[Dplr-commits] r784 - in pkg/dplR: . man

Tue Apr 8 06:03:42 CEST 2014

Author: andybunn
Date: 2014-04-08 06:03:36 +0200 (Tue, 08 Apr 2014)
New Revision: 784

Modified:
   pkg/dplR/ChangeLog
   pkg/dplR/TODO
   pkg/dplR/man/rwl.stats.Rd
   pkg/dplR/man/sens1.Rd
   pkg/dplR/man/sens2.Rd
Log:
Editing of help files. Editing TODO list.

Modified: pkg/dplR/ChangeLog
===================================================================

--- pkg/dplR/ChangeLog	2014-04-07 20:33:44 UTC (rev 783)
+++ pkg/dplR/ChangeLog	2014-04-08 04:03:36 UTC (rev 784)
@@ -2,7 +2,7 @@
 
 File: TODO
 -------------------------
-- Added a TODO list. This is exciting.
+- Added a TODO list that follows the todo.ell format.
 
 File: NAMESPACE
 -------------------------
@@ -13,7 +13,6 @@
 
 File: powt.R
 ------------
-
 - Originally, the transformed series were rescaled to their
   original mean and variance, which can lead to negative values for
   the (supposedly) raw tree-ring data.  This is not necessary, and

Modified: pkg/dplR/TODO
===================================================================
--- pkg/dplR/TODO	2014-04-07 20:33:44 UTC (rev 783)
+++ pkg/dplR/TODO	2014-04-08 04:03:36 UTC (rev 784)
@@ -1,15 +1,31 @@
 *  In rwi.stats and any place a correlation is calculated, offer an argument to
-   to specify which correlation method (e.g., spearman). Note that I implemented
-   this in interseries.cor - but will have to do this throughout. The default
-   should be spearman.
+   to specify which correlation method (e.g., spearman). Note that this is 
+   implemented in interseries.cor - but will have to do this throughout. 
+   The default should be spearman.
 
 *  In detrend(method=“ModNegExp”) there should be a verbose option that writes 
    how each series was handled including the parameters of the model.
 
-o [mvkorpel] Write a MAKEFILE for vignettes that removes any of the temp files 
-  that get produced when typesetting the vignette pdf? The tex files, etc.
-  I've been compiling the vignettes in Rstudio which leaves a lot of junk
-  behind when it's done.
+* Should there be a makefile for vignettes that removes 
+  the temp files that get produced when typesetting the vignette pdf? 
+  (the tex files and intermediate pdfs, etc.) I've been compiling the 
+  vignettes in Rstudio which leaves a lot of junk
+  behind when it's done. I made this makefile for my use. I'm not sure if 
+  this should sit in the pkg directory or just be for my use. Thoughts?
+      output = .output
+      rnwfile = intro-dplR
+      
+      all:
+        R CMD Sweave $(rnwfile).Rnw
+      	-mkdir $(output)
+      	-cp *.sty $(output)
+      	-cp *.bib $(output)
+      	-mv *.tex *.pdf *.pdf $(output)
+      	cd $(output); R CMD texi2pdf $(rnwfile).tex 
+      
+      clean:
+      	-rm $(output)/*
+      	-rmdir $(output)
 
 * Decide when to use class('rwl') in functions dealing with rwl objects.
   Other than the plot and summary S3Method for rwl, are there cases when 
@@ -26,18 +42,4 @@
     y <- ar.func(y)
     return(y)
 
-* Dummy item
-   This is a sample item.
 
-- Sub-item
-   Any number of sub-items can be added.
-
-o [mvkorpel] Another dummy item
-   This one shows how to mark a to-do item as assigned to somebody.
-   By default, this seems to show the user's login name.  The notation
-   is from todoo.el, an Emacs mode for editing TODO files.  Using the
-   mode, it is easy to reorder and hide / show items.  Also in the
-   mode, headings of items and sub-items are automatically
-   highlighted.  It should be easy enough to adhere to the format even
-   if the text editor does not support it.
-

Modified: pkg/dplR/man/rwl.stats.Rd
===================================================================
--- pkg/dplR/man/rwl.stats.Rd	2014-04-07 20:33:44 UTC (rev 783)
+++ pkg/dplR/man/rwl.stats.Rd	2014-04-08 04:03:36 UTC (rev 784)
@@ -44,9 +44,16 @@
   two measures of sensitivity, the Gini coefficient, and first order
   autocorrelation (\code{"skew"}, \code{"\link{sens1}"},
   \code{"\link{sens2}"}, \code{"\link{gini.coef}"}, \code{"ar1"}).
+  
+  Note that that mean sensitivity is not a robust statitic that should rarely,
+  if ever, be used (Bunn et al. 2013).
 }
 \references{
 
