R/examples/ex-seasons.R

In eco-hydro/phenofit2: Extract Remote Sensing Vegetation Phenology

{
    library(phenofit)
    data("MOD13A1")

    df <- tidy_MOD13(MOD13A1$dt)
    st <- MOD13A1$st

    date_start <- as.Date("2013-01-01")
    date_end <- as.Date("2016-12-31")

    sitename <- "CA-NS6" # df$site[1]
    d <- df[site == sitename & (date >= date_start & date <= date_end), ]
    sp <- st[site == sitename, ]
    south <- sp$lat < 0
    nptperyear <- 23

    # global parameter
    IsPlot = TRUE
    print = FALSE
    ypeak_min = 0.05
    wFUN = wTSM
}

profvis::profvis({
    IsPlot = FALSE
    # add one year in head and tail
    # dnew <- add_HeadTail(d, south = south, nptperyear = nptperyear)
    INPUT <- check_input(d$t, d$y, d$w,
        QC_flag = d$QC_flag,
        nptperyear = nptperyear, south = south,
        maxgap = nptperyear / 4, alpha = 0.02, wmin = 0.2
    )
    # all year as a whole
    # brks <- season(INPUT,
    #     rFUN = smooth_wWHIT, wFUN = wFUN,
    #     lambda = 10,
    #     plotdat = d, IsPlot = IsPlot, IsPlot.OnlyBad = FALSE
    # )
    for (i in 1:20) {
        # curve fitting by year
        brks2 <- season_mov(INPUT,
                            rFUN = smooth_wWHIT, wFUN = wFUN,
                            lambda = 10,
                            plotdat = d, IsPlot = IsPlot, IsPlot.OnlyBad = FALSE
        )
    }
})