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Add option to omit plots #2

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Add option to omit plots #2

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fb14503
Add option to omit plots
trashbirdecology Dec 4, 2018
fd53165
Ensure obj `timeseries` is of class "timeseries"
trashbirdecology May 7, 2019
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6 changes: 4 additions & 2 deletions earlywarnings/R/generic_ews.R
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@

# Author: Vasilis Dakos, January 2, 2012

generic_ews<-function(timeseries,winsize=50,detrending=c("no","gaussian","linear","first-diff"),bandwidth=NULL,logtransform=FALSE,interpolate=FALSE,AR_n=FALSE,powerspectrum=FALSE){
generic_ews<-function(timeseries,winsize=50,detrending=c("no","gaussian","linear","first-diff"),bandwidth=NULL,logtransform=FALSE,interpolate=FALSE,AR_n=FALSE,powerspectrum=FALSE, create.plots = FALSE){

require(lmtest)
require(nortest)
Expand Down Expand Up @@ -166,6 +166,7 @@ generic_ews<-function(timeseries,winsize=50,detrending=c("no","gaussian","linear

# Plotting
# Generic Early-Warnings
if(create.plots == T){
dev.new()
par(mar=(c(0,2,0,1)+0),oma=c(7,2,3,1),mfrow=c(5,2))
plot(timeindex,Y,type="l",ylab="",xlab="",xaxt="n",las=1,xlim=c(timeindex[1],timeindex[length(timeindex)]))
Expand Down Expand Up @@ -239,9 +240,10 @@ generic_ews<-function(timeseries,winsize=50,detrending=c("no","gaussian","linear
contour(x=(spectfft$freq[2:length(spectfft$freq)]),y=(seq(1,ncol (nSPECT),by=1)),log(nSPECT[2:length(spectfft$freq),]),add=TRUE)
mtext("Power spectrum within rolling windows",side=3,line=0.2, outer=TRUE)
}
} # End plotting

# Output
out<-data.frame(timeindex[mw:length(nsmY)],nARR,nSD,nSK,nKURT,nCV,nRETURNRATE,nDENSITYRATIO,nACF)
colnames(out)<-c("timeindex","ar1","sd","sk","kurt","cv","returnrate","densratio","acf1")
return(out)
}
}
5 changes: 3 additions & 2 deletions earlywarnings/R/sensitivity_ews.R
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Expand Up @@ -49,7 +49,8 @@ sensitivity_ews<-function(timeseries,indicator=c("ar1","sd","acf1","sk","kurt","
require(moments)
require(fields)

#timeseries<-ts(timeseries) #strict data-types the input data as tseries object for use in later steps
# Ensure obj timeseries is of class "timeseries"
if(!is.ts(timeseries)) timeseries <- ts(timeseries) #strict data-types the input data as tseries object for use in later steps
timeseries<-data.matrix(timeseries)
if (dim(timeseries)[2]==1){
Y=timeseries
Expand Down Expand Up @@ -218,4 +219,4 @@ for (ti in 1:length(tw)){
out<-data.frame(Ktauestind)
rownames(out)<-tw
return(out)
}
}