Back-Calculation of Fish Length

Helps fisheries scientists collect measurements from calcified structures and back-calculate estimated lengths at previous ages using standard procedures and models. This is intended to replace much of the functionality provided by the now out-dated 'fishBC' software.


News

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. 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.

RFishBC 0.1.2 9-Dec-18

  • Added dependency to 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.

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 and showTransect=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).
  • 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().

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 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().

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 to ignore.case=.
  • getID(): Modified. Slightly simplified code. Added tests.

RFishBC 0.0.11 26-Jul-18

  • 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 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).

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. 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().

RFishBC 0.0.9 18-May-18

  • Added rlang, stringr, and tidyr to Imports.
  • Added tests.
  • Updated "Collect Data" vignette for changes to combineData().
  • Changed "Back-calculating Lengths" vignette for new 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.

RFishBC 0.0.8 13-May-18

  • Added tests.
  • Changed to using .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.

RFishBC 0.0.7 10-May-18

  • Updated tests.
  • 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.

RFishBC 0.0.6 9-May-18

  • Added some tests.
  • Added importFrom for 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.

RFishBC 0.0.5 29-Apr-18

  • Changed license from MIT to GPL-3.
  • 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.

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 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().

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" 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().

RFishBC 0.0.2 27-Apr-18

  • 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).

RFishBC 0.0.1 16-Apr-18

  • First version. Everything is new.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("RFishBC")

0.2.0 by Derek Ogle, 4 months ago


http://derekogle.com/RFishBC


Report a bug at https://github.com/droglenc/RFishBC/issues


Browse source code at https://github.com/cran/RFishBC


Authors: Derek Ogle [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Imports graphics, grDevices, cli, clisymbols, crayon, readbitmap, rlang, settings, stringr, tidyr, withr

Suggests FSA, covr, pkgdown, testthat


See at CRAN