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ChangeLog
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* CHANGES IN dplR VERSION 1.7.9
File: rwi.stats ans sss help
----------------
* Changed verbiage after emails with Stefan Klesse and Allan Buras
File: powt
----------------
- Added SK's universalPOWT function and condensed the existing cook powt
function into a single function with a method call.
File: rwl.stats
----------------
- Added kurtosis to summary stats
File: glk
----------------
- Man file updated to improve example. See https://github.com/OpenDendro/dplR/issues/26
File: detrend.series
----------------
- Small change to Ar method to get mean right. See https://github.com/OpenDendro/dplR/issues/22
File: read.fh
----------------
- Added an extra check for the end and start date, in case there is an error in the FH-file, with the end date before the start date.
File: ffcsaps
----------------
- ffcsaps is deprecated as it has been replaced with caps. Will be defunct after 1.7.8
At the moment ffcsaps calls caps using the lifecycle::deprecate_warn()
File: dplR.c .h, redfit.c
----------------
- Resolved R CMD check NOTE by using a well documented, conditionally backported function instead of a non-API entrypoint
* CHANGES IN dplR VERSION 1.7.7
File: DESCRIPTION
----------------
- Changing the home of the repo to opendendro's GH
File: bakker.R .Rd, zo.rwl, zo.anc
----------------
- Added SK's bakker func
File: read.tucson.R
----------------
- Added a verbose flag
File: rwl.report.R
----------------
- Added in years with all zeros in the report. And a warning that it can break dplR.
- Removing plyr as an import -- very simple fix to get rid of alply
- Setting a new ouptput for consecutive zeros. Those make me nervous.
- Removing invisible so the rwl report can be useful as an object.
- Adding a new check for unconnected flaoters
- Changing arg names to better match dplR conventions
File: ssf.R
----------------
- Found a bug where input data with rows of all zero caused div0 problems. Added a check to stop program if input has all zero rows.
- Removing pos.slope as an argument and hardcoding to TRUE.
- Changed default to caps rather than ads.
- Added a difference option for making rwi.
- Changed output so that iter0 is incuded in the output arrays when return.info is true
File: caps.R
----------------
- Added arg so that nyrs can be between 0 and 1 and then treated as a %. Changed default to be 2/3 rather than 1/2 of n
* CHANGES IN dplR VERSION 1.7.6
File: caps.R
----------------
- Added a % option to the spline so that values of nyrs between 0 and 1 are a percentage of the length of y.
- Changed the default otion for nyrs to a 2/3 spline
* CHANGES IN dplR VERSION 1.7.5
File: read.compact.Rd
----------------
- Added an example.
File: read.compact.c
----------------
- warning on # of args in two spots. Looked at it after email from Kurt H
File: detrend.series.Rd
----------------
- missing \ in man page
File: adsf.f95 and capsf.f95
----------------
- Replaced DFLOAT with DBLE as per BDR's reasonable demand.
File: ssf
----------------
- Changed output to be class(crn) for list with long output
File: chron.ci
----------------
- Changed output to be class(crn)
File: crn.plot and plot.crn
----------------
- Finally reconciled the misnaming of crn.plot vs plot.crn etc. The new default plot method is simpler and cleaner. Help pages updated and a warning crn.plot is called directly.
File: chron.stabilized
----------------
- Added class crn to returned value as per github issue #18
File: read.fh
----------------
- Ron Visser added a BC correction to the function.
File: read.rwl
----------------
- Edited function to look for commas (",") in lower blocks of data as opposed to the header
File: csv2rwl
----------------
- Added a stop error and message when there are duplicate series IDs
File: read.tucson
----------------
- Changed error message when there are duplicate series IDs to be more informative
File: normalize1
----------------
- Found a bug so that when hanning was used (in say corr.rel.seg) a div0 error could occur resulting in a Nan that got propogated forward. Dealt with in the same way as detrend.series by setting 0 to 0.001.
