PhenoFlex function

PhenoFlex

Combined model of the dynamic model for chill accumulation and the GDH model

PhenoFlex(
  temp,
  times,
  A0 = 6319.5,
  A1 = 5.939917e+13,
  E0 = 3372.8,
  E1 = 9900.3,
  slope = 1.6,
  Tf = 4,
  s1 = 0.5,
  Tu = 25,
  Tb = 4,
  Tc = 36,
  yc = 40,
  Delta = 4,
  Imodel = 0L,
  zc = 190,
  stopatzc = TRUE,
  deg_celsius = TRUE,
  basic_output = TRUE
)

Arguments

• temp: Vector of temperatures.
• times: numeric vector. Optional times at which the temperatures where measured, if not given, hourly temperatures will be assumed
• A0: numeric. Parameter $A0$ of the dynamic model
• A1: numeric. Parameter $A1$ of the dynamic model
• E0: numeric. Parameter $E0$ of the dynamic model
• E1: numeric. Parameter $E1$ of the dynamic model
• slope: numeric. Slope parameter for sigmoidal function
• Tf: numeric. Transition temperature (in degree Kelvin) for the sigmoidal function
• s1: numeric. Slope of transition from chill to heat accumulation
• Tu: numeric. GDH optimal temperature
• Tb: numeric. GDH base temperature (lower threshold)
• Tc: numeric. GDH upper temperature (upper threshold)
• yc: numeric. Critical value defining end of chill accumulation
• Delta: numeric. Width of Gaussian heat accumulation model
• Imodel: integer. Heat accumulation model: 0 for GDH and 1 for Gaussian
• zc: numeric. Critical value of z determining the end of heat accumulation
• stopatzc: boolean. If TRUE, the PhenoFlex is applied until the end of the temperature series. Default is to stop once the value zc has been reached.
• deg_celsius: boolean. whether or not the temperature vector and the model temperature parameters are in degree Celsius (Kelvin otherwise)
• basic_output: boolean. If TRUE, only the bloomindex is returned as a named element of the return list.

Returns

A list is returned with named element bloomindex, which is the index at which blooming occurs. When basic_output=FALSE also x, y, z and xs are returned as named element of this list, which are numeric vectors of the same length as the input vector temp containing the hourly temperatures.

Examples

data(KA_weather)
hourtemps <- stack_hourly_temps(KA_weather, latitude=50.4)
iSeason <- genSeason(hourtemps, years=c(2009))
zc <- 190
yc <- 40
x <- PhenoFlex(temp=hourtemps$hourtemps$Temp[iSeason[[1]]],
               times=c(1: length(hourtemps$hourtemps$Temp[iSeason[[1]]])),
               zc=zc, stopatzc=TRUE, yc=yc, basic_output=FALSE)
DBreakDay <- x$bloomindex
ii <- c(1:DBreakDay)
plot(x=ii, y=x$z[ii], xlab="Hour Index", ylab="z", col="red", type="l")
abline(h=zc, lty=2)
plot(x=ii, y=x$y[ii], xlab="Hour Index", ylab="y", col="red", type="l")
abline(h=yc, lty=2)

Author(s)

Carsten Urbach urbach@hiskp.uni-bonn.de