Updated my (DHO) e-mail address in description and all@author tags in the documentation files.
Removed use of captioner package in vignettes as it is no longer available on CRAN (address #54).
Removed itemize() in @return section ofdigitizeRadii() documentation (addresses note in R-devel CRAN check).
Replaced itemize() with describe() in@details section of RFBCoptions()documentation (addresses note in R-devel CRAN check).
backCalc(): replaced use of gather() andspread() with pivot_longer() andpivot_wider() as gather() andspread() 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.
Fixed RFishBC-package \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.
Fixed URL links to “issues” in NEWS, some of the documentation pages, and some of the vignettes.
RFishBC 0.2.4 12-Feb-2022
Last version maintained by Derek Ogle. Transferring to fishR Core Team for next version.
Removed Travis-CI and appveyor.
No longer using coveralls for coverage statistics. Changed to codecov.io.
Added GitHub Action for CI/CD (usedusethis::use_github_action_check_standard()).
Added GitHub Action for pkgdown (usedusethis::use_github_action("pkgdown")).
Added GitHub Action for code coverage with codecov.io.
Now using ROxygen2 7.1.1.
showDigitizedRadii(): Modified. Now returns the window size in windowSize and the pixel width to height ratio inpixW2H. This better allows the user to save theshowDigitizedRadii() image as an image file in a loop (see examples in aaaMakeDataVignetts.R). Eventually this will be used to address #43.
RFishBC 0.2.3 11-December-19
Now using ROxygen2 7.0.1.
digitizeRadii(): Modified. Fixed bug withaddNote= when restarting an image. Thanks to Ben Neely for pointing out the issue.
RFishBC 0.2.2 2-May-19
Added URL for fishBC software per CRAN request.
Added a directive to ignore Rplots* files when building the package (i.e., to .rbuildignore). This reduces the size of the tar-ball per CRAN request.
RFishBC 0.2.1 1-May-19
Updated vignettes.
Added more tests.
addNote(): Added (addresses #41; thanks to Rory Feeney).
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 whensnap2transect=TRUE andmakeTransect=FALSE.
findNotes(): Added (addresses #41; thanks to Rory Feeney).
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 addingshowScaleBarLength= and cex.scaleBar=(addresses #36).
RFishBC 0.2.0 18-Dec-18
Added several items (mostly images) to .Rbuildignore to lower bloat of package.
Added .Rbuildignore to remove sticker folder from package directory.
Added validation tests (still need to be run manually) from Sullivan data.
combineData(): Modified. ChangedoutFormat= to formatOut=. AddedoutType= to allow user to choose either radial or incremental measurements as output.
digitizeRadii(): Modified. ChangedshowTransect= to makeTransect. Changed so thatsnap2Transect is changed to FALSE if it isTRUE 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 includesmakeTransect= used in digitizeRadii(). Now includes connect=, col.connect=, andlwd.connect= used in showDigitizedImage(). Because of those changes showTransect= has been removed.
showDigitizedImage(): Modified. ChangedshowTransect= to connect=,col.transect= to col.connect=, andlwd.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.
RFishBC 0.1.2 9-Dec-18
Added dependency to cli package forDONE(), 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 usecat_line() from cli package (removed my hack).
findScalingFactor(): Modified. Changed console output directions to use RULE() instead ofNOTE().
NOTE(): Modified. Changed to usecat_line() from cli package (removed my hack).
RULE(): Added.
RFishBC 0.1.1 12-Nov-18
Released to CRAN.
Removed automatic webpage construction from Travis-CI. Did not work with some of the updated vignettes.
Put fishBC in the Description field into single quotes as directed by CRAN.
digitizeRadii(). Modified. Added a note that draws attention when snap2Transect=TRUE andshowTransect=FALSE (i.e., “snapping” to a transect that is not shown). At least partially addresses #30.
RFishBC 0.1.0 7-Nov-18
iSnap2Transect(): Modified. Changed to handle bugs related to perfectly vertical or perfectly horizontal transects. Addresses #27(Thanks to Ben Neely).
showDigitizedImage(): Modified. RemovedcloseWindow= and sepWindow().
RFishBC 0.0.13 6-Oct-18
combineData(): Modified. Changed so that an age-0 fish with all plus-growth is still included in the returned data.frame whendeletePlusGrowth=TRUE (the ann andrad 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 andr button equivalencies for f andd. Added the ability for the user to start over (resulting in no file to be written, but the current image stays live; uses thez 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 fordigitizeRadii().
RFishBC 0.0.12 3-Oct-18
Excluded many of the interactive lines from the coverage statistics. Updated other tests (aiming for comprehensiveness).
Started a cran-comments document to begin preparations for a CRAN release.
Added Encoding: UTF-8 to DESCRIPTION.
bcFuns(): Modified. Fixed bug in verbose=result when BCM=18.
listFiles(): Modified. Fixed bug related toignore.case=.
Set TravisCI to auto-update the webpage documentation (See this).
Updated “Collect Radii Data” and the “Workflow” vignettes for changes below.
Updated the webpage for changes below.
digitizeRadii(): Modified. Moved the main code toiDigitizeRadii1(), which is basically the oldedigitizeRadii() for working with only one image. The newdigitizeRadii() allows nm= andid= 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 newIDpattern=.
RFBCoptions(): Modified. Added IDpattern=(Part of addressing #20).
