Updatedtest-coverage.yaml and moved a# nocov start and# nocov end inbootstrap.r to address the errors withtest-coverage.yaml. Addresses#118.
RemovedDescTools,plyr,psych from Suggests (and all their uses in tests and linkedcode in documentation). Removedggplot2,marked,rcapture, andtibble fromSuggests (and use in examples was put in a\dontrun()).
AddedFlexParamCurve to Imports for use ofmodpar() infindGrowthStarts(param="Richards")andpurrr for use ofmap2_chr() inshowGrowthFun().
Removed my ORCID from DESCRIPTION to alleviate note on WinBuilderfor R4.4.3.
Added the following “articles”.
FSA.FSA.FSA.internals: Added functions to return a logical about whether avalue is less than, less than or equal, greater than, or greater than orequal (i.e.,is.lte(),is.lt(),is.gte(), andis.gt()). Added functions thatuse those logical and return an informative error if the logical isFALSE (i.e.,iChkLTE(),iChkLT(),iChkGTE(), andiChkGT()). The errors can“grab” the name of the object so that the error can be specific thoughthe function is general.
internals: ModifiedSTOP() andWARN()to usestrwrap() rather than hard-coded line breaks. AddedMESSAGE(). AddediStrCollapse(), largely foruse withSTOP(),WARN(), andMESSAGE().
throughout: Changed manydf[-which(CONDITION),]constructs todf[!CONDITION] as suggestedhere.
findGrowthStarts(): Added. This replacesvbStarts() and includes starting values for Gompertz,logistic, and Richards functions, and seasonal and tag-recapture vonBertalanffy parameterizations. Note thatconstvals= andfixed= must now be numeric vectors (and not lists) and thatthe returned starting values are in a numeric vector.
fishR(): Modified. Added link to teachingresources.
GompertzFuns(): Deprecated (replaced withmakeGrowthFun()).
GrowthData1,GrowthData2,GrowthData3: Added for testing growth functions.
growthFunShow(): Deprecated (replaced withshowGrowthFun()). But also fixed expression forQuinnDeriso3 parameterization of the Gompertz function (i.e., erroneoust* changed to t0 … related to fixing#113). Alsochanged a parameter to b in Ricker2 and QuinnDeriso1, and a to c inRicker3 and QuinnDeriso2, to distinguish it from a in the Originalparameterization. Will be deleted in future versions.
logisticFuns(): Deprecated (replaced withmakeGrowthFun()).
makeGrowthFun(): Added. This replacesvbFuns(),GompertzFuns(),logisticFuns(),RichardsFuns(),Schnute(),SchnuteRichards(). Along the way,the following changes were made.
param= andmoved names topname=. Some names were changed.findGrowthStarts(). Removed theother two parameterizations as they were essentially the same as thefirst except for how the exponent was defined, which has no biologicalmeaning.peek(): Modified. Addressed#125.
psdAdd(): Modified. Addedgroup= tohandle the change for sub-groups inPSDlit. ModifiedaddLens= to more closely match howaddLens=words inpsdCalc() and, thus, removedaddSpecs=.
psdCalc(): Modified. Addedgroup= tohandle the change for sub-groups inPSDlit. Made othercoding changes that did not affect forward-facingfunctionality.
PSDLit: Modified.
group variable to handle species with specifiedsub-groups.psdVals(): Modified. Addedgroup= tohandle the change for sub-groups inPSDlit. Made othercoding changes that did not affect forward-facingfunctionality.
RichardsFuns(): Deprecated (replaced withmakeGrowthFun()).
Schnute(): Deleted (made defunct) as it was added tomakeGrowthFun() (useSchnute <- makeGrowthFun("Schnute") instead). Note thatorder of arguments was changed so that the parameters appear before theconstants to be consistent with other growth functions.
SchnuteRichards(): Deleted (made defunct) as it wasadded tomakeGrowthFun() (useSchnuteRichards <- makeGrowthFun("Schnute-Richards")instead) and was likely little used.
showGrowthFun(): Added. ReplacesGrowthFunShow(). Updated to allow user to send an objectfromnls() and have the coefficient values extracted andput in the expression. Also, can either return a string or an expressionto allow more flexibility in use (especially withggplot2).
vbFuns(): Deprecated (replaced withmakeGrowthFun()).
vbStarts(): Deprecated (replaced withmakeGrowthStarts(). But also streamlined some of theinternal functions, fixed some typos, and replacediVBStartsPlot() withiPlotGrowthStarts() to bemore general.
wrAdd(): Modified. AddedWsOpts= tohandle species where the user must make a choice about which standardweight equation to use.
WSLit: Modified.
type variable (will depend on whetherquad isNA or not).group variable that took the parentheticalgroupings fromspecies for things like Walleye, CutthroatTrout, etc. Nowspecies is an actual species name and if asub-group of that exists then it is defined withgroup.wsVal(): Modified.
group= to handle species for which equations werederived for sub-groups of the species (e.g., separately for males andfemales, or lentic and lotic). See related changes toWSlit.method= to handle species for which equationsderived from more than one method are available (e.g., “ArcticGrayling”).ref=,units=,etc. and provided more descriptive error messages.Updated testing to usetestthat v3.0.0.
DESCRIPTION including addingtidyr in Suggests (for example inremoval()).expect_is() withexpect_equal(class()) idioms.expect_equivalent() withexpect_equal() asexpect_equivalent() was notneeded to begin with.expect_equivalent() withexpect_equal(,ignore_attr=TRUE) asexpect_equivalent() was deprecated.matrixbut the class wasc("matrix","array").require() in individual files totestthat.R. This removed manyrequire() thatwere not needed.Fixed four minor errors in documentation from legacy uses of\R{} rather than\code{}.
Made some accessibility changes and rebuilt favicons as suggestedbypkgdown.
alkPlot(): Modified. Added note in documentationpointing to a fishR blog post on usingggplot2 to makesimilar plots.
catchCurve(): Modified. Addedas.df= toextractor functions andincl.est= toconfint.catchCurve() to match functionality added todepletion().
chapmanRobson(): Modified. Addedas.df=to extractor functions andincl.est= toconfint.chapmanRobson() to match functionality added todepletion().
depletion(): Modified to address#111.
depletion() washchanged to a method call anddepletion.default() anddepletion.formula() were added. Tests for the formula wereincluded.as.df= tocoef.depletion(),confint.depletion(), andsummary.depletion()so that the result is returned as a data.frame when set toTRUE (default isFALSE to maintain backwardcompatability).incl.est= toconfint.depletion() tomake it easier to get away from the clunkycbind("Est"=coef(),confint()) code.GompertzFuns(): Modified. Accepted pull requestrelated to#112 thatfixed several typos and dead links in the documentation … thanks Arni.Corrected the erroneous reference to t* (should have been t0) in thedocumentation for the Gompertz function (fixes#113 …thanks again to Arni).
metaM(): Modified to address#114.
rFAMS).justM= and its functionality (not needed withdata.frame returned).verbose= to allow user to limit some of what isreturned in data.frame.print.metaM() method.Mmethods(): Modified. Changedwhat= tomethod= for simplicity withmetaM().
removal(): Modified.
depletion().just.ests=. Functionality will be largelyreplaced withincl.ests= inconfint().Replaced split-apply example with a new one that performs similarlywithoutjust.ests= and is more in-line with examples indepletionet al.coef() extractor function.confint() andsummary() extractorfunctions to better matchdepletion().pkgdown.yaml GitHub action tov2.Changed action to only run on a release (rather than a push) but it canberunmanually as well.R-CMD-check.yaml GitHub action tov2.Note that I had to add theextra code fordealing with graphics on the Mac version.fishR(),FSA(), andREADME.md. Partially address#86._pkgdown.yml to match that ofFSAdata and more closely matchfishR.pkgdownpicks up the CRAN release date to add.CITATION (to match that required for nextversion of R).alkIndivAge(): Modified. Added a catch forNAs in the length sample. Also added a test. This addresses#88.confint.boot(): Modified. Changed hard-coding ofcolumns that contained the confidence interval values to find thosecolumns bygrep()ing for the% sign. Thisfixes an issue related tocar::Confint() returning thecoef() results for functions that have acoef() method but not for those that do not. Also updatedtests to use results fromcar::Boot() rather than the oldcar::bootCase().PSDcalc: Modified. Changed code to allow for missingspecies= as long asaddLens= is used. Thisallows the user to provide length categories for a species for whichGabelhouse lengths are not defined. Several new tests were added andsome were modified to handle the changing message re: a missingspecies=. The documentation was modified accordingly. This(finally) addresses#58.PSDlit: Modified. Added info for Redbreast Sunfish andSpotted Sunfish from Bonvecchioet al. (2023). This addresses#100).wSlit: Modified documentation. Described theRLP andEmP acronyms and provided referencesfor them. This addresses#95). Addedinfo for Redbreast Sunfish and Spotted Sunfish from Bonvecchioetal. (2023). This addresses#100).dplyr fromimports tosuggests (needed because functions were removed in lastversion; however it is still used in some examples; partially addresses#87).sciplot fromimports (becausefunctions were removed in last version; partially addresses#87).ksTest() to handle issues on the CRANM1 build machine (per e-mail from Prof. Ripley on 15-Feb-22; partiallyaddresses#87).droglenc github that wererelated toFSA orFSAdata to be to thefishR-Core-Team github.filterD():REMOVED (toFSAmisc).fitPlot():REMOVED (toFSAmisc).fsaNews() andFSANews():Removed.psdAdd(): Modified. Changed the wayPSDlitwas loaded into the function environment so thatFSA::psdAdd() will work. Addresses#85.PSDLit: Modified. Added info for Utah Chub (fromhere;address#84).psdVal(): Modified. Changed the wayPSDlitwas loaded into the function environment so thatFSA::psdVal() will work. Addresses#85.residPlot():REMOVED (toFSAmisc).wrAdd(): Modified. Changed the wayWSlitwas loaded into the function environment so thatFSA::wrAdd() will work. Addresses#85.WSLit: Modified. Added info for Utah Chub (fromhere;address#84).wsVal(): Modified. Changed the wayWSlitwas loaded into the function environment so thatFSA::wsVal() will work. Addresses#85.catchCurve() andchapmanRobson() as directed by CRAN on 17-Jul-21. Issuelikely caused by changes tofishmethods package.AUThor.plyr from Imports to Suggests.alkPlot(): Modified. Removed use ofchooseColors() (see below).binCI(): Modified. Changed to useiCheckConfLevel() (which addresses#66).bootCase():REMOVED. Users can usecar::Boot(), which partially addresses#65.plot.boot():REMOVED. Conflicted withboot::plot.boot() which caused an error with CRAN. Samefunctionality is available withpairs(<boot object>$t).catchCurve(): Modified. Removed hard-coding ofylim= forplot.catchCurve() (this addresses#70 … Thanksto Brendan Runde). Addedround.est= so that the user cancontrol the decimals on mortality estimate values. Changed to useiCheckConfLevel() (which addresses#66).chapmanRobson(): Modified. Removed hard-coding ofylim= forplot.chapmanRobson(). Addedround.est= so that the user can control the decimals onmortality and survival estimate values. Changed to useiCheckConfLevel() (which addresses#66).chooseColors():REMOVED. This was anexported function that should have been internal. Regardless, where itwas used has been removed and the user is now allowed to provide theirown vector of colors. SeeiCheckMultColors(). Partiallyaddresses#65.compIntercepts():REMOVED (toFSAmisc). Added toFSA-defunct. Partiallyaddresses#65.compSlopes():REMOVED (toFSAmisc). Added toFSA-defunct. Partiallyaddresses#65.depletion(): Modified. Changed to useiCheckConfLevel() (which addresses#66).filterD():DEPRECATED (partiallyaddresses#65).fitPlot():DEPRECATED (partiallyaddresses#65). Priorto that removed use ofchooseColors() (see above).diags():REMOVED (moved toFSAmisc). Added toFSA-defunct. Partiallyaddresses#65.hoCoef():REMOVED (moved toFSAmisc). Added toFSA-defunct. Partiallyaddresses#65.hyperCI(): Modified. Changed to useiCheckConfLevel() (which addresses#66).iCheckConfLevel(): Added (internal to address#66).iCheckMultColors(): Added (internal). Part of removingchooseColors() andpaletteChoices().iRichColors():REMOVED (as part ofremovingchooseColors()).mapvalues():REMOVED. Added toFSA-defunct. Partially addresses#65.mrClosed(): Modified. Changed to useiCheckConfLevel() (which addresses#66).mrOpen(): Modified. Added a warning for when r==0,which causes the SE of M and thus N to beInfinity (thisaddresses#69). Addeda similar warning for when R==0 (but not the last time period). Addedtests for the warning messages. Changed one use ofapply()torowSums() for ease of reading. Changed to useiCheckConfLevel() (which addresses#66).paletteChoices():REMOVED. SeechooseColors() above. Partially addresses#65.poiCI(): Modified. Changed to useiCheckConfLevel() (which addresses#66).psdAdd(): Modified. Changed alevels() iniPSDlitCheck() tounique() becausespecies is no longer a factor due to updatingPSDlit (i.e., rdata file changed with newread.csv()).psdCalc(): Modified. Added a catch for when “tibble”sare sent indata= (addresses#75).Changed to useiCheckConfLevel() (which addresses#66).psdCI(): Modified. Changed to useiCheckConfLevel() (which addresses#66).PSDlit: Modified. Added length categories for ShoalBass and Pallid Sturgeon. Added Striped Bass (Hybrid) and Striped Bass xWhite Bass; though these are the same as the existing Palmetto Bass.Added “source”s for each entry.psdVal(): Modified. Changed alevels() iniPSDlitCheck() andiListSpecies() tounique() becausespecies is no longer a factordue to updatingPSDlit (i.e., rdata file changed with newread.csv()). Added ashowJustSource= argumentthat will show the source info (ifTRUE) or not (ifFALSE; default), which partially addresses#76.removal(): Modified. Added check and then warning ifnon-whole numbers are incatch= (addresses#60). Alsomodified checks of data integrity to be more robust (e.g., if acharacter vector is sent). Changed to useiCheckConfLevel()(which addresses#66).residPlot():DEPRECATED (partiallyaddresses#65). Priorto that removed use ofchooseColors() (see above).Subset():REMOVED. Added toFSA-defunct. Partially addresses#65.wrAdd(): Modified. Changed alevels() iniwsLitCheck() tounique() becausespecies is no longer a factor due to updatingWSlit (i.e., rdata file changed with newread.csv()).WSlit: Modified. Addresses#68.wsVal(): Modified. Changed alevels() iniwsLitCheck() tounique() becausespecies is no longer a factor due to updatingWSlit (i.e., rdata file changed with newread.csv()).usethis::use_github_action_check_standard()).usethis::use_github_action("pkgdown")).tests\plottests\ to speed up testing. Thetests\plottests\ was added to.Rbuildignore.hist.formula(): Modified. Fixed bug with y-axes whenfreq=FALSE is used (fixes#62; thankstofitPlot(): Modified. Fixed bugs with handling modelsthat used character rather than factor variables.plotBinResp(): REMOVED. Removed as a user-facingfunction, but made as an internal function for continued use infitPlot() whilefitPlot() is deprecated.psdAdd(): Modified. Fixed bug relate to species thatwereNA (fixes#64; thanksto Dan Shoup). Added more tests and fixed some typos in thedocumentation.psdPlot(): Modified. Fixed bug with box around the plotwhenadd.psd=FALSE. Added 5% expansion to top of y-axis sothat bars did not run into the box.residPlot(): Modified. Fixed bugs with handling modelsthat used character rather than factor variables.tibble to suggests (see comment aboutheadtail() below).RichardsFuns() (documentation did not change when parameterletters were changed for the Age and Growth book).headtail() to useas_tibble() fromtibble package rather thantbl_df() fromdplyr package. Required addingtibble to suggests.nlsTracePlot(): Modified. Created a conditional catchdepending on the version of R as the results ofnls(*,trace=TRUE) are changing in v4.1.0 (per e-mail fromMartin Maechler on 2-Nov-20).rhub::check_for_cran() for checkingbefore sending to CRAN.Summarize() andksTest()that useddata.frame(). This should have been done withv0.8.28.ksTest() that were identifiedusing R-hub.fishR(): Modified. Changed base URL tohttps: (fromhttp:). Addedopen=,primarily to allow not opening a browser during testing.epitools package as it may soonbe orphaned. See changes tobinCI() andpoiCI() outlined below.binCI(): Modified. Added internal functions that arebased on (but not identical to) functions in theepitoolspackage which will possibly be deprecated soon (per note from CRAN on7-Mar-20).poiCI(): Modified. Added internal functions that arebased on (but not identical to) functions in theepitoolspackage which will possibly be deprecated soon (per note from CRAN on7-Mar-20).fitPlot(): Modified. Changed so that lines are plottedafter the points in the IVR versions.ksTest(): Modified. Changed documentation examples tohandle R’s new way of handlingstringsAsFactors= (perrequest from CRAN on 27-Feb-20).psdAdd(): Modified. Changed testing to handle R’s newway of handlingstringsAsFactors= (per request from CRAN on27-Feb-20).gplots package as it is noworphaned. Required addingiRichColors() internalfunction.lwCompPreds(): Removed\dots fromarguments as it was not in usage (per request from CRAN on3-Feb-20).repeatedRows2Keep(): Modified. Now makes comparisons asifNAs are regular values.R >=3.5.0, because that isthe latest version required by a package (i.e.,car) thatFSA imports or suggests. Used the“check_r_versions_of_package_dependencies” shiny app by “ateucher” (onGithub) to help determine this.asbio package from suggests as it hung upTravis-CI build (because of the need for the TCLTK package).capFirst(): Modified. Fixed bug related to anNA item.psdAdd(): Modified. Changedspec= tospecies= to be consistent withpsdCalc() andpsdPlot().peek(): Added.repeatedRows2Keep(): Modified. Added a catch if thedata.frame only contains one row (it then returnsTRUE sothat that row is kept).agePrecision(): Modified. Changed so that PE2 and CV2use the median in the entire calculation rather than just in thedenominator.iHndlColsUseIgnore(): Modified. Changed so that a 0indice returns an error.repeatedRows2Keep(): Added.vbStarts(): Modified. Corrected bug related to pointtransparenty whenplot=TRUE and there is no age/lengthcombination repeats (i.e., all age/length combinations are unique).Corrected bug ofcol.main= being ignored whenplot=TRUE.\concept in Rd files per CRANrequest.testthat folder as suggested intestthat release notes.Subset() (replaced withfilterD()).fitPlot(): Modified. Fixed bug related to y-axis limitsnot extending to contain the data, confidence bands, or prediction bands(infitPlot.slr()). This addresses#3 listed forNCStats).hist.formula(): Modified. Fixed bug related tosubsequent calls after a call that usediaxs=FALSE. Thisaddresses#46.iLegendHelp(): Modified. Added a catch if a properkeyword is not supplied.nlsTracePlot(): Modified. Moved error catching forimproper keyword for legend placement forward.SchnuteRichards(): Added. This addresses#54.fishmethods package(vblrt() replaced withgrowthlrt() andT= replaced withTC= inM.empirical()) per CRAN request.withr to Imports (see usages below).Encoding: UTF-8 to DESCRIPTION.method="Burnham" toremoval().dunnTest(). Should have done this longago.data() in examples that referred to datafrom this package. Included thepackage= argument indata() that loaded from other packages.seealso, with links to which functions use thedata for examples, to docmentation for all data.frames.