NEWS.md
@author tags in the documentation files.captioner package in vignettes as it is no longer available on CRAN (address #54).itemize() in @return section of digitizeRadii() documentation (addresses note in R-devel CRAN check).itemize() with describe() in @details section of RFBCoptions() documentation (addresses note in R-devel CRAN check).backCalc(): replaced use of gather() and spread() with pivot_longer() and pivot_wider() as gather() and spread() are no longer actively developed.backCalc(): added ability to retain fish for which no radial measurements were made (addresses #49).backCalc(): added a warning if the r-squared value for the length-structure relationship used in the back-calculation technique is below 0.80 (only for those functions that use a linear model). This attempts to address #47.backCalc(): Added simple examples to documentation.saveDigitizedImage(): Added (address #44).showDigitizedImage(): Added Encoding() to unicode “arrows” for plotting to address an issue in the upcoming R v4.4.0 (will address #59).test-coverage.yaml to latest version.pkgdown.yaml to latest version.listFiles(): Corrected URL errors in documentation.listFiles() update (per CRAN request on 28-Aug-2023).CITATION file to meet CRAN requirements.pkgdown.yaml GitHub action to v2. Changed action to only run on a release (rather than a push) but it can be run manually as well.R-CMD-check.yaml GitHub action to v2. Note that I had to add the extra code for dealing with graphics on the Mac version.\alias problem using the “automatic approach” (i.e., adding a "_PACKAGE" line to RFishBC-package.R) suggested in an e-mail from Kurt Hornik on 19-Aug-2023.NEWS, some of the documentation pages, and some of the vignettes.usethis::use_github_action_check_standard()).usethis::use_github_action("pkgdown")).showDigitizedRadii(): Modified. Now returns the window size in windowSize and the pixel width to height ratio in pixW2H. This better allows the user to save the showDigitizedRadii() image as an image file in a loop (see examples in aaaMakeDataVignetts.R). Eventually this will be used to address #43.digitizeRadii(): Modified. Fixed bug with addNote= when restarting an image. Thanks to Ben Neely for pointing out the issue.addNote(): Added (addresses #41; thanks to Rory Feeney).backCalc(): Modfified to address #34.combineData(): Modified. Fixed two bugs related to how age-0 fish with no measured annuli are combined (thanks to Rory Feeney). Fixed how returned results are sorted (by id, reading, and ann; rather than just id and ann).digitizeRadii(): Modified. Added sbUnits= for addressing #36. Added addNotes and note that allows adding a special note to the R Data file (addresses #41; thanks to Rory Feeney) Added “kill” functionality to stop processing of all images in a queue (addresses #40; thanks to Rory Feeney). Fixed poor warning message when snap2transect=TRUE and makeTransect=FALSE.findNotes(): Added (addresses #41; thanks to Rory Feeney).RFBCoptions(): Modified. Added addNote, showScaleBarLength=, scaleBarUnits=, and cex.scaleBar=.showDigitizedImage(): Modified. Rewrote the function to be less redundant; allow pch.show=, col.show=, and cex.show= to be appropriate vectors (when only one reading is displayed); allowed pch.show="arrows" to plot arrows (addresses #38); assure that all values in annuliLabels= exist in the data; allow col.ann= and cex.ann to be appropriate vectors; provide offset.ann=; and show units of the scale-bar beneath the scale-bar (if it was digitized) by adding showScaleBarLength= and cex.scaleBar= (addresses #36).combineData(): Modified. Changed outFormat= to formatOut=. Added outType= to allow user to choose either radial or incremental measurements as output.digitizeRadii(): Modified. Changed showTransect= to makeTransect. Changed so that snap2Transect is changed to FALSE if it is TRUE and makeTransect=FALSE. Radii are now computed as the cumulative sum of increments rather than the distance from the selected point back to the structure center. This addresses #32 [Thanks to Alan Hanke].RFBCoptions(): Modified. Now includes makeTransect= used in digitizeRadii(). Now includes connect=, col.connect=, and lwd.connect= used in showDigitizedImage(). Because of those changes showTransect= has been removed.showDigitizedImage(): Modified. Changed showTransect= to connect=, col.transect= to col.connect=, and lwd.transect= to lwd.connect= (this helps address #32) [Thanks to Alan Hanke]. Also removed the points that are plotted at the structure center and, if not an annulus, margin (this addresses #31). Made more robust checks for when the user tries to plot two images from different structures.cli package for DONE(), NOTE(), and RULE() (see below).digitizeRadii(): Modified. Changed console output directions to use RULE() instead of NOTE(). Fixed bug that produced error related to closing the last window when working with multiple images.DONE(): Modified. Changed to use cat_line() from cli package (removed my hack).findScalingFactor(): Modified. Changed console output directions to use RULE() instead of NOTE().NOTE(): Modified. Changed to use cat_line() from cli package (removed my hack).RULE(): Added.digitizeRadii(). Modified. Added a note that draws attention when snap2Transect=TRUE and showTransect=FALSE (i.e., “snapping” to a transect that is not shown). At least partially addresses #30.iSnap2Transect(): Modified. Changed to handle bugs related to perfectly vertical or perfectly horizontal transects. Addresses #27 (Thanks to Ben Neely).digitizeRadii(): Modified. Removed sepWindow(). Added deviceType=.findScalingFactor(): Modified. Removed sepWindow(). Added deviceType=.getID(): Modified. Added IDreplace=. Added more examples of use of IDpattern= and IDreplace= and more tests.iGetimage(): Modified. Removed sepWindow=. Added deviceType=.RFBCoptions(): Modified. Removed sepWindow(). Added deviceType= and IDreplace=.showDigitizedImage(): Modified. Removed closeWindow= and sepWindow().combineData(): Modified. Changed so that an age-0 fish with all plus-growth is still included in the returned data.frame when deletePlusGrowth=TRUE (the ann and rad variables will both be NA). Thanks to Ben Neely.digitizeRadii(): Modified. Removed restriction that one point be selected as an annulus, which allows for handling age-0 fish (addresses #25; thanks to Ben Neely for the suggestion). Removed the q and r button equivalencies for f and d. Added the ability for the user to start over (resulting in no file to be written, but the current image stays live; uses the z key) (addresses #22; thanks to Ben Neely for the suggestion). Added the ability for the user to abort a processing (resulting in no file to be written and moving to the next image if using multiple images; uses the q key) (addresses #24; thanks to Ben Neely for the suggestion).findScalingFactor(): Modified. Changed to allow the user to abort or restart the process, similar to for digitizeRadii().Encoding: UTF-8 to DESCRIPTION.bcFuns(): Modified. Fixed bug in verbose= result when BCM=18.listFiles(): Modified. Fixed bug related to ignore.case=.getID(): Modified. Slightly simplified code. Added tests.digitizeRadii(): Modified. Moved the main code to iDigitizeRadii1(), which is basically the olde digitizeRadii() for working with only one image. The new digitizeRadii() allows nm= and id= to be vectors with length greater than 1 so that multiple images (and corresponding IDs) can be given to the function at once (or selected via a dialog box). Thus, this function now handles single or multiple images. This addresses #20 (thanks to B. Utrup and J-M. Hessenauer). Also changed so that the dialog box for entering fish IDs is populated with a better guess at the fish’s ID by using getID() with the new IDpattern=.getID(): Added. Part of addressing #20.RFBCoptions(): Modified. Added IDpattern= (Part of addressing #20).combineData(): Modified. Allowed first argument to be an RFishBC object saved from digitizeRadii() (partially addresses #16; thanks to Jason Doll).digitizeRadii(): Modified. Added closeWindow= (addresses #14). Changed so that the rownames of the pts data.frame in the returned object includes “center” and “edge.” See changes to iSelectPt().findScalingFactor(): Modified. Added closeWindow= (addresses #14). See changes to iSelectPt().iSelectPt(): Modified. Added numPts= with several “catches” for whether this target number of points is met when the “f” key (for “finished”) was pressed. Alters behavior in digitizeRadii() and findScalingFactor() (addresses #17; thanks to Jason Doll).RFBCoptions(): Modified. Added closeWindow= (addresses #14).showDigitizedImage(): Modified. Fixed bug in iShowAnnuliLabels() (addressed #12; thanks to Liuyong Ding). Allowed first argument to be an RFishBC object saved from digitizeRadii() (partially addresses #16; thanks to Jason Doll). Changed nm= to nms= to be consistent with combineData().rlang, stringr, and tidyr to Imports.combineData().backCalc().aStandard(): Added. Addresses #10.backCalc(): Added.bcFuns(): Modified. Changed to using STOP(). Changed all Lc to Lcap, Rc to Rcap, agec to Acap, and agei to Ai. Changed all BPH-related models to use a, b, and c and all SPH-related models to use A, B, and C. Started using iGetBCMethod(). Removed verbose= (moved to within the returned function).bcUtilChecker(): Modified. Changed to using STOP() and WARN().combineData(): Modified. Added outFormat= and deletePlusGrowth= arguments (and corresponding tests).findScalingFactor(): Modified. Added a catch for non-positive knownLength=.iGetBCMethod(): Added. Used in backCalc() and bcFuns().SMBassWB1: Added.SMBassWB2: Added.StdIntLit: Added..rds files rather than .RData files to save the data. This required using saveRDS() in digitizeRadii() and readRDS() in showDigitizedImage() and combineData().combineData(): Modified. See note above. Added a check that the file is an “R Data” file (using isRData()) and of the RFishBC class.digitizeRadii(): Modified. See note above. Added the RFishBC class to the saved and returned object.showDigitizedImage(): Modified. See note above. Added a check that the file is an “R Data” file (using isRData()) and of the RFishBC class.isRdata(): Added.digitizeRadii(): Modified. Added ability (using iSelectPt()) to delete points after selection for scale-bar, transect, and annuli selection. This removed the use of locator() and thus key-presses are used to terminate the selection of points. Added the pch.del= and col.del= arguments. Removed the orig.pts data.frame from the returned object.findScalingFactor(): Modified. Added ability (using iSelectPt()) to delete points after selection for scale-bar. Added pch.sel=, col.sel=, cex.sel=, pch.del=, and col.del= arguments.RFBCoptions(): Modified. Added the pch.del= and col.del= arguments. Removed pch.show2=, col.show2=, and cex.show2=
