phenthau: Calculate PHENTHAUproc model

In PHENTHAUproc: Phenology Modelling of Thaumetopoea Processionea

Calculate PHENTHAUproc model

Description

"phenthau" implements the early warning system PHENTHAUproc created by Halbig et al. 2024 in R.

Usage

phenthau(x, params = NULL, def_hatch = "first", budswelling = NULL)

Arguments

x	SpatRaster list/SpatRaster/data.frame - numeric - with time attribute/date column (see Details for Input requirements)
params	list with parameter (see Details for Input requirements)
def_hatch	"first" or "mean": PHENTHAUproc has three hatch models integrated (for details see: Custers 2003, Wagenhoff et al. 2014, Meurisse et al. 2012). With "first" (Default) the first hatch-model which predicts hatch, with "mean", the mean day of all hatch-models will be used for further calculations.
budswelling	SpatRaster/numeric with DOY (Day of year) - If budswelling is provided, internal calculation of budswelling will be replaced. For raster input provide a raster with same extend and crs as x.

Details

Overview

phenthau function combines multiple phenology models:

• bud swelling & leaf unfolding of Quercus robur or Quercus petraea(still in development)

• hatch of oak processionary moth using 3 different hatch models (Custers 2003, Wagenhoff et al. 2014 and Meurisse et al. 2012)

• development stages of OPM (0 egg - 8 adult)

Input requirements

For different input type different parameter sets are needed. If params is not provided it will be selected dependent on datatype and names(x) so follow the name convention!

daily raster input with tmean, tmin and tmax:

• a list of 3 named objects: "tmean", "tmin" and "tmax"

• each object is a SpatRaster with one layer per day

• terra::time for each SpatRaster has to be set to Date -> parameter("dailymeanminmax", year)

daily raster input with tmean:

• a SpatRaster

• one layer per day

• terra::time has to be set to Date

• params has to be set manually! -> parameter("dailymean", year)

hourly raster input:

• a SpatRaster

• one layer per hour

• terra::time has to be set to Date -> parameter("hour", year)

daily data.frame input with tmean, tmin and tmax:

• a data.frame with 4 columns: "date", "tmean", "tmin", "tmax"

• one row per day -> parameter("dailymeanminmax", year)

daily data.frame input with tmean:

• a data.frame with 2 columns: "date", "tmean"

• one row per day

• "date" column is.Date -> parameter("dailymean", year)

hourly data.frame input:

• a data.frame with 2 columns: "date", "hour", "tmean"

• 24 rows per day

• "date" column is.Date -> parameter("hour", year)

Parametrisation

Additional parametrization is provided but has not yet been tested.

Use parameter() to return a data.frame with all possible parametrization options or choose a model. The default is "dailymeanminmax" and not dependent on the data input anymore.

• "dailymean": Regional PHENTHAUproc how described in Halbig et al. 2024 for daily mean temperature data

• "hour": Local PHENTHAUproc how described in Halbig et al. 2024 for hourly temperature data

• "dailymeanminmax": PHENTHAUproc for daily mean, max and min temperature data adapted to open access DWD raster data

Output

Regional Output:
A list with all model calculations as SpatRaster objects:

• stages: SpatRaster with one layer per day - numeric - values from 0-8 (0 egg stage - 8 adult stage). -> use get_legend("stages") to show id/cover/colors

• custers/wagenhoff/meurisse - one layer per day - logical - TRUE/FALSE for hatch or no hatch

• budswelling: one layer per day - logical - TRUE/FALSE for budswelling or no budswelling

• leafunfolding: one layer per day - logical - TRUE/FALSE for leafunfolding or no leafunfolding -> plot the first day of a logical SpatRaster with plot_date()

• mortality: one layer - integer - mortality in %

• ppa_biocide: one layer per day - numeric - 0 application of plant protection agents (PPA) and biocides not yet effective, 1 application effective, 2 appliaction not effective anymore

Local Output:
A data.frame with two columns:

• model: name of model

• date: date of first appearing of event

Presentation

Regional Output:

• plot_stages is a wrapper around terra::plot to preset legend, names, colors and day to plot.

• plot_date is a wrapper around terra::plot to plot the date of first TRUE in multiple layered SpatRaster

Local Output:

• plot_station_step is for local weather station data and creates a stepwise graph for the development stages

Value

data.frame or list of SpatRaster with all PHENTHAUproc model outputs (see Details)

Author(s)

Bachfischer Lorenz, Department of Forest Protection FVA (2024) [e-mail]

References

Halbig et al. 2024: Halbig, P., Stelzer, A. S., Baier, P., Pennerstorfer, J., Delb, H., & Schopf, A. (2024). PHENTHAUproc–An early warning and decision support system for hazard assessment and control of oak processionary moth (Thaumetopoea processionea). Forest Ecology and Management, 552, 121525
Custers 2003: Custers, C. (2003). Climate change and trophic synchronisation. English Wageningen UR, Chairgroup Environmental Systems Analysis.
Wagenhoff et al. 2014: Wagenhoff, E., Wagenhoff, A., Blum, R., Veit, H., Zapf, D., & Delb, H. (2014). Does the prediction of the time of egg hatch of Thaumetopoea processionea (Lepidoptera: Notodontidae) using a frost day/temperature sum model provide evidence of an increasing temporal mismatch between the time of egg hatch and that of budburst of Quercus robur due to recent global warming?. European Journal of Entomology, 111(2).
Meurisse et al. 2012: Meurisse, N., Hoch, G., Schopf, A., Battisti, A., & Grégoire, J. C. (2012). Low temperature tolerance and starvation ability of the oak processionary moth: implications in a context of increasing epidemics. Agricultural and forest entomology, 14(3), 239-250.

See Also

Other Main: get_legend(), mortality(), parameter(), phenology()

Examples

srl <- load_test()
phen <- phenthau(srl)

PHENTHAUproc documentation built on June 22, 2024, 7:12 p.m.