\dontrun()s from thebootCaserelated examples now thatcar package is updated. Thisaddresses#45.addZeroCatch(): Modified. Added a catch that turns a“tibble” into a regular data.frame (which obviates some errors thatoccur with tibbles). Minor changes to documentation and comments in thecode.agePrecision(): Modified. Added intermediate andsummary calculations for median and modal age; average absolutedeviation and standard deviation; APE and CV with the median rather thanthe mean as the divisor; and index of precision (D). Addedshow.prec2=. Updated tests and examples. Other minormodifications to the function code. Addresses#41 and#49.alkIndivAge(): Modified. Replaced anoptions(warn=-1) withsuppressWarnings().alkPlot(): Modified. Changed to usingwithr::local_par() (partially addresses#38).Replaced anoptions(warn=-1) withsuppressWarnings().alkSummaries(): Modified. Replaced anoptions(warn=-1) withsuppressWarnings().withr::local_par() (partially addresses#38).capHistSum(): Modified. Changed to usingwithr::local_par() (partially addresses#38).chapmanRobson(): Modified. Changed to usingwithr::local_par() (partially addresses#38).fishR(): Modified. Changed examples in documentation tonot be run (so as not to open an external webpage).FSAnews(): Modified. Changed examples in documentationto not be run (so as not to open an external webpage).withr::local_par() (partially addresses#38).hist.formula(): Modified. Changed to usingwithr::local_par() (partially addresses#38).lwCompPreds(): Modified. Changed to usingwithr::local_par() (partially addresses#38).plotAB(): Modified. Now in its own documentation file(rather than withageBias()).psdCalc(): Modified. Better handled the situation wherethe user asks for summaries with some fish greater than stock size butno fish greater than quality size (addresses#50; thanksto Timothy Spier for the bug report).removal(): Modified. Addedmethod="Burhnam" via the#51 fromPowell Wheeler.residPlot(): Modified. Changed to usingwithr::local_par() (partially addresses#38).SMBassWB: Modified. Fixed minor data entry error in row383.vbFuns(): Modified. AddedFrancis3 to thelist of models.asbio,DescTools,nlme,andpsych packages to Suggests because they are used intests (and as will soon be required by CRAN … per an e-mail from CRAN on17-May-18).addRadCap(): Removed. Moved toRFishBCpackage.bcFuns(): Removed. Moved toRFishBCpackage.gConvert(): Removed. Moved toRFishBCpackage.mrClosed(): Modified. Fixed a bug that was related topoiCI() returning results from all four types. NowmrClosed() will use only one type. Thanks to Timothy Spiersfor pointing out this bug.SMBassWB: Modified. Fixed minor data entry error in row404. Changed link in documentation fromalr3 toalr4 package.addZeroCatch(): Modified. Changed two1:nrow() structures toseq_len(nrow())(partially addressing#36).ageBias(): Modified. Changed all1:structures toseq_len() (partially addressing#36).agePrecision(): Modified. Changed all1:structures toseq_len() (partially addressing#36).bcFuns(): Modified. Changed three1:length() structures toseq_along()(partially addressing#36).bootCase() methods: Modified. Changed all1: structures toseq_len() (partiallyaddressing#36).capHistConvert(): Modified. Changed all1:structures toseq_len() orseq_along()(partially addressing#36).capHistSum(): Modified. Changed all1:structures toseq_len() (partially addressing#36).chooseColors(): Modified. Changed all1:structures toseq_len() (partially addressing#36).compSlopes(): Modified. Changed all1:structures toseq_len() (partially addressing#36).compIntercepts(): Modified. Changed all1:structures toseq_len() (partially addressing#36).extraSS(): Modified. Changed all1:structures toseq_len() orseq_along()(partially addressing#36).headtail(): Modified. Changed all1:structures toseq_len() (partially addressing#36).hist.formula() methods: Modified. Changed all1: structures toseq_len() (partiallyaddressing#36).htest.boot(): Removed (added last version) until I cantest more.iHndlFormula(): Modified. Now categorizes a charactervariable as a factor variable. This addresses#35) forhist.formula() andSummarize().lrt(): Modified. Changed all1: structurestoseq_len() orseq_along() (partiallyaddressing#36).lwCompPreds(): Modified. Changed all1:structures toseq_len() orseq_along()(partially addressing#36).mrClosed(): Modified. Changed two1:length() structures toseq_along()(partially addressing#36).nlsBoot() methods: Modified. Changed all1: structures toseq_len() (partiallyaddressing#36).plot.boot(): Removed (added last version) until I cantest more.predict.boot(): Removed (added last version) until Ican test more.psdAdd(): Modified. Changed three1:structures toseq_len() orseq_along()(partially addressing#36).residPlot(): Modified. Changed three1:length() structures toseq_along()(partially addressing#36).Summarize(): Modified. Changed one1:length() structure toseq_along() (partiallyaddressing#36).wrAdd(): Modified. Changed three1:structures toseq_len() orseq_along()(partially addressing#36).R >=3.2.0, because that isthe latest version required by a package (i.e.,car) thatFSA imports or suggests. Used the“check_r_versions_of_package_dependencies” shiny app by “ateucher” (onGithub) to help determine this.testthat package.bootCase(): Added. This was added becausebootCase() will soon be removed from thecarpackage. It was added so that the code in the Introductory FisheriesAnalyses with R book will still work. It is largely a wrapper toBoot() incar withmethod="case".The documentation was updated somewhat.catchCurve(): Modified. Changed the weighted regressionmethod so that negative weights are set to zero rather than the minimumof the positive values (brought to my attention by Vaskar Nepal KC).Also added anrSquared() method (per request by VaskarNepal KC).depletion(): Modified. Added anrSquared()method.expandCounts(): Modified. Minor changes todocumentation.hTest.boot(): Added.plot.boot(): Added.plotAB(): Modified. Addedcol.numbers= toallow users to modify the color of the numbers whenwhat="numbers" is used (addresses#34).predict.boot(): Added.psdPlot(): Modified. Minor changes to documentation andlook of the function code.rSquared(): Added fromNCStats, butincluding a generic method so that it can be used for other models(e.g.,catchCurve()).vbFuns(): Modified. SwitchedFabens andFabens2 parameterizations to better matchWang(i.e., increment model first). AddedFrancis2parameterization for tag-recapture data.vbStarts(): Modified. Fixed some spacing issues withthe warnings when starting values for Linf was poorly estimated. Addedan argument toivbStarts.LinfK() to suppress checking thevalue of Linf. This argument reduces the change of double-printing thewarning message when there are bad estimates of starting values for Linfand K.dunnTest(): Modified. Adjusted code to handle theaddition ofaltp= to and modified output fromdunn.test() indunn.test. Added additionaltests and corrected some issues in the documentation.GompertzFuns(): Modified. Fixed error in message (i.e.,msg=TRUE) forparam="Ricker2".growthFunShow(): Modified. Fixed error in expressionfortype="Logistic" andparam="CampanaJones1".helpers directory that will testthat all required packages are installed.iAddOutlierTestResults(): Modified. Fixed bug relatedto point labels inresidPlot() when the data.frame for theoriginal model hadNA values.removal(): Modified document by merging pull request#33.srStarts(): Modified. Addedfixed=. Addedsome catches for poor starting values. Added relevant tests. Addresses#30.dunn.test andlmtest toimports to help with portability for workshops.ageBias(): Modified. Fixed bug inplot()so that the tick marks on the marginal histograms match the tick markson the main plot. Changed the defaulthist.panel.size= inplot() so that it more reliably prints the values on theaxes of the marginal histograms.removal(): Modified. Added “warnings” for when allcatches are zeroes (an object is still returned with allNAs). Thanks to Daniel Hanks for pointing out thisissue.Summarize(): Modified. Fixed bug whenpercZero!="always" and there are no valid values such thatthe calculated percent of zeroes isNA.ageBias(): Modified. A complete rebuild ofplot. Major changes are to addplotAB() whichis primarily used to make the “legacy” age bias plots of Campana,removal of the “sunflower” plot option, new sets of defaults for many ofthe arguments that reflect my preferences for visualizing agecomparisons (which includes defaulting to plotting differences in ages),addition of the ability to add marginal histograms (xHist=,yHist=,col.hist=, andhist.panel.size=), better handling of axis ticks and labels(primarily to show ticks at integers and make sure 0 is included fordifferences), and allowing the ability to add “summary layers” to themain plot (seeallowAdd=). Many examples were added. Somefunctionality from previous versions will be broken.capFirst(): Modified. Changed someif()swithclass()es toinherits().compIntercepts(): Modified. Replaced twodim() calls withnrow().fact2num(): Modified. Changed someif()swithclass()es toinherits().lagratio(): Modified. Changed someif()swithclass()es toinherits().iHndlCols2UseIgnore(): Modified. Changed someif()s withclass()es toinherits().iLegendHelp(): Modified. Changed someif()s withclass()es toinherits().iPredictBoot(): Modified. Changed someif()s withclass()es toinherits().is.CapHist(): Added.iTypeoflm(): Modified. Added a catch for a linear modelthat has a character variable (now alerts the user with a warning).mrClosed(): Modified. Changed someif()swithclass()es tois.CapHist().mrOpen(): Modified. Changed someif()swithclass()es tois.CapHist().nlsTracePlot(): Modified. Changed someif()s withclass()es toinherits().perc(): Modified. Changed someif()s withclass()es toinherits().plotAB(): Added. See description above forageBias().plotBinResp(): Modified. Changed how defaulttransparency level is calculated and set the maximum transparency to 50(changed from 500). Fixed bug in how the width of the proportionswindows were calculated by default. These changes will affectfitPlot() for logistic regression models.psdAdd(): Modified. Changed someif()swithclass()es toinherits().residPlot(): Modified. Changed default forloess= fromTRUE toFALSE.Changed someif()s withclass()es toinherits().wrAdd(): Modified. Changed someif()s withclass()es toinherits().devtools::spell_check().fishmethods and changes to R v3.4.0.metaM(): Modified. ChangedT= toTemp= to reduce potential for conflicts withTRUE abbreviation.reproInfo(): Modified. Addedind= toselect a CRAN mirror to help with a common problem I have whenknitting.srStarts(): Modified. Corrected mis-spelling indirective toFSAsim package.vbStarts(): Modified. Added a catch that Linf cannot beautomatically estimated with fewer than three ages. Correctedmis-spelling in directive toFSAsim package.stop()s toSTOP()s and allwarning()s toWARN(). This modified nearly allfunctions.paste()s that usedsep="" topaste0()s.sep=""s frommessage()s.Hmisc from, but addedepitools to,imports. Removed all links toHmisc to remove CRAN checkwarnings..onAttach(): Modified. Streamlined package startupmessage.addZeroCatch(): Modified. Added more “catches” for baddata types or arguments.ageBias(): Modified. Changed allmessage()s insummary() tocat()s.agePrecision(): Modified. Changed allmessage()s insummary() tocat()s.binCI(): Modified. Changed from usingbinconf() inHmisc tobinom.exact(),binom.wilson(), andbinom.approx() fromepitools (this removesdependency onHmisc which was causing problems). Allowedmultipletypes to be chosen. Now only accepts whole numbersforx andn. Addedverbose= sothat the result can include all of the information returned from theepitools functions. Added a catch for badconf.levels. Added some more tests.catchCurve(): Modified. Made sure thatcoef() method returned a vector (addresses#19).Modifiedconfint() code for efficiency, made sure matrix isalways returned.chapmanRobson(): Modified. Made sure thatcoef() method returned a vector (addresses#19).Modifiedconfint() code for efficiency, made sure matrix isalways returned.chooseColors(): Modified. Addedrev= forreturning reverse ordered (from default) colors.depletion(): Modified. Changedcoef()method so that it returned a named vector (addresses#19).Modifiedconfint() code for efficiency, made sure matrix isalways returned. Removedtype= to match other functions(incorporated that functionality intoparm=). Removeddigits= to match other functions.expandLenFreq(): Modified. Changed allmessage()s tocat()s. Removed “names” fromprinted items for a cleaner look.fitPlot(): Modified. Addedcex.leg= andbox.lty.leg= to IVR plots.hist.formula(): Modified. Fixed a bug with adding thehorizontal line at 0 when the user usesplot=FALSE, whichoccurs withhist.bootCase().hyperCI(): Modified. Now only accepts whole numbers forM,n, orm. Added catch for badconf.levels and multiple values ofM,n, orm.iAddLoessLine(): Modified. Changed used ofiMakeColor() tocol2rgbt().iGetDecimals(): Modified. Added warning for situationswherex will be presented in exponential notation. Alsoreturned a decimal of zero in this situation. Helps with a bug inhist.formula().iHndlCols2use(): Deleted. Changed toiHndlCols2UseIgnore().iHndlCols2UseIgnore(): Added. Previously wasiHndlCols2use(). Completely reworked to catch more problemsincluding having both positive and negative indices (fixes#24) andchoosing variable names that don’t exist (fixes#25).iHndlFormula(): Modified. Added code to deal with aformula that is a single “variable” sent in an array. Addresses#21 for thesimple situation of single “variable.”iHndlMultWhat(): Modified. Addedtype= toallow use withmessage() orcat().iPlotExists(): Added. Helps with bug fix inhist.formula().is.wholenumber(): Added. Needed for changes tobinCI(),hyperCI(), andpoiCI().kCounts(): Modified. Fixed bug withcapitalize= andzero. Streamlined code. Addedtests.metaM(): Modified. Fixed bug with the way messages wereoutput when multiplemethods were provided andjustM=FALSE. Added more tests.mrClosed(): Modified. Addedpoi.type= tohandle new choices for Poisson confidence interals. Added some checksfor non-vector uses ofM= andR= (partiallyaddresses#22). Fixedbug in how inputs for subgroups were output fromsummary()whenverbose=TRUE.mrOpen(): Modified. Changed allmessage()sinsummary() tocat()s. Fixed bug wherereturned value fromsummary() was not a data.frame if onlyone parameter was selected.nlsTracePlot(): Added.plotBinResp(): Modified. Changed used ofiMakeColor() tocol2rgbt().poiCI(): Modified. Completely rebuilt to use thefunctions fromepitools. Now only accepts whole numbers forx.predict.bootCase(): Modified. Modified so thatsituations where other than values of the dependent variable are in thedots argument (as would occur if making predictions for the Francisparameterization of the VBGF).predict.nlsBoot(): Modified. See note forpredict.bootCase().psdCalc(): Modified. Fixed bug in output if more thantwo additional lengths were supplied.removal(): Modified. Added a check and a returned errorifmethod="Schnute" and the last of three catches is zero(addresses#26) Fixedbug related to sending catches in a one column data.frame. Fixed bugrelated to selecting only oneparm= inconfint(). Added tests.residPlot(): Modified. Addedcex.leg= andbox.lty.leg= to IVR plots. Removed extra spaces in maintitle ifmain="MODEL". Added some tests.tictactoe(): Modified. Changed used ofiMakeColor() tocol2rgbt().vbFuns(): Modified. AddedOgle to list ofparameterizations. Changed order ofL0 andKparameters in returned function whenparam="Original".vbStarts(): Modified. Added themethLinf=argument that allows the user to choose if Linf is estimated from aWalford plot (methLinf="Walford"; the default and oldfunctionality), as the mean of fish in a certain number of old ages(methLinf="oldAge"), or as the mean of a certain number ofthe longest fish (methLinf="longFish"). The number of agesor long fish is given innum4Linf=. Added methods fortype="Ogle".alkIndivAge(): Modified. Addedna.rm=TRUEto the checks on the minimum and maximum length data.catchCurve(): Modified. Removedtype= andblended that functionality intoparm= for methods. Madeparm= consistent across methods.chapmanRobson(): Modified. Addedaxis.age=argument that allows the user to choose which type of x-axis isdisplayed (see examples; this addresses#20) Alsomodified code that adds the axes so that they should “look better” inmore instances. Addedna.rm=TRUE to y-range calculation forthe plot method. Added acoef() method. Added aparm= argument to theconfint() andsummary() methods. Added tests.confint.nlsBoot(),confint.bootCase().Modified. Result is now a matrix even if only one parameter is chosen(previously it was an unnamed vector). Theparm= nowproperly handles negative values. Streamlined plotting results. Addedtests.depletion(): Modified. Checked for badconf.level= inconfint() method.GompertzFuns(): Modified. Fixed bug related toselectingQuinnDeriso3.htest.nlsBoot(),htest.bootCase().Modified. Theb0 now defaults to 0. Matrix of results nowinclude the parameter as the rowname. Modified the internals of how thedata are handled. Added tests.iAddLoessLine(): Modified. Suppressed warnings relatedto the loess line predictions.mrClosed(): Modified. Checked for badconf.level= inconfint() method.mrOpen(): Modified. Checked for badconf.level= inconfint() method.predict.nlsBoot(),predict.bootCase().Modified. The... argument can now contain a vector ofvalues such that predictions can be made for multiple values of theindependent variable. Modified the output matrix to handle thismodification. RemovedMARGIN as it will always be1 fornlsBoot andbootCaseobjects. Added checks forFUN=,conf.level=,anddigits=. Added tests.removal(): Modified. Checked for badconf.level= inconfint() method. Changedinternal functions from using a loop to usingapply().Changed internal functions from usinglog() andchoose() to usinglchoose().Summarize(): Modified. Addednvalid= andpercZero to only print the nvalid and percZero result ifthey are “interesting” (i.e., different than n or zero, respectively) bydefault (may be manually over-ridden). Modified tests.vbStarts(): Modified. Addedna.rm=TRUE tochecking of Linf values.ageComparison(): Modified. Removed an internal call tofact2num() because of changes toSummarize()below. Should not impact user experience.diags(): Added.gompertzFuns(): Modified. Fixed some spacing around themessage whenmsg=TRUE.logisticFuns(): Modified. Fixed some spacing around themessage whenmsg=TRUE.Summarize(): Modified. Removed all uses where the mainvariable was a factor (this functionality was largely unneeded andunused, was inelegant and difficult to maintain). Removed pass-throughtosummary. Removed warnings about the RHS variables beingconverted to factors. Columns for “levels” of the RHS variables are nowreturned in their original model (i.e., if the variable was numeric inthe original data.frame it is now numeric in the data.frame returnedfrom this function) – this should reduce need for usingfact2num() when using the results of this function forvariables that were originally numeric. Added more examples and testsfor the numeric data.growthFunShow(): Modified. Added Pauly et al. (1992)seasonal cessation function. Addedcase= for use withSchnute model.vbFuns(): Modified. Added Pauly et al. (1992) seasonalcessation function. Slightly modified messages for “Typical” and“Original” parameterizations.vbStarts(): Modified. Addedfixed= so thatthe user can define some of the starting values. Added Pauly etal. (1992) seasonal cessation function. Added tests forfixed=.relax fromSuggests. SeesrStarts() andvbStarts() notes below. Thisaddresses#17.gdata fromImports. SeefilterD() andSubset() notes below. Thisaddresses#5.ageKeyPlot(),capHistSum(),hist.formula(),histFromSum(),lwCompPreds(),plot.agebias(),plot.CatchCurve(),plot.ChapmanRobson(),plot.Depletion(),plotBinResp(),print.compSlopes(),print.compIntercepts(),print.metaM(),psdPlot(),residPlot(),srModels(),srStarts(), andvbStarts().ageKey(): Removed. Deprecated since 0.4.24. UsealkIndivAge().ageKeyPlot(): Removed. Deprecated since 0.4.24. UsealkPlot().bcFuns(): Modified. Changedmsg= toverbose=.capHistSum(): Added tests.filterD(): Modified. Changed to usedroplevels() frombase rather thandrop.levels() fromgdata. Addedexcept=.fitPlot(): Modified. Changed the way colors, plottingcharacters, and line types were handled for most of the models. Shouldmake their use more flexible. Fixed errors that occurred in IVR modelswhen the factor variable preceded the covariate in the model (fixes#18).Started to add tests for error and warning messages.GompertzFuns(): Modified. Changedtype= toparam=.GompertzModels(): Removed. Replaced withgrowthFunShow().iGetDecimals(): Modified. Fixed a bug that occured whenan integer was provided.lenFreqExpand(): Removed. Deprecated since 0.4.32. UseexpandLenFreq().logisticFuns(): Modified. Changedtype= toparam=.LogisticModels(): Removed. Replaced withgrowthFunShow().residPlot(): Modified. Changed the way colors, plottingcharacters, and line types were handled for most of the models. Shouldmake their use more flexible. Now matches coding infitPlot(). Fixed bug with main titling, but now asks userto decide if they want the model call or not. Started to add tests forerror and warning messages.RichardsFuns(): Modified. Changedtype= toparam=.RichardsModels(): Removed. Replaced withgrowthFunShow().growthFunShow(): Added.srFunShow(): Added.srModels(): Removed. Replaced withsrFunShow().srStarts(): Modified. RemoveddynamicPlot=TRUE option. Moved it toFSAsimpackage. Modified plot whenplot=TRUE by adding “STARTINGVALUES” to title and moving starting values to within the plot. Addedcex.main= andcol.main=.Subset(): MOdified. Changed to usedroplevels() frombase rather thandrop.levels() fromgdata.vbFuns(): Modified. Changedtype= toparam=.vbModels(): Removed. Replaced withgrowthFunShow().vbStarts(): Modified. RemoveddynamicPlot=TRUE option. Moved it toFSAsimpackage. Addedparam= to match othervbXXX()(works as doestype=). Modified plot whenplot=TRUE by adding “STARTING VALUES” to title and movingstarting values to within the plot. Added andcol.main=.Made warnings and error tests more explicit.sumTable() in ALK related tests andSummarize() in age comparisons tests. Prompted byforthcoming changes totestthat.News.md from.Rbuildignore(apparently now supported by CRAN).alkPlot(): Modified. Changed so thatxlim=andylim= would work whentype="area" andtype="bar". This fixes#10 (Thanksto Joseph Feldhaus).hist.formula(): Modified. Added thebreaks= argument (mostly a pass-through) and thew= argument that allows the user to just set the width ofthe bins without having to set eachbreak value. Thisshould complete#15.iCheckStartCatW(): Modified. Now useiGetDecimals() to extract the number of decimals instartcat andw.iCheckStartcat(): Added.iCheckW(): Added.iGetDecimals(): Added.lencat(): Modified. Changed order ofstartcat= andbreaks=. Slight modifications todocumentation.psdAdd(): Modified. Minor changes todocumentation.psdPlot(): Modified. Fixed bug related to PSD valuesbeing printed when only PSD-Q existed (needed to adddrop0Est=FALSE to thepsdCalc() call; thisfixes#13). Madethe histogram bars flush with the x-axis rather than hovering above it(addedyaxis="i" tohist(); this fixes#12). Minorchanges to documentation.psdVal(): Modified. Minor changes todocumentation.purl2(): Modified. AddeddelHeader=argument and functionality.Added URL for fishR webpage in DESCRIPTION per CRAN request.Removed it from the URL field in DESCRIPTION.
