optim_pheno

Interface of optimization functions for double logistics and other parametric curve fitting functions.

optim_pheno(
  prior,
  sFUN,
  y,
  t,
  tout,
  method,
  w,
  nptperyear,
  ylu,
  iters = 2,
  wFUN = wTSM,
  lower = -Inf,
  upper = Inf,
  constrain = TRUE,
  verbose = FALSE,
  ...
)

Arguments

prior	A vector of initial values for the parameters for which optimal values are to be found. prior is suggested giving a column name.
sFUN	The name of fine curve fitting functions, can be one of 'FitAG', 'FitDL.Beck', 'FitDL.Elmore', 'FitDL.Gu' and 'FitDL.Klos', 'FitDL.Zhang'.
y	Numeric vector, vegetation index time-series
t	Numeric vector, Date variable
tout	Corresponding doy of prediction.
method	The name of optimization method to solve fine fitting, one of 'BFGS','CG','Nelder-Mead', 'L-BFGS-B', 'nlm', 'nlminb', 'ucminf' and 'spg','Rcgmin','Rvmmin', 'newuoa','bobyqa','nmkb','hjkb'.
w	(optional) Numeric vector, weights of y. If not specified, weights of all NA values will be wmin, the others will be 1.0.
nptperyear	Integer, number of images per year, passed to wFUN. Only wTSM() needs nptperyear. If not specified, nptperyear will be calculated based on t.
ylu	ymin, ymax, which is used to force ypred in the range of ylu.
iters	How many times curve fitting is implemented.
wFUN	weights updating function, can be one of 'wTSM', 'wChen' and 'wBisquare'.
lower	vectors of lower and upper bounds, replicated to be as long as start. If unspecified, all parameters are assumed to be unconstrained.
upper	vectors of lower and upper bounds, replicated to be as long as start. If unspecified, all parameters are assumed to be unconstrained.
constrain	boolean, whether to use parameter constrain
verbose	Whether to display intermediate variables?
...	other parameters passed to I_optim() or I_optimx().

Value

fFIT object, see fFIT() for details.

See also

FitDL(), stats::nlminb()

Examples

# library(magrittr)
# library(purrr)

# simulate vegetation time-series
FUN = doubleLog_Beck
par  = c( mn  = 0.1 , mx  = 0.7 , sos = 50 , rsp = 0.1 , eos = 250, rau = 0.1)
par0 = c( mn  = 0.15, mx  = 0.65, sos = 100, rsp = 0.12, eos = 200, rau = 0.12)

t    <- seq(1, 365, 8)
tout <- seq(1, 365, 1)
y <- FUN(par, t)
#> Error in doubleLogMain(`_phenofit_cdoubleLog_Beck`, par, t, pred): object '_phenofit_cdoubleLog_Beck' not found

methods = c("BFGS", "ucminf", "nlm", "nlminb")
opt1 <- I_optim(par0, doubleLog_Beck, y, t, methods) # "BFGS", "ucminf", "nlm",
#> Error in I_optim(par0, doubleLog_Beck, y, t, methods): object 'y' not found
# opt2 <- I_optimx(prior, fFUN, y, t, tout, )

sFUN   = "doubleLog.Beck" # doubleLog.Beck
r <- optim_pheno(par0, sFUN, y, t, tout, method = methods[4],
                 nptperyear = 46, iters = 2, wFUN = wTSM, verbose = FALSE, use.julia = FALSE)
#> Error in optim_pheno(par0, sFUN, y, t, tout, method = methods[4], nptperyear = 46,     iters = 2, wFUN = wTSM, verbose = FALSE, use.julia = FALSE): object 'y' not found