File: powt.series
----------------
- Adding function so that a power transform can be done on a single series alone
* CHANGES IN dplR VERSION 1.7.4
File: chron.ci
----------------
- New function that calculates conf intervals for a chron via boot
File: detrend.series
----------------
- Fixed bug with method Ar using difference.
- Added in a flag for dirtyDogs to return.info
* CHANGES IN dplR VERSION 1.7.3
File: Various
----------------
- Replaced ffcsaps with caps in most instances across the package.
- Removing prefix argument from chron.
- Removing all vingettes and pointing to Learning to Love dplR on startup
- Typos and code cleanup in several files
File: zzz
----------------
- Adding startup message when dplR is loaded
File: crn.plot
----------------
- Added crn names to plot. helpful for ars crn and var stab crn plotting.
File: ssf
----------------
- A simple signal free implementation.
File: chron.ars
----------------
- The ARSTAN chronology at long last.
File: detrend
----------------
- When dopar is used for the looping, the series name wasn't being passed in. So modified code to take the series name. I think I did it marginally right. But dopar, foreach, and do.call are all prety opaque to me.
File: detrend.series
----------------
- Went to heroic efforts to improve the warnings that the user sees when there are negative fits from detrending. It was a huge time sink and hassle.
File: nm046
----------------
- Added new data file, nm046 is a rwl file that has a dirty dog in it (one where spline fits are negative in detrending).
File: ffcsaps
----------------
- Added `ties = "ordered"` to approx() to avoid warning thrown by regularize.values
File: caps
----------------
- Added new function caps() for Cook and Peters Spline. This is a function to calculate the classic ARSTAN spline. The work is done in Fortran and involved a C wrapper for the Fortran code. As a result the new files are caps.R, caps.Rd for the main files and the help function. But there are new Fortran and C files (caps.f95, caps.c) and changes to init.c and registered.h. Oh and NAMESPACE too. Note that this function is 1000s of times faster than ffcsaps.
File: ads
----------------
- Added new function ads(). This is a function to calculate age-dependent splines that came via Ed Cook. The work is done in Fortran and involved a C wrapper for the Fortran code. As a result the new files are ads.R, ads.Rd for the main files and the help function. But there are new Fortran and C files (adsf.f95, adsc.c) and changes to init.c and registered.h. Oh and NAMESPACE too.
File: bai.out, bai.in
----------------
- Added check to make sure `d2pith` and `diam` are data.frames and not, say, tibbles
File: ca533.Rd, cana157.Rd, co021.Rd, wa082.Rd
----------------
- Updated access dates and changed ftp to https per email from BDR on April 20 2021
* CHANGES IN dplR VERSION 1.7.2
File: glk.R sgc.R
----------------
- Revising glk for speed and adding sgc as a new function from Ronald Visser
File: chron.stabilized.R
----------------
- Adding variance stabilization from Stefan Kleese see https://github.com/AndyBunn/dplR/issues/3
File: time.rwl.R
----------------
- Adding `time<-` as a method for `time.rwl<-` and `time.crn<-` so that
times can be set as well as retrieved from rwl and crn. Getting the NAMESPACE,
and .Rd files right was unpleasant.
File: powt.R
----------------
- C Zang added rescale arguemnt to powt to have results align better with
ARSTAN output.
* CHANGES IN dplR VERSION 1.7.1
File: ccf.series.rwl.R
----------------
- Fixed stringsAsFactors issue pointed out by Kurt H
File: xdate.floater.R and .Rd
----------------
- New function to cross date a floating series (i.e., one with no dates).
* CHANGES IN dplR VERSION 1.7.0
File: insert.ring.R and delete.ring.R
----------------
- Adding an argument fix.length to maintain the length of the input and output. This makes it much easier to edit series and insert them back into a rwl object as needed.
File: plot.crs.R
----------------
- This is a new S3 method for plotting the ouptut from corr.rwl.seg. The rationale for this is to reduce computational overhard in the shiny app I'm developing for xdating.