Updated all references to Ogle (2016) in documentation.
ageBias(): Modified. Minor corrections to thedocumentation.
agePrecision(): Modified. Fixed bug related tocomputations of percent agreement whenNA values werepresent. There was an inconsistency between whenwhat="precision" andwhat="difference" wasused insummary(). The bug fix now properly divides by the“valid sample size” forwhat="precision". This fixes#9 (Thanks toJoseph Feldhaus). Now returnsvalidn. Modifications to thedocumentation.
histFromSum(): Added. Addresses#4.
metaM(): Modified. Changed order of methods inmethods=. Minor corrections and additions todocumentation.
mrClosed(): Modified. Now sends warning if anNA appears in the first position ofm, thefirst position ofM, or the last position ofRand converts these to 0 so that the procedure can continue. Each ofthese positions is ignored in the calculations. This fixes#8 (Thanks toJoe Mrnak).
reproInfo(): Modified. Made changes toiGetAllDependencis() based on forthcoming changes topackage.dependencies() (as notified by CRAN).
vbStarts(): Modified. Fixed bug whendynamicPlot=TRUE was used.
requireNamespaces() from some functionsand moved those packages fromSuggests toImports so that those functions would work better withother packages. The onlyrequireNamespaces() that remainare related to functions that require therelax package (sotcltk is not installed until needed) andknitr,dunn.test, andlmtest as these are unlikely tobe used by other packages and will keep the packages that are loadedwithFSA to a minimum. Packages moved fromSuggests toDepends areHmisc(for use inbinCI),gdata (for use infilterD() andSubset()),dplyr(for use infilterD()),sciplot (for use infitPlot()),car (for use inresidPlot()), andgplots (for use withcolors).addZeroCatch(): Modified tests (to reduce warnings thatwere not part of tests).geomean(): Added.geosd(): Added.lencat(): Modified. Fixed a bug related to using atbl_df object.sumTable(): Modified tests (but withdimnames()).data-raw to CSV files.\href{}{} and\url{} codes towebsites that I don’t control. The addresses are now “naked” such thatthe user will need to copy-and-paste them into a browser to view the webpage rather than clicking on a hyper link. Hopefully this will eliminateproblems with R CMD CHECK.ChinookArg: Updated help documentation.Ecoli: Added a Topics section.Mirex: Added a Topics section.PikeNYPartial1: Updated help documentation.SpotVA1: Updated help documentation.col2rgbt(): Added.compIntercepts(): Added.compSlopes(): Added.dunn.test for use indunnTest() (see below).agePrecision(): Modified. Changedcombn()toutils::combn() andsd() toutils::sd() (within anapply()).catchCurve(): Modified. Changedna.exclude() tostats::na.exclude().dunnTest(): Modified. Changed to more throughly usedunn.test() fromdunn.test. Added thetwo.sided= argument todunnTest() anddunn.test.results= toprint.dunnTest().expandLenFreq(): Modified. Changedrunif()tostats::runif().extraSS(): Modified. Changedanova() tostats::anova() in anlapply().fishR(): Modified. ChangedbrowseURL() toutils::browseURL().fsaNews(): Modified. ChangedbrowseURL()toutils::browseURL().headtail(): Modified. Changedhead() toutils::head() andtail() toutils::tail().hist.bootCase(): Modified. Changedhist()tohist.formula().iAgeBiasPlot(): Modified. ChangedgrconvertY() tographics::grconvertY().iALKMean.QD(): Modified. Changedvar() tostats::var() (withinsumTable()).iBubblesAdd(): Modified. Changedrgb() togrdevices::rgb().iChkComplexModel(): Modified. Changeddf.residual() tostats::df.residual().iCIboot(): Modified. Changedhist() tohist.formula().iEvent2Indiv(): Modified. Changedunstack() toutils::unstack().iGetAllDependencies(): Modified. Changedinstalled.packages() toutils::installed.packages().iHistResids(): Modified. Removedgraphics::hist() and changed tohist.formula().iHndlFormula(): Modified. Changedterms()tostats::terms().iHndlResidType(): Modified. Changedrstandard() tostats::rstandard() andrstudent() tostats::rstudent().iHtestBoot(): Modified. Removedgraphics::hist() and changed tohist.formula().iMakeColor(): Modified. Changedrgb() togrdevices::rgb().iMakeModelHeading(): Modified. Changedformula() tostats::formula() (within anlapply()).iMoran(): Modified. Changedoptimize() togrdevices::optimize().iProcessSessionInfo(): Modified. Changedsessioninfo() toutils::sessioninfo().iSchnute(): Modified. Changedoptimize()togrdevices::optimize().iTypeoflm(): Modified. Changedformula()tostats::formula().plot.AgeBias(): Modified. Changedrgb() togrdevices::rgb().plot.CatchCurve(): Modified. Changedpredict() tostats::predict().print.extraTest(): Modified. ChangedprintCoefMat() tostats::printCoefMat().psdAdd(): Modified. Changeddata() toutils::data().psdVal(): Modified. Changeddata() toutils::data().reproInfo(): Modified. Changedgraphics.off() togrdevices::graphics.off().removal(): Modified. Removed some of the examples fromthe help page to reduce the elapsed time for CRAN.vbStarts(): Modified. Changedrgb() togrdevices::rgb().wrAdd(): Modified. Changeddata() toutils::data().wsVal(): Modified. Changeddata() toutils::data().test_AgeLengthKey: Modified. Altered tests that hadused== to useexpect_equivalent() which usesall.equal() withcheck.attributes=FALSE.test_PSD: Modified. Altered tests that had used== to useexpect_equivalent() which usesall.equal() withcheck.attributes=FALSE..txt files to.Rda files.Original.txt files are in thedata-rawdirectory which was added to.Rbuildignore.purl2(): Addednewname= to allow theoutput file to have a name other than the same as the intput file.reproInfo(): Addedmarkdown to theout= types.README.md andDESCRIPTION for newwebsites.fishR(): Modified. Updated for the new websites.ageComparison(): Modified. Changedwhat="McNemars" andwhat="Bowkers" towhat="McNemar" andwhat="Bowker". Fixed bug ifall ages areNA.catchCurve(): Modified. Fixed bug related toNA values in the catch vector.chapmanRobson(): Modified. Fixed bug related toNA values in the catch vector.validn(): Modified. Fixed bug related to when a1-dimensional numeric vector was not recognized as a vector.ageBias(): Modified. Changed default forpch.mean= to 95 (from 175). Ifwhat= has onlyone item, then results will now be invisibly returned so that resultscan be saved to an object.agePrecision(): Modified. Addedtrunc.diff=. Ifwhat= has only one item, thenresults will now be invisibly returned so that results can be saved toan object.mapvalues(): Modified. Corrected to exportproperly.removal(): Modified. Minor edits to labels ifverbose=TRUE. Added some more tests.vbStarts(): Modified. MadeyngAge thedefault formeth0=. Fixed bug that occured whenmeth0='yngAge' and sample sizes at all ages were 1.Summarize(): Modified. Converted to usingiHndlFormula(). Changed output for quantitative data(validn is always returned,NAs is neverreturned). Changed output for two-way factor data (not returned as acharacter fromformatC()). Removed... fromcode in several places as it was buggy and not used. Added more checksand modified check messages. Fixed bug from when a 1-d matrix ofcharacters was sent. Added tests.sumTable(): Modified. Converted to usingiHndlFormula(). Added tests.addRadCap(): Modified. Streamlined code. Changeddefaultin.pre= toNULL (frominc). Added some tests for returned data.BluegillLM: Removed. Moved toFSAdata.gConvert(): Modified. Streamlined code. Changedtype= toout.type=. Changed defaultin.pre= andin.var= toNULL (frommissing). Changed code to handle changes inin.pre= andin.var=. Added some tests for returned data.gReshape(): Removed. Moved toFSAmisc.binCI(): Modified. Check forHmisc withrequireNamespaces() before processing body of function.This allowed movingHmisc intoSuggestsdeclarations rather thanImports.chooseColors(): Modified. Check forgplotswithrequireNamespaces() before processing body offunction. This allowed movinggplots intoSuggests declarations rather thanImports.filterD(): Modified. Check fordplyr andgdata withrequireNamespaces() beforeprocessing body of function. This allowed movingdplyr andgdata intoSuggests declarations rather thanImports.fitPlot(): Modified. Check forsciplot withrequireNamespaces() before adding intervals tot he plot.This allowed movingsciplot intoSuggestsdeclarations rather thanImports.lrt(): Modified. Check forlmtest withrequireNamespaces() before processing body of function.This allowed movinglmtest intoSuggestsdeclarations rather thanImports.mapvalues(): Modified. Changed so that it is a directimportFrom andexport without creating a helpfile inFSA.purl2(): Modified. Check forknitr withrequireNamespaces() before processing body of function.This allowed movingknitr intoSuggestsdeclarations rather thanImports.residPlot(): Modified. Check forcar withrequireNamespaces() before highlighting outliers on theplot. This allowed movingsciplot intoSuggests declarations rather thanImports.srStarts(): Modified. Check forrelax withrequireNamespaces() before constructing the dynamic plot.This allowed movingrelax intoSuggestsdeclarations rather thanImports.Subset(): Modified. Check forgdata withrequireNamespaces() before processing body of function.This allowed movinggdata intoSuggestsdeclarations rather thanImports.vbStarts(): Modified. Check forrelax withrequireNamespaces() before constructing the dynamic plot.This allowed movingrelax intoSuggestsdeclarations rather thanImports.importFrom() directives and went tohard-wiring to packages with::. Addedimports() directives forstats,graphics,tools, andgrDevices.Removedimports() directive formultcomp().vbStarts(): Modified. Changed default methos formethEV=. Changed order of starting values fortype="Mooij" in order to match that fromvbFuns(). This also fixed a bug whendynamicPlot=TRUE was used withtype="Mooij".Added tests to determine if parameter order is the same betweenvbStarts() andvbFuns() for allparameterizations.ageBias(): Modified. Corrected bug with labeling ofx-axis on age-bias plot whenref.lab= andnref.lab= were not given by the user. Changed default fornYpos= from1.1 to1.03. Addedcex.n= to allow control of the size of the sample sizelabels.agePrecision(): Modified. Changedwhat="detail" towhat="details". Note thatwhat="detail" still works.dunnTest(): Modified. Added a note to the help fileabout the use of complete cases. Suggested from PauleBodson-Clermont.vbFuns(): Modified. AddedOriginal andTypical to thetype= options. This allows botha capitalized and uncapitalized version for these twoparameterizations.vbModels(): Modified. Changed order ofOriginal andTypical (Typical isnow shown first). Fixed in error in how the equation for theWeisberg parameterization was displayed.vbStarts(): Modified. Addedcex.main= asan argument and defaulted to0.75. Addedraw=TRUE topoly() which is used whenmeth0="poly". AddedOriginal andTypical to thetype= options. This allows botha capitalized and uncapitalized version for these twoparameterizations.ageBias(): Modified. Moved into a single file withagePrecision(). Cleaned-up help file. No change inbehavior.agePrecision(): Modified. Moved into a single file withageBias(). Cleaned-up help file. No change inbehavior.alkAgeDist(): Modified. Moved into a single file withalkMeanVar(). Cleaned-up help file. Added someerror/warning tests. No change in behavior.alkIndivAge(): Modified. Clean-up help file. Added astronger test fortype="SR" method. No change inbehavior.alkMeanVar(): Modified. Moved into a single file withalkAgeDist(). Cleaned-up help file. No change inbehavior.alkPlot(): Cleaned-up help file and tests. No change inbehavior.confint.bootCase(): Modified. Created a common internalfunction for use withconfint.nlsBoot(). Added the abilityto plot histograms with confidence intervals superimposed (similar towhat was inconfint.nlsBoot()).confint.nlsBoot(): Modified. Created a common internalfunction for use withconfint.bootCase().GompertzFuns(): Moved intogrowthModelsfile. Did not change behavior.gompertzModels(): Modified. Changedtype=tofamily= to avoid confusion in the help file withtype= ingompertzFuns(). Moved intogrowthModels file.growthRadPlot(): Deleted. Moved toFSAmiscpackage.hist.formula(): Modified. Fixed so thatymax= also sets the y-axis limit when only one histogram ismade (it was previously ignored).htest.bootCase(): Modified. Created a common internalfunction for use withhtest.nlsBoot().htest.nlsBoot(): Modified. Created a common internalfunction for use withhtest.bootCase().iHndlFormula(): Modified. Addedna.action=NULL tomodel.frame() so that NAvalues will not be omitted.logisticFuns(): Moved intogrowthModelsfile. Did not change behavior.logisticModels(): Modified. Changedtype=tofamily= to avoid confusion in the help file withtype= inlogisticFuns(). Moved intogrowthModels file.predict.bootCase(): Modified. Created a common internalfunction for use withpredict.nlsBoot().predict.nlsBoot(): Modified. Created a common internalfunction for use withpredict.bootCase().psdAdd(): Modified. Fixed bug that never tested if alllengths wereNA. Required change toiHndlFormula.RichardsFuns(): Moved intogrowthModelsfile. Changedparam= totype= to better matchsimilar functions.RichardsModels(): Moved intogrowthModelsfile. Did not change behavior.Schnute(): Moved intogrowthModels file.Changedparam= totype= to better matchsimilar functions.SchnuteModels(): Moved intogrowthModelsfile. Did not change behavior.vbFuns(): Moved intogrowthModels file.Did not change behavior.vbModels(): Modified. Changedtype= tofamily= to avoid confusion in the help file withtype= invbFuns(). Moved intogrowthModels file.hist.formula(): Modified. Rebuilt to useiHndlFormula(). Modified howxlab= is used(result is the same). Added some tests.ksTest(): Modified. Rebuilt to useiHndlFormula(). Added some tests for messages and to makesure results matchedks.test().alkPrep(): Deleted. Moved toFSAmiscpackage (on GitHub).changesPos(): Deleted. Moved toFSAmiscpackage (on GitHub).chapmanPlot(): Deleted. Moved toFSAmiscpackage (on GitHub).dietOverlap(): Deleted. Moved toFSAmiscpackage (on GitHub).Garvey1: Deleted. Moved toFSAmisc package(on GitHub).Garvey4a: Deleted. Moved toFSAmiscpackage (on GitHub).KS2D_NR: Deleted. Moved toFSAmisc package(on GitHub).ks2d1(): Deleted. Moved toFSAmisc package(on GitHub).ks2d1p(): Deleted. Moved toFSAmiscpackage (on GitHub).ks2d2(): Deleted. Moved toFSAmisc package(on GitHub).ks2d2p(): Deleted. Moved toFSAmiscpackage (on GitHub).popSizesPlot(): Deleted. Moved toFSAmiscpackage (on GitHub).posadj(): Deleted. Moved toFSAmiscpackage (on GitHub).TroutDietSL: Deleted. Moved toFSAmiscpackage (on GitHub).walfordPlot(): Deleted. Moved toFSAmiscpackage (on GitHub).alkIndivAge(): Modified. Switched to usingiHndlFormula() at the beginning. Added more checks andtests.expandLenFreq(): Modified. Added more checks. Addedsome tests.wsVal(): Modified. Added more tests.ageBias(): Modified. Fixed bugs related to axes onnumbers plot and sunflower plot.filterD(): Modified. Addedreorder=FALSEtodrop.levels() so that the order of levels is not changedwhen levels are dropped.residPlot.nlme(): Added.extraSS(): Modified. Addedsim.name= toallow for a common typing mistake.logbtcf(): Modified. Slight change to handle a check oflm class.lrt(): Modified. Addedsim.name= to allowfor a common typing mistake.pcumsum(): Modified. Modified to handletable,matrix, anddata.frameclasses as long as they are 1-dimensional.rcumsum(): Modified. Modified to handletable,matrix, anddata.frameclasses as long as they are 1-dimensional.srStarts(): Modified. Corrected some bugs related tochecks. Added more tests.addRadCap(): Modified. Modified so thatin.pre= string must be at the start of the variable names.Added a check for when thein.pre= string does not exist atthe start of any variable names. Added a check for whether allin.var= variables exist. Added some simple tests (needmore).bcFuns(): Modified. Removedtype=;BCM= can now be either numeric or a string. Allowed stringto be in any case (will be converted to the required all upper-case).Corrected some errors for whenmsg=TRUE. Added some simpletests.gConvert(): Modified. Modified so thatin.pre= string must be at the start of the variable names.Added a check for when thein.pre= string does not exist atthe start of any variable names. Added some simple tests (needmore).gReshape(): Modified. Modified so thatin.pre= string must be at the start of the variable names.Added a check for when thein.pre= string does not exist atthe start of any variable names. Added some simple tests (needmore).gompFuns(): Deleted.gompModels(): Deleted.GompertzFuns(): Added. ReplacedgompFuns(). Addedtype="Troynikov1" andtype="Troynikov1".GompertzModels(): Added. ReplacedgompModels(). Addedcex= andtype=.logisticFuns(): Modified. Changedtype="Richards" totype="Karkach". Addedtype=HaddonI.logisticModels(): Modified. Added “Karkach” model.Addedcex= andtype=.RichardsFuns(): Modified. Added two moreparameterizations from Tjorve and Tjorve (2010).schnute(): Deleted.schnuteModels(): Deleteed.Schnute(): Added. Replacedschnute().Fixed bugs with the wayt1= andt3= arehandled.SchnuteModels(): Added. ReplacedschnuteModels(). Addedcex=.vbFuns(): Modified. Addedtype="Polacheck"which is equivalent totype="Laslett". Added a newreference in the help file.vbModels(): Modified. Addedcex= andtype=.RichardsFuns(): Added.RichardsModels(): Added.cat() to usingmessage() so that they can be suppressed withsuppressMessage() ormessage=FALSE in knitr.See “One comment on messages” at http://yihui.name/knitr/demo/output/.Specific functions modified are listed below.ageBias(): Modified. Changed allcat() tomessage()s. Changed so that messages (result headers) areonly printed ifwhat= contains more than one item.agePrecision(): Modified. Changed allcat() tomessage()s. Changed so that messages(result headers) are only printed ifwhat= contains morethan one item.bcFuns(): Modified. Changed allcat() tomessage()s.chapmanRobson(): Modified. Changed allcat() tomessage()s. Deleted “Estimates withStandard Errors” message.depletion(): Modified. Changed allcat()tomessage()s.dietOverlap(): Modified. Changed allcat()tomessage()s. Slightly modified messages.expandLenFreq(): Modified. Changed allcat() tomessage()s. Fixed bug with one of themessages.ks2d1(): Modified. Rewrote theprint()method. This removed a number ofcat()s.ks2d1p(): Modified. Rewrote theprint()method. This removed a number ofcat()s.ks2d2(): Modified. Rewrote theprint()method. This removed a number ofcat()s.ks2d2p(): Modified. Rewrote theprint()method. This removed a number ofcat()s.metaM(): Modified. Changed allcat() tomessage()s.mrOpen(): Modified. Changed allcat() tomessage()s.removal(): Modified. Changed allcat() tomessage()s.srFuns(): Modified. Changed allcat() tomessage()s. Created some tests.extraSS(): Modified. Added more message tests and somecalculational tests (compared toanova() results).gompFuns(): Modified. Changed allcat()stomessage()s and slightly modified the messages. Fixedminor bugs in some created functions. Created some tests.logisticFuns(): Modified. Changed allcat()s tomessage()s and slightly modified themessages. Fixed minor bugs in some created functions. Created sometests.lrt(): Modified. Added more message tests and somecalculational tests (compared tolrtest() fromlmtest package results).vbFuns(): Modified. Changed allcat()s tomessage()s and slightly modified the messages. Fixed minorbugs in some created functions. Created some tests.extraSS(): Modified. Addedsim_names= andcom_name= so that simple descriptive names could be givento the model and printed in the heading of the output. Added checks forwhether the complex model appears more complex or not. Added tests forwarning and error messages.fishR(): Modfiied. Fixed bug withwhere="news". Added tests.fitPlot(): Modified. Added ability to modify y-axislimits for the nonlinear regression model. Thanks to Gabriela N. forasking for this.hoCoef(): Modified. Changedlmobj= toobject=, added degrees-of-freedom to the output matrix,streamlined the code, added some checks, and added some tests.lrt(): Modified. Addedsim_names= andcom_name= so that simple descriptive names could be givento the model and printed in the heading of the output. Added checks forwhether the complex model appears more complex or not. Added tests forwarning and error messages.addZeroCatch(): Modified. Deleted extraneousprint() statement.lencat(): Modified. Major re-write to make it easier totrouble-shoot. Fixed bug related to empty category on end whenas.fact=TRUE anduse.names=TRUE. Added moretests.psdCalc(): Modified. Removed extra open-ended category(e.g., PSD-T-) for PSD intervals.importFrom formapvalues() fromplyr.changesPos(): Modified. Added some checks with errormessages. Added suite of tests.chooseColors(): Modified. Added some checks with errormessages. Added suite of tests.confint.nlsBoot():Modified. Fixed bug if maximum numberinparm= was greater than the number of parameters in themodel.dunnTest(): Modified. Change class type fromDunnTest todunnTest to eliminate conflictwithDunnTest() inDescTools package. Thanksto Sal Mangiafico for pointing out this conflict.fact2num(): Modified. Added some checks with errormessages. Added suite of tests.filterD(): Modified. Changed to usingdrop.levels fromgdata rather thandroplevels. Added a warning if the resultant data.frame haszero rows (same as inSubset). Added some checks with errormessages. Added suite of tests.fitPlot(): Modified. Replaced the