A variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website < http://derekogle.com/fishR/>.
stop()s to STOP()s and all warning()s to WARN(). This modified nearly all functions.paste()s that used sep="" to paste0()s.sep=""s from message()s.Hmisc from, but added epitools to, imports. Removed all links to Hmisc to remove CRAN check warnings..onAttach(): Modified. Streamlined package startup message.addZeroCatch(): Modified. Added more "catches" for bad data types or arguments.ageBias(): Modified. Changed all message()s in summary() to cat()s.agePrecision(): Modified. Changed all message()s in summary() to cat()s.binCI(): Modified. Changed from using binconf() in Hmisc to binom.exact(), binom.wilson(), and binom.approx() from epitools (this removes dependency on Hmisc which was causing problems). Allowed multiple types to be chosen. Now only accepts whole numbers for x and n. Added verbose= so that the result can be include all of the information return from the epitools functions. Added a catch for bad conf.levels. Added some more tests.catchCurve(): Modified. Made sure that coef() method returned a vector (addresses #19). Modified confint() code for efficiency, made sure matrix is always returned.chapmanRobson(): Modified. Made sure that coef() method returned a vector (addresses #19). Modified confint() code for efficiency, made sure matrix is always returned.chooseColors(): Modified. Added rev= for returned reverse ordered (from default) colors.depletion(): Modified. Changed coef() method so that it returned a named vector (addresses #19). Modified confint() code for efficiency, made sure matrix is always returned. Removed type= to match other functions (incorporated that functionality into parm=). Removed digits= to match other functions.expandLenFreq(): Modified. Changed all message()s to cat()s. Removed "names" from printed items for a cleaner look.fitPlot(): Modified. Added cex.leg= and box.lty.leg= to IVR plots.hist.formula(): Modified. Fixed a bug with adding the horizontal line at 0 when the user uses plot=FALSE, which occurs with hist.bootCase().hyperCI(): Modified. Now only accepts whole numbers for M, n, or m. Added catch for bad conf.levels and multiple values of M, n, or m.iAddLoessLine(): Modified. Changed used of iMakeColor() to col2rgbt().iGetDecimals(): Modified. Added warning for situations where x will be presented in exponential notation. Also returned a decimal of zero in this situation. Helps with a bug in hist.formula().iHndlCols2use(): Deleted. Changed to iHndlCols2UseIgnore().iHndlCols2UseIgnore(): Added. Previously was iHndlCols2use(). Completely reworked to catch more problems including having both positive and negative indices (fixes #24) and choosing variable names that don't exist (fixes #25).iHndlFormula(): Modified. Added code to deal with a formula that is a single "variable" sent in an array. Addresses #21 for the simple situation of single "variable."iHndlMultWhat(): Modified. Added type= to allow use with message() or cat().iPlotExists(): Added. Helps with bug fix in hist.formula().is.wholenumber(): Added. Needed for changes to binCI(), hyperCI(), and poiCI().kCounts(): Modified. Fixed bug with capitalize= and zero. Streamlined code. Added tests.metaM(): Modified. Fixed bug with the way messages were output when multiple methods were provided and justM=FALSE. Added more tests.mrClosed(): Modified. Added poi.type= to handle new choices for Poisson confidence interals. Added some checks for non-vector uses of M= and R= (partially addresses #22). Fixed bug in how inputs for subgroups were output from summary() when verbose=TRUE.mrOpen(): Modified. Changed all message()s in summary() to cat()s. Fixed bug where returned value from summary() was not a data.frame if only one parameter was selected.nlsTracePlot(): Added.plotBinResp(): Modified. Changed used of iMakeColor() to col2rgbt().poiCI(): Modified. Completely rebuilt to use the functions from epitools. Now only accepts whole numbers for x.predict.bootCase(): Modified. Modified so that situations where other than values of the dependent variable are in the dots argument (as would occur if making predictions for the Francis parameterization of the VBGF).predict.nlsBoot(): Modified. See note for predict.bootCase().psdCalc(): Modified. Fixed bug in output if more than two additional lengths were supplied.removal(): Modified. Added a check and a returned error if method="Schnute" and the last of three catches is zero (addresses #26) Fixed bug related to sending catches in a one column data.frame. Fixed bug related to selecting only one parm= in confint(). Added tests.residPlot(): Modified. Added cex.leg= and box.lty.leg= to IVR plots. Removed extra spaces in main title if main="MODEL". Added some tests.tictactoe(): Modified. Changed used of iMakeColor() to col2rgbt().vbFuns(): Modified. Added Ogle to list of parameterizations. Changed order of L0 and K parameters in returned function when param="Original".vbStarts(): Modified. Added the methLinf= argument that allows the user to choose if Linf is estimated from a Walford plot (methLinf="Walford"; the default and old functionality), as the mean of fish in a certain number of old ages (methLinf="oldAge"), or as the mean of a certain number of the longest fish (methLinf="longFish"). The number of ages or long fish is given in num4Linf=. Added methods for type="Ogle".alkIndivAge(): Modified. Added na.rm=TRUE to the checks on the minimum and maximum length data.catchCurve(): Modified. Removed type= and blended that functionality into parm= for methods. Made parm= consistent across methods.chapmanRobson(): Modified. Added axis.age= argument that allows the user to choose which type of x-axis is displayed (see examples; this addresses #20) Also modified code that adds the axes so that they should "look better" in more instances. Added na.rm=TRUE to y-range calculation for the plot method. Added a coef() method. Added a parm= argument to the confint() and summary() 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). The parm= now properly handles negative values. Streamlined plotting results. Added tests.depletion(): Modified. Checked for bad conf.level= in confint() method.GompertzFuns(): Modified. Fixed bug related to selecting QuinnDeriso3.htest.nlsBoot(),htest.bootCase(). Modified. The b0 now defaults to 0. Matrix of results now include the parameter as the rowname. Modified the internals of how the data are handled. Added tests.iAddLoessLine(): Modified. Suppressed warnings related to the loess line predictions.mrClosed(): Modified. Checked for bad conf.level= in confint() method.mrOpen(): Modified. Checked for bad conf.level= in confint() method.predict.nlsBoot(), predict.bootCase(). Modified. The ... argument can now contain a vector of values such that predictions can be made for multiple values of the independent variable. Modified the output matrix to handle this modification. Removed MARGIN as it will always be 1 for nlsBoot and bootCase objects. Added checks for FUN=, conf.level=, and digits=. Added tests.removal(): Modified. Checked for bad conf.level= in confint() method. Changed internal functions from using a loop to using apply(). Changed internal functions from using log() and choose() to using lchoose().Summarize(): Modified. Added nvalid= and percZero to only print the nvalid and percZero result if they are "interesting" (i.e., different than n or zero, respectively) by default (may be manually over-ridden). Modified tests.vbStarts(): Modified. Added na.rm=TRUE to checking of Linf values.ageComparison(): Modified. Removed an internal call to fact2num() because of changes to Summarize() below. Should not impact user experience.diags(): Added.gompertzFuns(): Modified. Fixed some spacing around the message when msg=TRUE.logisticFuns(): Modified. Fixed some spacing around the message when msg=TRUE.Summarize(): Modified. Removed all uses where the main variable was a factor (this functionality was largely unneeded and unused, was inelegant and difficult to maintain). Removed pass-through to summary. Removed warnings about the RHS variables being converted to factors. Columns for "levels" of the RHS variables are now returned in their original model (i.e., if the variable was numeric in the original data.frame it is now numeric in the data.frame returned from this function) -- this should reduce need for using fact2num() when using the results of this function for variables that were originally numeric. Added more examples and tests for the numeric data.growthFunShow(): Modified. Added Pauly et al. (1992) seasonal cessation function. Added case= for use with Schnute model.vbFuns(): Modified. Added Pauly et al. (1992) seasonal cessation function. Slightly modified messages for "Typical" and "Original" parameterizations.vbStarts(): Modified. Added fixed= so that the user can define some of the starting values. Added Pauly et al. (1992) seasonal cessation function. Added tests for fixed=.relax from Suggests. See srStarts() and vbStarts() notes below. This addresses #17.gdata from Imports. See filterD() and Subset() notes below. This addresses #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(), and vbStarts().ageKey(): Removed. Deprecated since 0.4.24. Use alkIndivAge().ageKeyPlot(): Removed. Deprecated since 0.4.24. Use alkPlot().bcFuns(): Modified. Changed msg= to verbose=.capHistSum(): Added tests.filterD(): Modified. Changed to use droplevels() from base rather than drop.levels() from gdata. Added except=.fitPlot(): Modified. Changed the way colors, plotting characters, and line types were handled for most of the models. Should make their use more flexible. Fixed errors that occurred in IVR models when the factor variable preceded the covariate in the model (fixes #18). Started to add tests for error and warning messages.GompertzFuns(): Modified. Changed type= to param=.GompertzModels(): Removed. Replaced with growthFunShow().iGetDecimals(): Modified. Fixed a bug that occured when an integer was provided.lenFreqExpand(): Removed. Deprecated since 0.4.32. Use expandLenFreq().logisticFuns(): Modified. Changed type= to param=.LogisticModels(): Removed. Replaced with growthFunShow().residPlot(): Modified. Changed the way colors, plotting characters, and line types were handled for most of the models. Should make their use more flexible. Now matches coding in fitPlot(). Fixed bug with main titling, but now asks user to decide if they want the model call or not. Started to add tests for error and warning messages.RichardsFuns(): Modified. Changed type= to param=.RichardsModels(): Removed. Replaced with growthFunShow().growthFunShow(): Added.srFunShow(): Added.srModels(): Removed. Replaced with srFunShow().srStarts(): Modified. Removed dynamicPlot=TRUE option. Moved it to FSAsim package. Modified plot when plot=TRUE by adding "STARTING VALUES" to title and moving starting values to within the plot. Added cex.main= and col.main=.Subset(): MOdified. Changed to use droplevels() from base rather than drop.levels() from gdata.vbFuns(): Modified. Changed type= to param=.vbModels(): Removed. Replaced with growthFunShow().vbStarts(): Modified. Removed dynamicPlot=TRUE option. Moved it to FSAsim package. Added param= to match other vbXXX() (works as does type=). Modified plot when plot=TRUE by adding "STARTING VALUES" to title and moving starting values to within the plot. Added and col.main=. Made warnings and error tests more explicit.sumTable() in ALK related tests and Summarize() in age comparisons tests. Prompted by forthcoming changes to testthat.News.md from .Rbuildignore (apparently now supported by CRAN).alkPlot(): Modified. Changed so that xlim= and ylim= would work when type="area" and type="bar". This fixes #10 (Thanks to Joseph Feldhaus).hist.formula(): Modified. Added the breaks= argument (mostly a pass-through) and the w= argument that allows the user to just set the width of the bins without having to set each break value. This should complete #15.iCheckStartCatW(): Modified. Now use iGetDecimals() to extract the number of decimals in startcat and w.iCheckStartcat(): Added.iCheckW(): Added.iGetDecimals(): Added.lencat(): Modified. Changed order of startcat= and breaks=. Slight modifications to documentation.psdAdd(): Modified. Minor changes to documentation.psdPlot(): Modified. Fixed bug related to PSD values being printed when only PSD-Q existed (needed to add drop0Est=FALSE to the psdCalc() call; this fixes #13). Made the histogram bars flush with the x-axis rather than hovering above it (added yaxis="i" to hist(); this fixes #12). Minor changes to documentation.psdVal(): Modified. Minor changes to documentation.purl2(): Modified. Added delHeader= 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 the documentation.