RFishBC 0.0.10 3-July-18
Added CITATION file.
Added hex sticker.
Added workflow vignette.
combineData(): Modified. Allowed first argument to be an RFishBC object saved from digitizeRadii()(partially addresses #16; thanks to Jason Doll).
digitizeRadii(): Modified. AddedcloseWindow= (addresses #14). Changed so that the rownames of the pts data.frame in the returned object includes “center” and “edge.” See changes toiSelectPt().
findScalingFactor(): Modified. AddedcloseWindow= (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 indigitizeRadii() and findScalingFactor()(addresses #17; thanks to Jason Doll).
showDigitizedImage(): Modified. Fixed bug iniShowAnnuliLabels() (addressed #12; thanks to Liuyong Ding). Allowed first argument to be an RFishBC object saved fromdigitizeRadii() (partially addresses #16; thanks to Jason Doll). Changednm= to nms= to be consistent withcombineData().
RFishBC 0.0.9 18-May-18
Added rlang, stringr, andtidyr to Imports.
Added tests.
Updated “Collect Data” vignette for changes tocombineData().
Changed “Back-calculating Lengths” vignette for newbackCalc().
bcFuns(): Modified. Changed to usingSTOP(). Changed all Lc to Lcap,Rc to Rcap, agec toAcap, and agei to Ai. Changed all BPH-related models to use a, b, andc and all SPH-related models to use A,B, and C. Started usingiGetBCMethod(). Removed verbose= (moved to within the returned function).
bcUtilChecker(): Modified. Changed to usingSTOP() and WARN().
findScalingFactor(): Modified. Added a catch for non-positive knownLength=.
iGetBCMethod(): Added. Used in backCalc()and bcFuns().
SMBassWB1: Added.
SMBassWB2: Added.
StdIntLit: Added.
RFishBC 0.0.8 13-May-18
Added tests.
Changed to using .rds files rather than.RData files to save the data. This required usingsaveRDS() in digitizeRadii() andreadRDS() in showDigitizedImage() andcombineData().
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 theRFishBC 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.
RFishBC 0.0.7 10-May-18
Updated tests.
digitizeRadii(): Modified. Added ability (usingiSelectPt()) to delete points after selection for scale-bar, transect, and annuli selection. This removed the use oflocator() and thus key-presses are used to terminate the selection of points. Added the pch.del= andcol.del= arguments. Removed the orig.ptsdata.frame from the returned object.
findScalingFactor(): Modified. Added ability (usingiSelectPt()) to delete points after selection for scale-bar. Added pch.sel=, col.sel=,cex.sel=, pch.del=, and col.del=arguments.
RFBCoptions(): Modified. Added thepch.del= and col.del= arguments. Removedpch.show2=, col.show2=, andcex.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.
RFishBC 0.0.6 9-May-18
Added some tests.
Added importFrom for clisymbols and crayonpackages.
combineData(): Modified. Added a check that the RData file has a radii object.
digitizeRadii(): Modified. Fixed bug related toshowTransect=. 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.
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.
RFishBC 0.0.4 29-Apr-18
Complete reworking of the code. The big difference is a requirement that the data files be 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 intodigitizeRadii().
iHndlID(): Deleted. Moved intodigitizeRadii().
iHndlScalingFactor(): Deleted.
iHndlScalingFactorFromScaleBar(): Added.
iProcessAnnuli(): Deleted. Moved intodigitizeRadii().
iPts2Rad(): Added.
iSelectAnnuli(): Deleted. Moved intodigitizeRadii().
iShowTransect(): Deleted. Deleted. Moved intodigitizeRadii() and showDigitizedImage().
RFishBC 0.0.3 28-Apr-18
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” ifsnap2Transect=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()). ChangedaddTransect= to showTransect= to make more similar to showDigitezedImages().
RFBCoptions(): Modified. AddedshowAnnuliLabels=, col.ann=, andcex.ann= for use in showDigitizedImage(). Changed defaults of mostly colors, pchs, and cexs.
showDigitizedImage(): Modified. AddedshowAnnuliLabels=, col.ann=, andcex.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 ofiSelectAnnuli().
iGetImage(): Modified. Streamlined code. Addednative=TRUE to read.bitmap() call to send to the underlying functions as this is apparently more efficient when usingrasterImage() (which this uses).
iOrderPts(): Added. Made it easier to add annuli labels in showDigitizedImage().
iSelectAnnuli(): Modified. Now callsiSelectTransect().
iShowAnnuliLabels(): Added. Made it easier to add annuli labels in showDigitizedImage().
ishowTransect(): Added. Moved this code out ofiSelectAnnuli(). Also called fromshowDigitizedImage().
RFishBC 0.0.2 27-Apr-18
digitizeRadii(): Modified. Addedsnap2Transect= to address #1. Modified how fname= was handled if missing (seeiHndlfname()) 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. AddedpopID= (again see iHndlID()). Fixed poor directions about the use of the escape key to terminatelocator(). Added showInfo=,pos.info=, cex.info=, andcol.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 indigitizeRadii(), showDigitizedImage(), andfindScalingFactor().
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 withdigitizeRadii()), which partially addresses #5.
iHndlScalingFactor(): Modified. AddedpixW2H= argument to receive the pixel width-to-height ratio to adjust distance calculations for non-square images.
showDigitizedData(): Modified. Movedfile.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).