Fine Curve fitting

Source: R/curvefits.R

Fine Curve fitting for INPUT time-series.

curvefits(INPUT, brks, options = list(), ...)

Arguments

INPUT

A list object with the elements of 't', 'y', 'w', 'Tn' (optional) and 'ylu', returned by check_input.

brks

A list object with the elements of 'fit' and 'dt', returned by season or season_mov, which contains the growing season division information.

options

see section: options for fitting for details.

...

other parameters to curvefit()

Value

List of phenofit fitting object.

options for fitting

  • methods (default c('AG', 'Beck', 'Elmore', 'Zhang')``): Fine curve fitting methods, can be one or more of c('AG', 'Beck', 'Elmore', 'Zhang', 'Gu', 'Klos')`. Note that 'Gu' and 'Klos' are very slow.

  • iters (default 2): max iterations of fine fitting.

  • wFUN (default wTSM): Character or function, weights updating function of fine fitting function.

  • wmin (default 0.1): min weights in the weights updating procedure.

  • use.rough (default FALSE): Whether to use rough fitting smoothed time-series as input? If false, smoothed VI by rough fitting will be used for Phenological metrics extraction; If true, original input y will be used (rough fitting is used to divide growing seasons and update weights.

  • use.y0 (default TRUE): boolean. whether to use original y0 as the input of plot_input, note that not for curve fitting. y0 is the original value before the process of check_input.

  • nextend (default 2): Extend curve fitting window, until nextend good or marginal points are found in the previous and subsequent growing season.

  • maxExtendMonth (default 1): Search good or marginal good values in previous and subsequent maxExtendMonth period.

  • minExtendMonth (default 0.5): Extend period defined by nextend and maxExtendMonth, should be no shorter than minExtendMonth. When all points of the input time-series are good value, then the extending period will be too short. In that situation, we can't make sure the connection between different growing seasons is smoothing.

  • minPercValid: (default 0, not use). If the percentage of good- and marginal- quality points is less than minPercValid, curve fiting result is set to NA.

  • minT: (not use). If Tn not provided in INPUT, minT will not be used. minT use night temperature Tn to define backgroud value (days with Tn < minT treated as ungrowing season).

See also

FitDL()

Examples

data("CA_NS6")
d = CA_NS6

nptperyear <- 23
INPUT <- check_input(d$t, d$y, d$w, QC_flag = d$QC_flag,
     nptperyear = nptperyear, south = FALSE,
     maxgap = nptperyear/4, alpha = 0.02, wmin = 0.2)
# plot_input(INPUT)

# Rough fitting and growing season dividing
wFUN <- "wTSM"
brks2 <- season_mov(INPUT,
    options = list(
        rFUN = "smooth_wWHIT", wFUN = wFUN,
        r_min = 0.05, ypeak_min = 0.05,
        lambda = 10,
        verbose = FALSE
    ))
# plot_season(INPUT, brks2, d)
# Fine fitting
fits <- curvefits(
    INPUT, brks2,
    options = list(
        methods = c("AG", "Beck", "Elmore", "Zhang"), #,"klos", "Gu"
        wFUN = wFUN,
        nextend = 2, maxExtendMonth = 2, minExtendMonth = 1, minPercValid = 0.2
    )
)

r_param = get_param(fits)
r_pheno = get_pheno(fits)
r_gof = get_GOF(fits)
d_fit = get_fitting(fits)
#> Warning: Unknown argument 'id' has been passed.
#> Warning: Unknown argument 'id' has been passed.
#> Warning: Unknown argument 'id' has been passed.
#> Warning: Unknown argument 'id' has been passed.
#> Warning: Unknown argument 'id' has been passed.
#> Warning: Unknown argument 'id' has been passed.
#> Warning: Unknown argument 'id' has been passed.

g <- plot_curvefits(d_fit, brks2)
grid::grid.newpage(); grid::grid.draw(g)