model.phenips.customize {barrks}R Documentation

Customize PHENIPS

Description

This page describes the parameters that can be used to customize PHENIPS. The model was developed by Baier et al. (2007). 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 calculating the beetles 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.

topt

Temperature for optimal development.

tlow, tup

Temperature below/above which no development happens.

func_btmean, func_btmax, func_btdiff

Functions to calculate the effective bark temperature (see Baier et al. 2007, equations A.3 to A5). Each parameter will be passed as SpatRaster:

  • tmean: mean air temperature

  • tmax: maximum air temperature

  • rad: radiation

  • btmax: maximum bark temperature

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 PHENIPS and specifies their default values.

model("phenips",

      # ==== onset ====

      dd_onset_start_date = '04-01',
      dd_onset_base = 8.3,
      dd_onset_threshold = 140,

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

      tfly = 16.5,

      # ==== development ====

      dd_development_base = 8.3,
      dd_total_dev = 557,
      dev_start = 0,
      dev_end = 1,
      dev_sister_brood = 0.5,
      dev_mortal_min = NULL,
      dev_mortal_max = 0.6,

      topt = 30.4,
      tlow = 8.3,
      tup = 38.9,

      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(btmax) {
        (-310.667 + 9.603 * btmax) / 24
      },

      model_end_date = '10-31',

      # ==== diapause ====

      daylength_dia = 14.5,

      # ==== mortality ====

      mortality_date = '10-31'
)

References

Baier P, Pennerstorfer J, Schopf A (2007). “PHENIPS—A comprehensive phenology model of Ips typographus (L.)(Col., Scolytinae) as a tool for hazard rating of bark beetle infestation.” Forest Ecology and Management, 249(3), 171–186. doi:10.1016/j.foreco.2007.05.020.

See Also

model(), phenology(), model.phenips.apply

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


[Package barrks version 1.1.1 Index]