agePrecision(): Modified. Fixed bug related to computations of percent agreement when NA values were present. There was an inconsistency between when what="precision" and what="difference" was used in summary(). The bug fix now properly divides by the "valid sample size" for what="precision". This fixes #9 (Thanks to Joseph Feldhaus). Now returns validn. Modifications to the documentation.
histFromSum(): Added. Addresses #4.
metaM(): Modified. Changed order of methods in methods=. Minor corrections and additions to documentation.
mrClosed(): Modified. Now sends warning if an NA appears in the first position of m, the first position of M, or the last position of R and converts these to 0 so that the procedure can continue. Each of these positions is ignored in the calculations. This fixes #8 (Thanks to Joe Mrnak).
reproInfo(): Modified. Made changes to iGetAllDependencis() based on forthcoming changes to package.dependencies() (as notified by CRAN).
vbStarts(): Modified. Fixed bug when dynamicPlot=TRUE was used.
requireNamespaces() from some functions and moved those packages from Suggests to Imports so that those functions would work better with other packages. The only requireNamespaces() that remain are related to functions that require the relax package (so tcltk is not installed until needed) and knitr, dunn.test, and lmtest as these are unlikedly to be used by other packages and will keep the packages that are loaded with FSA to a minimum. Packages moved from Suggests to Depends are Hmisc (for use in binCI), gdata (for use in filterD() and Subset()), dplyr (for use in filterD()), sciplot (for use in fitPlot()), car (for use in residPlot()), and gplots (for use with colors).addZeroCatch(): Modified tests (to reduce warnings that were not part of tests).geomean(): Added.geosd(): Added.lencat(): Modified. Fixed a bug related to using a tbl_df object.sumTable(): Modified tests (but with dimnames()).data-raw to CSV files.\href{}{} and \url{} codes to websites that I don't control. The addresses are now "naked" such that the user will need to copy-and-paste them into a browser to view the web page rather than clicking on a hyper link. Hopefully this will eliminate problems 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 in dunnTest() (see below).agePrecision(): Modified. Changed combn() to utils::combn() and sd() to utils::sd() (within an apply()).catchCurve(): Modified. Changed na.exclude() to stats::na.exclude().dunnTest(): Modified. Changed to more throughly use dunn.test() from dunn.test. Added the two.sided= argument to dunnTest() and dunn.test.results= to print.dunnTest().expandLenFreq(): Modified. Changed runif() to stats::runif().extraSS(): Modified. Changed anova() to stats::anova() in an lapply().fishR(): Modified. Changed browseURL() to utils::browseURL().fsaNews(): Modified. Changed browseURL() to utils::browseURL().headtail(): Modified. Changed head() to utils::head() and tail() to utils::tail().hist.bootCase(): Modified. Changed hist() to hist.formula().iAgeBiasPlot(): Modified. Changed grconvertY() to graphics::grconvertY().iALKMean.QD(): Modified. Changed var() to stats::var() (within sumTable()).iBubblesAdd(): Modified. Changed rgb() to grdevices::rgb().iChkComplexModel(): Modified. Changed df.residual() to stats::df.residual().iCIboot(): Modified. Changed hist() to hist.formula().iEvent2Indiv(): Modified. Changed unstack() to utils::unstack().iGetAllDependencies(): Modified. Changed installed.packages() to utils::installed.packages().iHistResids(): Modified. Removed graphics::hist() and changed to hist.formula().iHndlFormula(): Modified. Changed terms() to stats::terms().iHndlResidType(): Modified. Changed rstandard() to stats::rstandard() and rstudent() to stats::rstudent().iHtestBoot(): Modified. Removed graphics::hist() and changed to hist.formula().iMakeColor(): Modified. Changed rgb() to grdevices::rgb().iMakeModelHeading(): Modified. Changed formula() to stats::formula() (within an lapply()).iMoran(): Modified. Changed optimize() to grdevices::optimize().iProcessSessionInfo(): Modified. Changed sessioninfo() to utils::sessioninfo().iSchnute(): Modified. Changed optimize() to grdevices::optimize().iTypeoflm(): Modified. Changed formula() to stats::formula().plot.AgeBias(): Modified. Changed rgb() to grdevices::rgb().plot.CatchCurve(): Modified. Changed predict() to stats::predict().print.extraTest(): Modified. Changed printCoefMat() to stats::printCoefMat().psdAdd(): Modified. Changed data() to utils::data().psdVal(): Modified. Changed data() to utils::data().reproInfo(): Modified. Changed graphics.off() to grdevices::graphics.off().removal(): Modified. Removed some of the examples from the help page to reduce the elapsed time for CRAN.vbStarts(): Modified. Changed rgb() to grdevices::rgb().wrAdd(): Modified. Changed data() to utils::data().wsVal(): Modified. Changed data() to utils::data().test_AgeLengthKey: Modified. Altered tests that had used == to use expect_equivalent() which uses all.equal() with check.attributes=FALSE.test_PSD: Modified. Altered tests that had used == to use expect_equivalent() which uses all.equal() with check.attributes=FALSE..txt files to .Rda files. Original .txt files are in the data-raw directory which was added to .Rbuildignore.purl2(): Added newname= to allow the output file to have a name other than the same as the intput file.reproInfo(): Added markdown to the out= types.README.md and DESCRIPTION for new websites.fishR(): Modified. Updated for the new websites.ageComparison(): Modified. Changed what="McNemars" and what="Bowkers" to what="McNemar" and what="Bowker". Fixed bug if all ages are NA.catchCurve(): Modified. Fixed bug related to NA values in the catch vector.chapmanRobson(): Modified. Fixed bug related to NA values in the catch vector.validn(): Modified. Fixed bug related to when a 1-dimensional numeric vector was not recognized as a vector.ageBias(): Modified. Changed default for pch.mean= to 95 (from 175). If what= has only one item, then results will now be invisibly returned so that results can be saved to an object.agePrecision(): Modified. Added trunc.diff=. If what= has only one item, then results will now be invisibly returned so that results can be saved to an object.mapvalues(): Modified. Corrected to export properly.removal(): Modified. Minor edits to labels if verbose=TRUE. Added some more tests.vbStarts(): Modified. Made yngAge the default for meth0=. Fixed bug that occured when meth0='yngAge' and sample sizes at all ages were 1.Summarize(): Modified. Converted to using iHndlFormula(). Changed output for quantitative data (validn is always returned, NAs is never returned). Changed output for two-way factor data (not returned as a character from formatC()). Removed ... from code in several places as it was buggy and not used. Added more checks and modified check messages. Fixed bug from when a 1-d matrix of characters was sent. Added tests.sumTable(): Modified. Converted to using iHndlFormula(). Added tests.addRadCap(): Modified. Streamlined code. Changed default in.pre= to NULL (from inc). Added some tests for returned data.BluegillLM: Removed. Moved to FSAdata.gConvert(): Modified. Streamlined code. Changed type= to out.type=. Changed default in.pre= and in.var= to NULL (from missing). Changed code to handle changes in in.pre= and in.var=. Added some tests for returned data.gReshape(): Removed. Moved to FSAmisc.binCI(): Modified. Check forHmisc with requireNamespaces() before processing body of function. This allowed moving Hmisc into Suggests declarations rather than Imports.chooseColors(): Modified. Check forgplots with requireNamespaces() before processing body of function. This allowed moving gplots into Suggests declarations rather than Imports.filterD(): Modified. Check for dplyr and gdata with requireNamespaces() before processing body of function. This allowed moving dplyr and gdata into Suggests declarations rather than Imports.fitPlot(): Modified. Check forsciplot with requireNamespaces() before adding intervals tot he plot. This allowed moving sciplot into Suggests declarations rather than Imports.lrt(): Modified. Check forlmtest with requireNamespaces() before processing body of function. This allowed moving lmtest into Suggests declarations rather than Imports.mapvalues(): Modified. Changed so that it is a direct importFrom and export without creating a help file in FSA.purl2(): Modified. Check forknitr with requireNamespaces() before processing body of function. This allowed moving knitr into Suggests declarations rather than Imports.residPlot(): Modified. Check forcar with requireNamespaces() before highlighting outliers on the plot. This allowed moving sciplot into Suggests declarations rather than Imports.srStarts(): Modified. Check forrelax with requireNamespaces() before constructing the dynamic plot. This allowed moving relax into Suggests declarations rather than Imports.Subset(): Modified. Check forgdata with requireNamespaces() before processing body of function. This allowed moving gdata into Suggests declarations rather than Imports.vbStarts(): Modified. Check forrelax with requireNamespaces() before constructing the dynamic plot. This allowed moving relax into Suggests declarations rather than Imports.importFrom() directives and went to hard-wiring to packages with ::. Added imports() directives for stats, graphics, tools, and grDevices. Removed imports() directive for multcomp().vbStarts(): Modified. Changed default methos for methEV=. Changed order of starting values for type="Mooij" in order to match that from vbFuns(). This also fixed a bug when dynamicPlot=TRUE was used with type="Mooij". Added tests to determine if parameter order is the same between vbStarts() and vbFuns() for all parameterizations.ageBias(): Modified. Corrected bug with labeling of x-axis on age-bias plot when ref.lab= and nref.lab= were not given by the user. Changed default for nYpos= from 1.1 to 1.03. Added cex.n= to allow control of the size of the sample size labels.agePrecision(): Modified. Changed what="detail" to what="details". Note that what="detail" still works.dunnTest(): Modified. Added a note to the help file about the use of complete cases. Suggested from Paule Bodson-Clermont.vbFuns(): Modified. Added Original and Typical to the type= options. This allows both a capitalized and uncapitalized version for these two parameterizations.vbModels(): Modified. Changed order of Original and Typical (Typical is now shown first). Fixed in error in how the equation for the Weisberg parameterization was displayed.vbStarts(): Modified. Added cex.main= as an argument and defaulted to 0.75. Added raw=TRUE to poly() which is used when meth0="poly". Added Original and Typical to the type= options. This allows both a capitalized and uncapitalized version for these two parameterizations.ageBias(): Modified. Moved into a single file with agePrecision(). Cleaned-up help file. No change in behavior.agePrecision(): Modified. Moved into a single file with ageBias(). Cleaned-up help file. No change in behavior.alkAgeDist(): Modified. Moved into a single file with alkMeanVar(). Cleaned-up help file. Added some error/warning tests. No change in behavior.alkIndivAge(): Modified. Clean-up help file. Added a stronger test for type="SR" method. No change in behavior.alkMeanVar(): Modified. Moved into a single file with alkAgeDist(). Cleaned-up help file. No change in behavior.alkPlot(): Cleaned-up help file and tests. No change in behavior.confint.bootCase(): Modified. Created a common internal function for use with confint.nlsBoot(). Added the ability to plot histograms with confidence intervals superimposed (similar to what was in confint.nlsBoot()).confint.nlsBoot(): Modified. Created a common internal function for use with confint.bootCase().GompertzFuns(): Moved into growthModels file. Did not change behavior.gompertzModels(): Modified. Changed type= to family= to avoid confusion in the help file with type= in gompertzFuns(). Moved into growthModels file.growthRadPlot(): Deleted. Moved to FSAmisc package.hist.formula(): Modified. Fixed so that ymax= also sets the y-axis limit when only one histogram is made (it was previously ignored).htest.bootCase(): Modified. Created a common internal function for use with htest.nlsBoot().htest.nlsBoot(): Modified. Created a common internal function for use with htest.bootCase().iHndlFormula(): Modified. Added na.action=NULL to model.frame() so that NA values will not be omitted.logisticFuns(): Moved into growthModels file. Did not change behavior.logisticModels(): Modified. Changed type= to family= to avoid confusion in the help file with type= in logisticFuns(). Moved into growthModels