[Dplr-commits] r791 - in pkg/dplR: . R man

[noreply at r-forge.r-project.org]

Author: andybunn
Date: 2014-04-08 18:58:14 +0200 (Tue, 08 Apr 2014)
New Revision: 791

Modified:
   pkg/dplR/R/detrend.series.R
   pkg/dplR/TODO
   pkg/dplR/man/detrend.Rd
   pkg/dplR/man/detrend.series.Rd
Log:
made a start on method "Ar" in detrend. This needs some work I expect. The help files have not been worked on yet. I'll do that. Mikko, can you check code?

Modified: pkg/dplR/R/detrend.series.R
===================================================================
--- pkg/dplR/R/detrend.series.R	2014-04-08 16:24:39 UTC (rev 790)
+++ pkg/dplR/R/detrend.series.R	2014-04-08 16:58:14 UTC (rev 791)
@@ -1,12 +1,12 @@
 `detrend.series` <-
     function(y, y.name = "", make.plot = TRUE,
-             method = c("Spline", "ModNegExp", "Mean"),
+             method = c("Spline", "ModNegExp", "Mean", "Ar"),
              nyrs = NULL, f = 0.5, pos.slope = FALSE,
              constrain.modnegexp = c("never", "when.fail", "always"))
 {
     stopifnot(identical(make.plot, TRUE) || identical(make.plot, FALSE),
               identical(pos.slope, FALSE) || identical(pos.slope, TRUE))
-    known.methods <- c("Spline", "ModNegExp", "Mean")
+    known.methods <- c("Spline", "ModNegExp", "Mean", "Ar")
     constrain2 <- match.arg(constrain.modnegexp)
     method2 <- match.arg(arg = method,
                          choices = known.methods,
@@ -133,7 +133,15 @@
     } else {
         do.mean <- FALSE
     }
-
+    if("Ar" %in% method2){
+      ## Fit an ar model - aka prewhiten
+      Ar <- ar.func(y2)
+      resids$Ar <- Ar / mean(Ar,na.rm=TRUE)
+      do.ar <- TRUE
+    } else {
+      do.ar <- FALSE
+    }
+    
     resids <- data.frame(resids)
 
     if(make.plot){
@@ -152,7 +160,8 @@
         if(do.spline) lines(Spline, col="green", lwd=2)
         if(do.mne) lines(ModNegExp, col="red", lwd=2)
         if(do.mean) lines(Mean, col="blue", lwd=2)
-
+        if(do.ar) lines(Ar, col="purple", lwd=2)
+        
         if(do.spline){
             plot(resids$Spline, type="l", col="green",
                  main=gettext("Spline", domain="R-dplR"),
@@ -177,6 +186,13 @@
                  ylab=gettext("RWI", domain="R-dplR"))
             abline(h=1)
         }
+        if(do.ar){
+          plot(resids$Ar, type="l", col="purple",
+               main=gettext("Ar", domain="R-dplR"),
+               xlab=gettext("Age (Yrs)", domain="R-dplR"),
+               ylab=gettext("RWI", domain="R-dplR"))
+          abline(h=1)
+        }
     }
 
     resids2 <- matrix(NA, ncol=ncol(resids), nrow=length(y))

Modified: pkg/dplR/TODO
===================================================================
--- pkg/dplR/TODO	2014-04-08 16:24:39 UTC (rev 790)
+++ pkg/dplR/TODO	2014-04-08 16:58:14 UTC (rev 791)
@@ -34,11 +34,9 @@
 - Consider the benefits and drawbacks of creating classes for chonologies. 
   One benefit would be an S3 plot method for chronologies.
 
-* Add 'prewhiten' as a detrending method.
+* Continue work on "Ar" as a detrending method.
   It would be nice to have a prewhitening option to detrend.series
-  (and therefore dentrend) that returns white noise 
-  This could be as easy as:
-    y <- detrend.series(x, method="Mean")
-    y <- ar.func(y)
-    return(y)
+  (and therefore dentrend) that returns white noise. This has been started but
+  needs more work. The help files have not been worked on beyond adding Ar as
+  a method.
 

Modified: pkg/dplR/man/detrend.Rd
===================================================================
--- pkg/dplR/man/detrend.Rd	2014-04-08 16:24:39 UTC (rev 790)
+++ pkg/dplR/man/detrend.Rd	2014-04-08 16:58:14 UTC (rev 791)
@@ -7,7 +7,7 @@
 }
 \usage{
 detrend(rwl, y.name = names(rwl), make.plot = FALSE,
-        method = c("Spline", "ModNegExp", "Mean"), nyrs = NULL,
+        method = c("Spline", "ModNegExp", "Mean", "Ar"), nyrs = NULL,
         f = 0.5, pos.slope = FALSE,
         constrain.modnegexp = c("never", "when.fail", "always"))
 }
@@ -25,7 +25,7 @@
   
   \item{method}{ a \code{character} vector to determine the detrending
     methods. See details below. Possible values are all subsets of
-    \code{c("Spline", "ModNegExp", "Mean")}. Defaults to using all the
+    \code{c("Spline", "ModNegExp", "Mean", "Ar")}. Defaults to using all the
     available methods.}
   
   \item{nyrs}{ a number giving the rigidity of the smoothing spline,

Modified: pkg/dplR/man/detrend.series.Rd
===================================================================
--- pkg/dplR/man/detrend.series.Rd	2014-04-08 16:24:39 UTC (rev 790)
+++ pkg/dplR/man/detrend.series.Rd	2014-04-08 16:58:14 UTC (rev 791)
@@ -7,7 +7,7 @@
 }
 \usage{
 detrend.series(y, y.name = "", make.plot = TRUE,
-               method = c("Spline", "ModNegExp", "Mean"),
+               method = c("Spline", "ModNegExp", "Mean", "Ar"),
                nyrs = NULL, f = 0.5, pos.slope = FALSE,
                constrain.modnegexp = c("never", "when.fail", "always"))
 }
@@ -23,7 +23,7 @@
 
   \item{method}{ a \code{character} vector to determine the detrending
     methods. See details below. Possible values are all subsets of
-    \code{c("Spline", "ModNegExp", "Mean")}. Defaults to using all the
+    \code{c("Spline", "ModNegExp", "Mean", "Ar")}. Defaults to using all the
     available methods.}
 
   \item{nyrs}{ a number giving the rigidity of the smoothing spline,