PhenoFlex: PhenoFlex

In chillR: Statistical Methods for Phenology Analysis in Temperate Fruit Trees

PhenoFlex

Description

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

Usage

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 A_0 of the dynamic model
A1	numeric. Parameter A_1 of the dynamic model
E0	numeric. Parameter E_0 of the dynamic model
E1	numeric. Parameter E_1 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.

Value

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.

Author(s)

Carsten Urbach <[e-mail]>

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)

chillR documentation built on Nov. 28, 2023, 1:09 a.m.