+  Bunn. A.G., Jansma E., Korpela M., Westfall R.D., and Baldwin J. (2013) 
+  Using simulations and data to evaluate mean sensitivity (zeta) as a useful 
+  statistic in dendrochronology Dendrochronologia 31 250–4.
+
   Cook, E. R. and Kairiukstis, L.A. (1990) \emph{Methods of
   Dendrochronology: Applications in the Environmental Sciences}.
   Springer.  \acronym{ISBN-13}: 978-0-7923-0586-6.

Modified: pkg/dplR/man/sens1.Rd
===================================================================
--- pkg/dplR/man/sens1.Rd	2014-04-07 20:33:44 UTC (rev 783)
+++ pkg/dplR/man/sens1.Rd	2014-04-08 04:03:36 UTC (rev 784)
@@ -15,8 +15,9 @@
   This calculates mean sensitivity according to Eq. 1 in Biondi and
   Qeadan (2008).  This is the standard measure of sensitivity in
   dendrochronology and is typically calculated on detrended series.
-  Users unfamiliar with sensitivity in tree-ring data should see Cook
-  and Kairiukstis (1990) and Fritts (2001) for further details.
+  However, note that that mean sensitivity is not a robust statitic and 
+  should rarely, if ever, be used (Bunn et al. 2013).
+
 }
 \value{ the mean sensitivity.
 }
@@ -25,12 +26,9 @@
   Biondi, F. and Qeadan, F. (2008) Inequality in Paleorecords.
   \emph{Ecology}, 89(4):1056\enc{–}{--}1067.
 
-  Cook, E. R. and Kairiukstis, L. A. (1990) \emph{Methods of
-  Dendrochronology: Applications in the Environmental Sciences}.
-  Springer.  \acronym{ISBN-13}: 978-0-7923-0586-6.
-
-  Fritts, H. C. (2001) \emph{Tree Rings and Climate}.  Blackburn.
-  \acronym{ISBN-13}: 978-1-930665-39-2.
+  Bunn. A.G., Jansma E., Korpela M., Westfall R.D., and Baldwin J. (2013) 
+  Using simulations and data to evaluate mean sensitivity (zeta) as a useful 
+  statistic in dendrochronology Dendrochronologia 31 250–4.
   
 }
 \author{ Mikko Korpela, based on original by Andy Bunn }

Modified: pkg/dplR/man/sens2.Rd
===================================================================
--- pkg/dplR/man/sens2.Rd	2014-04-07 20:33:44 UTC (rev 783)
+++ pkg/dplR/man/sens2.Rd	2014-04-08 04:03:36 UTC (rev 784)
@@ -14,9 +14,9 @@
 \details{
   This calculates mean sensitivity according to Eq. 2 in Biondi and
   Qeadan (2008).  This is a measure of sensitivity in dendrochronology
-  that is typically used in the presence of a trend.  Users unfamiliar
-  with sensitivity in tree-ring data should see Cook and Kairiukstis
-  (1990) and Fritts (2001) for further details.
+  that is typically used in the presence of a trend.  However, note 
+  that that mean sensitivity is not a robust statitic and should rarely, 
+  if ever, be used (Bunn et al. 2013).
 }
 \value{ the mean sensitivity.
 }
@@ -25,12 +25,9 @@
   Biondi, F. and Qeadan, F. (2008) Inequality in Paleorecords.
   \emph{Ecology}, 89(4):1056\enc{–}{--}1067.
 
-  Cook, E. R. and Kairiukstis, L. A. (1990) \emph{Methods of
-  Dendrochronology: Applications in the Environmental Sciences}.
-  Springer.  \acronym{ISBN-13}: 978-0-7923-0586-6.
-
-  Fritts, H. C. (2001) \emph{Tree Rings and Climate}.  Blackburn.
-  \acronym{ISBN-13}: 978-1-930665-39-2.
+  Bunn. A.G., Jansma E., Korpela M., Westfall R.D., and Baldwin J. (2013) 
+  Using simulations and data to evaluate mean sensitivity (zeta) as a useful 
+  statistic in dendrochronology Dendrochronologia 31 250–4.
   
 }
 \author{ Mikko Korpela, based on original by Andy Bunn }