File: corr.rwl.seg.R
----------------
- Added class crs to the output object as well as added some new items to the list that are returned (e.g., the rwi, seg legnths and so on). This is done so that I could make a new S3 method for plotting objects `plot.crs()`. New output ites are explained in man file. The plotting code if make.plot=TRUE is gone and replaced with a call to plot.crs.
File: redfit.R
----------------
- Fixed bug where the handling of series with duplicate times (ages)
would produce an error. Thanks to Mark Hall for reporting.
File: plotRings.R and .Rd
----------------
- Making plotRings defunct as there were too many issues with the animation library and especially ImageMagick integrating smoothly for some users. Suggested to Darwin that he make plotRings a stand alone library.
File: xdate-dplR.Rnw
----------------
- Rewritten to explain new args in ccf.
File: xskel.ccf.plot.R and .Rd
----------------
- Added new argument to allow user to specify whether a series or master gets
passed to ccf as x. The convention was screwy.
File: ccf.series.rwl.R and .Rd
----------------
- Added new argument to allow user to specify whether a series or master gets
passed to ccf as x. The convention was screwy.
File: series.rwl.plot
----------------
- Cosmetic changes to plot
File: intro-dplR
----------------
- typos
* CHANGES IN dplR VERSION 1.6.9
File: sss.R and .Rd
----------------
- Adding subsample signal strength as a stand alone function
File: spag.plot.R and .Rd
----------------
- Small bug fix
File: crn.plot.R and .Rd
----------------
- Small bug fix
File: as.rwl.R and .Rd
----------------
- Adding a convenience function to transform data.frame or matrix to class rwl
File: powt.R and .Rd
----------------
- Small change so that powt returns class rwl as well as data.frame
File: pass.filt.R and .Rd
----------------
- Adding a wrapper function for signal::butter and signal::filtfilt to get low-pass, high-pass, band-pass filtering implemented as per a user request.
File: rwl.stats.R and .Rd
----------------
- Removing sens1 and sens2 from this function. At world dendro I'm still seeing these being used by dplR users. It's a terrible stat. I'm taking it out. Help file amended.
File: detrend.series.R and .Rd
----------------
- The function will now return the curves used for detrending the series if return.info is TRUE. Help file amended.
- Added the Hugershoff curve as an method for detrending. It's done along the lines of ModNegExp with straight line if the nls call fails.
- Added option to compute differences via subtraction rather than division.
File: detrend.R
----------------
- See above.
File: wavelet.plot.R
----------------
- Typos.
* CHANGES IN dplR VERSION 1.6.8
- Note that Darwin Alexander Pucha Cofrep has been added as a developer to work on plotRings() etc.
File: DESCRIPTION
----------------
- Fixing the version requirement for "animation" (>= 2.0-2)
- Fixing the version requirement for "R.utils" (>= 1.32.1)
- Introducing version requirement (>= 3.6) for suggested package "forecast"
File: plotRings.R
----------------
- Big change made is to aspect so that the plot area is square: par(pty="s"). Will contact author to check on the reasonableness of this. Other changes. R CMD CHECK was throwing flags. Notes an issue in the length.unit arg to the function given differently in the Rd file vs the R file. Made a quick fix. Also made a small adjustment to the axis limits as it seemed there was a lot of extra white space in the plot. Removed bty for the legend. Adjusted par. Added documentation language. Not sure if I understand the full rationale behind the way the function is written though. There is a lot of redundant code. -AGB
File: csv2rwl.R
----------------
Adding new function to read csv files in as rwl objects. Also adding that capability into read.rwl. Mikko should see if the error checks etc pass muster.
File: read.crn.R
----------------
Adding argument 'long' (default is TRUE) for supporting (non-standard) long
series with more than 4 characters used for the decade field. Use FALSE to
revert to the old way of assuming 6 characters for site ID and 4 characters
for decade. Thanks to Richard Telford for notcing the bug.
File: read.rwl.R
----------------
Adding read2csv into read.rwl both as a format specification and as an auto detect. Mikko should see if the error checks etc pass muster.