use ofnobs() fromgdata in the internal functioniCIfp1() withvalidn(). This removed onedependency ongdata.headtail(): Modified. Internally removetbl_df class (fromdplyr) if it exists. Addedsome checks with error messages. Added suite of tests.lagratio(): Modified. Corrected incorrect explanationofdifferences= in help file. Addedrecursion=anddirection=. Added suite of tests.mapvalues(): Deleted. Deleted the function fromFSA but imported it fromplyr and thenexported it fromFSA so that it would be available tofisheries users without having to loadplyr.oddeven(): Modified. Added some checks with errormessages. Added suite of tests.perc(): Modified. Added ability to use “and equals” ornot to the items indir= (i.e., there are now four items indir=). Fixed a bug related to usingna.rm=FALSE and a “less than” situation. Added some checkswith error messages. Added suite of tests.pcumsum(): Modified. Added some checks with errormessages. Added suite of tests.rcumsum(): Modified. Added some checks with errormessages. Added suite of tests.se(): Modified. Added some checks with error messages.Added suite of tests.Subset(): Modified. Added some checks with errormessages. Added suite of tests.validn(): Modified. Added some checks with errormessages. Added suite of tests.ageBias(): Modified. Corrected bugs withshow.pts=TRUE and “sunflower plot” that came from changesmade in version 0.5.1.residPlot(): Modified. Deletedstudent=.Addedresid.type= which allows used of standardized(internally studentized) and (externally) studentized residuals forlinear models (along with raw residuals). Added code followingnlsResiduals() fromnlstools for standardizedresiduals for nonlinear models.gompFuns(): Added.gompModels(): Added.logisticFuns(): Added.logisticModels(): Added.reproInfo(): Modified. Added theout=argument to allow the output to be straight R or LaTeX. Removed thelistFiles= argument. Changed the output to be moresuccinct. Streamlined the code.vbFuns(): Modified. Fixed a bug with the Laslettmodel.kCounts(): Added. WasswvCounts().kPvalue(): Added. WasswvPvalue().purl2(): Added. WasswvCode(). Addedtimestamp= argument for adding a timestamp to the createdscript.reproInfo(): Added. WasswvFinish().swvANOVA(): Deleted. Moved toNCStats.swvCode(): Deleted. Changed topurl2().swvCounts(): Deleted. Changed tokCounts().swvFinish(): Deleted. Changed toreproInfo().swvGLHT(): Deleted. Moved toNCStats.swvHtest(): Deleted. Moved toNCStats.swvPvalue(): Deleted. Changed tokPvalue().swvREG(): Deleted. Moved toNCStats.fishR(): Modified. AddedIFAR as anoption. Updated code to be more simple.capHistConvert(): Modified. Added a warning section andan example of problems that can occur if the data are in event formatbut the event variable contains unused levels as may occur followingsubsetting. Thanks to Joseph Feldhaus for pointing out thisproblem.extraSS(): Modified. Changed algorithm to determine ifthe models were of the same class or not. The modification allows amodel to have multiple classes.iHndlCols2Use (Intrnal Function): Modified. Fixed bugwith how the columns were selected. Added a suite of tests for thisfunction. This will fix bugs incapHistConvert() andcapHistSum(). Thanks to Joseph Feldhaus for pointing outthis egregious error.lrt(): Modified. Changed algorithm to determine if themodels were of the same class or not. The modification allows a model tohave multiple classes.LazyData: true.se(): Added. RemovedimportFrom ofse() fromsciplot.plot.capHist(): Modified. Changed default plot lookwhich can now be controlled withpch=,cex.pch=, andlwd=. Modified the two y-axisscales to useplotmath characters.capHistConvert(): Modified. Streamlined code aroundcreatingvar.lbls. Madeevent the defaultvalue forvar.lbls.pre=. Added some checks tovar.lbls.pre= if it starts with a number or has too manyvalues. Addedcols2use= and modified use ofcols2ignore= viaiHndlCols2use().capHistSum(): Modified.iHndlCol2use(): Added. Added this internal function tohandlecols2use= andcols2ignore= incapHistConvert() andcapHistSum().catchCurve(): Modified. Changed howages2use= was handled so that negative values can be usedto exclude some ages. Will also now send an error if a mix of positiveand negative ages are sent inages2use=. Better handled thesituation whereages2use= had more ages than theage variable. Checked for non-positive weights ifweighted=TRUE and returned a warning and changed thenon-positive weights to the minimum of the positive weights.chapmanRobson(): Modified. Changed howages2use= was handled so that negative values can be usedto exclude some ages. Will also now send an error if a mix of positiveand negative ages are sent inages2use=. Better handled thesituation whereages2use= had more ages than theage variable.expandCounts(): Modified. Changed so that``message()’’s are printed at the end instead of along the way. Thisreduces confusion of what appear to be messages of success followed byan error. Thanks to Dan Oele bringing this confusion to myattention.plotBinResp(): Modified. Changed the way the breakswere calculated (useslencat() now).srFuns(): Modified. Changed function returned whensimplify=FALSE so that if the parameters are named that thename is dropped. Thus, when the function is used, the returned resultwill not be annoyingly named as the first parameter. Added functionalityfor the “density-independence” model.srStarts(): Modified. Added functionality for the“density-independence” model.vbFuns(): Modified. Changed function returned whensimplify=FALSE so that if the parameters are named that thename is dropped. Thus, when the function is used, the returned resultwill not be annoyingly named as the first parameter.growthModelSim(): Deleted. The simulation functionalitywas moved to theFSAsim package. The functionality relatedto finding starting values for the von Bertalanffy modesl was moved tovbStarts().srFuns(): Modified. A complete rebuild to make similartovbFuns(). Addedsimple=. Addedtype='Shepherd' for the Shepherd (1982) three parametermodel andtype='SailaLorda' for the “Saila-Lorda” threeparameter model from Iles (1994). Added tests for error messages.srModels(): Modified. A complete rebuild to makesimilar togrowthModels(). Added “Shepherd” and“Saila-Lorda” models.srSims(): Deleted. The simulation functionality wasmoved to theFSAsim package. The functionality related tofinding starting values was moved tosrStarts().srStarts(): Modified. A complete rebuild to streamline.Removed default method (i.e., a formula must be used now). Added“Shepherd” and “Saila-Lorda” models. Modified plotting routine,including addingcol.mdl=,lwd.mdl=, andlty.mdl=. Moved the dynamic modeling aspects ofsrSim() into this function and is called with the newargumentdynamicPlot=TRUE. Also addedminmax.ratio= anddelta.prop= for use with thedynamic plots.vbStarts(): Modified. A complete rebuild to streamlineand fix some bugs that had not been found. Modified plotting routine,including addingcol.mdl=,lwd.mdl=, andlty.mdl=. Also added all of the von Bertalanffyparameterizations ingrowthModelSim() into this functionand is called with the new argumentdynamicPlot=TRUE. Addeddynamics plots for the “Francis” and “Schnute” parameterizations.psdPlot(): Modified. Fixed bug related toNAs inmax.brks variable.ageBias(): Modified. Reversed the order of the formula… it is nownrefvar~refvar. This more closely matches otherR functions where the tilde may be interpreted as the word “by”. Inother words, the formula now reads as “nonreference variable byreference variable” (i.e., Y by X). Thanks for Richard McBride for thesuggestion. Modified the age-bias plot extensively … addedsfrac= and defaulted to 0 to remove ends of the confidenceintervals, addedcex.mean= to control the size of thesymbol for the mean point, addedlwd= that will controlandset all of thelwd defaults to 1.agePrecision(): Modified. Changed all “CV” results to“ACV”.catchCurve(): Modified. Updated the help file regardingzmethod="Smithetal".capFirst(): Modified. Added a check to make sure theinputted object was either a character or factor class. Added code toreturn the object as the same class of the original object.lencat(): Modified. Added a catch for bad choices ofarguments. Added a catch to send a warning if the vector contains allNA values (this happens whenlencat() is usedwithin a loop or as part ofpsdAdd()). Added tests forerror and warning messages. Changed how the formula was handled in theformula method.psdAdd(): Modified. Fixed a bug with names when usinglabels. Addedverbose=. Added catches and sent messages ifverbose=TRUE for when no Gabelhouse lengths are know for aspecies and if the lengths for a species are all missing (see note forlencat() above).PSDlit: Modified. Fixed the trophy length for WhiteBass (from 15 to 18). This solved a bug related to non-uniquebreaks.expandCounts(): Modified. Made message regarding rowswith zero counts more useful. Added missing counts to the catch of zerocounts. Made changes to handle more “odd” data entries (see “details” inthe help file). Made some tests. Added some tests.psdCalc(): Modified. Corrected “bug” withunits=. Also modified warning message when no “stock” fishwere present in the data.frame to further note whatunits=were used (i.e., this problem is likely to happen if the data is inchesbut the user uses the defaultunits='mm'). Thanks to S.Mather for inspring this fix.dunnTest(): Modified. Corrected “bug” in the order thatthe groups are subtracted (i.e., they were flipped).catchCurve(): Modified. Changed default forpos.est= totopright. Addedcex.pos= (and set default to slightly smaller value).chapmanRobson(): Modified. Changed default forpos.est= totopright. Addedcex.pos= (and set default to slightly smaller value).hist.formula(): Modified. Changed use ofpar() to eliminate modifications to the gridding of plotsafter the function is complete. Also removed the setting ofmar= andmgp= inpar().mrOpen(): Modified. Removed pretty printing forsummary() andconfint() methods. These got inthe way of being able tocbind() the results together for asuccinct display.residPlot(): Modified. Changed use ofpar() to eliminate modifications to the gridding of plotsafter the function is complete..onAttach(): Modified. Centered the message andadjusted for different lengths of version numbers.alkPlot(): Modified. Fixed bug when usingadd=TRUE withtype="bubble".capHistSum(): Modified. Changed to returnpar() options to what they were before the function wascalled.catchCurve(): Modified. Changedplot() todefault to slighly lighter colored dots and a black line.chapmanRobson(): Modified. Changedplot()to default to slighly lighter colored dots. Changed to returnpar() options to what they were before the function wascalled.growthModelSim(): Modified. Changed to returnpar() options to what they were before the function wascalled.growthRadPlot(): Modified. Changed to returnpar() options to what they were before the function wascalled.hist.formula(): Modified. Changed to returnpar() options to what they were before the function wascalled.lwCompPreds(): Modified. Changedquant.lens= toqlens=. Changed defaultqlens= to have the 5th and 95th percentiles rather than theminimum and maximum values. Addedqpens.dec= so that theuser could control the number of decimals for the lengths derived fromqlens=.srSim(): Modified. Changed to returnpar()options to what they were before the function was called.mrOpen(): Modified. Changedsummary() andconfint() methods to allow single, multiple, or all choicesof parameters to return results for. Also added code to print theresults more prettily.swvCode(): Modified. Fixed bug related toblanks='extra'.filterD(): Added.catchCurve(): Modified. Removed the use of largerpoints in theplot().chapmanRobson(): Modified. Removed the use of largerpoints in theplot().metaM(): Modified. Deletedgroup= (andcreatedmethod="ZhangMegreyD" andmethod="ZhangMegreyP"). Added geometric mean regressonmethods for Hoenig. Changed default forjustM= toTRUE. Fixed several minor bugs from the originalimplementation. Added some checks for reasonableness of some arguments.Created tests for several methods to see if the results matched thosefrom Kenchington (2014). Added code to compute with several methods atonce.Mmethods(): Added. Added as a function and removed as avector.lencat(): Modified. Fixed a bug that occurred ifbreaks= were given but the vector containedNAs. Thanks to Ben Neely for pointing this out.catchCurve(): Modified. Changeduse.weights= toweighted=. Added some checksfor the formula in the formula version and for the variables in thedefault version. Add unit tests for warnings and errors and tow testsfor values.chapmanRobson(): Modified. Added themethod="Smithetal" methodology for estimating the SE of Z(and made it the default). Added some checks for the formula in theformula version and for the variables in the default version. Addedverbose= tosummary(). Add unit tests forwarnings and errors and two tests for values.alkPlot(): Modified. Changed behavior for adding alegend to alleviate a bug.metaM(): Added.confint.nlsBoot(): Modified. Changed default forerr.col= toblack fromred. Fixedexample due to changes innlsBoot package.extraSS(): Modified. Added a catch to make sure allmodels are of the same type. Added a catch to note that the functiondoes not work with other thatlm() ornls()models. Fixed a bug related to the labels for results fromanova() being different depending on whetherlm() ornls() models were given. Added someexamples.hist.formula(): Modified. Fixed bug (originated in lastversion) that nothing was returned when only one histogram wasconstructed.lrt(): Modified. Changed call tolrtest()to a call tolrtest.default(). Added a catch to make sureall models are of the same type. Note that degrees-of-freedom fromlrtest() are not error df; thus, modified to report errordf to matchextraSS(). Added some examples.hist.formula(): Modifiied. Addediaxs=,which when set to the default value ofTRUE will usexaxs="i" andyaxs="i" to remove the “floating”x-axis produced byhist() in base R.lwCompPreds(): Modified. Added theyaxs=argument.psdCalc(): Modified. AddedshowIntermediate= to allow showing intermediate values inthe calculation of the PSD indices. AddedjustAdds= toallow the user to return just those results that pertain to the valuesinaddLens=. Added ability to use a named vector inaddLens= and then not useaddNames=. Changeddigits=1 todigits=0. Thanks to Ben Neely forthe suggestions.psdVal(): Modified. Added ability to use a named vectorinaddLens= and then not useaddNames=. Theoriginal functionality is still there. Added a check that one of theGabelhouse lengths is not also one of theaddLens= values.Deleted theaddLens= value if it was (the user might havesent a name with this value and will want that name to appear in theresults).residPlot(): Modiifed. Addedxpd=TRUE tothe loess line routine so that the curve and polygon would stay withinthe plotting region.tictactoe(): Modified. Add the ability to handledifferences between whenxaxs="r" andyaxs="r"are used and whenxaxs="i" andyaxs="i" areused.dunnTest(): Added.addZeroCatch(): Modified. Removedidvar=,forced theeventvar= andspeciesvar= variablesin the returned data.frame to be numeric if they were numeric in theoriginal data.frame, allowedspeciesvar= to have more thanone variable, and addedna.rm=. Multiple values forspecvar= will allow the user to add zeros based on acombination of variables (e.g., species and size category). Thena.rm= argument allows the user to remove “missing”species, which are common if some sampling events did not capture anyfish.growthModelSim(): Modified. Changed all “K0” objects to“t50”.headtail(): Added.logbtcf(): Added.lwCompPreds(): Modified. Addedbase= toallow the function to work with logarithms to a different base. Theoriginal function was hard-wired to only use natural logarithms. Updatedthe examples and the tests.vbFuns(): Modified. Changed all “K0” objects to“t50”.vbStarts(): Modified. Changed all “K0” objects to“t50”.expandcounts(): Added (fromfishWiDNRpackage).expandLenFreq(): Added. Same aslenFreqExpand() but thought that this name fits better withexpandCounts().pcumsum(): Added.rcumsum(): Modified. Completely new code (muchsimpler).validn(): Added.plyr.addZeroCatch(): Modified. Slight modifications to helpfile. Fixed bug related to error checking the number of variables. Addedsome tests.lencat() Modified. Addeddroplevels= andkeptdrop.levels= as I could not consistently remember whatthe name of the argument was – i.e., the user can use either one, butdroplevels= is preferred.mapvalues(): Added. This is the exact same functionfrom theplyr package. Included here to minimize conflictsbetween functions indplyr andplyr that havethe same name (i.e., don’t have to installplyr just formapvalues() when also usingdplyr).perc(): Added.psdCalc(): Modified. Minor change related todroplevels= inlencat().psdVal(): Modified. Changed name for the “zero” groupto “substock.”swvCode(): Modified. Removed ability to Stangle thecode and thus removedmethod=. Modified code to allow usageof .Rmd files in addition to .Rnw files.plyr, for examples usingmapvalues().lencat(): Modified. Changedas.fact= todefault to same asuse.names=. This will result in the samebehavior as before. However, it also allows the user to setuse.names=TRUE andas.fact=FALSE to return acharacter vector (that is not a factor).psdAdd(): Modified. AddedaddSpec= andaddLens= so that the user can have non-Gabelhouse lengthsfor individual species.PSDlit: Modified. Changed “Walleye x Sauger” to“Saugeye” and “White Bass x Striped Bass” to “Palmetto Bass”. Updatedthe Palmetto Bass values based on Dumont and Neely (2011), but kept oldvalues as “Palmetto Bass (original)”. Deleted redundant entries for somespecies.recodeF(): Deleted. Functionality is inmapvalues() fromplyr. Ease come easy go(i.e., added in last version).dplyr.capFirst(): Modified. Changedwords= towhich=.psdAdd(): Modified. Added a default and a formulaversion to allow efficiency withdplyr. Added examples.Updated tests.recodeF(): Added.recodeSpecies(): Deleted. Functionality replaced byrecodeF() in combination withcapFirst().wrAdd(): Modified. Added a default and a formulaversion to allow efficiency withdplyr. Added examples.Updated tests.WSlit: Modified. Added results for Sardine.psdAdd(): Added.psdDataPrep(): Deleted. Functionality replaced bypsdAdd().recodeSpecies(): Modified. Completely re-written butwith the same basic functionality. This new version returns a vectorthat can then be appended to an existing data.frame rather than the oldfunction that returned a whole data.frame. This function should allowease of use withmutate() fromdplyr. Addedmore catches for badformuala=s. Added some tests.wrAdd(): Modified. Completely re-written withcompletely new functionality. This new version returns a vector that canthen be appended to an existing data.frame rather than the old functionthat returned a whole data.frame. This function should allow ease of usewithmutate() fromdplyr. Added more catchesfor badformuala=s. Added some tests.wrDataPrep(): Deleted. Functionality replaced by newwrAdd().hist.formula(): Modified. Slight modifications towarning messages.Summarize(): Modified. Slight modification to warningmessages.tictactoe(): Modified. Changedpredbal= topredobj=,preybal= topredbal=,xlab= topredlab=,ylab= topreylab=,bal.col= toobj.col=,andbal.trans= toobj.trans=.vbStarts(): Modified. Fixed a bug related toplot=TRUE whentype="Francis" ortype="Schnute".wrAdd(): Modified. Modified how quadratic functions andthe handling of fish less than the minimum applicable length werehandled because of changes towsVal().wsLit: Modified. Changed order of variables, changedhybrid species names to match that of Neumann et al. (2012), updatecomments to related to Neumman et al. (2012) rather than Blackwell etal. (2012), and added information for the Riffle Dace.wsVal(): Modified. Changed the names of themin.len andmax.len variables to be eithermin.TL andmax.TL ormin.FL andmax.TL as appropriate. Suppressed the return ofmax.len andquad if they did not exist andsuppressed return ofcomment if it wasnone.Added a catch if more than one species was given inspecies=. Created some tests.capFirst() Modified. Added an option to handle a vectorof strings rather than just a single string.lencat(): Modified. Fixed bug with category names whenuse.names=TRUE. Moved all internal functions outside oflencat() environment (and renamed them). Cleaned upcode.psdCI(): Modified. Added more catches for calls withmistakes. Create some internal functions to modularize the computations.Added tests.psdVal(): Modified. Added more catches for calls withmistakes. Added tests.psdCalc(): Modified. Completely redone. Changed defaultto use multinomial rather than binomial method for confidence intervals(addedmethod= argument to control CI type). Changed tothrow an error of a species is not given in ``species=’’. Addedtests.psdDataPrep(): Modified. Changeduse.catnames= touse.names andpsdname= tovname= to be consistent withpsdVal(). Removed duplicitousfactor() callsfor the length category and species name variables in the returneddata.framed.psdPlot(): Modified. Completely redone (fixed severalbugs and overall sloppy code). Addedpsd.add=. Changedlegend.pos= andlegend.cex= topsd.pos= andpsd.cex=.recodeSpecies(): Modified. Made changes to reflect