From 4a48fd44f279382d7c84c73051def8aff45ff483 Mon Sep 17 00:00:00 2001
From: Henrike Dierkes <58042175+henriDierkes@users.noreply.github.com>
Date: Tue, 5 Dec 2023 13:35:47 +0100
Subject: [PATCH 1/3] Bfastlite() as force-udf in R

---
 rstats/ts/dynamic-habitat-indices/bfast.R | 88 +++++++++++++++++++++++
 1 file changed, 88 insertions(+)
 create mode 100644 rstats/ts/dynamic-habitat-indices/bfast.R

diff --git a/rstats/ts/dynamic-habitat-indices/bfast.R b/rstats/ts/dynamic-habitat-indices/bfast.R
new file mode 100644
index 0000000..151bebd
--- /dev/null
+++ b/rstats/ts/dynamic-habitat-indices/bfast.R
@@ -0,0 +1,88 @@
+#load libraries
+lib <- "../../rlib"
+
+.libPaths(c(.libPaths(), lib))
+
+sfLibrary(zoo, lib.loc = lib)
+sfLibrary(sandwich, lib.loc = lib)
+sfLibrary(strucchangeRcpp, lib.loc = lib)
+sfLibrary(bfast, lib.loc = lib)
+
+
+# dates:     vector with dates     of input data (class: Date)
+# sensors:   vector with sensors   of input data (class: character)
+# bandnames: vector with bandnames of input data (class: character)
+force_rstats_init <- function(dates, sensors, bandnames){
+	return(c("Breakdate1", "Breakdate2", "Breakdate3", "NR", "RMSD1", 
+	         "RMSD2", "RMSD3", "Trend1", "Trend2", "Trend3",  "Trend4"))
+}
+  
+# inarray:   2D-array with dim = c(length(dates), length(bandnames))
+#            No-Data values are encoded as NA.  (class: Integer)
+# dates:     vector with dates     of input data (class: Date)
+# sensors:   vector with sensors   of input data (class: character)
+# bandnames: vector with bandnames of input data (class: character)
+# nproc:     number of CPUs the UDF may use. Always 1 for pixel functions (class: Integer)
+
+force_rstats_pixel <- function(inarray, dates, sensors, bandnames, nproc){
+  
+  # check for missing and zero values
+  if (all(inarray == 0) | all (is.na(inarray))){
+    
+    return(rep(-99999, 11))
+  } 
+  
+  # extract year and doy from date information of inarray
+  years <- dates |>
+    format("%Y") |>
+    as.numeric()
+  
+  doy <- dates |>
+    format("%j") |>
+    as.numeric()
+  
+  # create year identifier for the time series
+  x <- years + doy/365
+
+  # check for non-unique values and create mean value if two observations per time from different sensors appear
+  y <- split(inarray[,1], x) |> sapply(mean, na.rm = TRUE)
+  
+  # check the uniqueness of x, otherwise zoo() will return an error
+  x <- unique(x)
+
+  # create time series
+  ts <- zoo(y, x, frequency = 365) |> 
+    as.ts()
+
+  #save(list = ls(), file = "workspace.RData", envir = environment())  
+
+  # apply bfast with 3 breaks
+  bf = bfastlite(ts, breaks = 3)
+
+  # get trend, breaks and break dates
+  breakpoints_table <- strucchangeRcpp::breakpoints(bf[["breakpoints"]])
+  breakpoints <- breakpoints_table$breakpoints
+  break_dates <- x[breakpoints]
+  
+  # if breakpoints are determined, retrieve magnitude, rmsd, and number of breakpoints
+  if (any(!is.na(breakpoints))){
+  mag <- magnitude(bf$breakpoints)
+  rmsd <- as.numeric(unlist(mag$Mag[,4]))
+  nr <- as.numeric(length(breakpoints))
+  
+  # calculate trend 
+  trendtable <- data.frame(coef(bf$breakpoints))
+  trendtable$trend_recl <- with(trendtable, ifelse(trend < 0, 1, 2))
+  trend <- as.numeric(trendtable[,9])
+  
+  # otherwise return 0 
+  }else {
+    break_dates <- rep(0,3)
+    rmsd <- rep(0,3)
+    nr <- 0
+    trend <- rep(0,4)  
+  }
+
+    return(c(break_dates[1],  break_dates[2],  break_dates[3],nr, rmsd[1], rmsd[2], rmsd[3], trend[1], trend[2], trend[3], trend[4]))
+
+}

From c7c67edccc0b374d6e4e49b4be49b09c6061e755 Mon Sep 17 00:00:00 2001
From: Henrike Dierkes <58042175+henriDierkes@users.noreply.github.com>
Date: Tue, 5 Dec 2023 13:38:55 +0100
Subject: [PATCH 2/3] move bfastlite.R and rename

---
 rstats/ts/{dynamic-habitat-indices/bfast.R => bfastlite.R} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename rstats/ts/{dynamic-habitat-indices/bfast.R => bfastlite.R} (100%)

diff --git a/rstats/ts/dynamic-habitat-indices/bfast.R b/rstats/ts/bfastlite.R
similarity index 100%
rename from rstats/ts/dynamic-habitat-indices/bfast.R
rename to rstats/ts/bfastlite.R

From e46c826f8556f0b27961866b065ff23da77cd02b Mon Sep 17 00:00:00 2001
From: Henrike Dierkes <58042175+henriDierkes@users.noreply.github.com>
Date: Tue, 5 Dec 2023 13:39:56 +0100
Subject: [PATCH 3/3] move to rstats/bfastlite.R

---
 rstats/{ts => }/bfastlite.R | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename rstats/{ts => }/bfastlite.R (100%)

diff --git a/rstats/ts/bfastlite.R b/rstats/bfastlite.R
similarity index 100%
rename from rstats/ts/bfastlite.R
rename to rstats/bfastlite.R