File: time.rwl.R
----------------
- Two convenience functions time.rwl and time.crn which extract the row.names of
rwl and crn objects as numerics. Used as a S3 method with class rwl and class crn.
This resulted in various changes to Rd files to make use of this capability.
File: seg.plot.R
----------------
- Fixed an issue with ylim and yaxs which should cut out extra white space.
File: xdate-dplR.Rnw
----------------
- Fixed typos
* CHANGES IN dplR VERSION 1.6.7
File: latexify.R
----------------
- Fixed a bug in latexDate() which was causing failure on R-Devel.
File: plotRings.R
----------------
- New function to plot a cross section. Contributed by Darwin Pucha-Cofrep and Jakob Wernicke
File: DESCRIPTION
----------------
- Added in new authors (Darwin Pucha-Cofrep and Jakob Wernicke)
- Added animation to Imports list
- Added gmp to Suggests
File: NAMESPACE
----------------
- Added plotRings to export and importFrom(animation, saveGIF) to support it
* CHANGES IN dplR VERSION 1.6.6
File: helpers.R
----------------
- Internal helper fix.names() is more robust when working in the C
locale.
- Added internal helper function check.tempdir()
- Added internal helper function requireVersion()
File: latexify.R
----------------
- Fixed conversion bugs in the latexify() utility when working in
the C locale.
File: rasterPlot.R
----------------
- In rasterPlot(Cairo = TRUE, ...), added a version check for the Cairo
package
- Check if temporary directory is missing before use
File: read.tucson.R
----------------
- Check if temporary directory is missing before use
File: redfit.R
----------------
- Computation of the exact acceptance region of number of runs
distributions in runcrit(), if not precomputed, depends on package
"gmp" being installed (now optional).
- Argument 'p' of redfit() and runcrit() may be numeric (which is
the default) or "bigq", but the latter now fails if "gmp" is not
installed.
File: DESCRIPTION
----------------
- Version requirement for stringi bumped up to >= 0.2-3. Should have been
done for dplR 1.6.1
- Version requirement for matrixStats bumped up to >= 0.50.2
because it's not possible to test 0.50.0, 0.50.1 with really old
versions of R, e.g. 2.15.2.
- Version requirement for png bumped up to >= 0.1-2: difficulties
compiling 0.1-1 on a test system (type voidp not defined).
Files: NAMESPACE, src/..., R/...
----------------
- Technical change: Native routines are registered.
<https://stat.ethz.ch/pipermail/r-devel/2017-February/073755.html>
- Technical change: Visibility of native routines has been
limited, following 6.15 "Controlling visibility" in R-exts.
- Package "gmp" is now in Suggests, not in Imports.
File: rcs.R
----------------
- Technical changes to facilitate the future implementation of
signal-free rcs.
File: src/redfit.c
----------------
- Fixed a pointer protection alert reported by rchk / Tomas
Kalibera. Seemed like a false alarm, but the code is slightly
cleaner as a result of the change.
* CHANGES IN dplR VERSION 1.6.5
File: combine.rwl.R
----------------
-Changed so that combine.rwl returns class data.frame and class rwl.
File: crn.plot.R
----------------
- Graphical parameters (xlim, ylim, ...) are handled better in crn.plot().
- Parameter 'ylim2' controls scale of secondary y axis.
File: detrend and detrend.series.Rd
-----------------
- Added Friedman under method argument in the help file. It was ommitted by mistake.
- Bug in detrend fixed where make.plot was hard coded as FALSE which kept TRUE
from being passed to detrend.series.
File: helpers.R
-----------------
- Added function find.internal.na() that reutrns the index of internal NA in a series. This will be used by the rwl.report() function and could be used (maybe) by the fill.internal.NA
File: rwl.report.R
-----------------
- Added function to provide a summary of information about an rwl object. This is still very much a work in progress.
