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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,108 @@ | ||
| #' Phenology extraction in Derivative method (DER) | ||
| #' | ||
| #' @inheritParams D | ||
| #' @inheritParams PhenoTrs | ||
| #' @param der1 the first order difference | ||
| #' | ||
| #' @references | ||
| #' 1. Filippa, G., Cremonese, E., Migliavacca, M., Galvagno, M., Forkel, M., | ||
| #' Wingate, L., … Richardson, A. D. (2016). Phenopix: A R package for | ||
| #' image-based vegetation phenology. Agricultural and Forest Meteorology, | ||
| #' 220, 141–150. \doi{10.1016/j.agrformet.2016.01.006} | ||
| #' | ||
| #' @seealso [PhenoTrs()], [PhenoGu()], [PhenoKl()] | ||
| #' @export | ||
| PhenoDeriv <- function(x, t, ...) UseMethod("PhenoDeriv", x) | ||
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|
||
| #' @rdname PhenoDeriv | ||
| #' @export | ||
| PhenoDeriv.fFIT <- function(x, t = NULL, | ||
| analytical = TRUE, smoothed.spline = FALSE, ...) { | ||
| if (!is.null(x$tout)) t <- x$tout | ||
| values <- last2(x$zs) | ||
| der1 <- D1.fFIT(x, t, analytical, smoothed.spline) | ||
| PhenoDeriv.default(values, t, der1, ...) | ||
| } | ||
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| #' @rdname PhenoDeriv | ||
| #' @param show.legend whether show figure lelend? | ||
| #' @export | ||
| PhenoDeriv.default <- function(x, t, der1, | ||
| IsPlot = TRUE, show.legend = TRUE, ...) | ||
| { | ||
| PhenoNames <- c("SOS", "POS", "EOS") | ||
| metrics <- setNames(rep(NA, 3), c("sos", "pos", "eos")) # template | ||
| n <- length(t) | ||
|
|
||
| # get peak of season position | ||
| half.season <- median(which.max(x)) # deal with multiple pos x | ||
| pos <- t[half.season] | ||
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|
||
| if (all(is.na(x))) return(metrics) | ||
| if (half.season < 5 || half.season > (n - 5)) return(metrics) | ||
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||
| # get SOS and EOS according to first order derivative | ||
| # fixed 20180510, ±5 to make sure sos and eos are not in the POP. | ||
| # I_sos <- median(which.max(der1[1:(half.season - 5)])) | ||
| # I_eos <- median(which.min(der1[(half.season+5):length(der1)])) + half.season | ||
|
|
||
| # der.sos (eos) is impossible to occur near the pop. | ||
| nmin <- 5 | ||
| I_sos <- findpeaks( der1[1:(half.season - 5)], | ||
| nups=nmin, ndowns=nmin, npeaks=1, sortstr=TRUE)$X$pos | ||
| I_eos <- findpeaks(-der1[(half.season+5):length(der1)], | ||
| nups=nmin, ndowns=nmin, npeaks=1, sortstr=TRUE)$X$pos + half.season + 4 | ||
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||
| # if half.season > length(der1), error will be occur | ||
| sos <- t[I_sos] | ||
| eos <- t[I_eos] | ||
| if (is_empty(sos)) { | ||
| I_sos <- findpeaks( der1[1:(half.season - 5)], | ||
| nups=nmin, ndowns=0, npeaks=1, sortstr=TRUE)$X$pos | ||
| sos <- t[I_sos] | ||
| if (is_empty(sos)) sos <- round((t[1] + pos)/2) | ||
| } | ||
| if (is_empty(eos)) { | ||
| I_eos <- findpeaks(-der1[(half.season+5):length(der1)], | ||
| nups=nmin, ndowns=0, npeaks=1, sortstr=TRUE)$X$pos + half.season + 4 | ||
| eos <- t[I_eos] | ||
| if (is_empty(eos)) eos <- round((t[n] + pos)/2) | ||
| } | ||
| # greenup <- .Greenup(x) | ||
| # if (is.na(sos)) { | ||
| # if (all(!rm_empty(greenup))) sos = pos | ||
| # } | ||
| # if (is.na(eos)) { | ||
| # if (all(rm_empty(greenup))) eos = pos | ||
| # } | ||
| metrics <- c(sos = sos, pos = pos, eos = eos)#, los = los | ||
|
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||
| if (IsPlot){ | ||
| main <- ifelse(all(par("mar") == 0), "", "DER") | ||
| PhenoPlot(t, x, main = main, ...) | ||
| if (show.legend) legend('topright', c("f(t)'"), lty = 2, col = "black", bty='n') | ||
|
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| abline(v = c(sos, eos), col = colors[c(1, 4)], lwd = linewidth) | ||
| abline(v = pos, col ="blue", lty = 1, lwd = linewidth) | ||
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||
| A <- diff(range(x)) | ||
| I_metrics <- match(metrics, t) | ||
| if (all(is.na(I_metrics))) { | ||
| ylons <- I_metrics | ||
| }else{ | ||
| ylons <- x[I_metrics] + c(1, -2, 1)*0.1*A | ||
| } | ||
| xlons <- metrics + c(-1, 1, 1)*5 | ||
| xlons[xlons < min(t)] <- min(t) | ||
| xlons[xlons > max(t)] <- max(t) | ||
|
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||
| I <- c(1); text(xlons[I], ylons[I], PhenoNames[I], col = colors[I], adj = c(1, 0)) | ||
| I <- 2:3 ; text(xlons[I], ylons[I], PhenoNames[I], col = c("blue", colors[4]), adj = c(0, 0)) | ||
|
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| #der1 last plot | ||
| op <- par(new = TRUE) | ||
| plot(t, der1, type= "l", lty = 2, lwd = linewidth, | ||
| col = "black", axes = FALSE) | ||
| } | ||
| return(metrics) | ||
| } |
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