Extract phenological metrics

Extract phenological metrics from a fitted time series.

extract_pheno(data, method = "trs", trs = 0.5, ...)

Arguments

data

List of fitted time series as generated by function fit_curve().

method

Thresholding method among "trs", "derivatives", "klosterman" and "gu" (see phenopix::PhenoExtract()).

trs

Argument passed to phenopix::PhenoExtract() if method = "trs". It is valid also for method = "derivatives" thanks to a {sen2rts} implementation (it will be documented soon). Other methods do not make use of this argument.

...

Additional arguments passed to phenopix::PhenoExtract().

Value

A data table with the following fields:

• id: the time series ID (see s2ts);

• year: the year (integer);

• cycle: the cycle ID (integer);

• begin, end, maxval: the dates of begin, end and maximum value in the cycle as computed by cut_cycles();

• other phenology metrics, depending on method:

  • if method = "trs" or "derivatives": sos, eos, los, pop, mgs, rsp, rau, peak, msp, mau (see phenopix::PhenoTrs() or phenopix::PhenoDeriv());

  • if method = "gu": UD, SD, DD, RD, maxline, baseline, prr, psr, plateau.slope (see phenopix::PhenoGu());

  • if method = "klosterman": Greenup, Maturity, Senescence, Dormancy (see phenopix::PhenoKl()).

Author

Luigi Ranghetti, PhD (2020) luigi@ranghetti.info

Examples

# Load input data
data("cf")
data("ts_filled") # used for plots

# Default extraction ("trs" method with 50% threshold)
dt_pheno <- extract_pheno(cf)
plot(ts_filled, fitted = cf, pheno = dt_pheno, plot_dates = TRUE)


# \donttest{
# Customize parameters (e.g. "derivatives" method with 30% threshold)
dt_pheno_2 <- extract_pheno(cf, method = "derivatives", trs = 0.3)
plot(ts_filled, fitted = cf, pheno = dt_pheno_2, plot_dates = TRUE)


# Other methods: Klosterman
dt_pheno_kl <- extract_pheno(cf, method = "klosterman")
plot(ts_filled, fitted = cf, pheno = dt_pheno_kl, plot_dates = TRUE)


# Other methods: Gu
dt_pheno_gu <- extract_pheno(cf, method = "gu")
plot(ts_filled, fitted = cf, pheno = dt_pheno_gu, plot_dates = TRUE)

# }