File: NAMESPACE
-----------------
- Added rwl.report to export
- Added rwl.report print method
- Added import from plyr
File: DESCRIPTION
-----------------
- Added plyr (>= 1.8.3) to imports
File: sea.R
-----------------
- Note on commit from Zang: sea() simplified and computation of p-values fixed; computation of p-values and CI bands for sea() now based on ecdf() and quantile() functions.
File: zzz.R
-----------------
- .onUnload(): DLL / shared library is unloaded together with package
* CHANGES IN dplR VERSION 1.6.4
File: DESCRIPTION
-----------------
- Version number requirement for matrixStats is now (>= 0.50.0).
File: chron-dplR-Rnw
------------------
- A new vignette for chronology building. This is pretty rough and could
use some expanding.
File: anos1.Rda
------------------
- The anos1 data from Christian Zang had been read into R incorrectly at
some point. AGB noticed negative ring widths in the file and emailed Zang
who sent along a corrected anos1.rda file.
File: rasterPlot.R
------------------
- Added option 'Cairo' to control the preferred bitmap
device. FALSE (the default) for png() as before, and TRUE for
Cairo() as a new option. If the preferred device is unavailable,
the other one will be tried.
- rasterPlot() now reverts to normal plotting if bitmap device is
unavailable or raster images are not supported. Previously an
error would be produced.
- The function now also works if no high level plot exists,
i.e. if plot.new() has not been called.
- Added option 'draw' to control whether the raster plot is to be drawn (TRUE,
the default) or returned (FALSE)
- png plot is initialized with plot.new() instead of the previous
plot(type = "n", ...) arrangement.
File: sea.R
-----------
- Updated sea() to return bootstrapped CIs.
File: treeMean.R
-------------
- Made a new function to calculate the mean value of each tree when there are
multiple cores.
File: wavelet.plot.R
--------------------
- wavelet.plot() now passes ... arguments to rasterPlot().
Files: detrend.R, detrend.series.R
----------------------------------
- New detrending method "Friedman" is Friedman's super smoother,
implemented in stats::supsmu().
- When 'return.info' is TRUE, also the "f" parameter of
method="Spline" is returned.
File: DESCRIPTION
-----------------
- New Suggested package: Cairo. Used (if available) in
rasterPlot() if the png() device is unavailable or if the user
specifies 'Cairo=TRUE'.
File: NAMESPACE
-------------
- Added treeMean function.
- Importing dev.capture() from grDevices.
Various .R files
----------------
- Argument values are checked more thoroughly: 'prec', 'header'.
- 'if (condition) optionA else optionB' is used instead of
'ifelse(condition, optionA, optionB)' where appropriate.
- Number of characters is used instead of display width where
appropriate, or vice versa. Counterparts:
strtrim() and substr();
nchar(type = "width") and nchar() with default 'type';
format(string, width = w, justify = "left") and
stringr::str_pad(string, w, side="right").
- Using 'rows' and 'cols' arguments of matrixStats functions where
appropriate. This should result in less time and memory being
used. Thanks to Henrik Bengtsson for the tip and code examples.
* CHANGES IN dplR VERSION 1.6.3
File: crn.plot.R
-------------
- Added default x and y labels to plot. It would be better to use match.call()
to check to see if xlab and ylab were passed in as dots but it is a very
cumbersome bit of code for only a little difference to the user.
File: spag.plot.R
--------------
- Change to ylim in the plotting area.
File: CITATION
--------------
- Removed a piece of obsolete code which raised a NOTE in recent R-devel
when checking --as-cran.
File: DESCRIPTION
-----------------
- A new field, MailingList, shows the address of the web interface
to the dplR-help mailing list hosted on Google Groups.
- New Imported packages: Matrix, matrixStats, R.utils.
- New Suggested package: testthat. Unit tests are now done with testthat
instead of RUnit.
- RUnit is no longer Suggested.
- Updated version requirement: gmp (>= 0.5-5). Earlier versions of gmp do
not export is.bigq() which is required by dplR. The previous version
requirement (>= 0.5-2) was a mistake.
- Updated version requirement: R (>= 2.15.2). For some reason, R
CMD check does not play nice with testthat on earlier versions of R.
