monitoR
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##  SUMMARY OF CHANGES AFFECTING USERS ##
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2015 APRIL 23
Version 1.0.3
* Added hours.offset argument to fileCopyRename() for manual override of 
timezone management.

* Global time-zone detection in binMatch() and corMatch() when time.source="filename".

* Streamlined database functions; most query arguments are now optional.

* Added write.wav argument to makeCorTemplate(), makeBinTemplate(),
corMatch(), and binMatch. If a Wave object is used for the first argument 
(clip or survey), these function no longer automatically write the object to file 
(but will do so if write.wav=TRUE). 

* makeBinTemplate() New behavior for dens argument: points are now randomly 
sampled, and repeated selection of an area increases the density. 

* New function templatePath() for extracting or replacing the paths for Wave 
files.

* Added option to plot template over detections using argument box="template" 
in showPeaks().

2014 MAY 15
Version 1.0.2
* Minor bug fixes.

2014 MARCH 28
Version 1.0.1
* seewave and its dependencies no longer required for installation of monitoR.

2014 MARCH 27
Version 1.0.0
Initial upload to CRAN.




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##  DETAILED LOG  ##
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2015 APRIL 22 Sasha Hafner and Jon Katz
Version 1.0.3
*fileCopyRename.R/Rd New argument hours.offset allows user to manually offset the modification date to transport recordings across time zones. 

*corMatch.R binMatch.R Now both use getClip function to see if survey is a wav
file, and now both include a write.wav argument (FALSE by default) so that
they will not create a wav file by default.

*corMatch.Rd and binMatch.Rd Added write.wav argument.

*makeTemplate.Rd, writeTemplates.Rd, readTemplates.Rd, template____.Rd and
several other Rd files Changed examples to prevent writing files outside of tempdir().

*monitoR_QuickStart.Rnw Changed examples so now now tempdir() is the only
location where files are created.

2015 APRIL 21 Jon Katz and Sasha Hafner
Version 1.0.3

*Fixed time-zone detection in _Match() when time.source='filename' to match global time zones

*binMatch.R and corMatch.R Forced time slot in templateScores object to character, to fix new
problem due to c.difftime method.

2015 APRIL 03 Sasha Hafner 
Version 1.0.3

*Several Rd files Added spaces to code to make it easier to read

*stft.R Removed require call and added fftw:: to all PlanFFT and FFT calls

*dbDownload.Rd Removed default values for last two arguments

2015 APRIL 02 Jon Katz
Version 1.0.3

*all db__ functions Removed require calls to RODBC and added RODBC:: where needed

*survey_anno.Rd set example to \dontrun{}

2015 APRIL 02 Sasha Hafner (sdh11@cornell.edu)
Version 1.0.3

*monitoR-package.Rd Changed examples around line 66

*binMatch.R, corMatch.R, bindEvents.R, findPeaks.R, readBinTemplates.R,
readCorTemplates, writeCorTemplates Removed require calls to parallel and added parallel::
where needed

*survey_anno.rda Changed R in extension to r

*monitoR_QuickStart.Rnw Added footnote on new write.wav argument

*makeTemplate.Rd See changes listed below in the R files.

*makeBinTemplate.R and makeCorTemplate.R Added write.wav argument. If FALSE
(default), functions will not create wav files from Wave objects but will
instead return an error if the clip argument is not a file. This is a
change in behavior.

*getClip.R Added write.wav argument. If FALSE (default) and the output
argument is "file", function will return an error.

*showPeaks.R and viewSpec For the "play" option, a wav file is written. This file is 
now named using the tempfile function and put in the directory given by the
tempdir function.

2015 MARCH 19 Jon Katz
Version 1.0.3

*viewSpec.R and showPeaks.R Argument "player" now calls shell() for Windows and system() 
elsewhere (original code called system()). In showPeaks spaces are removed from the 
tempname to avoid quotes in call.

*viewSpec.Rd and showPeaks.Rd Details regarding the player argument updated to instruct 
on Windows syntax

2015 JANUARY 21 Sasha Hafner (sdh11@cornell.edu)
Version 1.0.3

*templatePath.R New file and new functions for extracting or replacing the paths for Wave 
files (clip.path slot)

*templatePath.Rd New help file for the new functions.

2014 NOVEMBER 07 Jon Katz and Sasha Hafner (sdh11@cornell.edu)
Version 1.0.3

*makeCorTemplate.R Added check for high or low dens values

*makeBinTemplate.R and makeCorTemplate.R Changed how dens argument is used, so
points are now randomly sampled, and repeated selection of an area (e.g., with
select = "rectangle") can increase the density of on or off points. Original
behavior was to select points in every nth row and nth column, so repeated
selection had no effect, and dens argument was approximate only.

*showPeaks.R Added option to plot template over detections using argument box='template' 

*binMatch.R Added error check so function will stop if it encounters a
template missing on or off points

*eventEval.R Removed single-template requirement, dropped unused "template" argument

*dbDownloadSurvey.R Made select inputs optional and capable of handling variable-length vectors
*dbDownloadTemplate.R Made select inputs optional and capable of handling variable-length vectors
*dbDownloadCardRecorderID.R Made select inputs optional and capable of handling variable-length vectors

*viewSpec.R Set 'no entry' to advance spectrogram equivalent to 'n'. Added identify option 'i' (not offered as an on-screen menu item) to measure RMS of a variable box size. 

2014 AUGUST 17 Sasha Hafner (sdh11@cornell.edu)
Version 1.0.3

*binMatch.R and corMatch.R Added tolower() for file.ext so WAV and MP3 are now
acceptable file extensions [this code removed on 2015 APRIL 15 so no longer
relevant. But getClip handles this issue properly.]

2014 MAY 15 Sasha Hafner (sdh11@cornell.edu) and Jon Katz
Version 1.0.2

* monitoR-package.Rd Added disclaimer, funding acknowledgement, and made 
small corrections.

* monitoR_QuickStart.Rnw Added disclaimer and funding acknowledgement.

* Methods-plot.R and showPeaks.R Changed how ask argument is used for plot 
methods for templateScores and TemplateList objects, and also for showPeaks
function, to make sure ask par is set back to the initial value. Also now
the ask par is not changed to the value of the ask argument until after the 
first plot has been produced.

2014 MARCH 28 Sasha Hafner (sdh11@cornell.edu)
Version 1.0.1

* Classes.R Replaced all slots=c() arguments in setClass calls with 
representation=representation() to make package compatible with R-oldrelease 
(R-2.15.3). Users should expect that this will be changed back to slots 
sometime in the future.

* Removed seewave import, and instead added seewave R code for functions stft,
dBweight, ftwindow, hamming.w, hanning.w, blacktop.w, flattop.w, and
rectangle.w to the package. The only effect for users is that seewave and its
dependencies are not required for installation of monitoR.

* Updated list of authors to include seewave and tuneR authors.

2014 MARCH 27
Version 1.0
