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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20  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 
ACP.table 
A table of every combination of offset period and accumulation period.for precipitation
ACP.table can be calculated using the 
ACT.table 
A table of every combination of offset period and accumulation period.for temperature
ACP.table can be calculated using the 
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

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

anu.VI 
The annual (Growing season) max VI. Must be a object of class 
acu.RF 
The optimal accumulated rainfall for anu.VI. Must be a object of class 
acu.TM 
The optimal accumulated rainfall for anu.TM. Must be a object of class 
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 
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 
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 
sig 
Significance of all the functions. defualt sig=0.05 
season 
See 
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 retest. 
h 
See 
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:
The method used to determine total change. (RESTREND see RESTREND
,
segmented.RESTREND see seg.RESTREND
, segmented.VPR see
seg.VPR
)
The total significant change. Residual.Change + VPR.HeightChange.
The change in the VPR Residuals over the time period
The change in VI at mean rainfall for a "ts" with a significant breakpoint in the VPR
p value of the regression model fitted to the VPR. See lm
p value of the regression model fitted to the VPR Residuals. See lm
the p value associated with the break height. See lm
The Year of the most significant breakpoint
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
)
summary of the most significant breakpoint.
Summary of every detected breakpoint
A matrix containing the coefficents for the CTS.fit, VPR.fit, RESTREND.fit and segVPR.fit
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27  ## 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)

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