Phenology Extraction methods

Source: R/PhenoExtractMeth.R

  • PhenoTrs Threshold method

  • PhenoDeriv Derivative method

  • PhenoGu Gu method

  • PhenoKl Inflection method

PhenoTrs(
  fFIT,
  approach = c("White", "Trs"),
  trs = 0.5,
  asymmetric = TRUE,
  IsPlot = TRUE,
  ...
)

PhenoDeriv(
  fFIT,
  analytical = TRUE,
  smoothed.spline = FALSE,
  IsPlot = TRUE,
  show.lgd = TRUE,
  ...
)

PhenoGu(fFIT, analytical = TRUE, smoothed.spline = FALSE, IsPlot = TRUE, ...)

PhenoKl(
  fFIT,
  analytical = TRUE,
  smoothed.spline = FALSE,
  IsPlot = TRUE,
  show.lgd = TRUE,
  ...
)

Arguments

fFIT

fFIT object returned by optim_pheno().
approach

to be used to calculate phenology metrics. 'White' (White et al. 1997) or 'Trs' for simple threshold.
trs

threshold to be used for approach "Trs", in (0, 1).
asymmetric

If true, background value in spring season and autumn season is regarded as different.
IsPlot

whether to plot?
...

other parameters to PhenoPlot
analytical

If true, numDeriv package grad and hess will be used; if false, D1 and D2 will be used.
smoothed.spline

Whether apply smooth.spline first?
show.lgd

whether show figure lelend?

Examples

library(phenofit)

#> Error in library(phenofit): there is no package called ‘phenofit’
# simulate vegetation time-series
fFUN = doubleLog.Beck
par  = c( mn  = 0.1 , mx  = 0.7 , sos = 50 , rsp = 0.1 , eos = 250, rau = 0.1)

t    <- seq(1, 365, 8)
tout <- seq(1, 365, 1)
y <- fFUN(par, t)

methods <- c("AG", "Beck", "Elmore", "Gu", "Zhang") # "Klos" too slow
fFITs <- curvefit(y, t, tout, methods)

#> [doubleLog.AG]: object '_phenofit_rcpp_wTSM' not found
#> [doubleLog.AG]: object '_phenofit_rcpp_wTSM' not found
#> [doubleLog.Beck]: object '_phenofit_rcpp_wTSM' not found
#> [doubleLog.Beck]: object '_phenofit_rcpp_wTSM' not found
#> [doubleLog.Elmore]: object '_phenofit_rcpp_wTSM' not found
#> [doubleLog.Elmore]: object '_phenofit_rcpp_wTSM' not found
#> [doubleLog.Gu]: object '_phenofit_rcpp_wTSM' not found
#> [doubleLog.Gu]: object '_phenofit_rcpp_wTSM' not found
#> [doubleLog.Zhang]: object '_phenofit_rcpp_wTSM' not found
#> [doubleLog.Zhang]: object '_phenofit_rcpp_wTSM' not found
fFIT  <- fFITs$fFIT$AG

par(mfrow = c(2, 2))
PhenoTrs(fFIT)

#> sos eos 
#>  50 250 
PhenoDeriv(fFIT)

#> sos pop eos 
#>  47 150 253 
PhenoGu(fFIT)

#>  UD  SD  DD  RD 
#>  29  70 230 272 
PhenoKl(fFIT)

#>    Greenup   Maturity Senescence   Dormancy 
#>         20         77        223        280