Customize PHENIPS

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 caused by 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 caclulate 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 .

Arguments

Details

References

See also