ADTS {spphpr} | R Documentation |
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 )
Arguments
S.arr |
the candidate starting dates for thermal accumulation (in day of year) |
Ea.arr |
the candidate activation free energy values (in kcal |
Year1 |
the vector of the years recording a particular phenological event |
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) when the climate data exist |
Temp |
the mean daily air temperature data (in |
DOY.ul |
the upper limit of |
fig.opt |
an optional argument of drawing the figures assoicated 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 of allowing users to suppress printing of computation progress |
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 the unique of Year2
,
and the intersection of two years will be finally kept. The unused years that have phenological
records but lack the climate data will be showed in unused.years
in the returned list.
\qquad
The numerical value of DOY.ul
should be larger than or equal to the maximum Time
.
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 |
RMSE.mat |
the matrix consisting of the RMSEs (in days) from different
combinations of |
AADTS.arr |
the AADTS values in different years
associated with the smallest value in |
Year |
The intersected years between |
Time |
The observed occurence times (day of year) in the intersected years
between |
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 |
AADD |
the expected AADTS |
RMSE |
the smallest RMSE (in days) in |
unused.years |
the years that have phenological records but lack the climate data |
Note
The entire mean daily temperature data in the spring of each year should be provided.
AADTS
is represented by the mean of AADTS.arr
in the output.
Author(s)
Peijian Shi pjshi@njfu.edu.cn, Zhenghong Chen chenzh64@126.com, Brady K. Quinn Brady.Quinn@dfo-mpo.gc.ca.
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. 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. doi:10.1093/aesa/sax063
See Also
Examples
data(apricotFFD)
data(BJMDT)
X1 <- apricotFFD
X2 <- BJMDT
Year1.val <- X1$Year
Time.val <- X1$Time
Year2.val <- X2$Year
DOY.val <- X2$DOY
Temp.val <- X2$MDT
DOY.ul.val <- 120
S.arr0 <- seq(40, 60, by = 1)
Ea.arr0 <- seq(10, 20, by = 1)
res3 <- ADTS( S.arr = S.arr0, Ea.arr = Ea.arr0, Year1 = Year1.val, Time = Time.val,
Year2 = Year2.val, DOY = DOY.val, Temp = Temp.val, DOY.ul = DOY.ul.val,
fig.opt = TRUE, verbose = TRUE)
res3
RMSE.mat0 <- res3$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()