showDigitizedImage(): Modified. Removed the ability to show the original (before snapping to the transect) points. Thus, removed showOrigPts=, pch.show2=, col.show2=, and cex.show2=.iSelectPt(): Added.clisymbols and crayon packages.combineData(): Modified. Added a check that the RData file has a radii object.digitizeRadii(): Modified. Fixed bug related to showTransect=. Added clisymbols to messages (and had to change message()s to cat()s). Added tests for the messages related to arguments (found early in the function).iHndlFilenames(): Modified. Slight modification of the error messages.combineData(): Modified. Better handles filenames (see iHndlFilenames()).digitizeRadii(): Modified. Better handles filenames (see iHndlFilenames()).findScalingFactor(): Modified. Better handles filenames (see iHndlFilenames()).showDigitizedImage(): Modified. Better handles filenames (see iHndlFilenames()). Streamlined the looping code. Made a catch for the situation where one of the multiple files selected does not appear to be derived from the same structure image as the first file.iHndlFilenames(): Modified. Streamlined and changed to using choose.files() to allow for more efficient selection of multiple files. Filtered the choices to image files or RData files. Now checks to see if the user is using Windows and if the selected files are in the current working directory.digitizeRadii(): Modified. Incorporated some of the internal files, completely rewored the list that is returned, dealt with working directory change.findScalingFactor(): Modified. Dealth with working directory chagne.showDigitizedImages(): Modified. Incorporated some of the internal files and dealt with working directory change.iFindTransect(): Deleted. Moved into digitizeRadii().iHndlID(): Deleted. Moved into digitizeRadii().iHndlScalingFactor(): Deleted.iHndlScalingFactorFromScaleBar(): Added.iProcessAnnuli(): Deleted. Moved into digitizeRadii().iPts2Rad(): Added.iSelectAnnuli(): Deleted. Moved into digitizeRadii().iShowTransect(): Deleted. Deleted. Moved into digitizeRadii() and showDigitizedImage().digitizeRadii(): Modified. Slight modification to the messages in the console. Re worked the code with locator() so that the points will be shown “snapped to the transect” if snap2Transect=TRUE (this addresses #7). Added an orig.pts data.frame to the RData object which contains the original (non-snapped to transect) points (which can be plotted with showDigitizedImage()). Changed addTransect= to showTransect= to make more similar to showDigitezedImages().RFBCoptions(): Modified. Added showAnnuliLabels=, col.ann=, and cex.ann= for use in showDigitizedImage(). Changed defaults of mostly colors, pchs, and cexs.showDigitizedImage(): Modified. Added showAnnuliLabels=, col.ann=, and cex.ann= to shown annuli numbers when just one transect is shown. Added showOrigPts=, pch.show2=, col.show2=, and cex.show2= to handle including original points on the image.iFindTransect(): Added. Moved this code out of iSelectAnnuli().iGetImage(): Modified. Streamlined code. Added native=TRUE to read.bitmap() call to send to the underlying functions as this is apparently more efficient when using rasterImage() (which this uses).iOrderPts(): Added. Made it easier to add annuli labels in showDigitizedImage().iSelectAnnuli(): Modified. Now calls iSelectTransect().iShowAnnuliLabels(): Added. Made it easier to add annuli labels in showDigitizedImage().ishowTransect(): Added. Moved this code out of iSelectAnnuli(). Also called from showDigitizedImage().digitizeRadii(): Modified. Added snap2Transect= to address #1. Modified how fname= was handled if missing (see iHndlfname()) and if selecting an image from outside of the current working directory. Allowed user to choose id= through a dialog box or a console prompt (see iHndlID()), which addresses #2. Added popID= (again see iHndlID()). Fixed poor directions about the use of the escape key to terminate locator(). Added showInfo=, pos.info=, cex.info=, and col.info= to address #6.iGetImage(): Added. Was iReadImage(). Calculated the pixel width-to-height ratio (from image dimensions) and returned in list.iHndlfname(): Added. Used in digitizeRadii(), showDigitizedImage(), and findScalingFactor().iHndlID(): Added. Used in digitizeRadii(). Was modified from initial to include the image filename sans extension as the default ID in the Windows dialog box (when used with digitizeRadii()), which partially addresses #5.iHndlScalingFactor(): Modified. Added pixW2H= argument to receive the pixel width-to-height ratio to adjust distance calculations for non-square images.iPlaceText(): Added. Used to address #6.iReadImage(): Removed. Changed to iGetImage().iSnap2Transect(): Added. Used in digitizeRadii().iProcessAnnuli(): Modified. Added pixW2H= argument to receive the pixel width-to-height ratio to adjust distance calculations for non-square images.RFBCoptions(): Modified. Added popID= (see iHndlID()). Added showInfo=, pos.info=, cex.inf=, and col.info= (see digitizeRadii()).showDigitizedData(): Modified. Moved file.choose() for fname= out of argument list and into the main function code. Also modified to allow the user to select an object out of the current working directory (only works with a single file).