file.predict.bootCase(): Modified. Created a common internal function for use with predict.nlsBoot().predict.nlsBoot(): Modified. Created a common internal function for use with predict.bootCase().psdAdd(): Modified. Fixed bug that never tested if all lengths were NA. Required change to iHndlFormula.RichardsFuns(): Moved into growthModels file. Changed param= to type= to better match similar functions.RichardsModels(): Moved into growthModels file. Did not change behavior.Schnute(): Moved into growthModels file. Changed param= to type= to better match similar functions.SchnuteModels(): Moved into growthModels file. Did not change behavior.vbFuns(): Moved into growthModels file. Did not change behavior.vbModels(): Modified. Changed type= to family= to avoid confusion in the help file with type= in vbFuns(). Moved into growthModels file.hist.formula(): Modified. Rebuilt to use iHndlFormula(). Modified how xlab= is used (result is the same). Added some tests.ksTest(): Modified. Rebuilt to use iHndlFormula(). Added some tests for messages and to make sure results matched ks.test().alkPrep(): Deleted. Moved to FSAmisc package (on GitHub).changesPos(): Deleted. Moved to FSAmisc package (on GitHub).chapmanPlot(): Deleted. Moved to FSAmisc package (on GitHub).dietOverlap(): Deleted. Moved to FSAmisc package (on GitHub).Garvey1: Deleted. Moved to FSAmisc package (on GitHub).Garvey4a: Deleted. Moved to FSAmisc package (on GitHub).KS2D_NR: Deleted. Moved to FSAmisc package (on GitHub).ks2d1(): Deleted. Moved to FSAmisc package (on GitHub).ks2d1p(): Deleted. Moved to FSAmisc package (on GitHub).ks2d2(): Deleted. Moved to FSAmisc package (on GitHub).ks2d2p(): Deleted. Moved to FSAmisc package (on GitHub).popSizesPlot(): Deleted. Moved to FSAmisc package (on GitHub).posadj(): Deleted. Moved to FSAmisc package (on GitHub).TroutDietSL: Deleted. Moved to FSAmisc package (on GitHub).walfordPlot(): Deleted. Moved to FSAmisc package (on GitHub).alkIndivAge(): Modified. Switched to using iHndlFormula() at the beginning. Added more checks and tests.expandLenFreq(): Modified. Added more checks. Added some tests.wsVal(): Modified. Added more tests.ageBias(): Modified. Fixed bugs related to axes on numbers plot and sunflower plot.filterD(): Modified. Added reorder=FALSE to drop.levels() so that the order of levels is not changed when levels are dropped.residPlot.nlme(): Added.extraSS(): Modified. Added sim.name= to allow for a common typing mistake.logbtcf(): Modified. Slight change to handle a check of lm class.lrt(): Modified. Added sim.name= to allow for a common typing mistake.pcumsum(): Modified. Modified to handle table, matrix, and data.frame classes as long as they are 1-dimensional.rcumsum(): Modified. Modified to handle table, matrix, and data.frame classes as long as they are 1-dimensional.srStarts(): Modified. Corrected some bugs related to checks. Added more tests.addRadCap(): Modified. Modified so that in.pre= string must be at the start of the variable names. Added a check for when the in.pre= string does not exist at the start of any variable names. Added a check for whether all in.var= variables exist. Added some simple tests (need more).bcFuns(): Modified. Removed type=; BCM= can now be either numeric or a string. Allowed string to be in any case (will be converted to the required all upper-case). Corrected some errors for when msg=TRUE. Added some simple tests.gConvert(): Modified. Modified so that in.pre= string must be at the start of the variable names. Added a check for when the in.pre= string does not exist at the start of any variable names. Added some simple tests (need more).gReshape(): Modified. Modified so that in.pre= string must be at the start of the variable names. Added a check for when the in.pre= string does not exist at the start of any variable names. Added some simple tests (need more).gompFuns(): Deleted.gompModels(): Deleted.GompertzFuns(): Added. Replaced gompFuns(). Added type="Troynikov1" and type="Troynikov1".GompertzModels(): Added. Replaced gompModels(). Added cex= and type=.logisticFuns(): Modified. Changed type="Richards" to type="Karkach". Added type=HaddonI.logisticModels(): Modified. Added "Karkach" model. Added cex= and type=.RichardsFuns(): Modified. Added two more parameterizations from Tjorve and Tjorve (2010).schnute(): Deleted.schnuteModels(): Deleteed.Schnute(): Added. Replaced schnute(). Fixed bugs with the way t1= and t3= are handled.SchnuteModels(): Added. Replaced schnuteModels(). Added cex=.vbFuns(): Modified. Added type="Polacheck" which is equivalent to type="Laslett". Added a new reference in the help file.vbModels(): Modified. Added cex= and type=.RichardsFuns(): Added.RichardsModels(): Added.cat() to using message() so that they can be suppressed with suppressMessage() or message=FALSE in knitr. See "One comment on messages" at http://yihui.name/knitr/demo/output/. Specific functions modified are listed below.ageBias(): Modified. Changed all cat() to message()s. Changed so that messages (result headers) are only printed if what= contains more than one item.agePrecision(): Modified. Changed all cat() to message()s. Changed so that messages (result headers) are only printed if what= contains more than one item.bcFuns(): Modified. Changed all cat() to message()s.chapmanRobson(): Modified. Changed all cat() to message()s. Deleted "Estimates with Standard Errors" message.depletion(): Modified. Changed all cat() to message()s.dietOverlap(): Modified. Changed all cat() to message()s. Slightly modified messages.expandLenFreq(): Modified. Changed all cat() to message()s. Fixed bug with one of the messages.ks2d1(): Modified. Rewrote the print() method. This removed a number of cat()s.ks2d1p(): Modified. Rewrote the print() method. This removed a number of cat()s.ks2d2(): Modified. Rewrote the print() method. This removed a number of cat()s.ks2d2p(): Modified. Rewrote the print() method. This removed a number of cat()s.metaM(): Modified. Changed all cat() to message()s.mrOpen(): Modified. Changed all cat() to message()s.removal(): Modified. Changed all cat() to message()s.srFuns(): Modified. Changed all cat() to message()s. Created some tests.extraSS(): Modified. Added more message tests and some calculational tests (compared to anova() results).gompFuns(): Modified. Changed all cat()s to message()s and slightly modified the messages. Fixed minor bugs in some created functions. Created some tests.logisticFuns(): Modified. Changed all cat()s to message()s and slightly modified the messages. Fixed minor bugs in some created functions. Created some tests.lrt(): Modified. Added more message tests and some calculational tests (compared to lrtest() from lmtest package results).vbFuns(): Modified. Changed all cat()s to message()s and slightly modified the messages. Fixed minor bugs in some created functions. Created some tests.extraSS(): Modified. Added sim_names= and com_name= so that simple descriptive names could be given to the model and printed in the heading of the output. Added checks for whether the complex model appears more complex or not. Added tests for warning and error messages.fishR(): Modfiied. Fixed bug with where="news". Added tests.fitPlot(): Modified. Added ability to modify y-axis limits for the nonlinear regression model. Thanks to Gabriela N. for asking for this.hoCoef(): Modified. Changed lmobj= to object=, added degrees-of-freedom to the output matrix, streamlined the code, added some checks, and added some tests.lrt(): Modified. Added sim_names= and com_name= so that simple descriptive names could be given to the model and printed in the heading of the output. Added checks for whether the complex model appears more complex or not. Added tests for warning and error messages.addZeroCatch(): Modified. Deleted extraneous print() statement.lencat(): Modified. Major re-write to make it easier to trouble-shoot. Fixed bug related to empty category on end when as.fact=TRUE and use.names=TRUE. Added more tests.psdCalc(): Modified. Removed extra open-ended category (e.g., PSD-T-) for PSD intervals.importFrom for mapvalues() from plyr.changesPos(): Modified. Added some checks with error messages. Added suite of tests.chooseColors(): Modified. Added some checks with error messages. Added suite of tests.confint.nlsBoot():Modified. Fixed bug if maximum number in parm= was greater than the number of parameters in the model.dunnTest(): Modified. Change class type from DunnTest to dunnTest to eliminate conflict with DunnTest() in DescTools package. Thanks to Sal Mangiafico for pointing out this conflict.fact2num(): Modified. Added some checks with error messages. Added suite of tests.filterD(): Modified. Changed to using drop.levels from gdata rather than droplevels. Added a warning if the resultant data.frame has zero rows (same as in Subset). Added some checks with error messages. Added suite of tests.fitPlot(): Modified. Replaced the use of nobs() from gdata in the internal function iCIfp1() with validn(). This removed one dependency on gdata.headtail(): Modified. Internally remove tbl_df class (from dplyr) if it exists. Added some checks with error messages. Added suite of tests.lagratio(): Modified. Corrected incorrect explanation of differences= in help file. Added recursion= and direction=. Added suite of tests.mapvalues(): Deleted. Deleted the function from FSA but imported it from plyr and then exported it from FSA so that it would be available to fisheries users without having to load plyr.oddeven(): Modified. Added some checks with error messages. Added suite of tests.perc(): Modified. Added ability to use "and equals" or not to the items in dir= (i.e., there are now four items in dir=). Fixed a bug related to using na.rm=FALSE and a "less than" situation. Added some checks with error messages. Added suite of tests.pcumsum(): Modified. Added some checks with error messages. Added suite of tests.rcumsum(): Modified. Added some checks with error messages. Added suite of tests.se(): Modified. Added some checks with error messages. Added suite of tests.Subset(): Modified. Added some checks with error messages. Added suite of tests.validn(): Modified. Added some checks with error messages. Added suite of tests.ageBias(): Modified. Corrected bugs with show.pts=TRUE and "sunflower plot" that came from changes made in version 0.5.1.residPlot(): Modified. Deleted student=. Added resid.type= which allows used of standardized (internally studentized) and (externally) studentized residuals for linear models (along with raw residuals). Added code following nlsResiduals() from nlstools for standardized residuals for nonlinear models.gompFuns(): Added.gompModels(): Added.logisticFuns(): Added.logisticModels(): Added.reproInfo(): Modified. Added the out= argument to allow the output to be straight R or LaTeX. Removed the listFiles= argument. Changed the output to be more succinct. Streamlined the code.vbFuns(): Modified. Fixed a bug with the Laslett model.kCounts(): Added. Was swvCounts().kPvalue(): Added. Was swvPvalue().purl2(): Added. Was swvCode(). Added timestamp= argument for adding a timestamp to the created script.reproInfo(): Added. Was swvFinish().swvANOVA(): Deleted. Moved to NCStats.swvCode(): Deleted. Changed to purl2().swvCounts(): Deleted. Changed to kCounts().swvFinish(): Deleted. Changed to reproInfo().swvGLHT(): Deleted. Moved to NCStats.swvHtest(): Deleted. Moved to NCStats.swvPvalue(): Deleted. Changed to kPvalue().swvREG(): Deleted. Moved to NCStats.fishR(): Modified. Added IFAR as an option. Updated code to be more simple.capHistConvert(): Modified. Added a warning section and an example of problems that can occur if the data are in event format but the event variable contains unused levels as may occur following subsetting. Thanks to Joseph Feldhaus for pointing out this problem.extraSS(): Modified. Changed algorithm to determine if the models were of the same class or not. The modification allows a model to have multiple classes.iHndlCols2Use (Intrnal Function): Modified. Fixed bug with how the columns were selected. Added a suite of tests for this function. This will fix bugs in capHistConvert() and capHistSum(). Thanks to Joseph Feldhaus for pointing out this egregious error.lrt(): Modified. Changed algorithm to determine if the models were of the same class or not. The modification allows a model to have multiple classes.LazyData: true.se(): Added. Removed importFrom of se() from sciplot.plot.capHist(): Modified. Changed default plot look which can now be controlled with pch=, cex.pch=, and lwd=. Modified the two y-axis scales to use plotmath characters.capHistConvert(): Modified. Streamlined code around creating var.lbls. Made event the default