TSSRESTREND: Time Series Segmentation of Residual Trends (MAIN FUNCTION)
In TSS.RESTREND: Time Series Segmentation of Residual Trends

Description Usage Arguments Value Note Author(s) See Also Examples

Time Series Segmented Residual Trend (TSS.RESTREND) methodology.Takes in a complete monthly time series of a VI and its corrosponding precipitation (and temperature). It then looks looks for breakpoints using the BFAST function. The significance of the breakpoin in the residuals and the VPR is assessed using a Chow test, then, the total time series change is calculated.

TSSRESTREND(
  CTSR.VI,
  ACP.table = FALSE,
  ACT.table = NULL,
  CTSR.RF = FALSE,
  CTSR.TM = NULL,
  anu.VI = FALSE,
  acu.RF = FALSE,
  acu.TM = NULL,
  VI.index = FALSE,
  rf.b4 = FALSE,
  rf.af = FALSE,
  sig = 0.05,
  season = "none",
  exclude = 0,
  allow.negative = FALSE,
  allowneg.retest = FALSE,
  h = 0.15,
  retnonsig = FALSE
)

`CTSR.VI`	Complete Monthly Time Series of Vegetation Index values. An object of class `'ts'` object without NA's.
`ACP.table`	A table of every combination of offset period and accumulation period.for precipitation ACP.table can be calculated using the `climate.accumulator`.
`ACT.table`	A table of every combination of offset period and accumulation period.for temperature ACP.table can be calculated using the `climate.accumulator`.
`CTSR.RF`	Complete Time Series of Rainfall. An object of class 'ts' object without NA's and be the same length and cover the same time range as CTSR.VI. If ACP.table is provided, CTSR.RF will be automitaclly calculated using the `ACP.calculator`
`CTSR.TM`	Complete Time Series of temperature. An object of class 'ts' object without NA's and be the same length and cover the same time range as CTSR.VI. Default (CTSR.TM=NULL). If ACT.table is provided, CTSR.RF will be automitaclly calculated using the `ACP.calculator`
`anu.VI`	The annual (Growing season) max VI. Must be a object of class `'ts'` without NA's. if anu.VI=FALSE, it will be calculated from the CTSR.VI using `AnMaxVI`.
`acu.RF`	The optimal accumulated rainfall for anu.VI. Must be a object of class `'ts'` without NA's and be of equal length and temporal range to anu.VI. if anu.RF=FALSE, it will be calculated from ACP.table usingthe `AnnualClim.Cal`
`acu.TM`	The optimal accumulated rainfall for anu.TM. Must be a object of class `'ts'` without NA's and be of equal length and temporal range to anu.TM. if anu.TM=FALSE, it will be calculated from ACT.table usingthe `AnnualClim.Cal`
`VI.index`	the index of the CTSR.VI ts that the anu.VI values occur at. Must be the same length as anu.VI. NOTE. R indexs from 1 rather than 0. if VI.index=FALSE, it will be calculated from the CTSR.VI using `AnMaxVI`.
`rf.b4`	If a breakpoint in the VPR is detected this is the optimial accumulated rainfall before the breakpoint. must be the same length as the anu.VI. If ACP.table is provided it will be generated using `AnnualClim.Cal`
`rf.af`	If a breakpoint in the VPR is detected this is the optimial accumulated rainfall after the breakpoint. must be the same length as the anu.VI. If ACP.table is provided it will be generated using `AnnualClim.Cal`
`sig`	Significance of all the functions. defualt sig=0.05
`season`	See `bfast`. This season value only applies to bfast done using the CTS VPR. if a non VPR adjusted BFAST is performed.a harmonic season is used.
`exclude`	A numberic vector containg months excluded from breakpoint detection. This was included to allow sensor transitions to be masked.
`allow.negative`	If true, will not preference positive slope in either CTSR or VI calculations. default=FALSE is set because negative associations between rainfall and vegetation in water limited ecosystems is unexpected If temperature data is included then this paramter is forced to TRUE.
`allowneg.retest`	default=FALSE If temperature data is provided but found to not be significant then a retest is performed. This paramter is to allow negative on re-test.
`h`	See `bfast`, The.minimal segment size between potentially detected breaks in the trend model given as fraction relative to the sample size (i.e. the minimal number of observations in each segment divided by the total length of the timeseries. Default h = 0.15.
`retnonsig`	Bool. New in v0.3.0. Allows TSSRESTREND to return change estimates of values that filed the sig component in the residual analysis. defualt FALSE will give the same result as eralier versions.

An object of class 'TSSRESTREND' is a list with the following elements:

summary

Method: The method used to determine total change. (RESTREND see RESTREND, segmented.RESTREND see seg.RESTREND, segmented.VPR see seg.VPR)
Total.Change: The total significant change. Residual.Change + VPR.HeightChange.
Residual.Change: The change in the VPR Residuals over the time period
VPR.HeightChange: The change in VI at mean rainfall for a "ts" with a significant breakpoint in the VPR
model.p: p value of the regression model fitted to the VPR. See lm
residual.p: p value of the regression model fitted to the VPR Residuals. See lm
VPRbreak.p: the p value associated with the break height. See lm
bp.year: The Year of the most significant breakpoint

ts.data

The Time series used in analysis. See Arguments for description

CTSR.VI
CTSR.RF
anu.VI
VI.index
acu.RF
StdVar.RF see seg.VPR)

ols.summary

chow.summary: summary of the most significant breakpoint.
chow.ind: Summary of every detected breakpoint
OLS.table: A matrix containing the coefficents for the CTS.fit, VPR.fit, RESTREND.fit and segVPR.fit

TSSRmodels

models of class "lm" lm and class "bfast" bfast generated.

if ACP.table = FALSE, CTSR.RF and acu.RF must be provided as well as rf.b4 and rf.af for 'ts' with a breakpoint in the VPR.

Arden Burrell, arden.burrell@unsw.edu.au

plot.TSSRESTREND
print.TSSRESTREND

## Not run: 
#To get the latest version of the package (Still in development)
install.packages("devtools")
library("devtools")
install_github("ArdenB/TSSRESTREND", subdir="TSS.RESTREND")
library(TSS.RESTREND)
#Find the path of the rabbitRF.csv dataset, read it in and turn it into a time series
rf.path<- system.file("extdata", "rabbitRF.csv", package = "TSS.RESTREND", mustWork = TRUE)
in.RF <- read.csv(rf.path)
rf.data <- ts(in.RF, end=c(2013,12), frequency = 12)

#Find the path of the rabbitVI.csv dataset and read it in
vi.path <- system.file("extdata", "rabbitVI.csv", package = "TSS.RESTREND", mustWork = TRUE)
in.VI <- read.csv(vi.path)
CTSR.VI <- ts(in.VI, start=c(1982, 1), end=c(2013,12), frequency = 12)

#Define the max accumuulation period
max.acp <- 12
#Define the max offset period
max.osp <- 4
#Create a table of every possible precipitation value given the max.acp and max.osp
ACP.table <- climate.accumulator(CTSR.VI, rf.data, max.acp, max.osp)
results <- TSSRESTREND(CTSR.VI, ACP.table)
print(results)
plot(results, verbose=TRUE)

## End(Not run)