- Removed one of the URLs in the URL field. BDR sent and email saying that
having two URLs was breaking R and that we should put a comma in betwixt
them. But the comma is problematic as it is a valid part of some URLs.
We decided the better part of valor was to keep only one URL and not fight
this particular battle.
File: NAMESPACE
---------------
- Importing captureOutput() from R.utils.
- Importing package Matrix.
- Importing various functions from matrixStats.
- Importing packageDescription() from utils, dropped installed.packages().
- Exporting net().
- Added previously missing imports. From grDevices:
dev.capabilities(), dev.cur(), png(), dev.off(), dev.set(),
devAskNewPage(). From utils: read.table(), write.csv(). As these
packages are attached by default, the missing imports would not
have been a problem in most cases.
Various .R files
----------------
- Using deparse.level=0 in some calls to cbind() and rbind() when names
are not needed in the result. Due to this change, the first column of
the $bins matrix in the return value of ccf.series.rwl(),
corr.rwl.seg(), and corr.series.seg() does not have (undocumented)
column names anymore.
- Using base::rowSums and functions from the matrixStats package
to speed up some operations on rows or columns of matrices.
- Reduced the number of calls to options() by one when setting and
restoring options
- Argument values, particularly those that should be character
vectors, are checked more thoroughly. This makes many functions
more robust against unusual values: wrong type, "bytes" encoding,
zero length or NA. Some values that previously failed are now
silently accepted by coercion to character, extraction of first
element when a single string is expected, and / or interpretation
of a zero length argument as an empty string. NA is equivalent to
"NA" in detrend.series() and skel.plot() where it is used for
plotting or text output, but forbidden otherwise, e.g. in chron().
File: ffcsaps.R
---------------
- Increased performance by using sparse matrices from the Matrix
package.
File: helpers.R
---------------
- Internal function vecMatched does not care if nzchar() starts
returning NA some day.
File: latexify.R
----------------
- Improved efficiency when handling a large number of strings with
the "bytes" Encoding. The code now uses R.utils::captureOutput()
instead of a home-baked re-implementation of (parts of)
utils::capture.output(), which is also a more compact solution in
terms of lines of code in dplR. See Henrik Bengtsson's notes at
http://www.jottr.org/2014/05/captureOutput.html (referenced on
2015-01-07).
- Removed an unused variable.
File: net.R
-----------
- New function for computing the NET parameter (Esper et al., 2001).
File: read.fh.R
---------------
- read.fh() now ignores empty lines at the end of series.
File: read.tucson.R
-------------------
- New argument 'edge.zeros', TRUE (default) or FALSE. If TRUE,
possible leading and trailing zero values in tree-ring series are
kept. If FALSE, such values are dropped. The latter is how the
function has worked between (pre-)release 1.5.5 and the previous
release, and may be considered a bug or a misfeature. To
reiterate, the default behavior has changed in some cases. The
alternative, 1.5.5--1.6.2 behavior can be restored by changing the
value of the argument. Reported by Daniel Bishop and Neil
Pederson.
File: redfit.R
--------------
- Fixed a bug where redfit() would fail if the "stats" package was
not attached.
File: series.rwl.plot.R
-----------------------
- Worked around a problem in graphics::abline(): the function
fails when a linear model is given and the "stats" package is not
attached. The solution is to extract the coefficients of the model
and use those in the call.
File: write.crn.R
-----------------
- Better coding style: avoid using assign().
File: write.tridas.R
--------------------
- Implementation detail: When checking the package version,
packageDescription() is now used instead of installed.packages().
* CHANGES IN dplR VERSION 1.6.2
No functional changes. A unit test was changed so it would not fail
on the solaris-sparc CRAN platform. Also in some other tests,
identicality checks were replaced with near equality checks.