value for var.lbls.pre=. Added some checks to var.lbls.pre= if it starts with a number or has too many values. Added cols2use= and modified use of cols2ignore= via iHndlCols2use().capHistSum(): Modified.iHndlCol2use(): Added. Added this internal function to handle cols2use= and cols2ignore= in capHistConvert() and capHistSum().catchCurve(): Modified. Changed how ages2use= was handled so that negative values can be used to exclude some ages. Will also now send an error if a mix of positive and negative ages are sent in ages2use=. Better handled the situation where ages2use= had more ages than the age variable. Checked for non-positive weights if weighted=TRUE and returned a warning and changed the non-positive weights to the minimum of the positive weights.chapmanRobson(): Modified. Changed how ages2use= was handled so that negative values can be used to exclude some ages. Will also now send an error if a mix of positive and negative ages are sent in ages2use=. Better handled the situation where ages2use= had more ages than the age variable.expandCounts(): Modified. Changed so that ``message()''s are printed at the end instead of along the way. This reduces confusion of what appear to be messages of success followed by an error. Thanks to Dan Oele bringing this confusion to my attention.plotBinResp(): Modified. Changed the way the breaks were calculated (uses lencat() now).srFuns(): Modified. Changed function returned when simplify=FALSE so that if the parameters are named that the name is dropped. Thus, when the function is used, the returned result will not be annoyingly named as the first parameter. Added functionality for the "density-independence" model.srStarts(): Modified. Added functionality for the "density-independence" model.vbFuns(): Modified. Changed function returned when simplify=FALSE so that if the parameters are named that the name is dropped. Thus, when the function is used, the returned result will not be annoyingly named as the first parameter.growthModelSim(): Deleted. The simulation functionality was moved to the FSAsims package. The functionality related to finding starting values for the von Bertalanffy modesl was moved to vbStarts().srFuns(): Modified. A complete rebuild to make similar to vbFuns(). Added simple=. Added type='Shepherd' for the Shepherd (1982) three parameter model and type='SailaLorda' for the "Saila-Lorda" three parameter model from Iles (1994). Added tests for error messages.srModels(): Modified. A complete rebuild to make similar to growthModels(). Added "Shepherd" and "Saila-Lorda" models.srSims(): Deleted. The simulation functionality was moved to the FSAsims package. The functionality related to finding starting values was moved to srStarts().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 adding col.mdl=, lwd.mdl=, and lty.mdl=. Moved the dynamic modeling aspects of srSim() into this function and is called with the new argument dynamicPlot=TRUE. Also added minmax.ratio= and delta.prop= for use with the dynamic plots.vbStarts(): Modified. A complete rebuild to streamline and fix some bugs that had not been found. Modified plotting routine, including adding col.mdl=, lwd.mdl=, and lty.mdl=. Also added all of the von Bertalanffy parameterizations in growthModelSim() into this function and is called with the new argument dynamicPlot=TRUE. Added dynamics plots for the "Francis" and "Schnute" parameterizations.psdPlot(): Modified. Fixed bug related to NAs in max.brks variable.ageBias(): Modified. Reversed the order of the formula ... it is now nrefvar~refvar. This more closely matches other R functions where the tilde may be interpreted as the word "by". In other words, the formula now reads as "nonreference variable by reference variable" (i.e., Y by X). Thanks for Richard McBride for the suggestion. Modified the age-bias plot extensively ... added sfrac= and defaulted to 0 to remove ends of the confidence intervals, added cex.mean= to control the size of the symbol for the mean point, added lwd= that will controland set all of the lwd defaults to 1.agePrecision(): Modified. Changed all "CV" results to "ACV".catchCurve(): Modified. Updated the help file regarding zmethod="Smithetal".capFirst(): Modified. Added a check to make sure the inputted object was either a character or factor class. Added code to return the object as the same class of the original object.lencat(): Modified. Added a catch for bad choices of arguments. Added a catch to send a warning if the vector contains all NA values (this happens when lencat() is used within a loop or as part of psdAdd()). Added tests for error and warning messages. Changed how the formula was handled in the formula method.psdAdd(): Modified. Fixed a bug with names when using labels. Added verbose=. Added catches and sent messages if verbose=TRUE for when no Gabelhouse lengths are know for a species and if the lengths for a species are all missing (see note for lencat() above).PSDlit: Modified. Fixed the trophy length for White Bass (from 15 to 18). This solved a bug related to non-unique breaks.expandCounts(): Modified. Made message regarding rows with zero counts more useful. Added missing counts to the catch of zero counts. Made changes to handle more "odd" data entries (see "details" in the help file). Made some tests. Added some tests.psdCalc(): Modified. Corrected "bug" with units=. Also modified warning message when no "stock" fish were present in the data.frame to further note what units= were used (i.e., this problem is likely to happen if the data is inches but the user uses the default units='mm'). Thanks to S. Mather for inspring this fix.dunnTest(): Modified. Corrected "bug" in the order that the groups are subtracted (i.e., they were flipped).catchCurve(): Modified. Changed default for pos.est= to topright. Added cex.pos= (and set default to slightly smaller value).chapmanRobson(): Modified. Changed default for pos.est= to topright. Added cex.pos= (and set default to slightly smaller value).hist.formula(): Modified. Changed use of par() to eliminate modifications to the gridding of plots after the function is complete. Also removed the setting of mar= and mgp= in par().mrOpen(): Modified. Removed pretty printing for summary() and confint() methods. These got in the way of being able to cbind() the results together for a succinct display.residPlot(): Modified. Changed use of par() to eliminate modifications to the gridding of plots after the function is complete..onAttach(): Modified. Centered the message and adjusted for different lengths of version numbers.alkPlot(): Modified. Fixed bug when using add=TRUE with type="bubble".capHistSum(): Modified. Changed to return par() options to what they were before the function was called.catchCurve(): Modified. Changed plot() to default to slighly lighter colored dots and a black line.chapmanRobson(): Modified. Changed plot() to default to slighly lighter colored dots. Changed to return par() options to what they were before the function was called.growthModelSim(): Modified. Changed to return par() options to what they were before the function was called.growthRadPlot(): Modified. Changed to return par() options to what they were before the function was called.hist.formula(): Modified. Changed to return par() options to what they were before the function was called.lwCompPreds(): Modified. Changed quant.lens= to qlens=. Changed default qlens= to have the 5th and 95th percentiles rather than the minimum and maximum values. Added qpens.dec= so that the user could control the number of decimals for the lengths derived from qlens=.srSim(): Modified. Changed to return par() options to what they were before the function was called.mrOpen(): Modified. Changed summary() and confint() methods to allow single, multiple, or all choices of parameters to return results for. Also added code to print the results more prettily.swvCode(): Modified. Fixed bug related to blanks='extra'.filterD(): Added.catchCurve(): Modified. Removed the use of larger points in the plot().chapmanRobson(): Modified. Removed the use of larger points in the plot().metaM(): Modified. Deleted group= (and created method="ZhangMegreyD" and method="ZhangMegreyP"). Added geometric mean regresson methods for Hoenig. Changed default for justM= to TRUE. Fixed several minor bugs from the original implementation. Added some checks for reasonableness of some arguments. Created tests for several methods to see if the results matched those from Kenchington (2014). Added code to compute with several methods at once.Mmethods(): Added. Added as a function and removed as a vector.lencat(): Modified. Fixed a bug that occurred if breaks= were given but the vector contained NAs. Thanks to Ben Neely for pointing this out.catchCurve(): Modified. Changed use.weights= to weighted=. Added some checks for the formula in the formula version and for the variables in the default version. Add unit tests for warnings and errors and tow tests for values.chapmanRobson(): Modified. Added the method="Smithetal" methodology for estimating the SE of Z (and made it the default). Added some checks for the formula in the formula version and for the variables in the default version. Added verbose= to summary(). Add unit tests for warnings and errors and two tests for values.alkPlot(): Modified. Changed behavior for adding a legend to alleviate a bug.metaM(): Added.confint.nlsBoot(): Modified. Changed default for err.col= to black from red. Fixed example due to changes in nlsBoot package.extraSS(): Modified. Added a catch to make sure all models are of the same type. Added a catch to note that the function does not work with other that lm() or nls() models. Fixed a bug related to the labels for results from anova() being different depending on whether lm() or nls() models were given. Added some examples.hist.formula(): Modified. Fixed bug (originated in last version) that nothing was returned when only one histogram was constructed.lrt(): Modified. Changed call to lrtest() to a call to lrtest.default(). Added a catch to make sure all models are of the same type. Note that degrees-of-freedom from lrtest() are not error df; thus, modified to report error df to match extraSS(). Added some examples.hist.formula(): Modifiied. Added iaxs=, which when set to the default value of TRUE will use xaxs="i" and yaxs="i" to remove the "floating" x-axis produced by hist() in base R.lwCompPreds(): Modified. Added the yaxs= argument.psdCalc(): Modified. Added showIntermediate= to allow showing intermediate values in the calculation of the PSD indices. Added justAdds= to allow the user to return just those results that pertain to the values in addLens=. Added ability to use a named vector in addLens= and then not use addNames=. Changed digits=1 to digits=0. Thanks to Ben Neely for the suggestions.psdVal(): Modified. Added ability to use a named vector in addLens= and then not use addNames=. The original functionality is still there. Added a check that one of the Gabelhouse lengths is not also one of the addLens= values. Deleted the addLens= value if it was (the user might have sent a name with this value and will want that name to appear in the results).residPlot(): Modiifed. Added xpd=TRUE to the loess line routine so that the curve and polygon would stay within the plotting region.tictactoe(): Modified. Add the ability to handle differences between when xaxs="r" and yaxs="r" are used and when xaxs="i" and yaxs="i" are used.dunnTest(): Added.addZeroCatch(): Modified. Removed idvar=, forced the eventvar= and speciesvar= variables in the returned data.frame to be numeric if they were numeric in the original data.frame, allowed speciesvar= to have more than one variable, and added na.rm=. Multiple values for specvar= will allow the user to add zeroes based on a combination of variables (e.g., species and size category). The na.rm= argument allows the user to remove "missing" species, which are common if some sampling events did not capture any fish.growthModelSim(): Modified. Changed all "K0" objects to "t50".headtail(): Added.logbtcf(): Added.lwCompPreds(): Modified. Added base= to allow the function to work with logarithms to a different base. The original function was hard-wired to only use natural logarithms. Updated the examples and the tests.vbFuns(): Modified. Changed all "K0" objects to "t50".vbStarts(): Modified. Changed all "K0" objects to "t50".expandcounts(): Added (from fishWiDNR package).expandLenFreq(): Added. Same as lenFreqExpand() but thought that this name fits better with expandCounts().pcumsum(): Added.rcumsum(): Modified. Completely new code (much simpler).validn(): Added.plyr.addZeroCatch(): Modified. Slight modifications to