newcapFirst() functionality.tictactoe(): Modfied.tictactoeAdd(): Removed. Directed user to useplotCI() fromplotrix instead.mrClosed(): Modified. Better handled a given value ofR=.psdCalc() Modified. Fixed a bug that appeared when no“zero” fish were present in the data. Moved all internal functionsoutside ofpsdCalc() environment (and renamed them).psdCI(): Added.psdPlot(): Modified. Fixed a bug that appeared when no“zero” fish were present in the data. UsedpsdCalc() tocompute the PSD values. Moved default legend position totopleft.swvCode(): Modified. Fixed bug when attempting to usethis function from outside of the directory where the .Rnw file exists.Added functionality to add a “note” to the first line(s) of the outputfile. Added code to remove the first line of the output file if it wasgoing to be blank.swvFinish(): Modified. Updated code becauseiGetFilePrefix() was deleted.ageKey(): Deprecated. SeealkIndAge().ageKeyPlot(): Deprecated. SeealkPlot().ageKeyPrep(): Deprecated. SeealkPrep().alkAgeDist(): Added.alkIndAge(): Added. WasageKey(). Addedseed= to help with reproducibility. Modified code to betterhandle when an age-length key has a whole row of missing data (as wouldhappen ifas.fact=TRUE anddrop.levels=FALSEinlencat()). Added some checks for the age-length keystructure. Moved all internal functions outside ofalkIndAge() environment (and renamed them).alkMeanVar(): Added.alkPlot(): Added. WasageKeyPlot(). Fixedbug with colors when adding legend to bar and area plots. Allowed legendto be removed from area plot. Added ability to add a legend to the linesand splines plot. Addedpal= to allow choice of colorpalette for areas in bar and area plot and lines in lines and splinesplots. Allowed an area plot when one row of age-length key sums to zero(previously did not allow this). Create internal functions for each plottype. Moved all internal functions outside ofalkPlot()environment (and renamed them). Added some checks on the age-length keystructure.alkPrep(): Added. WasageKeyPrep(). Addedsome checks on the age-length key structure.iCheck ALK(): Added as an internal function (used totest the structure of the age-length keys in several otherfunctions).summary.mrOpen(): Modified. Removed “Estimates” headingifverbose=FALSE.Summarize(): Modified. Moved all internal functionsoutside ofSummarize() environment (and renamed them).removal(): Modified. Completely modified the code sothat the examples withapply() andlapply()would also provide confidence intervals. Also changed the code toreflect that\(\sum_{i=1}^{k-1}T_{i}\)from Schnute (1983) is the same asremoval() without having to useas.numeric(). Modified and added examples of the use ofapply() andlapply().ageKey(): Modified. Changed to usingall.equal() to check if the ALK has rows that don’t sum to1. This was an attempt to minimize the number of “false negatives”caused byRFAQ 7.31. Changed the check of whether the longest fish in thelength sample is greater than the longest length bin in the ALK towhether the longest fish in the length sample is greater than thelongest length bin in ALK PLUS the minimum width of length categories.This last change is an attempt to minimize the number of warnings thatoccur when the longest fish in the length sample would be in the lastlength category ALK but because the length categories are labelled bytheir minimum length it looks like it is not. The minimum width is usedto still allow unevent length categories and, thus, this check may stillproduce some “false negatives.”ageKeyPlot(): Modified. Removedbubble.ylab=. Modifiedylab= to handle whatbubble.ylab= used to handle.removal(): Modified. Added options to perform Moran(1951) and Schnute (1983) removal methods. Added examples of the newfunctionality. Updated the tests for the new functionality.depletion(): Modified. Changedtype= tomethod= and addedDeLury as an option tomethod= (and leftDelury). Changedricker.mod= toRicker.mod=. Added somechecking for bad arguments. Created internal functions specific to theLeslie and DeLury methods (for isolation). Modified some clunky code.Added references to specific sections in Seber (2002) for SE equations.Updated examples. Added tests and error checking.coef.depletion(): Modified. Addeddigits=.confint.depletion(): Modified. Addeddigits=. Modified theparm= list to be moreefficient.plot.depletion(): Modified. Removed internalpar() settings.summary.depletion(): Modified. Addedverbose= anddigits=.removal(): Modified. Made"CarleStrub" thedefault method. Changedtype= tomethod=.Changed internalmeth object tolbl. Moved allinternal functions outside ofmrOpen() environment andadded other internal functions to isolate all intermediate calculations.Added averbose= andparm= tosummary(). Streamlined clunky code inconfint() including removing theall andboth options fromparm=. Added more checks forabd inputs, notes in the code as to sources for the fomulae, andtests.capHistSum(): Modified. Changed column and row labelsfor$methodB.top and column labels for$methodB.bot. Added a m-array object for when more than twosampling events are present. Added calculations for the number of fishfirst seen on event i (ui), the number of fish last seen on event i(vi), and the number of fish seen i times (fi) to$sum.jolly(): Added. Same asmrOpen(), addedonly for convenience.mrClosed(): Modified. Fixed bugs around printing of CItype with Schnabel and the ignoring ofconf.level= withSchnabel.mrOpen: Modified. Changedci.type= totype= andphi.type= tophi.full=.Removedtype= fromsummary() and added averbose= which will print only the estimates ifFALSE or both observables and estimates ifTRUE. Added averbose= toconfint() to control whether the message about the type ofconfidence interval is printed or not. Moved all internal functionsoutside ofmrOpen() environment and added other internalfunctions to isolate all intermediate calculations. Changes to row andcolumn labels incapHistSum() resulted in changes to rowlables forsummary() andconfint() results.Streamlined some clunky code. Added checks for misformedmb.top= andmb.bot=. Added tests and notes inthe code as to sources for the fomulae.plot.CapHistSum(): Added.plot.mrClosed(): Modified. Changed axis labels as theexpressions did not print with some fonts and devices.marked for the example incapHistConvert().ageBias(): Modified. Changed default value ofmin.n.CI= from 5 to 3. Added anna.rm=TRUE tothemin() andmax() that produced the ageranges for the age agreement table.BluegillJL: Modified. Corrected lake name and added acitation.capHistConvert(): Modified. This should probably beconsidered as a new function if updating from the old version.Modifications included simplifying the structure allowed for the inputdata.frames (they can have only an id or a freq column and then columnsrelated to the capture history … this makes the function less flexiblebut simplifies its use for those that are most likely to use it), movedto a series of internal functions, created a common intermediate dataformat (which streamlined the code considerably), changed the name oftheFSA format toindividual and theRcapture format tofrequency, added anout.type='event' format, addedin.type='RMark'andin.type='marked'formats, fixed the bug with outputtingRMark format, changed the default for new frequencyvariables fromFreq tofreq, removed themch= andevent= arguments, replacedcols= withcols2ignore=, added theinclude.id= argument, changed thein.type=default, coded some “catches” for common mistakes in use, coded to keepthe unique fish identifier inid= or event name given inthe variable names as much as possible, fixed a bug withevent.ord=. Added several new examples.capHistSum(): Modified. Changecols=argument tocols2use=. Moved all internal functions outsideofcapHistSum() environment.CutthroatAL: Modified. Updated from a new source toinclude many more years of samples.fitPlot(): Modified. Changedtrans.pt= totransparency=.mrClosed(): Modified. Completely re-built the internalfile structure. Changedincl.inputs= toverbose=. Added the ability to construct a CI for theoverall PE when multiple groups are used in a Petersen family method(thus, added aincl.all= toconfint()).Changed default forincl.all= fromFALSE toTRUE. Modified the messages whenverbose=TRUE.plot.AgeBias(). Modified. Fixed bug that produced awarning if all of the bias t-tests were either significant or notsignificant. Changedcol.err= tocol.CI=,lwd.err= tolwd.CI=,col.err.sig=tocol.CIsig=,col.ref= tocol.agree=,lwd.ref= tolwd.agree=,lty.ref= tolty.agree=,show.rng= toshow.range=,col.rng= tocol.range=,lwd.rng= tolwd.range=. Removedcol.lab= androw.lab= which were deprecated several minor versions ago.Changed default values forlwd.rng= andlwd.CI= from 2 to 1. Added acex.numbers=argument for controlling the size of the numbers in the “numbers plot”(defaults to 0.9).plotBinResp(): Modified. Changedtrans.pt=totransparency=.confint.mrClosed(): Modified. Moved all internalfunctions outside ofconfint.mrClosed() environment (seeiCI.MRCMultiple() andiCI.MRCSingle()).Changedci.type= to justtype=. Streamlinedbinomial method for single census. UsediMRCSingleSE() toget SE for whentype="normal" for Chapman, Bailey, andRicker methods.extraSS(): Modified. Slight change to row labels inoutput table.iMRCMultiple(): Added. Wasmrc2() internalfunction inside ofmrClosed() environment.iMRCSingle(): Added. Wasmrc1() internalfunction inside ofmrClosed() environment.iMRCSingleSE(): Added. Moved functionality out ofsummary.mrClosed(). Checked and documented all formulaswith sources (in code and in Rd file).lrt(): Modified. Slight change to row labels in outputtable.mrClosed(): Modified. Moved all internal functionsoutside ofmrClosed() environment (seeiMRCMultiple() andiMRCSingle()). Changedtype= argument tomethod=. Added more catchesfor argument problems (required settingn=,m=,M= andR= toNULL). Streamlined warning message for whenincl.SE=TRUE is used with Schnabel or Schumacher-Eschmeyermethod. Added tests and reported results in the help file for populationsize, SE, and CI estimates for each method.plot.mrClosed(): Modified. Removed setting ofpar(). Changed from usinglowess() to usingloess() and set better default values. Added descriptivetext to help file.summary.mrClosed(): Modified. Moved SE calculationsinto an internal function (seeiMRCSingleSE()).BluegillLM: Modified. Added a seealso.residPlot(): Modified. Changed the loess-relatedmethods to useloess(), to put an approximate confidentband with the line, the line and band are “under” the points, the lineis lighter. Put the horizontal reference line at zero under the points.Madeloess=TRUE the default.iAddLoessLine(): Modified. SeeresidPlot().iHndlFormula(): Modified. COrrected the positioning ofthe explanatory variables when the model has a response variable.iMakeBaseResidPlot(): Added as an internal function toresidPlot() to simplify some coding.iMakeColor(): Modified. More intelligently handlesvalues that are greater than 1 (converts them to decimals byinverting.)lwPredsComp(): Modified. Changedmdl= toobject=. Added use of internaliHndlFormula()and moved two internal functions outside the main function. Changeddefault for intervals fromboth toconfidenceand changed so that if only the confidence or prediction intervals areplotted they will be black withlwd= width (if both areplotted the CI is now black and the PI is now blue). Added ashow.preds argument. Changedconnect.means= toconnect.preds=. Changed defaultlwd= value andhow it is used for CIs, PIs, and the connection lines. Addedcol.connect= argument. Removedmar andmgp frompar() call (leftmfrow).Added more examples. Added tests for error messages.residPlot(): Modified. AddedinclHist=argument. Corrected a bug around the use ofthigmophobe()iniAddOutlierTest(). Changed default forstudent= toFALSE. Modified and added moreexamples.SMBassWB: Modified. Added a seealso.addLoessLine(): Deleted. Moved functionality toiAddLoessLine() and moved code toresidPlot()file..addOutlierTestResults(): Deleted. Moved functionalitytoiAddOutlierTestResults() and moved code toresidPlot() file.capHistConvert(): Added aninteractive()to theRcapture example in the help file.checkStartcatW(): Deleted. Moved functionality toiCheckStartcatW().ci.fp(): Deleted. Moved functionality toiCIfp() and moved code tofitPlot() file.ci.fp.1(): Deleted. Moved functionality toiCIfp1() and moved code tofitPlot()file.ciLabel(): Deleted. Moved functionality toiCILabel().getAllDependencies(): Deleted. Moved functionality toiGetAllDependencies() and moved code toswvUtils file.getFilePrefix(): Deleted. Moved functionality toiGetFilePrefix() and moved code toswvUtilsfile.getMainTitle(): Deleted. Moved functionality toiGetMainTitle() and moved code toresidPlot()file.getVarFromFormula(): Deleted. Moved functionality toiGetVarFromFormula().hndlFormula(): Deleted. Moved functionality toiHndlFormula().hndlMultWhat(): Deleted. Moved functionality toiHndlMultWhat().iAddLoessLine(): Added. WasaddLoessLine().iAddOutlierTestResults(): Added. WasaddOutlierTestResults().iCheckStartcatW(): Added. WascheckStartcatW().iCIfp(): Added. Wasci.fp().iCIfp1(): Added. Wasci.fp.1().iCILabel(): Added. WasciLabel().iGetAllDependencies(): Added. WasgetAllDependencies().iGetFilePrefix(): Added. WasgetFilePrefix().iGetMainTitle(): Added. WasgetMainTitle().iGetVarFromFormula(): Added. WasgetVarFromFormula().iHndlFormula(): Added. WashndlFormula().iHndlMultWhat(): Added. WashndlMultWhat().iLegendHelp(): Added. WaslegendHelp().iMakeColor(): Added. WasmakeColor().iMakeFilename(): Added. WasmakeFilename().iMakeItemsToRemove(): Added. WasmakeItemsToRemove().iProcessSessionInfo(): Added. WasprocessSessionInfo().iPSDLitCheck(): Added. WaspsdLitCheck().is.even(): Added.is.odd(): Added. Wasodd().iTypeoflm(): Added. Wastypeoflm().iwsLitCheck(): Added. WaswsLitCheck()legendHelp(): Deleted. Moved functionality toiLegendHelp().listSpecies(): Deleted. Moved functionality toiListSpecies().makeColor(): Deleted. Moved functionality toiMakeColor().makeFilename(): Deleted. Moved functionality toiMakeFilename() and moved code toswvUtilsfile.makeItemsToRemove(): Deleted. Moved functionality toiMakeItemsToRemove() and moved code toswvUtils file.odd(): Deleted. Moved functionality tois.odd().predict.nlsBoot(): Added aninteractive()to thenlstools example in the help file.printProgressMsg(): Deleted. Not used anywhere.processSessionInfo(): Deleted. Moved functionalityiProcessSessionInfo() and moved code toswvUtils file.PSDLitCheck(): Deleted. Moved functionality toiPSDLitCheck() and moved code topsdVals()file.pssCalc(): Deleted. Was deprecated several versionsago. SeepsdCalc().pssDataPrep(): Deleted. Was deprecated several versionsago. SeepsdDataPrep().pssPlot(): Deleted. Was deprecated several versionsago. SeepsdPlot().pssVal(): Deleted. Was deprecated several versions ago.SeepsdVal().typeoflm(): Deleted. Moved functionality toiTypeoflm().wsLitCheck(): Deleted. Moved functionality toiwsLitCheck() and moved code towsVals()file.test_VonB2b.R) to assure that groupcomparisons of von Bertalanffy parameters equal those in Kimura (1980)andvblrt() infishmethods.lmtest forlrt().Also used in testing (test_VonB2b.R).confint.nlsBoot(): Modified. Modified the plotting tousehist.formula(), removedpar(mar=)definitions, and addederr.col= andlwd.col=to control the color and line width of the confidence interval line onthe plot.extraSS(): Added.growthModels(): Modified. Added Weisbergparameterization. ChangedvbGallucciQuinn tovbGQ.growthModelSim(): Modified. Added Weisbergparameterization. AddedvbGQ abbreviation (synonymous withvbGallucciQuinn).lrt(): Added.vbFuns(): Modified. Added Weisberg parameterization.AddedvbGQ abbreviation (synonymous withvbGallucciQuinn). Simplified the functions for whensimple=FALSE (no error checking now).vbModels(): Modified. Added Weisberg parameterization.ChangedvbGallucciQuinn tovbGQ.vbStarts(): Modified. Added Weisberg parameterization.AddedvbGQ abbreviation (synonymous withvbGallucciQuinn). Added an internal function for checkingwhther the starting values for K and Linf made sense.Date: Jun14
added testthat files for error checking ofchapmanPlot(),vbFuns(),vbStarts(), andwalfordPlot(). Added atestthat file for checking that the von Bertalanffy fitting usingvbFuns() andvbStarts() matches othersources.
ageBias(): Modified. Deprecatedcol.lab= androw.lab= and replaced withref.lab= andnref.lab=. Moved all functionsthat were internal to main functions to being internal to the package.In the process, I changed the names of the internal functions slightly,made explicit the argument passing, and added internal descriptions ofthe internal files. Changed several if else strings in the plot methodto aswitch().
agePrecision(): Modified. Changed some messages sothey were not as wide.
chapmanPlot(): Modified. Removed S3 functions sothatvbStarts() has to use a formula. Added some checkingrelated to the formula.
growthModels(): Modified. Created an internalfunction that eliminates repetitiveness between this andvbModels(). Changed theGompX types toGompertzX.
growthModelSim(): Modified. Removed S3 functions sothatgrowthModelSim() has to use a formula. Added somechecking related to the formula. Changed the order of the arguments sothatformula= anddata= come beforetype=. This allows a similar interface withvbStarts(). Included a hack that still allows the user toenter a type as the first argument (and thus not have to typetype= if any parameterization besides thevbTypical is being used). Corrected spelling of Galluccifor Gallucci and Quinn model.
hndlFormula(): Modified. Fixed bug with expectednumber of response variables value in return list.
SpotVA1: Modified. Updated reference.
vbFuns(): Modified. Changedschnuteparameterization to use L3 instead of L2 and t3 instead of t2.
vbModels(): Modified. Created an internal functionthat eliminates repetitiveness between this andgrowthModels().
vbStarts(): Modified. Removed S3 functions so thatvbStarts() has to use a formula. Added some checkingrelated to the formula. ChangedtFrancis= toages2use=. Changed the Schnute method to use the ages inages2use= rather than being hard-wired to use the minimumand maximum observed age. Both the Schnute and Francis methods will usethe minimum and maximum observed ages ifages2use=NULL.Added a catch for ifages2use= are in descending order(should be in ascending order). ChangedSchnuteparameterization to use L3 instead of L2.
walfordPlot(): Modified. Removed S3 functions sothatvbStarts() has to use a formula. Added some checkingrelated to the formula.
Date: May14
added Suggests fortestthat,fishmethods,FSAdata for testing andpopbio for an example that was made “interactive” from“dont run”(see below).
added testthat files forageBias() andagePrecision().
ageBias(): Modified. Removed unit testings fromexamples and put in the testing file.
agePrecision(): Modified. Removed deprecatedwhat="agreement".
confint.nlsBoot(): Modified. Changed example from“dont run” to “interactive.”
fact2num(): Modified. Changed example from “dontrun” to “interactive.”
fishR(): Modified. Removednews andaddedposts to thewhere= argument. Cleaned upthe Rd file. Changed example from “dont run” to “interactive.”
FSA(): Modified. Cleaned up the Rd file.
FSANews(),fsaNews(): Modified. Cleanedup and fixed the Usage section in the Rd file. Changed example from“dont run” to “interactive.”
growthRadPlot(): Modified. Changed example from“dont run” to “interactive.”
htest.nlsBoot(): Modified. Changed example from“dont run” to “interactive.”
lagratio(): Modified. Changed example from “dontrun” to “interactive.”
lencat(): Modified. Changed Rd file for deletion ofview().
popSizesPlot(): Modified. Changed example from “dontrun” to “interactive.”
TroutDietSL: Modified. Changed Rd file for deletionofview().
view(): Deleted. Moved to NCStats package.
wrDataPrep(): Modified. Changed Rd file for deletionofview().
Date: May14
Removed Roxygen directives in DESCRIPTION (with changes toroxygen2 4.0.1).
Changed@S3method and@method to@export in the following files according to changes inROxygen2 as described at stackoverflow.com/questions/7198758/, amongseveral other places:ageBias,agePrecision,bootCase,catchCurve,chapmanRobson,confint.nlsboot,depletion,dietOverlap,fitPlot,hist.formula,htest.nlsBoot,ks2d1,ks2d1p,ks2d2,ks2d2p,ksTest,lencat,mrClosed,mrOpen,plotBinResp,predict.nlsBoot,removal,residPlot,srStarts,Subset,Summarize,sumTable,vbStarts,andwalfordChapmanPlot.
addZeroCatch(): Modified. Added a catch for thesituation where no zeros need to be added to the data.frame. Cleaned-upthe help file, modified the examples, and added another example. Thanksto Ben Neely for bringing this bug (handling where zeros are not needed)to my attention.
capHistSum(): Modified. Cleaned up the code (nochanges in functionality).
catchCurveSim(): Deleted. Moved to FSAsimpackage.
checkstartcatw(): Modified. Changed the catch forwhether the starting category value was greater than the minimumobserved value to correct for a pathological case where they were equalbut not with machine rounding.
lenFreqExpand(): Modified. Slightly changed theexamples in the help file.
lwPredsComp(): Modified. Streamlined the code (nochanges to functionality).
mrOpen(): Modified. Streamlined the code (no changesto functionality). Removed all explicity partial matching options inswitch()es as these were already caught with previousmatch.arg()s.
