spphpr (version 1.0.0)

ADTS: Function for Implementing the Accumulated Days Transferred to a Standardized Temperature Method

Description

Estimates the starting date (\(S\), in day-of-year) and activation free energy (\(E_{a}\), in kcal \(\cdot\) mol\({}^{-1}\)) in the accumulated days transferred to a standardized temperature (ADTS) method using mean daily air temperatures (Konno and Sugihara, 1986; Aono, 1993; Shi et al., 2017a, 2017b).

Usage

ADTS( S.arr, Ea.arr, Year1, Time, Year2, DOY, Temp, DOY.ul = 120, 
      fig.opt = TRUE, verbose = TRUE )

Value

mAADTS.mat

a matrix consisiting of the means of the annual accumulated days transferred to a standardized temperature (AADTS) values from the combinations of \(S\) and \(E_{a}\)

RMSE.mat

the matrix consisting of the RMSEs (in days) from different combinations of \(S\) and \(E_{a}\)

AADTS.arr

the AADTS values in different years associated with the smallest value in RMSE.mat

Year

The overlapping years between Year1 and Year2

Time

The observed occurence times (day-of-year) in the overlapping years between Year1 and Year2

Time.pred

the predicted occurence times in different years

S

the determined starting date (day-of-year)

Ea

the determined activation free energy values (in kcal\(\cdot\)mol\({}^{-1}\))

AADD

the expected AADTS

RMSE

the smallest RMSE (in days) in RMSE.mat from different combinations of \(S\) and \(E_{a}\)

unused.years

the years that have phenological records but lack climate data

Arguments

S.arr

the candidate starting dates for thermal accumulation (in day-of-year)

Ea.arr

the candidate activation free energy values (in kcal \(\cdot\) mol\({}^{-1}\))

Year1

the vector of the years in which a particular phenological event was recorded

Time

the vector of the occurence times (in day-of-year) of a particular phenological event across many years

Year2

the vector of the years recording the climate data corresponding to the occurrence times

DOY

the vector of the dates (in day-of-year) for which climate data exist

Temp

the mean daily air temperature data (in \({}^{\circ}\)C) corresponding to DOY

DOY.ul

the upper limit of DOY used to predict the occurrence time

fig.opt

an optional argument to draw the figures associated with the determination of the combination the starting date and activation free energy, and a comparision between the predicted and observed occurrence times

verbose

an optional argument allowing users to suppress the printing of computation progress

Author

Peijian Shi , Zhenghong Chen , Brady K. Quinn .

Details

When fig.opt is equal to TRUE, it will show the contours of the root-mean-square errors (RMSEs) based on different combinations of \(S\) and \(E_{a}\).

\(\qquad\)The function does not require that Year1 is the same as unique(Year2), and the intersection of the two vectors of years will be kept. The unused years that have phenological records but lack climate data will be showed in unused.years in the returned list.

\(\qquad\)The numerical value of DOY.ul should be greater than or equal to the maximum Time.

References

Aono, Y. (1993) Climatological studies on blooming of cherry tree (Prunus yedoensis) by means of DTS method. Bulletin of the University of Osaka Prefecture. Ser. B, Agriculture and life sciences 45, 155\(-\)192 (in Japanese with English abstract).

Konno, T., Sugihara, S. (1986) Temperature index for characterizing biological activity in soil and its application to decomposition of soil organic matter. Bulletin of National Institute for Agro-Environmental Sciences 1, 51\(-\)68 (in Japanese with English abstract).

Shi, P., Chen, Z., Reddy, G.V.P., Hui, C., Huang, J., Xiao, M. (2017a) Timing of cherry tree blooming: Contrasting effects of rising winter low temperatures and early spring temperatures. Agricultural and Forest Meteorology 240\(-\)241, 78\(-\)89. tools:::Rd_expr_doi("10.1016/j.agrformet.2017.04.001")

Shi, P., Fan, M., Reddy, G.V.P. (2017b) Comparison of thermal performance equations in describing temperature-dependent developmental rates of insects: (III) Phenological applications. Annals of the Entomological Society of America 110, 558\(-\)564. tools:::Rd_expr_doi("10.1093/aesa/sax063")

See Also

predADTS

Examples

data(apricotFFD)
data(BJDAT)
X1 <- apricotFFD
X2 <- BJDAT

Year1.val  <- X1$Year
Time.val   <- X1$Time
Year2.val  <- X2$Year
DOY.val    <- X2$DOY
Temp.val   <- X2$MDT
DOY.ul.val <- 120
S.arr0     <- seq(40, 60, by = 1)
Ea.arr0    <- seq(10, 20, by = 1)

# \donttest{
  res3 <- ADTS( S.arr = S.arr0, Ea.arr = Ea.arr0, Year1 = Year1.val, Time = Time.val, 
                Year2 = Year2.val, DOY = DOY.val, Temp = Temp.val, DOY.ul = DOY.ul.val, 
                fig.opt = TRUE, verbose = TRUE)
  res3

  RMSE.mat0  <- res3$RMSE.mat
  RMSE.range <- range(RMSE.mat0)

  dev.new()
  par1 <- par(family="serif")
  par2 <- par(mar=c(5, 5, 2, 2))
  par3 <- par(mgp=c(3, 1, 0))
  image( S.arr0, Ea.arr0, RMSE.mat0, col = terrain.colors(200), axes = TRUE, 
         cex.axis = 1.5, cex.lab = 1.5, xlab = "Starting date (day-of-year)", 
         ylab = expression(paste(italic(E["a"]), " (kcal" %.% "mol"^{"-1"}, ")", sep = "")))
  points( res3$S, res3$Ea, cex = 1.5, pch = 16, col = 2 )
  contour( S.arr0, Ea.arr0, RMSE.mat0, levels = round(seq(RMSE.range[1], 
           RMSE.range[2], len = 20), 4), add = TRUE, cex = 1.5, col = "#696969", labcex = 1.5)
  par(par1)
  par(par2)
  par(par3)

  resu3 <- ADTS( S.arr = 47, Ea.arr = seq(10, 20, by = 0.5), Year1 = Year1.val, Time = Time.val, 
                 Year2 = Year2.val, DOY = DOY.val, Temp = Temp.val, DOY.ul = DOY.ul.val, 
                 fig.opt = TRUE, verbose = TRUE)
  resu3

  # graphics.off()

# }