help file. Fixed bug related to error checking the number of variables. Added some tests.lencat() Modified. Added droplevels= and kept drop.levels= as I could not consistently remember what the name of the argument was -- i.e., the user can use either one, but droplevels= is preferred.mapvalues(): Added. This is the exact same function from the plyr package. Included here to minimize conflicts between functions in dplyr and plyr that have the same name (i.e., don't have to install plyr just for mapvalues() when also using dplyr).perc(): Added.psdCalc(): Modified. Minor change related to droplevels= in lencat().psdVal(): Modified. Changed name for the "zero" group to "substock."swvCode(): Modified. Removed ability to Stangle the code and thus removed method=. Modified code to allow usage of .Rmd files in addition to .Rnw files.plyr, for examples using mapvalues().lencat(): Modified. Changed as.fact= to default to same as use.names=. This will result in the same behavior as before. However, it also allows the user to set use.names=TRUE and as.fact=FALSE to return a character vector (that is not a factor).psdAdd(): Modified. Added addSpec= and addLens= so that the user can have non-Gabelhouse lengths for individual species.PSDlit: Modified. Changed "Walleye x Sauger" to "Saugeye" and "White Bass x Striped Bass" to "Palmetto Bass". Updated the Palmetto Bass values based on Dumont and Neely (2011), but kept old values as "Palmetto Bass (original)". Deleted redundant entries for some species.recodeF(): Deleted. Functionality is in mapvalues() from plyr. Ease come easy go (i.e., added in last version).dplyr.capFirst(): Modified. Changed words= to which=.psdAdd(): Modified. Added a default and a formula version to allow efficiency with dplyr. Added examples. Updated tests.recodeF(): Added.recodeSpecies(): Deleted. Functionality replaced by recodeF() in combination with capFirst().wrAdd(): Modified. Added a default and a formula version to allow efficiency with dplyr. Added examples. Updated tests.WSlit: Modified. Added results for Sardine.psdAdd(): Added.psdDataPrep(): Deleted. Functionality replaced by psdAdd().recodeSpecies(): Modified. Completely re-written but with the same basic functionality. This new version returns a vector that can then be appended to an existing data.frame rather than the old function that returned a whole data.frame. This function should allow ease of use with mutate() from dplyr. Added more catches for bad formuala=s. Added some tests.wrAdd(): Modified. Completely re-written with completely new functionality. This new version returns a vector that can then be appended to an existing data.frame rather than the old function that returned a whole data.frame. This function should allow ease of use with mutate() from dplyr. Added more catches for bad formuala=s. Added some tests.wrDataPrep(): Deleted. Functionality replaced by new wrAdd().hist.formula(): Modified. Slight modifications to warning messages.Summarize(): Modified. Slight modification to warning messages.tictactoe(): Modified. Changed predbal= to predobj=, preybal= to predbal=, xlab= to predlab=, ylab= to preylab=, bal.col= to obj.col=, and bal.trans= to obj.trans=.vbStarts(): Modified. Fixed a bug related to plot=TRUE when type="Francis" or type="Schnute".wrAdd(): Modified. Modified how quadratic functions and the handling of fish less than the minimum applicable length were handled because of changes to wsVal().wsLit: Modified. Changed order of variables, changed hybrid species names to match that of Neumann et al. (2012), update comments to related to Neumman et al. (2012) rather than Blackwell et al. (2012), and added information for the Riffle Dace.wsVal(): Modified. Changed the names of the min.len and max.len variables to be either min.TL and max.TL or min.FL and max.TL as appropriate. Suppressed the return of max.len and quad if they did not exist and suppressed return of comment if it was none. Added a catch if more than one species was given in species=. Created some tests.capFirst() Modified. Added an option to handle a vector of strings rather than just a single string.lencat(): Modified. Fixed bug with category names when use.names=TRUE. Moved all internal functions outside of lencat() environment (and renamed them). Cleaned up code.psdCI(): Modified. Added more catches for calls with mistakes. Create some internal functions to modularize the computations. Added tests.psdVal(): Modified. Added more catches for calls with mistakes. Added tests.psdCalc(): Modified. Completely redone. Changed default to use multinomial rather than binomial method for confidence intervals (added method= argument to control CI type). Changed to throw an error of a species is not given in ``species=''. Added tests.psdDataPrep(): Modified. Changed use.catnames= to use.names and psdname= to vname= to be consistent with psdVal(). Removed duplicitous factor() calls for the length category and species name variables in the returned data.framed.psdPlot(): Modified. Completely redone (fixed several bugs and overall sloppy code). Added psd.add=. Changed legend.pos= and legend.cex= to psd.pos= and psd.cex=.recodeSpecies(): Modified. Made changes to reflect new capFirst() functionality.tictactoe(): Modfied.tictactoeAdd(): Removed. Directed user to use plotCI() from plotrix instead.mrClosed(): Modified. Better handled a given value of R=.psdCalc() Modified. Fixed a bug that appeared when no "zero" fish were present in the data. Moved all internal functions outside of psdCalc() environment (and renamed them).psdCI(): Added.psdPlot(): Modified. Fixed a bug that appeared when no "zero" fish were present in the data. Used psdCalc() to compute the PSD values. Moved default legend position to topleft.swvCode(): Modified. Fixed bug when attempting to use this function from outside of the directory where the .Rnw file exists. Added functionality to add a "note" to the first line(s) of the output file. Added code to remove the first line of the output file if it was going to be blank.swvFinish(): Modified. Updated code because iGetFilePrefix() was deleted.ageKey(): Deprecated. See alkIndAge().ageKeyPlot(): Deprecated. See alkPlot().ageKeyPrep(): Deprecated. See alkPrep().alkAgeDist(): Added.alkIndAge(): Added. Was ageKey(). Added seed= to help with reproducibility. Modified code to better handle when an age-length key has a whole row of missing data (as would happen if as.fact=TRUE and drop.levels=FALSE in lencat()). Added some checks for the age-length key structure. Moved all internal functions outside of alkIndAge() environment (and renamed them).alkMeanVar(): Added.alkPlot(): Added. Was ageKeyPlot(). Fixed bug with colors when adding legend to bar and area plots. Allowed legend to be removed from area plot. Added ability to add a legend to the lines and splines plot. Added pal= to allow choice of color palette for areas in bar and area plot and lines in lines and splines plots. Allowed an area plot when one row of age-length key sums to zero (previously did not allow this). Create internal functions for each plot type. Moved all internal functions outside of alkPlot() environment (and renamed them). Added some checks on the age-length key structure.alkPrep(): Added. Was ageKeyPrep(). Added some checks on the age-length key structure.iCheck ALK(): Added as an internal function (used to test the structure of the age-length keys in several other functions).summary.mrOpen(): Modified. Removed "Estimates" heading if verbose=FALSE.Summarize(): Modified. Moved all internal functions outside of Summarize() environment (and renamed them).removal(): Modified. Completely modified the code so that the examples with apply() and lapply() would also provide confidence intervals. Also changed the code to reflect that $\sum_{i=1}^{k-1}T_{i}$ from Schnute (1983) is the same as $X$ from Carle and Strub (1978), the $\sum_{i=1}^{k-1}T_{i}-C_{1}$ in Schnute (1983) is the same as $X-(k-1)C_{1}$, and $q$ in Schnute (1983) is $p$ in most other resources. These changes allowed some efficiencies and connected the theory behind the methods more firmly. Removed the check for character data. Kept the check for whether catch was a vector or not but if catch is a one row or one column matrix or data.frame then it will be converted to a vector to continue. The latter change allows one to extract one row from a data.frame to send to removal() without having to use as.numeric(). Modified and added examples of the use of apply() and lapply().ageKey(): Modified. Changed to using all.equal() to check if the ALK has rows that don't sum to 1. This was an attempt to minimize the number of "false negatives" caused by R FAQ 7.31. Changed the check of whether the longest fish in the length sample is greater than the longest length bin in the ALK to whether the longest fish in the length sample is greater than the longest length bin in ALK PLUS the minimum width of length categories. This last change is an attempt to minimize the number of warnings that occur when the longest fish in the length sample would be in the last length category ALK but because the length categories are labelled by their minimum length it looks like it is not. The minimum width is used to still allow unevent length categories and, thus, this check may still produce some "false negatives."ageKeyPlot(): Modified. Removed bubble.ylab=. Modified ylab= to handle what bubble.ylab= used to handle.removal(): Modified. Added options to perform Moran (1951) and Schnute (1983) removal methods. Added examples of the new functionality. Updated the tests for the new functionality.depletion(): Modified. Changed type= to method= and added DeLury as an option to method= (and left Delury). Changed ricker.mod= to Ricker.mod=. Added some checking for bad arguments. Created internal functions specific to the Leslie 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. Added digits=.confint.depletion(): Modified. Added digits=. Modified the parm= list to be more efficient.plot.depletion(): Modified. Removed internal par() settings.summary.depletion(): Modified. Added verbose= and digits=.removal(): Modified. Made "CarleStrub" the default method. Changed type= to method=. Changed internal meth object to lbl. Moved all internal functions outside of mrOpen() environment and added other internal functions to isolate all intermediate calculations. Added a verbose= and parm= to summary(). Streamlined clunky code in confint() including removing the all and both options from parm=. Added more checks for abd inputs, notes in the code as to sources for the fomulae, and tests.capHistSum(): Modified. Changed column and row labels for $methodB.top and column labels for $methodB.bot. Added a m-array object for when more than two sampling events are present. Added calculations for the number of fish first 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 as mrOpen(), added only for convenience.mrClosed(): Modified. Fixed bugs around printing of CI type with Schnabel and the ignoring of conf.level= with Schnabel.mrOpen: Modified. Changed ci.type= to type= and phi.type= to phi.full=. Removed type= from summary() and added a verbose= which will print only the estimates if FALSE or both observables and estimates if TRUE. Added a verbose= to confint() to control whether the message about the type of confidence interval is printed or not. Moved all internal functions outside of mrOpen() environment and added other internal functions to isolate all intermediate calculations. Changes to row and column labels in capHistSum() resulted in changes to row lables for summary() and confint() results. Streamlined some clunky code. Added checks for misformed mb.top= and mb.bot=. Added tests and notes in the code as to sources for the fomulae.plot.CapHistSum(): Added.plot.mrClosed(): Modified. Changed axis labels as the expressions did not print with some fonts and devices.marked for the example in capHistConvert().ageBias(): Modified. Changed default value of min.n.CI= from 5 to 3. Added an na.rm=TRUE to the min() and max() that produced the age ranges for the age agreement table.BluegillJL: Modified. Corrected lake name and added a citation.capHistConvert(): Modified. This should probably be considered as a new function if updating from the old version. Modifications included simplifying the structure allowed for the input data.frames (they can have only an id or a freq column and then columns related to the capture history ... this makes the function less flexible but simplifies its use for those that are most likely to use it), moved to a series of internal functions, created a common intermediate data format (which streamlined the code considerably), changed