Date: May14
Added Roxygen directives to DESCRIPTION.
Updated to Roxygen2 4.0.0 which modified several helpfiles.
ageBias(): Modified. Cleaned-up the helpfile.
agePrecision(): Modified. Cleaned-up the helpfile.
ageKey(): Modified. Cleaned-up the help file andmodified the example.
ageKeyPlot(): Modified. Added more description andcleaned-up the help file.
ageKeyPrep(): Modified. Added more description andcleaned-up the help file.
lenFreqExpand(): Modified. Correctedtotal= to uselength(x) rather thannrow(df), which was left over from a previous change.Cleaned-up the help file.
mrClosed(): Modified. Increased the readability ofthe code (added comments, usedwith() for some longcalculations, added spacing). Added specific citations to equations inthe help file. Changed the degrees-of-freedom in the confidence intervalcalculation for the Schnabel methods from number of samples minus 2 tonumber of samples minus 1 (following Krebs).
poiCI(): Modified. Cleaned-up the helpfile.
psdDataPrep(): Modified. Fixed error arounduse.catnames=.
swvCounts(): Modified. Fixed error inoutput.
Date: May14
Removed nlme dependencies (with removal ofvbDataGen()).
ageComp(): Deleted. Fully deprecated. UseageBias() andagePrecision() instead.
cohortSim(): Deleted. Moved to FSAsimpackage.
depletion(): Modified. Remove link toleslieSim().
lengthWeightSim(): Deleted. Moved to FSAsimpackage.
leslieSim(): Deleted. Moved to FSAsimpackage.
lwModelSim(): Deleted. Moved to FSAsimpackage.
mrClosed(): Modified. Remove link tomrClosed1Sim().
mrClosed1Sim(): Deleted. Moved to FSAsimpackage.
srCobWeb(): Deleted. Moved to FSAsimpackage.
vbComp(): Deleted. Moved to FSAsim package.
vbDataGen(): Deleted. Moved to FSAsimpackage.
vbFuns(): Modified. Remove link tovbComp().
VBGMlit(): Deleted. Moved to FSAsimpackage.
ageBias(): Modified. Added the ability to use multiplewhat= arguments withc(). Addedwhat="n" to get the sample size on the age-agreement table.AddednYpos= toplot() to allow control of theposition of the sample size values on the plot. Changed the order of theprinting of results whenwhat="symmetry" is used insummary(). The order more closely follows the “level ofcomplexity” of the tests. Added unit test examples to the helpfile.agePrecision(): Modified. Added the ability to usemultiplewhat= arguments withc().hndlMultWhat(): Added. An internal file to helpageBias() andagePrecision handle multiplewhat= arguments.Date: Apr14
Removed all of the functions related to constructing andvalidating standard weight equations. These are now in theFSAWs package. This is thestart of an effort to streamline the FSA package.
Removed importFrom quantreg (only used for standard weightmethods).
ChinookArg: Added (from FSAdata).
emp(): Removed.
FroesWs(): Removed.
lencatOLD(): Removed (from FSA-internals).
lwPredsComp(): Modified. Changed example to usingChinookArg rather thanRuffeWs becauseRuffeWs was moved to the FSAWs package.
LMBassWs: Removed.
rlp(): Removed.
RuffeWs: Removed.
WalleyeGerowLW: Removed.
wsValidate(): Removed.
WalleyeGerowLW: Removed.
Date: Apr14
Changed to compiling under R 3.1.0
Importedstackpoly() from plotrix for use inageKeyPlot().
Added concepts (that largely match those in the FSAdata pacakge)to most of the data files.
Made some grammatical changes and added author sections to Rdfiles.
ageKeyPlot(): Added.
dietOverlap(): Modified. Changed examples in helpfile to reflect changes tolencat().
lencat(): Modified. Added generic functions.lencat.default() accepts a vector as its first argument andreturns a single vector.lencat.formula() accepts a formulaas its first argument and thedata= argument. Thelencat.formula() is the same as the oldlencat() andlencat.default() provides newfunctionality. Additionally, the default forstartcat= isnowNULL and a value forstartcat= is foundautomatically (though a value can still be supplied by the user). Theuse.catnames= was changed touse.names=. Otherchanges were made to simplify the code.
lenFreqExpand(): Modified. Removed thedf= andcl= arguments and replaced withx=, which is simply a vector of length measurements.Changed tostartcat=NULL so that that the starting categoryvalue can be determined automatically (or can still be set by theuser).
Date: Apr14
Converted to using github as a repository.
Changed NEWS to NEWS.md
Added ImportFrom for relax package (see below).
ageBias(): Modified. Added a plot that shows thenumber of observations at each combined age. Changed the coding slightlyaround Bowker’s test (added an internal function) and implemented Evansand Hoenig’s and McNemar’s test. These changes resulting in adding a“table” choice towhat= that will print just theage-agreement table. Whenwhat="symmetry" is chosen allthree ob Bowker’s, McNemar’s, and Evans-Hoenig results will be output asa table. The age-agreement table is no longer printed whenwhat="symmetry". In addition,what="Bowkers",what="EvansHoenig", andwhat="McNemars" can beused to see the Bowker’s, Evans and Hoenig, and McNemars test results,respectfully. Added acont.corr= argument for use withMcNemars test.
agePrecision(): Modified. Added the ability to showraw (vs. absolute value) differences between structures. This resultedin the removal ofwhat="agreement" (though it isdeprecated, with a message, for now) and the addition ofwhat="difference" andwhat="absolute difference".
fishR(): Modified. Changed to point to the githubNEWS.md whenwhere="news".
fitPlot(): Modified. Changed the logistic regressioncode to handle the changes toplotBinResp() (see below). Inaddition, a temporary fix was added so that the size of the y-axislabels could be modified with an external call topar().This was a fix for Glen Sutton but will ultimately need to be handledmore elegantly.
fsaNews(): Modified. Changed to point to the githubNEWS.md.
catchCurveSim(): Added back from FSATeach (requiredadding ImportFrom for relax package).
cohortSim(): Added back from FSATeach (requiredadding ImportFrom for relax package).
growthModelSim(): Added back from FSATeach (requiredadding ImportFrom for relax package).
lengthWeightSim(): Added back (waslwModelSim()) from FSATeach (required adding ImportFrom forrelax package).
leslieSim(): Added back from FSATeach (requiredadding ImportFrom for relax package).
mrClosed1Sim(): Added back from FSATeach (requiredadding ImportFrom for relax package).
plotBinResp(): Modified. Addedyaxis1.ticks= andyaxis1.lbls= arguments sothat the user can control the tick-mark locations and labels for theleft y-axis (the defaults are to show ticks every 0.1 units but onlylabel 0, 0.5, and 1). Addedyaxis2.show= argument to allowthe user to “turn-off” the right y-axis (defaults to being on) which islabeled with the level labels.
srSim(): Added back from FSATeach (required addingImportFrom for relax package).
ageKeyPrep(): Added.agePrecision(): Modified. Fixed the bug where the APEand CV were over-estimated in situations where the multiple ages agreedat an age=0 (thanks to Richard McBride for pointing out thiserror).wsLit: Modified. Added Pursak chub information fromSulun et al. (2014).ageBias(): Added. Extracted the age-bias relatedmaterial fromageComp(). Modified the code to removeunneeded code. FromageComp(), remove thewhat= argument related to differences and added adifference= argument. Also changedwhat="bias.diff" towhat="diff.bias" to allowfor a quicker partial matching (i.e. separate more fromwhat="bias"). Major modifications to how the axis limitsare created if none are provided. Modified where the sample size isshown on the age-bias plot. Added themin.n.CI= argument.Added an example usingWhitefishLC to be consistent withagePrecision().ageComp(): Modified. Split intoageBias()andagePrecision(). Added a warning that this function isdeprecated and will be removed in the future.ageKey(): Modified. Fixed a bug that occurred when adata frame that already contained an LCat variable was provided.agePrecision(): Added. Extracted age precision relatedmaterial fromageComp(). Modified the code to allow forcalculations across more than two structures. Code was streamlineddramatically from what was inageComp(). Added an exampleusing WhitefishLC as it allows for demonstrating more than two ageassignments.capFirst(): Modified. Added functionality, controlledby the new words= parameter, to allow all words, rather than just thefirst word, to be capitalized.capHistConvert(): Modified the help file by commentingout the example that depends on the RCapture package. This is needed forthe RForge site for the time being.fitPlot(): Modified Rd. Added two polynomial regressionexamples.fitPlot.IVR(): Modified. Changed to use newtypeoflm(), changedinterval= argument,removed automatic main title, removed a bunch of unneeded code.fitPlot.logreg(): Modified. Removed automatic maintitle.fitPlot.nls(): Modified. Removed automatic maintitle.fitPlot.ONEWAY(): Modified. Changed to use newtypeoflm(), removed automatic main title, removed one lineof unneeded code.fitPlot.SLR(): Modified. Changed to use newtypeoflm(), changedinterval= argument,removed automatic main title.fitPlot.TWOWAY(): Modified. Changed to use newtypeoflm() and removed automatic main titlegReshape(): Modified. Added adrop=argument so that the user can drop some variables before reshaping.Also, addednew.row.names=1:100000 to thereshape() call to work-around issues with duplicate rownames (which were particularly problematic if any of theid.vars= had missing values.)growthModels(): Modified. Corrected spelling ofGallucci for Gallucci and Quinn model.hist.formula(): Modified. Add acol=argument that defaults to “gray90”.hndlFormula(): Added. An internal function to handlevarious assessments related to using formulas.lencat(): Modified. Added the ability to add names ifthe vector sent inbreaks= is named.confint.mrClosed(): Modified. Removed extra linespacesin printed output. Changed default forincl.inputs= toFALSE.summary.mrClosed(): Modified. Removed extra linespacesin printed output. Changed default forincl.inputs= toFALSE.predict.nlsBoot(): Modified the help file by commentingout the example that depends on the nlsBoot package. This is needed forthe RForge site for the time being.psdCalc(): Added (waspssCalc()).psdDataPrep(): Added (waspssDataPrep())and modified. Deleted the code in this function that added categorynames as this functionality was added tolencat(). Seelencat() above.PSDlit: Added (wasPSSlit) and modified.Changed all species names to have both words capitalized so as to followthe latest AFS guidelines.psdPlot(): Added (waspssPlot()).psdVal(): Added (waspssVal()).rsdCalc(): Deleted.rsdVal(): Deleted.recodeSpecies(): Modified. ChangedcapFirst= todoCapFirst= to minimize confusionwithcapFirst(). ChangedoCapFirst= to acharacter that behaves likewords= incapFirst(), rather than as a logical.SpotVA1: Modified. Removed link to source documentsbecause it caused a problem when making the PDF manual.StripedBass1: Deleted. Moved to FSAdata as no longerneeded because some examples were changed to useWhitefishLC.Subset(): Modified. Added aresetRownames=argument.swvCode(): Modified. Added anout.dir=argument.swvCounts(): Modified. Added acapitalize=argument.typeoflm(): Modifed. Changed to usehndlFormula(). Made an internal function.vbFuns(): Modified. Corrected spelling of Gallucci forGallucci and Quinn model.vbStarts(): Modified. Corrected spelling of Galluccifor Gallucci and Quinn model.WhitefishLC: Added (from FSAdata).wsLit: Modified. Changed all species names to have bothwords capitalized so as to follow the latest AFS guidelines.Date: Dec13
Changed to compiling under R 3.0.2.
Removed dependency on reshape package (see changes foremp(),gReshape(), andssValidate() below) and the relax, tcltk, and TeachingDemospackages (see changes forcatchCurveSim(),cohortSim(),growthModelSim(),leslieSim(),lwModelSim(),mrClosed1Sim(),simAgeBias(),simAges(),simLenFromAge(),simLenSelect(), andsrSim() below).
.onAttach(): Modified. Added notes to usecitation().
bcFuns(): Modified. Added “BPH” and “SPH” options totype= argument (same as “LBPH” and “LSPH”, respectively).Changed a catch usingcat() to usingmessage(). Added some specificity to the help file (more isneeded).
catchCurveSim(): Deleted. Moved to FSATeachpackage.
changesPos(): Added.
cohortSim(): Deleted. Moved to FSATeachpackage.
emp(): Modified. Replaced use ofcast()withaggregate().
gReshape(): Modified. Replaced use ofmelt() withreshape() from base package. Fixedbug if name of “increments” was not “inc” (now catches thatin.pre= value is used). Fixed bug thatna.rm=was ignored. Modified so that rownames are not created until after theNAs are moved or not. Changed the default name invar.name=from “age” to “prvAge” to reduce the highly possible chance that theremight be another variable in the data frame named “age.”
growthModelSim(): Deleted. Moved to FSATeachpackage.
growthRadPlot(): Modified. Slightly changed thexlab= argument default.
leslieSim(): Deleted. Moved to FSATeachpackage.
lwModelSim(): Deleted. Moved to FSATeachpackage.
mrClosed1Sim(): Deleted. Moved to FSATeachpackage.
simAgeBias(): Deleted. Moved to FSATeachpackage.
simAges(): Deleted. Moved to FSATeachpackage.
simLenFromAge(): Deleted. Moved to FSATeachpackage.
simLenSelect(): Deleted. Moved to FSATeachpackage.
srSim(): Deleted. Moved to FSATeachpackage.
summary.ageComp(): Modified. Added azero.print= argument with a default of a single dash foruse when printing an age-agreement table. Addedflip.table=argument to allow ease of comparison between the age-agreement table andthe age-bias plot. Changed so that ifwhat="prec.stats" thesummary percentages by absolute differences is also printed. Modifiedthe print of several data frames (forwhat="bias","symmetry", and"prec.stats") so that rownames (i.e., row numbers) are not printed.
sumTable(): Added. Brought over fromNCStats.
vbFuns(): Modified. Changed all non-simple growthmodel functions with checks for the number of model parameters anddefinitions sent. Changed the Francis parameterization model to takeonly two values oft= (i.e., the intermediate value is notused and, thus, is not required); thus, thet2= argumentwas removed.
vbGen(): Modified. Fixed bug that developed whenchanges togReshap() were made. Added warning suppressionrelated to “calculations” on NAs.
vbStarts(): Modified. Changed tFrancis argument touse only two ages. Changed the default formeth.EV= to“poly”. Removed jittering and added a transparency to the plot. Removedthe box around the legend and moved the legend to the “bottomright.”Fixed a typo in the plot heading.
wsValidate(): Modified. Replaced use ofcast() withaggregate().
Date: Oct13
Changed R dependency to >3.0.0 (because gplots package hasthat dependency).
Added importFrom forcast(),is.formula(), andmelt() in reshapepackage.
capHistConvert(): Corrected the formatting of thedocumentation.
capHistSum(): Corrected the documentation. Added asecond example.
dietOverlap(): Modified. Changed the “Morista”option to “Morisita” to be consistent with the correct spelling of thename.
Garvey1: Added. Used in examples inks2d1().
Garvey4a: Added. Used in examples inks2d1().
histStack(): Deleted, moved to plotrix package.Arguments were changed there.
ks2d(): Deleted, changed toks2d2().
ks2d1(): Added.
ks2d2(): Added, wasks2d().
ks2dp(): Deleted, changed toks2d2p().
ks2d2p(): Added, wasks2dp().
mrClosed(): Modified. Changed all “messages” usingcat() to usingmessage() so that they can besuppressed withsuppressMessage() ormessage=FALSE in knitr. See “One comment on messages” athttp://yihui.name/knitr/demo/output/.
pkolgomorov1x(): Added to FSAinternals (fromks2d()).
plotH(): Deleted, moved to plotrix package.
quad_dens(): Added to FSAinternals (fromks2d()).
Date: Jun13
Corrected all pointers to fishR vignettes (because of newwebpage).
Removed importFrom color.scale from plotrix because of changes todischarge() andwetPerim().
removed importFrom %nin% from Hmisc. See multiple changes becauseof this below.
.onAttach(): Added, was.onLoad().
.onLoad(): Deleted, now.onAttach().
addMargins(): Deleted, moved back toNCStats.
addSigLetters(): Deleted, moved back toNCStats.
addZeroCatch(): Modified. Changed the loopingstructure for finding the sampling event and species combinations thatneed zeros. This should speed things up substantially. Also, modified toallow noidvar= variables. Finally, the returned data framehas the variables (columns) in the same order as the original data frame(rather than having the order modified).
ageComp(): Modified some of the code to adjust forname changes inSummarize(). Modified to use a formulanotation.
ageKey(): Modified to using a formula notation. Thisremoved thedl=,cl=, andca=arguments. Made minor adjustments to the help pages (in addition tochanges related to the argument modifications).
bcFuns(): Removed use of %nin%.
capFirst(): Modified so that ONLY the first letteris capitalized (previous version would de-capitalize the first letter inthe second word but leave the rest of the letters capitalized).
capHistSum(): Modified to correct an error thatoccurred when computing the Method B table when a capture historyoccurred only once or not at all.
chapmanRobson(): Modified by adding the Hoenig etal. (1983) bias correction formula for the estimate of Z as the defaultoption.
confint.nlsBoot(): Removed use of %nin%.
discharge(): Deleted, moved to NCStats (to reduceoverhead here).
histStack(): Modified by adding a formula method(histStack.formula()) which required adding a defaultmethod (histStack.default()).
htest.nlsBoot(): Removed use of %nin%.
lencat(): Modified by changing to using a formulanotation and adata= argument. This means that thedf= andcl= arguments are no longer used. Inaddition, the warning about fish larger than the larger category hasbeen turned off. The method to handle this was not changed, the warningwas just turned off.
lencatOLD(): Added as an internal file totemporarily allow me not to change all functions that were affected bythe changes tolencat(). The functions that required thisareemp() andwsValidate().
lenFreqExpand(): Modified to deal withlencat() change.
limnoProfilePlot(): Deleted, moved to NCStats (toreduce overhead here).
mrClosed(): Removed use of %nin%.
plotBinResp(): Modified by movingmakeColor() internal function to FSA-internals so that itcan also be used bytictactoe().
predict.bootCase(): Added.
PSSLit: added from RSDLit. Added from Ogle andWinfield (2009) for ruffe, Bonvechio et al. (2010) for Suwannee bass,and from Phelps and Willis (2013) for several “carp” species.
PSSLitCheck(): Added this internal file. ModifiedpssVal(),pssCalc(), andpssPlot() accordingly.
psdVal(): Deprecated, will delete, becamepssVal().
pssCalc(): Added, wasrsdCalc().Modified to using a formula notation and adata=argument.
pssDataPrep(): Added.
pssPlot(): Added, wasrsdPlot().Modified to using a formula notation and adata= argument,to handle the default change forincl.zero= inpssVal(), and changed the defaultpss.lty=settings.
pssVal(): Added, wasrsdVal(). Changedincl.zero=TRUE to be the default.
recodeSpecies(): Added.
rsdCalc(): Deleted, becamepssCalc().
rsdLit(): Deleted, becamePSSLit().
rsdPlot(): Delted, becamepssPlot().
rsdVal(): Deprecated, will delete, becamepssVal().
sigLetters(): Deleted,cld() inmultcomp has been modified to deprecate this.
simLenSelect(): Modified to deal withlencat() change.
Summarize(): Modified by calculating the percentageof zeros for quantitative data. Also changed the names in the returnedvectors or data frames to reduce capitalization, spaces, andpunctuation. Removed use of %nin%.
tictactoe(): Modified by changing the way the “inbalance” regions are depicted. This resulted in the addition of thebal.trans= argument.
tictactoeAdd(): Modified by changing PSD labels toPSS.
vbStarts(): Removed use of %nin%.
wetPerim(): Deleted, moved to NCStats (to reduceoverhead here).
wrAdd(): Modified. Major modifications to accountfor changes toWSlit. Added thecapFirst()check for species name. ChangedsubNA= toremove.submin= to make consistent withwrDataPrep().
wrDataPrep(): Added.
wrVal(): Deleted.
WSlit: Modified. Completely rebuilt so thatquadratic equation using EmP could be incorporated into the database.Also added equations for several new species.
WSLitCheck(): Added this internal file. ModifiedwsVal(),wrVal(), andwrAdd()accordingly.
wsVal(): Modified. A major modification to accountfor the major changes toWSLit.
wsValidate(): Removed use of %nin%.
