monitoR Version 1.0.7 2018 Feb 13 Sasha D. Hafner monitoR_QuickStart.Rnw Removed reference to placeins and natbib packages. corMatch.R Added missing ! back in freq.step check. (Change made 8 days earlier) Version 1.0.7 2018 Feb 13 Jon Katz corMatch.R and binMatch.R Removed unused argument "warn" Added argument "quiet", when TRUE will suppress updates to the console: based on attempted merge by github user "gannebamm" at unofficial github repo spectro Added argument "/dots", allows users to include arg "warn" in calls to binMatch and corMatch Version 1.0.6 2017 June 23 Sasha D. Hafner corMatch.R and binMatch.R Changed warning and template adjustment to error for case when time step or frequency step doesn't match between template and survey. batchDetection.Rd Fixed second example when a template list in environment is used. Version 1.0.5 2017 February 16 Sasha D. Hafner *cutw.R Removed file *NAMESPACE Removed cutw *cutw.Rd Removed file *survey_anno.Rda Changed extension to rda 2015 December 11 Jon Katz Version 1.0.4 *cutw.Rd Removed \alias{biogas-deprecated} 2015 September 18 Sasha D. Hafner Version 1.0.4 *NAMESPACE Added cutWave to export() *cutWave.Rd Switched cutw to cutWave in example. 2015 September 17 Sasha D. Hafner Version 1.0.4 *makeBinTemplate.R, makeCorTemplate.R Used 'if' construct to return appropriate message for ending interactive graphical input (or moving onto the next input) depending on whether .Device is X11 or not. Original message always was "...right click". 2015 September 17 Jon Katz Version 1.0.4 *binMatch.R, corMatch.R, fileCopyRename.R Added optional argument rec.tz to allow manual specification of the timezone in which a survey was recorded. This change was originally made in April 2015 for version 1.0.3. 2015 September 12 Sasha D. Hafner Version 1.0.4 *monitoR_QucikStart.Rnw Added spaces to R code. 2015 September 7 Sasha D. Hafner Version 1.0.4 *dbDownloadCardRecorderID.R, dbDownloadTemplate.R, dbUploadResult.R, dbDownloadResult.R, dbSchema.R, dbUploadSurvey.R, dbDownloadSurvey.R, dbUploadAnno.R, dbUploadTemplate.R Fixed indentation of usage lines, plus other small changes. 2015 September 6 Sasha D. Hafner Version 1.0.4 *dbDownloadCardRecorderID.R, dbDownloadTemplate.R, dbUploadResult.R, dbDownloadResult.R, dbSchema.R, dbUploadSurvey.R, dbDownloadSurvey.R, dbUploadAnno.R, dbUploadTemplate.R Added check at start of functions to make sure RODBC package is installed. *dbDownloadResults.R, fileCopyRename.R, getClip.R, Methods-plot.R, viewSpec.R Added tuneR:: to all readWave() calls. *viewSpec.R Added tuneR:: to all channel() calls. *getClip.R, showPeaks.R, viewSpec.R Added tuneR:: to all writeWave() calls. *collapseClips.R Added tuneR:: to bind() call. *templateComment.R, templateCutoff.R, templateNames.R, templatePath.R Removed space before <- in, e.g., templatePath<-, that had been added by a Perl command earlier. *templateComment.Rd, templateCutoff.Rd, templateNames.Rd, templatePath.Rd Removed space before <- in, e.g., \alias{templatePath<-}, that had been added by a Perl command earlier. *index-methods.Rd, plot-methods.Rd, show-methods.Rd Removed space after comma in, e.g., \alias{[,templateScores-method}, added earlier by Perl command. *Methods-plot.R Replaced 'ext' with 'file.ext' in error message on line 29. *monitoR_QuickStart.Rnw Changed reference to cutw to cutWave. *binMatch.R, corMatch.R Removed space in {1, 7}, apparently added by Perl command earlier. *dbSchema.Rd, mp3Subsamp.Rd, readMP3.Rd Removed space added around = in URL. *NAMESPACE Added "image" and "plot" to importFrom for graphics package. Only saw a NOTE on this after removing tuneR import from file as a test. Switch to importFrom for tuneR functions. *NAMESPACE (This change made a month or two ago) Added import and importFrom directives for all non-base package functions. 2015 August 8 Sasha D. Hafner Version 1.0.4 *collapseClips.R, makeBinTemplate.R, makeCorTemplate.R, Methods-plot.R, showPeaks.R, viewSpec.R Replaced calls to cutw() with calls to cutWave() using Perl. 2015 August 1 Sasha D. Hafner Version 1.0.4 *cutWave.R New name for old cutw() function. *cutw.R Added call to .Deprecated. The cutw() function will be removed in the future. *All Rd files Added spaces to examples to make them easier to read. Fixed typos. 2015 July 21 Sasha D. Hafner Version 1.0.4 All R files Added spaces around <-, after commas, and around =, ==, and != using Perl. 2015 MAY 15 Jon Katz Version 1.0.4 *viewSpec.Rd and showPeaks.Rd Details regarding the player argument updated to instruct on correct Windows syntax with tempfiles. * showPeaks.R Fixed bug identifying when there are no hits to show, originally failed when 1 hit is present. Changed fd.rat default from 2 to 4. * getPeaks.R/getDetections.R Added return of an empty data frame when no peaks/detections are present. * dbDownloadSurvey.R dropped first AND operator included in SQL query 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