the name of the FSA format to individual and the Rcapture format to frequency, added an out.type='event' format, added in.type='RMark' and in.type='marked'formats, fixed the bug with outputting RMark format, changed the default for new frequency variables from Freq to freq, removed the mch= and event= arguments, replaced cols= with cols2ignore=, added the include.id= argument, changed the in.type= default, coded some "catches" for common mistakes in use, coded to keep the unique fish identifier in id= or event name given in the variable names as much as possible, fixed a bug with event.ord=. Added several new examples.capHistSum(): Modified. Change cols= argument to cols2use=. Moved all internal functions outside of capHistSum() environment.CutthroatAL: Modified. Updated from a new source to include many more years of samples.fitPlot(): Modified. Changed trans.pt= to transparency=.mrClosed(): Modified. Completely re-built the internal file structure. Changed incl.inputs= to verbose=. Added the ability to construct a CI for the overall PE when multiple groups are used in a Petersen family method (thus, added a incl.all= to confint()). Changed default for incl.all= from FALSE to TRUE. Modified the messages when verbose=TRUE.plot.AgeBias(). Modified. Fixed bug that produced a warning if all of the bias t-tests were either significant or not significant. Changed col.err= to col.CI=, lwd.err= to lwd.CI=, col.err.sig= to col.CIsig=, col.ref= to col.agree=, lwd.ref= to lwd.agree=, lty.ref= to lty.agree=, show.rng= to show.range=, col.rng= to col.range=, lwd.rng= to lwd.range=. Removed col.lab= and row.lab= which were deprecated several minor versions ago. Changed default values for lwd.rng= and lwd.CI= from 2 to 1. Added a cex.numbers= argument for controlling the size of the numbers in the "numbers plot" (defaults to 0.9).plotBinResp(): Modified. Changed trans.pt= to transparency=.confint.mrClosed(): Modified. Moved all internal functions outside of confint.mrClosed() environment (see iCI.MRCMultiple() and iCI.MRCSingle()). Changed ci.type= to just type=. Streamlined binomial method for single census. Used iMRCSingleSE() to get SE for when type="normal" for Chapman, Bailey, and Ricker methods.extraSS(): Modified. Slight change to row labels in output table.iMRCMultiple(): Added. Was mrc2() internal function inside of mrClosed() environment.iMRCSingle(): Added. Was mrc1() internal function inside of mrClosed() environment.iMRCSingleSE(): Added. Moved functionality out of summary.mrClosed(). Checked and documented all formulas with sources (in code and in Rd file).lrt(): Modified. Slight change to row labels in output table.mrClosed(): Modified. Moved all internal functions outside of mrClosed() environment (see iMRCMultiple() and iMRCSingle()). Changed type= argument to method=. Added more catches for argument problems (required setting n=, m=, M= and R= to NULL). Streamlined warning message for when incl.SE=TRUE is used with Schnabel or Schumacher-Eschmeyer method. Added tests and reported results in the help file for population size, SE, and CI estimates for each method.plot.mrClosed(): Modified. Removed setting of par(). Changed from using lowess() to using loess() and set better default values. Added descriptive text to help file.summary.mrClosed(): Modified. Moved SE calculations into an internal function (see iMRCSingleSE()).BluegillLM: Modified. Added a seealso.residPlot(): Modified. Changed the loess-related methods to use loess(), to put an approximate confident band with the line, the line and band are "under" the points, the line is lighter. Put the horizontal reference line at zero under the points. Made loess=TRUE the default.iAddLoessLine(): Modified. See residPlot().iHndlFormula(): Modified. COrrected the positioning of the explanatory variables when the model has a response variable.iMakeBaseResidPlot(): Added as an internal function to residPlot() to simplify some coding.iMakeColor(): Modified. More intelligently handles values that are greater than 1 (converts them to decimals by inverting.)lwPredsComp(): Modified. Changed mdl= to object=. Added use of internal iHndlFormula() and moved two internal functions outside the main function. Changed default for intervals from both to confidence and changed so that if only the confidence or prediction intervals are plotted they will be black with lwd= width (if both are plotted the CI is now black and the PI is now blue). Added a show.preds argument. Changed connect.means= to connect.preds=. Changed default lwd= value and how it is used for CIs, PIs, and the connection lines. Added col.connect= argument. Removed mar and mgp from par() call (left mfrow). Added more examples. Added tests for error messages.residPlot(): Modified. Added inclHist= argument. Corrected a bug around the use of thigmophobe() in iAddOutlierTest(). Changed default for student= to FALSE. Modified and added more examples.SMBassWB: Modified. Added a seealso.addLoessLine(): Deleted. Moved functionality to iAddLoessLine() and moved code to residPlot() file..addOutlierTestResults(): Deleted. Moved functionality to iAddOutlierTestResults() and moved code to residPlot() file.capHistConvert(): Added an interactive() to the Rcapture example in the help file.checkStartcatW(): Deleted. Moved functionality to iCheckStartcatW().ci.fp(): Deleted. Moved functionality to iCIfp() and moved code to fitPlot() file.ci.fp.1(): Deleted. Moved functionality to iCIfp1() and moved code to fitPlot() file.ciLabel(): Deleted. Moved functionality to iCILabel().getAllDependencies(): Deleted. Moved functionality to iGetAllDependencies() and moved code to swvUtils file.getFilePrefix(): Deleted. Moved functionality to iGetFilePrefix() and moved code to swvUtils file.getMainTitle(): Deleted. Moved functionality to iGetMainTitle() and moved code to residPlot() file.getVarFromFormula(): Deleted. Moved functionality to iGetVarFromFormula().hndlFormula(): Deleted. Moved functionality to iHndlFormula().hndlMultWhat(): Deleted. Moved functionality to iHndlMultWhat().iAddLoessLine(): Added. Was addLoessLine().iAddOutlierTestResults(): Added. Was addOutlierTestResults().iCheckStartcatW(): Added. Was checkStartcatW().iCIfp(): Added. Was ci.fp().iCIfp1(): Added. Was ci.fp.1().iCILabel(): Added. Was ciLabel().iGetAllDependencies(): Added. Was getAllDependencies().iGetFilePrefix(): Added. Was getFilePrefix().iGetMainTitle(): Added. Was getMainTitle().iGetVarFromFormula(): Added. Was getVarFromFormula().iHndlFormula(): Added. Was hndlFormula().iHndlMultWhat(): Added. Was hndlMultWhat().iLegendHelp(): Added. Was legendHelp().iMakeColor(): Added. Was makeColor().iMakeFilename(): Added. Was makeFilename().iMakeItemsToRemove(): Added. Was makeItemsToRemove().iProcessSessionInfo(): Added. Was processSessionInfo().iPSDLitCheck(): Added. Was psdLitCheck().is.even(): Added.is.odd(): Added. Was odd().iTypeoflm(): Added. Was typeoflm().iwsLitCheck(): Added. Was wsLitCheck()legendHelp(): Deleted. Moved functionality to iLegendHelp().listSpecies(): Deleted. Moved functionality to iListSpecies().makeColor(): Deleted. Moved functionality to iMakeColor().makeFilename(): Deleted. Moved functionality to iMakeFilename() and moved code to swvUtils file.makeItemsToRemove(): Deleted. Moved functionality to iMakeItemsToRemove() and moved code to swvUtils file.odd(): Deleted. Moved functionality to is.odd().predict.nlsBoot(): Added an interactive() to the nlstools example in the help file.printProgressMsg(): Deleted. Not used anywhere.processSessionInfo(): Deleted. Moved functionality iProcessSessionInfo() and moved code to swvUtils file.PSDLitCheck(): Deleted. Moved functionality to iPSDLitCheck() and moved code to psdVals() file.pssCalc(): Deleted. Was deprecated several versions ago. See psdCalc().pssDataPrep(): Deleted. Was deprecated several versions ago. See psdDataPrep().pssPlot(): Deleted. Was deprecated several versions ago. See psdPlot().pssVal(): Deleted. Was deprecated several versions ago. See psdVal().typeoflm(): Deleted. Moved functionality to iTypeoflm().wsLitCheck(): Deleted. Moved functionality to iwsLitCheck() and moved code to wsVals() file.test_VonB2b.R) to assure that group comparisons of von Bertalanffy parameters equal those in Kimura (1980) and vblrt() in fishmethods.lmtest for lrt(). Also used in testing (test_VonB2b.R).confint.nlsBoot(): Modified. Modified the plotting to use hist.formula(), removed par(mar=) definitions, and added err.col= and lwd.col= to control the color and line width of the confidence interval line on the plot.extraSS(): Added.growthModels(): Modified. Added Weisberg parameterization. Changed vbGallucciQuinn to vbGQ.growthModelSim(): Modified. Added Weisberg parameterization. Added vbGQ abbreviation (synonymous with vbGallucciQuinn).lrt(): Added.vbFuns(): Modified. Added Weisberg parameterization. Added vbGQ abbreviation (synonymous with vbGallucciQuinn). Simplified the functions for when simple=FALSE (no error checking now).vbModels(): Modified. Added Weisberg parameterization. Changed vbGallucciQuinn to vbGQ.vbStarts(): Modified. Added Weisberg parameterization. Added vbGQ abbreviation (synonymous with vbGallucciQuinn). Added an internal function for checking whther the starting values for K and Linf made sense.chapmanPlot(), vbFuns(), vbStarts(), and walfordPlot(). Added a testthat file for checking that the von Bertalanffy fitting using vbFuns() and vbStarts() matches other sources.ageBias(): Modified. Deprecated col.lab= and row.lab= and replaced with ref.lab= and nref.lab=. Moved all functions that 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 of the internal files. Changed several if else strings in the plot method to a switch().agePrecision(): Modified. Changed some messages so they were not as wide.chapmanPlot(): Modified. Removed S3 functions so that vbStarts() has to use a formula. Added some checking related to the formula.growthModels(): Modified. Created an internal function that eliminates repetitiveness between this and vbModels(). Changed the GompX types to GompertzX.growthModelSim(): Modified. Removed S3 functions so that growthModelSim() has to use a formula. Added some checking related to the formula. Changed the order of the arguments so that formula= and data= come before type=. This allows a similar interface with vbStarts(). Included a hack that still allows the user to enter a type as the first argument (and thus not have to type type= if any parameterization besides the vbTypical is being used). Corrected spelling of Gallucci for Gallucci and Quinn model.hndlFormula(): Modified. Fixed bug with expected number of response variables value in return list.SpotVA1: Modified. Updated reference.vbFuns(): Modified. Changed schnute parameterization to use L3 instead of L2 and t3 instead of t2.vbModels(): Modified. Created an internal function that eliminates repetitiveness between this and growthModels().vbStarts(): Modified. Removed S3 functions so that vbStarts() has to use a formula. Added some checking related to the formula. Changed tFrancis= to ages2use=. Changed the Schnute method to use the ages in ages2use= rather than being hard-wired to use the minimum and maximum observed age. Both the Schnute and Francis methods will use the minimum and maximum observed ages if ages2use=NULL. Added a catch for if ages2use= are in descending order (should be in ascending order). Changed Schnute parameterization to use L3 instead of L2.walfordPlot(): Modified. Removed S3 functions so that vbStarts() has to use a formula. Added some checking related to the formula.testthat, fishmethods, FSAdata for testing and popbio for an example that was made "interactive" from "dont run"(see below).ageBias() and agePrecision().ageBias(): Modified. Removed unit testings from examples and put in the testing file.agePrecision(): Modified. Removed deprecated what="agreement".confint.nlsBoot(): Modified. Changed example from "dont run" to "interactive."fact2num(): Modified. Changed example from "dont run" to "interactive."fishR(): Modified. Removed news and added posts to the where= argument. Cleaned up the Rd file. Changed example from "dont run" to "interactive."FSA(): Modified. Cleaned up the Rd file.FSANews(), fsaNews(): Modified. Cleaned up 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 "dont run" to "interactive."lencat(): Modified. Changed Rd file for deletion of view().popSizesPlot(): Modified. Changed example from "dont run" to "interactive."TroutDietSL: Modified. Changed Rd file for deletion of view().view(): Deleted. Moved to NCStats package.wrDataPrep(): Modified. Changed Rd file for deletion of view().Removed Roxygen directives in DESCRIPTION (with changes to roxygen2 4.0.1).