Date: Jan13
added special “fishR Vignette” sections with links to severalhelp files.
binCI(): Modified so that result is a matrix ratherthan sometimes (when only one set of CIs were computed) being avector.
catchCurve(): Modified by minorly adjusting howconfint() produced CIs. Also, disallowed usingparm= when the user asks for CIs for the linear model. Thisallowed usingmatch.arg() as a check for appropriateparm= values. Modified the examples in the help fileslightly and added an example of using the weighted regressionmethod.
plot.catchCurve(): Modified so that log(catch)values less than 0 will be plotted.
chapmanRobson(): Modified by minorly adjusting howconfint() produced CIs.
depletion(): Modified by minorly adjusting howconfint() produced CIs and added acat()tedoutput to thesummary() method describing whether theLeslie or DeLury method was used.
growthModelSim(): Modified. Streamlined the code(removed some “junk” and unneeded redundancies). Also corrected theerror where the fourth parameter in the vbSchnute and Schnute were notobserved to be connected to sliders. Also changed a few default slidervalues. Also set the minimum age (t.min) to 0 and cannot beover-ridden (was previously controlled by a slider). Thus, removed theminimum age slider. Also moved the maximum age slider to the bottom ofthe sliders. Changed the calls for the Gompertz models to use the fullname (i.e.,Gompertz1 instead ofGomp1).Changed model= to type= to be more consistent with other similarfunctions.
hyperCI(): Modified so that the result is a matrixrather than a vector.
leslieSim(): Modified by addinghscale=1.5 to resampling version.
mrClosed(): Modified to handle the changes inhyperCI() andbinCI(). Also modified messagesinsummary() andconfint() (tostreamline).
predict.nlsBoot(): Added.
removal(): Modified by minorly adjusting howconfint() produced CIs and removed acat()tedline from the summary() method. Also, modified the “catches” for the 2-and 3-pass specific methods to disallow using anything but a vector witheither 2 or 3 samples.
srCobWeb(): Added.
srSim(): Modified. Streamlined the code (lots of“junk” code that did not do anything and some unneeded redundancies)were removed. Modified the default values and the axis labels so as toproduce generally more interesting simulations. Modified the graphic toshow the peak recruitment level and, if a Ricker model, the stock sizewhere the peak recruitment occurs. Changed a long series of if-else forthe different parametrizations to aswitch(). Changedmodel= totype= to be consistent with othersrXXX functions.
vbFuns(): Modified slightly the messages ifmsg=TRUE. Added a message for the Wang2 model and correctedan error for the Somers2 model.
view(): Modified to remove the ability to print to awindow (use method built into RStudio instead). Also generalized to usefor both a matrix or a data.frame (eliminates some warningmessages).
Date: 21Dec12
Added ImportFrom forslider() andgslider() from the relax package. Deleted the ImportFromforslider() from theTeachingDemos package.These functions were the same but it was being deprecated fromTeachingDemos.
General: addedcall.=FALSE to severalstop()s andwarning()s.
General: replacedpaste() inside of severalcat()s.
ageKey(): Modified to usematch.arg()with type=.
binCI(): Modified to useciLabel() (seebelow).
catchCurveSim(): Modified in a variety of ways.First, moved the ability to control the recruitment age and thesteadiness of the Z and N*changes to function arguments rather than slider controls. Second, streamlined the internal functions. Third, converted to usinggslider()instead ofslider()`.Fourth, made minor cosmetic changes to the plot. Fifth, I edited thehelp file somewhat.
checkStartcatW(): Added this internalfunction.
ciLabel(): Added this internal function.
cohortSim(): Modified in a variety of ways. First,streamlined the internal functions so that the plot can be createdindividually. Second, converted to usinggslider() insteadofslider().
confint.bootCase(): Modified to useciLabel().
confint.catchCurve(): Modified to useciLabel().
confint.chapmanRobson(): Modified to useciLabel().
confint.depletion(): Modified to useciLabel().
confint.mrClosed(): Modified to useciLabel().
confint.nlsBoot(): Modified to useciLabel().
confint.removal(): Modified to useciLabel().
dietOverlap(): Added.
fsa.news(), FSA.news(): Deleted, renamed tofsaNews() andFSANews().
fsaNews(), FSANews(): Renamed versions offsa.news() andFSA.news().
FSAsims(): Deleted. Rarely used and not supported innon-windows and RStudio.
growthModelSim(): Modified in a variety of ways.First, streamlined the internal functions so that the plot can becreated individually. Second, converted to usinggslider()instead ofslider().
hyperCI(): Modified to useciLabel().
lencat(): Modified by using the newcheckStartcatW() internal function.
lenFreqExpand(): Modified by adding show.summary=argument and using the newcheckStartcatW() internalfunction.
leslieSim(): Modified in a variety of ways. First,combined the code fromleslieSim2() into this function.This required deleting the use.rand= argument and adding atype= argument. In addition, theleslieRandRun() internal function was moved to this Rdocument (from FSA-internals). Second, the functions were allstreamlined with new internal functions. Third, converted to usinggslider() instead ofslider(). Fourth, mademinor cosmetic changes to each plot (including adding a small legend tothe oldleslieSim2()).
leslieSim2(): Deleted. SeeleslieSim().
lwModelSim(): Modified in a variety of ways. First,streamlined the internal functions so that the plot can be createdindividually (will ultimately allow use of the manipulate package).Second, converted to usinggslider() instead ofslider().
mrClosed(): Modified by removingnumdigs= argument.
mrClosed1Sim(): Modified in a variety of ways.First, streamlined the internal functions so that the plot can becreated individually. Second, converted to usinggslider()instead ofslider().
poiCI(): Modified to useciLabel().
rlp(): Modified by replacingdecimals=argument with digits= argument.
srSim(): Modified in a variety of ways. First,streamlined the internal functions so that the plot can be createdindividually. Second, converted to usinggslider() insteadofslider(). Third, removed the S3methods.
Summarize(): Modified by removingnumdigs argument.
TroutDietSL: Added for use withdietOverlap().
vbStarts(): Modified by including a catch fornegative starting values of K or starting values of Linf that are 50%smaller or larger than the observed maximum length in the dataset.
Date: 1Dec12
Changed R dependency to >2.14.0.
Added a ImportsFrom for knitr (purl() in swvCode() addedbelow).
Moved gdata to an ImportsFrom from Suggests. Needed for nobs() inci.fp1() which is used in fitPlot.ONEWAY and drop.levels() used in theexample in RuffeWs.
Deleted dependency on FSAdata.
Added the following data files from FSAdata: BluegillJL,BluegillLM, BrookTroutTH, CodNorwegian, CutthroatAL, Ecoli, KS2D_NR,LMBassWs, Mirex, PikeNY, PikeNYPartial1, RSDlit, RuffeWs, SMBassLS,SMBassWB, SpotVA1, StripedBass1, VBGMlit, WalleyeGerowLW, WR79, WSlit.This allowed removing the depending on FSAdata.
.onLoad(): modified slightly with a suggestion fromSimon Urbanek to eliminate a warning on RCMD Check (that showed up onrforge.net, but not locally).
addMargins(): added from NCStats.
addSigLetters(): added from NCStats. Modified toallow the use of a result from sigLetters() in lets=.
`bootCase methods: added from NCStats. Needed to import bootCasefrom car.
hist.formula(): added from NCStats.
lencat(): made some warning messages moreconcise.
lsmean(): deleted. Functionality is replaced bylsmeans() in the lsmeans package.
psdVal(), rsdCalc(), rsdVal(), rsdPlot(): added codeto eliminate “global bindings” note when performing RCMD Check.Solutions came from Adrian Alexa’s response to this question:https://groups.google.com/forum/?fromgroups=#!topic/cambridge-r-user-group/c7vf8o3QwDo
sigLetters(): added. Hopefully this will eventuallybe replaced by changed to cld() in the multcomp package.
Summarize(): made some warning messages moreconcise.
swvCounts(), swvPvalue(), swvANOVA(), swvGLHT(), swvREG(), swvHtest(), swvCode(), swvFinish():added from miscOgle.
view(): added from NCStats.
wsVal(), wrAdd(): added code to eliminate “globalbindings” note when performing RCMD Check. Solutions came from AdrianAlexa’s response to this question:https://groups.google.com/forum/?fromgroups=#!topic/cambridge-r-user-group/c7vf8o3QwDo
Date: 25Nov12
Switched to using the Project mode in RStudio.
Switched to using semantic versioning for the version number(which means that the hyphen before the last number has been replaced bya period).
Switched to using roxygen to construct help files.
Set some values =NULL to eliminate “global bindings” warning whenperforming the RCMD check – emp(), pos2adj(), psdVal(), simAgeBias(),srStarts(), vbStarts(), and wsValidate(). This did not work for theWSlit and RSDlit problems in rsdCalc(), rsdPlot(), rsdVal() andwsVal().
Added an importFrom for lineplot.CI()) and se() from sciplot(used in fitPlot()).
Added an importFrom for outlierTest() from car for use inresidPlot().
Deleted importFrom for alias() from stats (was used inwlgm()).
Deleted importFrom for boxcox() from MASS (was used inwlgm()).
Deleted depends on NCStats (moved many functions here (see below)and then made NCStats depend on FSA).
Deleted suggests for exactRankTests (apparently no longerneeded).
Moved nlstools from depends to suggests (only needed for anexample in confint.nlsboot that is not run because of the timerequired).
Moved plotrix from depends to importsFrom for color.scale(),plotCI(), and thigmophobe().
Moved quantreg from depends to importsFrom for rq() (used inemp()).
Attempted to move reshape to importsFrom but had problems withmissing is.formula() from plyr.
ageComp(): modified class name to “ageComp” from“AgeComp”.
capFirst(): added.
catchCurve(): modified class name to “catchCurve”from “CC”.
chapmanRobson(): modified class name to“chapmanRobson” from “CR”.
coefPlot(): deleted (Weisberg’s LGM is nowout-dated).
depletion(): modifed class name to “depletion” from“Depletion”.
discharge(): modified class name to “discharge” from“StrmDschrg”.
emp(): modified class names to “empXX” from“EMPxx”.
fitPlot(): added from NCStats.
FroeseWs(): modified class name to “FroeseWs” from“FROESE”.
histStack(): added.
hoCoef(): added from NCStats.
ks2d(): modified class name to “ks2d” from“ks2d”.
ks2dp(): modified class name to “ks2dp” from“ks2dp”.
legendHelp(): added (internal) fromNCStats.
mrClosed(): modified by moving the two internalfunctions – mrc1() and mrc2() – to inside mrClosed, moving the twointernal functions – ci.mrc1() and ci.mrc2() – to insideconfint.mrClosed(), removed the “MRC1” and “MRC2” classes, changed the“MRC” class name to “mrClosed”, and added a catch to plot.mrClosed() tostop if the user tries to plot with single-census data.
mrOpen(): modified class name to “mrOpen” from“MRO”.
plotBinResp(): added from NCStats.
plotH(): minor modifications to the Rdfile.
pos2adj(): modified the labels for the positions byincluding full names for all directions, eliminating the single lettersfor the four main directions, but also leaving the four “off” directionsas abbreviations.
psdVal(), rsdVal(), rsdCalc(), rsdPlot(): modifiedto use capFirst so that the user does not need to focus oncapitalization of the species name.
removal(): modified class name to “removal” from“Removal”.
residPlot(): added from NCStats.
rlp(): modified class name to “rlp” from“RLP”.
Summarize(): added from NCStats.
typeoflm(): added from NCStats.
wetPerim(): modified class name to “wetPerim” from“WetPerim”.
wlgm(): deleted (Weisberg’s LGM is nowout-dated).
wsValidate(): modified the classnames to “willis”from “WILLIS” and “empq” from “EMPQ”. Also made minor modificationbecause of class name change in FroeseWs()
ycPlot(): deleted (Weisberg’s LGM is nowout-dated).
Date: 8-Nov-12
Moved several functions from NCStats that are used quite oftenfor fisheries analyses. Ultimately, I want to remove the dependency toNCStats.
Deleted an importFrom for gtools, created an internal odd()instead.
Added an importFrom for gplots, to get rich.colors() forchooseColors().
Added an importFrom and removed an import for NCStats.
ageComp(): modified to use internal odd(), ratherthan odd() imported from gtools.
binCI(): moved from NCStats.
chooseColors(): copied from NCStats (i.e., samefunction still in NCStats).
confint.nlsBoot(): moved from NCStats.
fact2num(): moved from NCStats.
htest(): copied from NCStats (i.e., same functionstill in NCStats).
htest.nlsBOot(): moved from NCStats.
hyperCI(): moved from NCStats.
ks2d(): moved from NCStats.
ks2dp(): moved from NCStats.
ksTest(): moved from NCStats.
lagratio(): moved from NCStats.
`lsmean(), and related internals: moved from NCStats.
mrClosed(): modified so as not to depend on ci.t()from NCStats.
plotH(): moved from NCStats.
poiCI(): moved from NCStats.
popSizesPlot(): moved from NCStats.
pos2adj(): moved from NCStats.
rcumsum(): moved from NCStats.
rsdPlot(): modified to handle situations wheresubstock fish are not present in the data. Thanks to Max Wolter forpointing out this issue.
Subset(): copied from NCStats (i.e., same functionstill in NCStats).
Date: 21Jun12
Switched to compiling under R version 2.14.1 (64-bit).
Changed license specification from “GPL version 2 or newer” to“GPL (>= 2)” to avoid warning on check.
Added a suggestion for gdata to fix warning with capHistConver.rd(see below).
`capHistConvert.rd: Modified the examples to not use“gdata::combine” by adding a “require(gdata)” in the examples andsuggesting gdata in the description file.
fishR(): Added.
simAgeBias(): changed width to widths in layout() toavoid warning on check.
simLenSelectM(): changed width to widths in layout()to avoid warning on check.
.onLoad(): Modified. Moved the startup message intopackageStartupMessage() in hopes of eliminating the warning whenchecking the package.catchCurveSim(): Modified. Changed max.age= to 15 (from10). Slightly changed the labels related to ‘Z Steady’ and ‘N*`Steady’.chapmanRobson(): Modified. Corrected a bug for when theages2use= argument contains ages that are not found in the data. Thanksto Eric Berglund for finding this bug.psdVal(): Modified. As described for rsdVal().rsdCalc(): Added.rsdPlot(): Modified. Modified to reflect changes inrsdVal().rsdVal(): Modified. Removed the metric= and mm=arguments in favor of a new argument, units=, where the user chooses theunits as a string. This streamlines, for example, the selection of mm.The modifications also resulted in mm being the default. Also, removedthe appended units names from the names attribute – i.e., “stock” ratherthan “stock.mm” or “stock.in”.wrAdd(): Added.wrVal(): Modified. As described for wsVal().wsVal(): Modified. Removed the justcoef= argument.Added the ab= and comment= arguments. Also, removed the appended unitsnames from the names attribute – i.e., “int” rather than “int.E” or“int.mm”.Date: 1Oct11
Switched to compiling under R version 2.13.1 (32-bit).
Removed importFroms that were required for updateFSA().
Removed splines package from imports list (not needed).
capHistConvert(): Modified. Modifications to handlechanges to capHistSum().
capHistSum(): Modified. Changed the returned liststructure. First, caphist.sum is now caphist. Second, if only twosamples are given, then only caphist and sum, where sum is a data frameof the required summaries for the Petersen method, are returned. If morethan two samples are given, then caphist, sum, methodB.top, andmethodB.bot are returned. Note that there is n* `longer an item labeledas schnabel.sum returned.
mrClosed(): Modified. Modifications to handle thechanges to capHistSum(). Also modified so that if only two samples weresummarized in a CapHist object and that object is supplied as the firstargument to mrClosed() then the Petersen method will find the data itneeds from the CapHist object.
rsdPlot(): Modified. Modified calls to min() andmax() to include na.rm=TRUE. This fixes bug related to vectors withmissing values.
updateFSA(): Removed.
vbFuns(): Modified. Added ‘Somers2’ option to type=argument.
vbStarts(): Modified. Added ‘Somers2’ option totype= argument.
Date: 19Aug11
Modified description file to show my e-mail address.
Addedcnvrt.coords() as an ImportFrom TeachingDemos.Needed forsimAgeBias() andsimLenSelectM().
ageKey(): Modified. Length categories in the lengthsample, if none are provided in len.breaks=, are constructed from thelength categories present in the age-length key rather than guessing ata starting value and width and creating evenly spaced categories. Thisshould fix the bug that occurred when an age-length key was originallycreated with even length categories but the key is so sparse that thelength categories with actual data are uneven. Also, changed the errorcatching so that the routine is stopped if a length in the length sampleis smaller than the smallest length category in the age length key butwill only elicit a warning if the largest length is greater than thelargest length category in the age-length key.
chapmanRobson(): Modified. Changed to have a.default and .formula method.
chapmanRobson.default(): Added.
chapmanRobson.formula(): Added.
FSAsims(): Modified. Corrected calls togrowthModelSim() for von Bertalanffy models.
growthModelSim(): Modified. Changed from modeling“size” to modeling “length” (or “weight” for just “vbTypicalW” and“vbOriginalW”). Changes required adding two new model options –“vbTypicalW” and “vbOriginalW” – for modeling weights and leaving all ofthe original model options as models for length. Added a max.wt=argument for use when modeling weights. Removed “vbBevertonHolt” as amodel option because it is covered by “vbTypical” and was not actuallyimplemented. Changed order of models so that “vbTypical” rather than“vbOriginal” is the default model used. Made slight cosmetic changes toslider bar options (e.g., “to” became “t_0”). Made changes and somecorrections to the .Rd file.
rsdPlot(): Added. Still needs more thoroughproofing.
simAgeBias(): Added.
simAges(): Added.
simApplyAgeBias(): Added.
simLenFromAge(): Added.
simLenSelectM(): Added.
simLenSelectP(): Added.
vbComp(): Modified. Streamlined the code. Changedthe t= argument to ages= to remove any possible confusion with t().Removed the option to model over ages provided in the (previous) t=argument. Instead the ages= argument can be used to represent themaximum age to model to. The ages= argument can be a vector such thateach simulation can have a different set of ages over which the model isevaluated. This allows for more realistinc modeling.
Date: 15Jun11
Switched to compiling under R version 2.13.0.
vbFuns(): Modified. Modified Wang’s formulas to befor length increments. Added a length increments version to Faben’smethod (“Fabens2”).
Date: 18Apr11
Updated citation file.
Added importFrom for tools and utils packages.
ageKey(): Modified. Added a len.breaks= argument sothat an age-length key with variable widths for the length categoriescan be used. Added an example to the Rd file to illustrate theuse.
confint.MRC(): Modified. Replaced numdigs= argumentwith digits= argument. Retained numdigs= for backwardscompatability.
`lwPredsComp.Rd: Modified. Replaced use of lgrep() with grepl()because of change in NCStats.
removal(): Modified. Changed order of items printedin the returned list. In addition, if the type is one of Zippin,CarleStrub, or Seber3 then a set of intermediate values (k, T, and X) isalso included in the returned list. The first change is cosmetic, thesecond change was made to help with some troubleshooting. Added anargument to allow choosing the method of contructing SE for theCarleStrub method. Created an internal function for computing the ZippinSE method to allow easier use with the other methods. The help file waschanged to make note of the non-estimable SE when No=T in the CarleStrubmethod under certain circumstances. These changes result in a differentSE being reported if the CarleStrub method is used and CS.se=“Zippin”(the default) is used. The “old” results can be obtained by usingCS.se=“Alternative”. I have yet to find a solid references for thisSE.
summary.MRC(): Modified. Replaced numdigs= argumentwith digits= argument. Retained numdigs= for backwardscompatability.
tictactoeAdd(): Modified. Added capability oflabeling points.
updateFSA(): Added. Had to add an importFrom fromthe tools package.
vbFuns(): Modified. Added Wang and Wang2functions.
