Customize CHAPY

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 caused by 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 .

Arguments

Details

References

See also