Changed @S3method and @method to @export in the following files according to changes in ROxygen2 as described here, among several 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, and walfordChapmanPlot.
addZeroCatch(): Modified. Added a catch for the situation where no zeroes need to be added to the data.frame. Cleaned-up the help file, modified the examples, and added another example. Thanks to Ben Neely for bringing this bug (handling where zeroes are not needed) to my attention.
capHistSum(): Modified. Cleaned up the code (no changes in functionality).
catchCurveSim(): Deleted. Moved to FSAsim package.
checkstartcatw(): Modified. Changed the catch for whether the starting category value was greater than the minimum observed value to correct for a pathological case where they were equal but not with machine rounding.
lenFreqExpand(): Modified. Slightly changed the examples in the help file.
lwPredsComp(): Modified. Streamlined the code (no changes to functionality).
mrOpen(): Modified. Streamlined the code (no changes to functionality). Removed all explicity partial matching options in switch()es as these were already caught with previous match.arg()s.
ageBias(): Modified. Cleaned-up the help file.agePrecision(): Modified. Cleaned-up the help file.ageKey(): Modified. Cleaned-up the help file and modified the example.ageKeyPlot(): Modified. Added more description and cleaned-up the help file.ageKeyPrep(): Modified. Added more description and cleaned-up the help file.lenFreqExpand(): Modified. Corrected total= to use length(x) rather than nrow(df), which was left over from a previous change. Cleaned-up the help file.mrClosed(): Modified. Increased the readability of the code (added comments, used with() for some long calculations, added spacing). Added specific citations to equations in the help file. Changed the degrees-of-freedom in the confidence interval calculation for the Schnabel methods from number of samples minus 2 to number of samples minus 1 (following Krebs).poiCI(): Modified. Cleaned-up the help file.psdDataPrep(): Modified. Fixed error around use.catnames=.swvCounts(): Modified. Fixed error in output.vbDataGen()).ageComp(): Deleted. Fully deprecated. Use ageBias() and agePrecision() instead.cohortSim(): Deleted. Moved to FSAsim package.depletion(): Modified. Remove link to leslieSim().lengthWeightSim(): Deleted. Moved to FSAsim package.leslieSim(): Deleted. Moved to FSAsim package.lwModelSim(): Deleted. Moved to FSAsim package.mrClosed(): Modified. Remove link to mrClosed1Sim().mrClosed1Sim(): Deleted. Moved to FSAsim package.srCobWeb(): Deleted. Moved to FSAsim package.vbComp(): Deleted. Moved to FSAsim package.vbDataGen(): Deleted. Moved to FSAsim package.vbFuns(): Modified. Remove link to vbComp().VBGMlit(): Deleted. Moved to FSAsim package.ageBias(): Modified. Added the ability to use multiple what= arguments with c(). Added what="n" to get the sample size on the age-agreement table. Added nYpos= to plot() to allow control of the position of the sample size values on the plot. Changed the order of the printing of results when what="symmetry" is used in summary(). The order more closely follows the "level of complexity" of the tests. Added unit test examples to the help file.agePrecision(): Modified. Added the ability to use multiple what= arguments with c().hndlMultWhat(): Added. An internal file to help ageBias() and agePrecision handle multiple what= arguments.Removed all of the functions related to constructing and validating standard weight equations. These are now in the FSAWs package. This is the start of an effort to streamline the FSA package.
Removed importFrom quantreg (only used for standard weight methods).
ChinookArg: Added (from FSAdata).
emp(): Removed.
FroesWs(): Removed.
lencatOLD(): Removed (from FSA-internals).
lwPredsComp(): Modified. Changed example to using ChinookArg rather than RuffeWs because RuffeWs was moved to the FSAWs package.
LMBassWs: Removed.
rlp(): Removed.
RuffeWs: Removed.
WalleyeGerowLW: Removed.
wsValidate(): Removed.
WalleyeGerowLW: Removed.
stackpoly() from plotrix for use in ageKeyPlot().ageKeyPlot(): Added.dietOverlap(): Modified. Changed examples in help file to reflect changes to lencat().lencat(): Modified. Added generic functions. lencat.default() accepts a vector as its first argument and returns a single vector. lencat.formula() accepts a formula as its first argument and the data= argument. The lencat.formula() is the same as the old lencat() and lencat.default() provides new functionality. Additionally, the default for startcat= is now NULL and a value for startcat= is found automatically (though a value can still be supplied by the user). The use.catnames= was changed to use.names=. Other changes were made to simplify the code.lenFreqExpand(): Modified. Removed the df= and cl= arguments and replaced with x=, which is simply a vector of length measurements. Changed to startcat=NULL so that that the starting category value can be determined automatically (or can still be set by the user).ageBias(): Modified. Added a plot that shows the number of observations at each combined age. Changed the coding slightly around Bowker's test (added an internal function) and implemented Evans and Hoenig's and McNemar's test. These changes resulting in adding a "table" choice to what= that will print just the age-agreement table. When what="symmetry" is chosen all three ob Bowker's, McNemar's, and Evans-Hoenig results will be output as a table. The age-agreement table is no longer printed when what="symmetry". In addition, what="Bowkers", what="EvansHoenig", and what="McNemars" can be used to see the Bowker's, Evans and Hoenig, and McNemars test results, respectfully. Added a cont.corr= argument for use with McNemars test.agePrecision(): Modified. Added the ability to show raw (vs. absolute value) differences between structures. This resulted in the removal of what="agreement" (though it is deprecated, with a message, for now) and the addition of what="difference" and what="absolute difference".fishR(): Modified. Changed to point to the github NEWS.md when where="news".fitPlot(): Modified. Changed the logistic regression code to handle the changes to plotBinResp() (see below). In addition, a temporary fix was added so that the size of the y-axis labels could be modified with an external call to par(). This was a fix for Glen Sutton but will ultimately need to be handled more elegantly.fsaNews(): Modified. Changed to point to the github NEWS.md.catchCurveSim(): Added back from FSATeach (required adding ImportFrom for relax package).cohortSim(): Added back from FSATeach (required adding ImportFrom for relax package).growthModelSim(): Added back from FSATeach (required adding ImportFrom for relax package).lengthWeightSim(): Added back (was lwModelSim()) from FSATeach (required adding ImportFrom for relax package).leslieSim(): Added back from FSATeach (required adding ImportFrom for relax package).mrClosed1Sim(): Added back from FSATeach (required adding ImportFrom for relax package).plotBinResp(): Modified. Added yaxis1.ticks= and yaxis1.lbls= arguments so that the user can control the tick-mark locations and labels for the left y-axis (the defaults are to show ticks every 0.1 units but only label 0, 0.5, and 1). Added yaxis2.show= argument to allow the user to "turn-off" the right y-axis (defaults to being on) which is labeled with the level labels.srSim(): Added back from FSATeach (required adding ImportFrom for relax package).ageKeyPrep(): Added.agePrecision(): Modified. Fixed the bug where the APE and CV were over-estimated in situations where the multiple ages agreed at an age=0 (thanks to Richard McBride for pointing out this error).wsLit: Modified. Added Pursak chub information from Sulun et al. (2014).ageBias(): Added. Extracted the age-bias related material from ageComp(). Modified the code to remove unneeded code. From ageComp(), remove the what= argument related to differences and added a difference= argument. Also changed what="bias.diff" to what="diff.bias" to allow for a quicker partial matching (i.e. separate more from what="bias"). Major modifications to how the axis limits are created if none are provided. Modified where the sample size is shown on the age-bias plot. Added the min.n.CI= argument. Added an example using WhitefishLC to be consistent with agePrecision().ageComp(): Modified. Split into ageBias() and agePrecision(). Added a warning that this function is deprecated and will be removed in the future.ageKey(): Modified. Fixed a bug that occurred when a data frame that already contained an LCat variable was provided.agePrecision(): Added. Extracted age precision related material from ageComp(). Modified the code to allow for calculations across more than two structures. Code was streamlined dramatically from what was in ageComp(). Added an example using WhitefishLC as it allows for demonstrating more than two age assignments.capFirst(): Modified. Added functionality, controlled by the new words= parameter, to allow all words, rather than just the first word, to be capitalized.capHistConvert(): Modified the help file by commenting out the example that depends on the RCapture package. This is needed for the RForge site for the time being.fitPlot(): Modified Rd. Added two polynomial regression examples.fitPlot.IVR(): Modified. Changed to use new typeoflm(), changed interval= argument, removed automatic main title, removed a bunch of unneeded code.fitPlot.logreg(): Modified. Removed automatic main title.fitPlot.nls(): Modified. Removed automatic main title.fitPlot.ONEWAY(): Modified. Changed to use new typeoflm(), removed automatic main title, removed one line of unneeded code.fitPlot.SLR(): Modified. Changed to use new typeoflm(), changed interval= argument, removed automatic main title.fitPlot.TWOWAY(): Modified. Changed to use new typeoflm() and removed automatic main titlegReshape(): Modified. Added a drop= argument so that the user can drop some variables before reshaping. Also, added new.row.names=1:100000 to the reshape() call to work-around issues with duplicate row names (which were particularly problematic if any of the id.vars= had missing values.)growthModels(): Modified. Corrected spelling of Gallucci for Gallucci and Quinn model.hist.formula(): Modified. Add a col= argument that defaults to "gray90".hndlFormula(): Added. An internal function to handle various assessments related to using formulas.lencat(): Modified. Added the ability to add names if the vector sent in breaks= is named.confint.mrClosed(): Modified. Removed extra linespaces in printed output. Changed default for incl.inputs= to FALSE.summary.mrClosed(): Modified. Removed extra linespaces in printed output. Changed default for incl.inputs= to FALSE.predict.nlsBoot(): Modified the help file by commenting out the example that depends on the nlsBoot package. This is needed for the RForge site for the time being.psdCalc(): Added (was pssCalc()).psdDataPrep(): Added (was pssDataPrep()) and modified. Deleted the code in this function that added category names as this functionality was added to lencat(). See lencat() above.PSDlit: Added (was PSSlit) and modified. Changed all species names to have both words capitalized so as to follow the latest AFS guidelines.psdPlot(): Added (was pssPlot()).psdVal(): Added (was pssVal()).rsdCalc(): Deleted.rsdVal(): Deleted.recodeSpecies(): Modified. Changed capFirst= to doCapFirst= to minimize confusion with capFirst(). Change doCapFirst= to a character that behaves like words= in capFirst(), rather than as a logical.SpotVA1: Modified. Removed link to source documents because it caused a problem when making the PDF manual.StripedBass1: Deleted. Moved to FSAdata as no longer needed because some examples were changed to use WhitefishLC.Subset(): Modified. Added a resetRownames= argument.swvCode(): Modified. Added an out.dir= argument.swvCounts(): Modified. Added a capitalize= argument.typeoflm(): Modifed. Changed to use hndlFormula(). Made an internal function.vbFuns(): Modified. Corrected spelling of Gallucci for Gallucci and Quinn model.vbStarts(): Modified. Corrected spelling of Gallucci for Gallucci and Quinn model.WhitefishLC: Added (from FSAdata).wsLit: Modified. Changed all species names to have both words capitalized so as to follow the latest AFS guidelines.Changed to compiling under R 3.0.2.
Removed dependency on reshape package (see changes for emp(), gReshape(), and ssValidate() below) and the relax, tcltk, and TeachingDemos packages (see changes for catchCurveSim(), cohortSim(), growthModelSim(), leslieSim(), lwModelSim(), mrClosed1Sim(), simAgeBias(), simAges(), simLenFromAge(), simLenSelect(), and srSim() below).
