '12-31',

      # ==== diapause ====

      daylength_dia = 13.6,

      # ==== mortality ====

      mortality_date = '12-31'
)

References

Ogris N, Ferlan M, Hauptman T, Pavlin R, Kavčič A, Jurc M, De Groot M (2019). “RITY–A phenology model of Ips typographus as a tool for optimization of its monitoring.” Ecological Modelling, 410, 108775. doi:10.1016/j.ecolmodel.2019.108775.

Ogris N, Ferlan M, Hauptman T, Pavlin R, Kavčič A, Jurc M, de Groot M (2020). “Sensitivity analysis, calibration and validation of a phenology model for Pityogenes chalcographus (CHAPY).” Ecological Modelling, 430, 109137. ISSN 0304-3800, doi:10.1016/j.ecolmodel.2020.109137.

See Also

model(), phenology(), model.chapy.apply

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


[Package barrks version 1.1.1 Index]