Date: 3Mar11
moved to compling under 2.12.1 (32-bit)
changed dependency to >2.11.1
ageComp(): modified dramatically. Primarily addedthe ability to test for bias by comparing the mean of the y-structure tothe value of the x-structure with t-tests adjusted for multiplecomparisons. Modified the code to allow this to happen more efficientlyand to output results in the plot() and summary() methods. Also modifiedthe plot() method so that the default is to just show the confidenceintervals rather than showing the CIs and the range of the data (useshow.rng=TRUE to see the old plot). Also changed the CI colors so thatsignificant differences are shown in red (default) and non-significantdifferences are shown in blue (default) (set both col.err= andcol.err.sig= to the same color to get the old plot).
lencat(): modified so that vname=NULL is thedefault. This will default to using “LCat” as the variable name (as inthe previous version). However, modified the way the vname is appendedto the new data frame so that if vname already exists in the data framea new name will be used (vname plus some number).
removal(): added just.ests= argument and changed theests part of the returned value to be a vector rather than a matrix.Both changes allowed for better use of lapply() for computing theremoval estimates on more than one group. Changed from an error to awarning for situations where the method could not compute populationestimates (i.e., because the population was not depleted). In addition,NAs are returned in situations where population estimates can not bemade. An example of computing the removal estimate for more than onegroup was added to the .rd file. Thanks to Jon Bolland for asking thequestion that motivated these changes.
catchCurve(): Modified by adding a formula method. Thisrequired moving the original code into a default method and changing theage= argument to x=.lenFreqExpand(): Modified by adding the additional=argument (which required modifying the total= argument and adding anerror check for the situation where the total fish to assign lengths isnot greater than the number of fish in the measured subsample)..onLoad(): modified. Changed to include version numberof loaded version.vbFuns(): Modified by adding simple= argument. Added a‘Somers’ seasonal growth oscillations model and ‘Fabens’ model fortag-recapture data. Also added, but did not check, a ‘Laslett’ ‘doublevon Bertalanffy’ model.vbStarts(): Modified by setting a catch to return asingle root for st0 or sL0 if the polynomial root found a double root.Thanks to Giacom* `Tavecchia for identifying this error. Added a‘Somers’ seasonal growth oscillations model.bcFuns(): Added. Still needs to be thoroughlyproofed.FSAsims(): Modified to reflect srSim() change describedbelow.listSpecies(): Moved internal function out of beingwithin RSDval() and WSval() and then added an argument for the dataframe containing the species names. The hope was that this would correctthe “n* `visible binding” warnings when performing RCMD check but it didnot.srModels(): Renamed from stockRecruitModels() to bemore consistent with the rest of the stock-recruitment functions.srSim(): Renamed from stockRecruitSim() to be moreconsistent with the rest of the stock-recruitment functions.vbDataGen(): Modified use of minAge argument – will nowalways back-calculate to age-1 but minAge denotes the minimumage-at-capture that will be modeled. Deleted use of cfAge variable incode.vbModels(): Added.stockRecruitModels() rather thanstock.recruit.models().ageComp(): renamed from age.comp().ageKey(): renamed from age.key().capHistConvert(): renamed from caphist.convert().capHistSum(): renames from caphist.sum().catchCurve(): renamed from catch.curve().catchCurveSim(): renamed from cc.sim().chapmanRobson(): renamed from chapman.robson().coefPlot(): renamed from coefplot().cohortSim(): renamed from cohort.sim().emp(): modified for name changes in NCStats.FroeseWs(): modified for name changes in NCStats.FSASims(): modified by updating to new names ofsimulation functions.gConvert(): renamed from g.convert().gReshape(): renamed from g.reshape().growthRadPlot(): renamed from growrad.plot().lenFreqExpand(): renamed from len.freq.expand().leslieRandRun(): renamed from leslie.rand.run(). Thisis an internal function.leslieSim(): renamed from leslie.sim().leslieSim2(): renamed from leslie.sim2().limnoProfilePlot(): renamed fromlimnoprofile.plot().lwModelSim(): renamed from lwmodel.sim().lwPredsComp(): renamed from comp.lwpreds().mrClosed(): renamed from mr.closed(). Modified for namechanges in NCStats.mrClosed1Sim(): renamed from mr.closed1.sim().mrOpen(): renamed from mr.open().psdVal(): renamed from PSDval().rcumsum(): deleted. Moved to NCStats package.rpl(): modified for name changes in NCStats.rsdVal(): renamed from RSDval().tictactoeAdd(): renamed from tictactoe.add(). Modifiedfor name changes in NCStats.vbComp(): renamed from vb.comp().wetPerim(): renamed from wetperim().wlgm(): modified for name changes in NCStats.wrVal(): renamed from WRval().wsVal(): renamed from WSval().wsValidate(): renamed from validateWs(). Also modifiedfor name changes in NCStats.ycPlot(): renamed from ycplot().Date: 20Aug10
moved to compiling under 2.11.1.
started changing my naming convention to “camel” type – e.g.,stockRecruitModels() rather thanstock.recruit.models(). In this version, I am only changingthe functions that I am working on. I will change the rest in the nextversion.
added an importFrom fornlme asgroupedData() was needed forvbDataGen().
age.key(): Modified the way that the lengthcategories in the age-length key is determined. Previously I just usedthe rownames found in the key, but this allows lengths with a row of allNA or zeros to be considered as a length found in the age length key.Now the row sums are found and the sums with NaN or 0 are removed. Inaddition, I added a warning message if the row sums d* `not sum to1.
caphist.convert(): Modified such that an “RMark”type can be output. 0 chapmanPlot()`: Added.
growmodel.sim(): Deleted. Changed togrowthModelSim(). See below. 0 growthModelSim()`: Added. Initially arenaming of growmodel.sim(). However, the model names were changed to bemore consistent with other functions and a method for the Mooij etal. paramaterization was added.
growthModels(): Added.
srFuns(): Added.
srStarts(): Added.
stock.recruit(): Deleted, along with all relatedgenerics.
stock.recruit.sim(): Deleted. Changed tostockRecruitSim(). See below.
stockRecruitModels(): Added.
stockRecruitSim(): Initially a renaming ofstock.recruit.sim. However, added a “formula” method which requiredadding generic and default methods. Changed the order of the S and Rarguments. Re-ordered, modified, and added models in accordance with thevignette. Updated the Rd file to reflect these changes and made a veryslight modification to the examples and added an example to illustratethe use of the formula. Found decent default values forsimulations.
stockRecruitSim.default(): Added. Seeabove.
stockRecruitSim.formula(): Added. Seeabove.
vbDataGen(): Added.
vbFuns(): Added.
vbStarts(): Added.
walfordPlot(): Added.
growmodel.sim(): added an option to fit the “original”von Bertalanffy function. Also added more “mis-spelling” options to theother model names.Date: 17Dec09
moved to compiling under 2.10.1.
`added a dependency to tcltk so that simulators would workproperly upon load of FSA.
age.comp(): added xlim= and ylim= arguments so usercan control x- and y-axis limits if desired. Changed code so that betterchoices for axis limits are selected automatically if xlim and ylim areboth NULL. Changed code so that the “extra” vertical space added whenshow.n=TRUE AND ylim is NLL is 10 percent of the y-axis range ratherthan just an extra one unit. Allowed function to work better withxaxt=“n” and yaxt=“n” in case the user wants to create their own axes.Removed a par() setting within the plotting function. Thanks to David A.Hewitt for pointing out the deficiences with the axis labeling.
age.key(): corrected how the age column is labeledif the column did not already exist in the data frame. Was alsoindirectly modified with lencat() modification. Also modified to stopand warn the user if the length sample has fish whose lengths are notpresent in the length-age key (previously there was a warning, but thenultimately there was an error).
catch.curve(): added a use.weights= argument toallow using weights in the catch curve regression as proposed by Maceinaand Bettoli (1998).
chapman.robson(): changed S result from a proportionto a percentage (i.e., * `100).
comp.lwpreds(): added center.value= argument toallow centering in the regressions. Added an example to the .rdfile.
fsa.news(): added to show user the NEWSfile.
FSA-package(): updated.
growmodel.sim(): added the ability to use a formulaand data= argument. Made the model argument not have a default value.Corrected an error when both x and y were NULL. Corrected errors in theRd file. Thanks to Jacek Szlakowski for pointing out theseproblems.
lencat(): modified so that an “extra” last lengthcategory (with no fish in it) was not included when as.fact=TRUE anddrop.levels=FALSE is used. This should correct the “problem” of an extraall-NA row in the age-length keys.
tictactoe.add(): added to the namespace export list.Changed order of items listed in the ci.type= argument to match that ofbin.ci() from NCStats.
.FirstLib(): removed (changed to .onLoad() because ofnamespace).age.comp(): modified by removing reference to “valid.n”(which is no longer used because of changes to Summarize() in NCStats).Modified to only attempt to compute SE if n>1 and st. dev >0.comp.lwpreds(): added. Exported in namespace.g.convert(): fixed major error in how the functionconverted increments to radii.growrad.plot(): added. Exported in namespace.mr.closed(): modified by changing library(Rcapture) torequire(Rcapture) in help page.plot.EMPQ(): modified by changing objectvalidateWs(): converted sign.slope variable in theWillis method to a factor to deal with situations where all results werepositive or negative.age.comp(): streamlined code (put bias and differenceplots in same function, used grconvertY for show.n, used plotCI forrange intervals, caught and corrected CI problems when n=1 or SD=0). N*`functionality difference, just improved code.growmodel.sim(): modified by determining some of theslider values from the data when x= and y= arguments are not null. Thismakes the graph more useful for determining starting values in nls()modeling.Date: 6Dec08
added a dependency to quantreg (forrq() inemp()).
added CITATION file.
age.comp(): modified the plot() function by adding a‘difference’ method to the what= argument. This allows creation of an“age-difference” plot as used in Muir et al. (2008).
caphist.convert(): modified by adding an event.ord=argument to allow the user to identify the order of the event names whenconverting from a capture-by-event type. This is particulary useful ifthe event names are things like ‘first’, ‘second’, ‘third’, ‘fourth’because R orders these alphabetically which adversely effects thecorrectness of the capture histories.
compute.Ws(): moved this internal function out ofvalidateWs() to be a stand-alone internal function. This allows usagewith animation routines.
discharge(), summary.StrmDschrg(), plot.StrmDschrg():added.
emp(): added probs= argument result to return list.Corrected ylab in plotting methods. Added a predict method. Added amethod= argument that allows choice of using linear regression orquantile regression to find the Ws equation. Modified objects in thereturn list (added rawdata component) and added the back-transformed Wqvalue in regdata (for comparison with Gerow’s Excel tool). Changed codefor finding summarized dataframes inside the function by using cast()from the reshape package – this resulted in a 3x reduction insystem.time().
mr.closed(): modified by correcting error in themultiple census methods if M, n, and m (but not R) were supplied. Alsocorrected an error in the examples.
rlp(): added probs= argument result to return list.Corrected ylab in plotting methods. Added a predict method.
PSDval(),RSDval(): added a check for missing speciesname so that the user can just type PSDval() to get the list of possiblespecies names. Also added a check to see if RSDlit was alreadyloaded.
validateWs(): added probs= argument result to returnlist. Corrected ylab in plotting methods. Added a predict method.Modified EmpQ() internal function to use predict() methods for emp andrlp objects. Streamlined some of the code by including a compute.Ws()internal function and using the update() function. Changed code forfinding summarized dataframes inside the function by using cast() fromthe reshape package – this resulted in a 1.5x reduction insystem.time().
wetperim(),summary.WetPerim(),plot.WetPerim():added.
wlgm(): major changes included moving some internalfunctions outside of wlgm(), adding the ability to use the data=argument, and adding the ability to fit weighted regressions on thesummary statistics. Other minor changes were also made. Updated the .Rdfile.
WSval(),WRval(): added a check for missing speciesname so that the user can just type WSval() to get the list of possiblespecies names. Also added a check to see if WSlit was alreadyloaded.
.First.lib: Addedadd.zerocatch(): added this function to add zeros tocatch records where a species of fish was not caught.limnoprofile.plot(): added this function to simplifyconstructing plots of depth versus limnological measure with the depthdecreasing from top to bottom.rlp(): changed default qtype= to 8 (from 7). Added aprobs= argument to allow other than 75th percentile calculations.emp(): updated the help page. Added a logical for ifp.n.low does not exist when using cutoff.tail. Renamed items in theoutput list. Added a table of number of individuals per length categoryto output list. Added a probs= argument to allow other than 75thpercentile calculations. Added its own generics – rather than relying onthe rlp() generics.FroeseWs(): added this function, and its generics, toperform the standard weight equation calculation as proposed by Froese(2006).validateWs(): added this function, and its generics, toperform the Willis and EmpQ methods for assessing length bias in thestandard weight equations. Added a probs= argument to allow other than75th percentile calculations. Added a mean= argument to allow use ofmeans rather than quantiles. Modified to accept an object of classFROESE.Date: 15May08
Moved to RForge.net.
changed to R2.7.0.
added a dependency toRcapture (for the example incaphist.convert()).
anova.RLP(): added this function to produce theanova table for the standard weight equation.
caphist.convert(): added this function convertbetween various capture history formats(FSA,event,MARK,Rcapture).
emp(): added this function, and its generics, toperform Gerow’s EmP method for obtaining a standard weightequation.
fit.plot.RLP(): added this function.
plot.RLP(): modified so that color palette with agradient rather than only a solid color can be used for the populations.In addition, added order.pop= argument that will order the populationsfrom smallest to largest predicted with in the first length interval.When used with the color gradients this will make it easier to see whichpopulations cross over other populations.
rlp(): modified function so that the user can chooseto use any-mm length intervals rather than having 10-mm hardwired.Modified output in list somewhat to more closely match the output ofemp().
lencat(): Modified by adding an as.fact= argument thatallows the user to decide if the resulting variable should be returnedas a factor variable or not. The default is set to return as a factorvariable. This allows tables of the new variable to include zeros forlevels of the new variable that contain no individuals. This makes someRSD/PSD (and likely age-length key) calculations simpler. Also added adrop.levels= argument to allow the user to drop unused levels if sodesired.mr.closed(): This function is a combination of the oldmr.closed1() and mr.closed2(). It also allows the user to compute singlecensus estimates with multiple sub-groups in the data (i.e., length- orage-classes). The function also allows the user to compute an overallpopulation esitmate of multiple sub-groups are present and an overall SEif the incl.SE=TRUE is used. It also corrects the SE computationsimplemented in version 0.0-9. This change caused the construction of ourinternal functions – mrc1, mrc2, ci.mrc1, and ci.mrc2.mr.closed1(): removed this function. Use mr.closed()instead.mr.closed2(): removed this function. Use mr.closed()instead.PSDval(): Added mm= argument so that metric result canbe returned in mm. Also added incl.zero= argument that will include azer* `value in the first position in the vector; this is useful for whencreating PSD/RSD values.rcumsum(): Added this function (from NCStats).RSDval(): See PSDval description.age.comp(): Corrected SE calculation used to constructthe CIs. Changed the CI plotting routine to use plotCI in plotrixpackage – this puts lines rather than points on the ends of the CIs.Added a check for computing SDs and CIs for when n=1 or when allmeasurements are the same. This reduces (eliminates?) the number ofwarnings that are given.catch.curve(): added na.rm=TRUE arguments to min() andmax() in plot.CC(). Changed type= argument so that “params” is thedefault rather than “lm”. This makes it more consistent with othersimulation programs.cc.sim(): Put in catch for situations where the CV forNo and Z were equal to zero. Originally, the program attempted tocomputed a random number from a normal distribution with a standarddeviation of zero. This corrected the problem of n* `lines appearingunless the CVs were greater than zero.ch.convert(): STARTED A FUNCTION to CONVERT B/W CAPTUREHISTORY FORMATS. N* `RD FILE YET.depletion(): Moved type= argument to third position.Will more easily allow type=“Leslie” as a default (i.e., can just entercatch and effort vector.FSAsims(): Added a “mark-recap” menu section. Added achapman 1-sample M-R item to the menu.leslie.sim(): corrected the conditionals on p.surv andr.prop so that it asks if any not the first value is less than 1. Thiscorrects the problem of R returning a large number of warnings.leslie.sim2(): corrected the call to depletion() sothat the type of model (“Leslie”) was the third rather than the firstargument. This was caused by a change in the usage of depletion inprevious version changes.mr.closed1(): Modified output list to include anestimate of the variance as described in Ricker(1975).summary.MRC1(): Modified output so that (1) the giveninformation is a little easier to read, (2) the population estimate isreturned in a matrix, (3) the SE from Ricker(1975) can be included inthe outputm, and (4) a label can be placed on row for the matrix output.The purpose of these changes was to allow the SE to be computed and toallow future functions to more flexibly use the output.Date: unknown
changed some to in RD files. Changed most hard-wired quotes to orin RD files. Changed some text-based equations to more latex-basedequations in or markups. This fixed the Latex compilation problems thatI was having when using RCMD check.
age.comp(): Removed single-letter values from thewhat= argument. Will rely on partial matching.
age.key(): Changed default name for new column withages from “Age” to “age”. Added example.
coefplot.WLGM(): Changed to use plotCI() from theplotrix package. This removed the for loop that I had programmed. Thisalso added the sfrac= and gap= arguments. Updated the RD.
depletion(): Removed single-letter and lower-casevalues from the type= argument. Will rely on partial matching.
lencat(): Changed d argument to df.
lenfreq.expand(): Changed d argument to df.
mr.open(): Added match.arg functionality to theci.type and phi.type arguments.
plot.RLP(): Added “object <- x” to allow x to beused inside the curve() function without confusion.
removal(): Removed abbreviated values from the type=argument. Will rely on partial matching.
rlp(): Added examples from Murphy etal. (1990)
stock.recruit(): Removed abbreviated values from thetype= argument – will rely on partial matching. Changed sumtype argumentto what.
stock.recruit.sim(): Changed model argument to typeand added param argument (to make compatible with stock.recruit). MovedR and S arguments to beginning of argument string (more compatible withstock.recruit). STILL NEED to ADD SECOND RICKER MODEL.
vb.comp(): Changed d argument to df.
wlgm.RD(): Added example code. Added somedetails.
Date: unknown
changed to compiling under R 2.6.1.
added FSA.R file that loads the required librarys.
now depends onMASS package because of the creationof theboxcox.WLGM() function and on theplotrix package for elements ofycplot().
add.radcap(): Created this function to add theradius-at-capture to a one-fish-per-line data frame ofincrements.
age.comp(): Added amatch.arg() callfor the what argument.
age.key(): Corrected=T or=F to=TRUE or=FALSE.
cc.sim(): Corrected the use ofz.paramwith correct use ofZ.param.
coefplot(): A new generic function for plottingcoefficients from a Weisberg Linear Growth Model analysis.
g.convert(): Changed arguments from data andmeasure.var to df and in.var. Includedmatch.arg() for thetype argument. Moved type argument as it now has a default. Added thein.pre argument that allows the user to identify all input variables bya common prefix rather than having to list them out in in.var. Added theout.pre argument that allows the user to control the prefix for thenewly created variables in the output data frame. Updated helpfile.
g.reshape(): Changed arguments from data and prefixto df and in.pre. Deleted the measure.var argument. Moved new in.preargument forward and na.rm argument backward in the argument list. Usedin.pre to identify the measure.var variables to send to the meltfunction. If id.var is left blank (and in.pre is not) then id.var is theremaining variables not identified by in.pre. The val.name argument wasset equal to in.pre as the default.
leslie.sim(): Corrected call to oldleslie() function with a correct call todepletion() function withtype="Leslie".
leslie.sim2(): Corrected two calls to oldleslie() function with correct calls todepletion() function withtype="Leslie".
leslie.rand.run(): Moved R Documentation alias toFSA-internal.RD.
mr.closed2(): Forced the function to use thelowess() function in the stats rather than the gplotspackage (which is loaded fromNCStats). Also changed theloess.f argument to f and added the iter argument forsending tolowess().
confint.MRO(): Put in a logical catch when printingthe confidence intervals because ifci.type="Manly" thenCIs for B are not computed.
summary.MRO(): Put in a logical catch when printingthe estimates because ifci.type="Manly" then SEs are notcomputed.
plot.RLP(): Corrected=T or=F to=TRUE or=FALSE.
wlgm(): Created a method with a number of generics(alias, anova, boxcox, coef, coefplot, confint, ycplot) for performingthe Weisberg Linear Growth Model.
ycplot(): A new generic function for creating ayear-class plot for the Weisberg Linear Growth Model analysis.
agebias.plot(): deleted and replaced with agecomp andplot.AgeComp functions.agesunflower.plot(): deleted and replaced with agecompand plot.AgeComp functions.agecomp(): a new function that, along with itsextractor functions, combines all of the functionality of the oldage.tests(),age.symmetry(),agebias.plot(), andagesunflower.plot().Allows for a more seamless comparison of ageing reads.plot.AgeComp(): an extractor function for objects savedfrom theagecomp() function. This replaces the oldagebias.plot() andagesunflower.plot()functions.summary.Agecomp(): an extractor function for objectssaved from theagecomp() function. This replaces the oldage.tests() andage.symmetry() functions.age.symmetry(): deleted and replaced withagecomp() andsummary.AgeComp()functions.age.tests(): deleted and replaced withagecomp() andsummary.AgeComp()functions.cc.sim(): modified graphic to (1) include assumptionviolation labels on top of the graph and (2) label y-axis with“log(Catch)” rather than “ln(Catch)”.delury(): deleted and replaced withdepletion() function. See notes fordepletion() function.depletion(): created a new function that performs theLeslie or Delury method as determined by a user-defined argument totype. This function replaces the oldleslie() anddelury() functions. All extractor functions for the class“LeslieDelury” have now been changed to class “Depletion”.plot.Depletion(): correct xlab so that it defaults to“Cumulative Effort” for the Delury method.leslie(): deleted and replaced with depletion function.See notes for depletion function.leslie.sim(): modified graphic to include assumptionviolation labels on top of the graph.mr.open(): modifiedest.N() internalfunction so that N is set equal to n if N<n. In other words, if thesample size at time i is larger than the estimated population size attime i then the estimated population size is set equal to the observedsample size. This corrects the problem of theN.secalculation attempting to take the square root of a negative numbercausing themr.open() function to shut down.pass.removal(): changed name to removal.removal(): new name for old pass.removal function.rlp(): new name for old (upper-case) RLP.RLP(): changed name to (lower-case) rlp.