* CHANGES IN dplR VERSION 1.6.1
File: glk.R and glk.Rd
-------------
- Modified by Christian Zang in response to a bug report by Allan Buras. In the
case of no change from year i to year i+1 in both series then the glk sign
will for both be 0 and the sum of both is then also 0 and will not be
accounted for correctly in the sum of synchronous years. Zang and Buras have
patched and Zang updated the help file to reflect the change as:
"This implementation improves the original formulation inasmuch as the case
of neighbouring identical measurements in the same years is accounted for.
Here, it is treated as full agreement, in contrast to only partial agreement
in the original formulation."
File: crn.plot.R
-------------
- Removed automatic plotting of chronology name in main title.
File: plot.wavelet.R
-------------
- Fixed small bug in ylim for the chronology in the plot.
File: NAMESPACE
---------------
- Added rasterPlot, latexify() and latexDate() to export list
- Import readPNG from png.
- Import more functions from grid.
- Import stri_trans_nfc from stringi.
File: DESCRIPTION
-----------------
- New Suggested packages: Biobase, dichromat, knitr, tikzDevice,
RColorBrewer. Of these, dichromat, knitr, and tikzDevice are for document
building (see math-dplR.pdf below). Biobase is for making access to
math-dplR.pdf easier with openPDF(). RColorBrewer provides an
alternative palette to an example in wavelet.plot.Rd.
- New Imported packages: png and stringi.
File: chron.R
-------------
- Added pass-through of arguments from chron() to ar()
Files: corr.rwl.seg.R, corr.series.seg.R, interseries.cor.R,
rwi.stats.running.R, xskel.ccf.plot.R, xskel.plot.R
------------------------------------------------------------
- Parameters not changed by assignment anymore (small technical detail)
File: common.interval.R
-----------------------
- Bug fix: make.plot=TRUE threw an error when input data.frame had leading
or trailing all-NA rows
File: corr.rwl.seg.R, skel.plot.R
---------------------------------
- Performance optimization, including the use of dev.hold() and dev.flush()
File: corr.series.seg.R
-----------------------
- Bug fix: Argument 'method' was not used for moving correlations.
Instead, the method used was always "spearman".
File: detrend.R
---------------
- Updated .export of foreach() to match previous changes to the loop body
File: latexify.R
----------------
- New utility functions latexify() and latexDate() for use in vignettes
New files in subdirectory inst/doc:
-----------------------------------
- math-dplR.pdf is a vignette-ish document about the mathematical details
of some dplR functions (room for expansion in the future). It is
packaged as a static PDF due to the long build time. However, the
source is available as required by the CRAN policies for an open
source package. Arguably the staticness also makes sense in light of
the document presenting non-changing information about the package. If
the functions analyzed in the document change fundamentally (which is not
to be expected), the relevant parts of the document must be rewritten
and the document recompiled. Compare this to the idea that regular
vignettes usually include concrete examples about how the package can be
used. In that case it makes sense to compile the document often to
verify that the examples work.
- math-dplR.Rnw.txt is the source of math-dplR.pdf, with extra file
extension .txt to prevent automatic rebuild by R CMD build and R CMD
check
- math-dplR.bib is the BibTeX bibliography of the document
- math-dplR.R is the R source extracted from the document
- build-math-dplR.R is a build script
File: morlet.R
--------------
- Added some input checks
File: powt.R
------------
- Handle cases where the running mean of a series is 0
New file rasterPlot.R
---------------------
- New function rasterPlot(). Adds a raster image drawn with low
level graphics commands to the current high level plot.
Files: rcompact.c, readloop.c
-----------------------------
- Made the C code of read.compact() and read.tucson() more
resilient to unusual inputs
File: redfit.c
--------------
- Avoid using the long double type in some cases. Hopefully this
will speed up otherwise unbearable computation times on some
systems.
Files: series.rwl.plot.R
------------------------
- Fixed clipping of text in the lower right corner of the plot
File: skel.plot.R
-----------------
- Adjusted alignment, size and clipping properties of viewports. Now a
plot with less than the full number of rows can fit in a smaller
device and text on the sides won't be clipped.
File: spag.plot.R
-----------------
- Added two options to spag.plot().