Merge pull request #56 from bfast2/20-bfast0n

Create a function for bfast0n

DESCRIPTION

@@ -43,4 +43,4 @@ URL: http://bfast.R-Forge.R-project.org/
 LazyLoad: yes
 LazyData: yes
 LinkingTo: Rcpp
-RoxygenNote: 5.0.1
+RoxygenNote: 7.1.0

NAMESPACE

@@ -22,6 +22,7 @@ S3method(residuals,bfast01)
 export(bfast)
 export(bfast01)
 export(bfast01classify)
+export(bfast0n)
 export(bfastmonitor)
 export(bfastpp)
 export(bfastts)

R/bfast0n.R

@@ -0,0 +1,41 @@
+#
+# This file is part of BFAST.
+#
+# BFAST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#
+# BFAST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BFAST.  If not, see <http://www.gnu.org/licenses/>.
+
+#' Detect multiple breaks in a time series
+#'
+#' A combination of \code{\link{bfastpp}} and \code{\link[strucchange]{breakpoints}}
+#' to do light-weight detection of multiple breaks in a time series
+#' while also being able to deal with NA values by excluding them
+#' via \code{bfastpp}.
+#'
+#' @param ... Additional arguments to \code{\link[strucchange]{breakpoints}}.
+#' @inheritParams bfastpp
+#' @inheritParams strucchange::breakpoints
+#' @example examples/bfast0n.r
+#'
+#' @export bfast0n
+
+bfast0n <- function(data, formula=response ~ trend + harmon, order = 3,
+                   lag = NULL, slag = NULL, na.action = na.omit,
+                   stl = c("none", "trend", "seasonal", "both"),
+                   decomp=c("stlplus", "stl"), sbins=1, ...)
+{
+  data_pp <- bfastpp(data, order = 3,
+                   lag = NULL, slag = NULL, na.action = na.omit,
+                   stl = c("none", "trend", "seasonal", "both"),
+                   decomp=c("stlplus", "stl"), sbins=1)
+  return(strucchange::breakpoints(formula=formula, data = data_pp, ...))
+}

examples/bfast0n.r

@@ -0,0 +1,13 @@
+plot(simts) # stl object containing simulated NDVI time series
+datats <- ts(rowSums(simts$time.series))
+# sum of all the components (season,abrupt,remainder)
+tsp(datats) <- tsp(simts$time.series) # assign correct time series attributes
+plot(datats)
+
+# Detect breaks
+bp = bfast0n(datats)
+
+# Default method of estimating breakpoints
+bp[["breakpoints"]]
+# Custom method
+strucchange::breakpoints(bp, breaks=2)