model.phenips_clim.apply {barrks}R Documentation

Use PHENIPS-Clim

Description

This page describes the usage of PHENIPS-Clim with phenology(). The model specific inputs are listed and its basic functionality is explained. PHENIPS-Clim is not published yet. This manual will be updated when a publication is available. It was parametrized for Ips typographus in southern Germany.

Arguments

...

See phenology() for a detailled description of the function. See phenology() for details.

tmin, tmean, tmax

Daily minimum/mean/maximum temperatures in °C. tmin is optional. If available it will be used to calculate the temperature amplitude. If not, (tmax - tmean) * 2 will be used as amplitude.

rad

Daily radiation in W * h / m^2.

daylength

Length of the day in hours. Can be created with create_daylength_rst() or create_daylength_rst().

sister_broods

Set FALSE to disable the calculation of sister broods.

scenario

Choose a scenario to use a suitable combination of parameters for specific situations. The scenario defines a default value for each value that can be overwritten by specifying a value for the respective parameter. The following scenarios are available:

  • mean: list(exposure = 'sunny', onset_mode = 0.5, diapause_mode = 'photoperiodic', oviposition_mode = 0.5)

  • max: list(exposure = 'sunny', onset_mode = 0.1, diapause_mode = 'thermal', oviposition_mode = 0.1)

exposure

Specifies the sun exposure. Can be 'sunny'(default) or 'shaded'.

onset_mode

Share of beetles that are already infesting trees necessary to trigger the onset. Must be 0.1, 0.5 or 0.9 if not customized.

oviposition_mode

Share of beetles that should have finished oviposition to trigger the beginning of the development. Must be 0.1, 0.5 or 0.9 if not customized.

diapause_mode

Determines how the diapause is initiated. Can be one of the following options:

  • 'photoperiodic': The diapause is initiated when the daylength falls below a specific threshold.

  • 'thermal': The diapause is initiated by a logistic model that depends on the daylength and the maximum temperature.

Share of beetles that already stopped reproducing necessary to trigger the diapause. Must be thermal or 'photoperiodic' if not customized. If 'photoperiodic' is chosen, the diapause is controlled by a daylength threshold (see parameter daylength_dia here).

Details

In barrks, phenology() is used to apply a model. The following code illustrates which inputs are required to apply PHENIPS-Clim and which additional parameters are available.

phenology("phenips-clim", ..., tmin, tmean, tmax, rad, daylength,
          sister_broods = TRUE, scenario = 'max', exposure = NULL,
          onset_mode = NULL, oviposition_mode = NULL, diapause_mode = NULL)

# calculate submodels separately
phenology("phenips-clim", ..., .submodels = 'onset', tmax, scenario = 'max', onset_mode = NULL)
phenology("phenips-clim", ..., .submodels = 'diapause', tmax, daylength, scenario = 'max', diapause_mode = NULL)
phenology("phenips-clim", ..., .submodels = 'mortality', tmin)
phenology("phenips-clim", ..., .submodels = 'development',
          .onset, .diapause = NULL, .mortality = NULL,
          tmin, tmean, tmax, rad, sister_broods = TRUE,
          scenario = 'max', exposure = NULL, oviposition_mode = NULL)

Functioning

In the following, the basic functioning of PHENIPS-Clim is explained.

Look here to find out how the model parameters affect the actual calculations and which values are used by default.

See Also

model(), phenology(), model.phenips_clim.customize

Other phenology applications: model.bso.apply, model.chapy.apply, model.joensson.apply, model.lange.apply, model.phenips.apply, model.rity.apply


[Package barrks version 1.0.0 Index]