.onAttach(): Modified. Added notes to use citation().
bcFuns(): Modified. Added "BPH" and "SPH" options to type= argument (same as "LBPH" and "LSPH", respectively). Changed a catch using cat() to using message(). Added some specificity to the help file (more is needed).
catchCurveSim(): Deleted. Moved to FSATeach package.
changesPos(): Added.
cohortSim(): Deleted. Moved to FSATeach package.
emp(): Modified. Replaced use of cast() with aggregate().
gReshape(): Modified. Replaced use of melt() with reshape() from base package. Fixed bug if name of "increments" was not "inc" (now catches that in.pre= value is used). Fixed bug that na.rm= was ignored. Modified so that rownames are not created until after the NAs are moved or not. Changed the default name in var.name= from "age" to "prvAge" to reduce the highly possible chance that there might be another variable in the data frame named "age."
growthModelSim(): Deleted. Moved to FSATeach package.
growthRadPlot(): Modified. Slightly changed the xlab= argument default.
leslieSim(): Deleted. Moved to FSATeach package.
lwModelSim(): Deleted. Moved to FSATeach package.
mrClosed1Sim(): Deleted. Moved to FSATeach package.
simAgeBias(): Deleted. Moved to FSATeach package.
simAges(): Deleted. Moved to FSATeach package.
simLenFromAge(): Deleted. Moved to FSATeach package.
simLenSelect(): Deleted. Moved to FSATeach package.
srSim(): Deleted. Moved to FSATeach package.
summary.ageComp(): Modified. Added a zero.print= argument with a default of a single dash for use when printing an age-agreement table. Added flip.table= argument to allow ease of comparison between the age-agreement table and the age-bias plot. Changed so that if what="prec.stats" the summary percentages by absolute differences is also printed. Modified the print of several data frames (for what="bias", "symmetry", and "prec.stats") so that row names (i.e., row numbers) are not printed.
sumTable(): Added. Brought over from NCStats.
vbFuns(): Modified. Changed all non-simple growth model functions with checks for the number of model parameters and definitions sent. Changed the Francis parameterization model to take only two values of t= (i.e., the intermediate value is not used and, thus, is not required); thus, the t2= argument was removed.
vbGen(): Modified. Fixed bug that developed when changes to gReshap() were made. Added warning suppression related to "calculations" on NAs.
vbStarts(): Modified. Changed tFrancis argument to use only two ages. Changed the default for meth.EV= to "poly". Removed jittering and added a transparency to the plot. Removed the box around the legend and moved the legend to the "bottomright." Fixed a typo in the plot heading.
wsValidate(): Modified. Replaced use of cast() with aggregate().
Changed R dependency to >3.0.0 (because gplots package has that dependency).
Added importFrom for cast(), is.formula(), and melt() in reshape package.
capHistConvert(): Corrected the formatting of the documentation.
capHistSum(): Corrected the documentation. Added a second example.
dietOverlap(): Modified. Changed the "Morista" option to "Morisita" to be consistent with the correct spelling of the name.
Garvey1: Added. Used in examples in ks2d1().
Garvey4a: Added. Used in examples in ks2d1().
histStack(): Deleted, moved to plotrix package. Arguments were changed there.
ks2d(): Deleted, changed to ks2d2().
ks2d1(): Added.
ks2d2(): Added, was ks2d().
ks2dp(): Deleted, changed to ks2d2p().
ks2d2p(): Added, was ks2dp().
mrClosed(): Modified. Changed all "messages" using cat() to using message() so that they can be suppressed with suppressMessage() or message=FALSE in knitr. See "One comment on messages" at http://yihui.name/knitr/demo/output/.
pkolgomorov1x(): Added to FSAinternals (from ks2d()).
plotH(): Deleted, moved to plotrix package.
quad_dens(): Added to FSAinternals (from ks2d()).
Corrected all pointers to fishR vignettes (because of new webpage).
Removed importFrom color.scale from plotrix because of changes to discharge() and wetPerim().
removed importFrom %nin% from Hmisc. See multiple changes because of this below.
.onAttach(): Added, was .onLoad().
.onLoad(): Deleted, now .onAttach().
addMargins(): Deleted, moved back to NCStats.
addSigLetters(): Deleted, moved back to NCStats.
addZeroCatch(): Modified. Changed the looping structure for finding the sampling event and species combinations that need zeroes. This should speed things up substantially. Also, modified to allow no idvar= variables. Finally, the returned data frame has 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 for name changes in Summarize(). Modified to use a formula notation.
ageKey(): Modified to using a formula notation. This removed the dl=, cl=, and ca= arguments. Made minor adjustments to the help pages (in addition to changes related to the argument modifications).
bcFuns(): Removed use of %nin%.
capFirst(): Modified so that ONLY the first letter is capitalized (previous version would de-capitalize the first letter in the second word but leave the rest of the letters capitalized).
capHistSum(): Modified to correct an error that occurred when computing the Method B table when a capture history occurred only once or not at all.
chapmanRobson(): Modified by adding the Hoenig et al. (1983) bias correction formula for the estimate of Z as the default option.
confint.nlsBoot(): Removed use of %nin%.
discharge(): Deleted, moved to NCStats (to reduce overhead here).
histStack(): Modified by adding a formula method (histStack.formula()) which required adding a default method (histStack.default()).
htest.nlsBoot(): Removed use of %nin%.
lencat(): Modified by changing to using a formula notation and a data= argument. This means that the df= and cl= arguments are no longer used. In addition, the warning about fish larger than the larger category has been turned off. The method to handle this was not changed, the warning was just turned off.
lencatOLD(): Added as an internal file to temporarily allow me not to change all functions that were affected by the changes to lencat(). The functions that required this are emp() and wsValidate().
lenFreqExpand(): Modified to deal with lencat() change.
limnoProfilePlot(): Deleted, moved to NCStats (to reduce overhead here).
mrClosed(): Removed use of %nin%.
plotBinResp(): Modified by moving makeColor() internal function to FSA-internals so that it can also be used by tictactoe().
predict.bootCase(): Added.
PSSLit: added from RSDLit. Added from Ogle and Winfield (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. Modified pssVal(), pssCalc(), and pssPlot() accordingly.
psdVal(): Deprecated, will delete, became pssVal().
pssCalc(): Added, was rsdCalc(). Modified to using a formula notation and a data= argument.
pssDataPrep(): Added.
pssPlot(): Added, was rsdPlot(). Modified to using a formula notation and a data= argument, to handle the default change for incl.zero= in pssVal(), and changed the default pss.lty= settings.
pssVal(): Added, was rsdVal(). Changed incl.zero=TRUE to be the default.
recodeSpecies(): Added.
rsdCalc(): Deleted, became pssCalc().
rsdLit(): Deleted, became PSSLit().
rsdPlot(): Delted, became pssPlot().
rsdVal(): Deprecated, will delete, became pssVal().
sigLetters(): Deleted, cld() in multcomp has been modified to deprecate this.
simLenSelect(): Modified to deal with lencat() change.
Summarize(): Modified by calculating the percentage of zeroes for quantitative data. Also changed the names in the returned vectors or data frames to reduce capitalization, spaces, and punctuation. Removed use of %nin%.
tictactoe(): Modified by changing the way the "in balance" regions are depicted. This resulted in the addition of the bal.trans= argument.
tictactoeAdd(): Modified by changing PSD labels to PSS.
vbStarts(): Removed use of %nin%.
wetPerim(): Deleted, moved to NCStats (to reduce overhead here).
wrAdd(): Modified. Major modifications to account for changes to WSlit. Added the capFirst() check for species name. Changed subNA= to remove.submin= to make consistent with wrDataPrep().
wrDataPrep(): Added.
wrVal(): Deleted.
WSlit: Modified. Completely rebuilt so that quadratic equation using EmP could be incorporated into the database. Also added equations for several new species.
WSLitCheck(): Added this internal file. Modified wsVal(), wrVal(), and wrAdd() accordingly.
wsVal(): Modified. A major modification to account for the major changes to WSLit.
wsValidate(): Removed use of %nin%.
added special "fishR Vignette" sections with links to several help files.
binCI(): Modified so that result is a matrix rather than sometimes (when only one set of CIs were computed) being a vector.
catchCurve(): Modified by minorly adjusting how confint() produced CIs. Also, disallowed using parm= when the user asks for CIs for the linear model. This allowed using match.arg() as a check for appropriate parm= values. Modified the examples in the help file slightly and added an example of using the weighted regression method.
plot.catchCurve(): Modified so that log(catch) values less than 0 will be plotted.
chapmanRobson(): Modified by minorly adjusting how confint() produced CIs.
depletion(): Modified by minorly adjusting how confint() produced CIs and added a cat()ted output to the summary() method describing whether the Leslie or DeLury method was used.
growthModelSim(): Modified. Streamlined the code (removed some "junk" and unneeded redundancies). Also corrected the error where the fourth parameter in the vbSchnute and Schnute were not observed to be connected to sliders. Also changed a few default slider values. Also set the minimum age (t.min) to 0 and cannot be over-ridden (was previously controlled by a slider). Thus, removed the minimum age slider. Also moved the maximum age slider to the bottom of the sliders. Changed the calls for the Gompertz models to use the full name (i.e., Gompertz1 instead of Gomp1). Changed model= to type= to be more consistent with other similar functions.
hyperCI(): Modified so that the result is a matrix rather than a vector.
leslieSim(): Modified by adding hscale=1.5 to resampling version.
mrClosed(): Modified to handle the changes in hyperCI() and binCI(). Also modified messages in summary() and confint() (to streamline).
predict.nlsBoot(): Added.
removal(): Modified by minorly adjusting how confint() produced CIs and removed a cat()ted line from the summary() method. Also, modified the "catches" for the 2- and 3-pass specific methods to disallow using anything but a vector with either 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 to produce generally more interesting simulations. Modified the graphic to show the peak recruitment level and, if a Ricker model, the stock size where the peak recruitment occurs. Changed a long series of if-else for the different parametrizations to a switch(). Changed model= to type= to be consistent with other srXXX functions.
vbFuns(): Modified slightly the messages if msg=TRUE. Added a message for the Wang2 model and corrected an error for the Somers2 model.
view(): Modified to remove the ability to print to a window (use method built into RStudio instead). Also generalized to use for both a matrix or a data.frame (eliminates some warning messages).
Added ImportFrom for slider() and gslider() from the relax package. Deleted the ImportFrom for slider() from the TeachingDemos package. These functions were the same but it was being deprecated from TeachingDemos.
General: added call.=FALSE to several stop()s and warning()s.
General: replaced paste() inside of several cat()s.
ageKey(): Modified to use match.arg() with type=.
binCI(): Modified to use ciLabel() (see below).
catchCurveSim(): Modified in a variety of ways. First, moved the ability to control the recruitment age and the steadiness of the Z and N* changes to function arguments rather than slider controls. Second, streamlined the internal functions. Third, converted to using gslider() instead of slider(). Fourth, made minor cosmetic changes to the plot. Fifth, I edited the help file somewhat.
checkStartcatW(): Added this internal function.
ciLabel(): Added this internal function.
cohortSim(): Modified in a variety of ways. First, streamlined the internal functions so that the plot can be created individually. Second, converted to using gslider() instead of slider().
confint.bootCase(): Modified to use ciLabel().
confint.catchCurve(): Modified to use ciLabel().
confint.chapmanRobson(): Modified to use ciLabel().
confint.depletion(): Modified to use ciLabel().
confint.mrClosed(): Modified to use ciLabel().
confint.nlsBoot(): Modified to use ciLabel().
confint.removal(): Modified to use ciLabel().
dietOverlap(): Added.
fsa.news(), FSA.news(): Deleted, renamed to fsaNews() and FSANews().
fsaNews(), FSANews(): Renamed versions of fsa.news() and FSA.news().
FSAsims(): Deleted. Rarely used and not supported in non-windows and RStudio.
growthModelSim(): Modified in a variety of ways. First, streamlined the internal functions so that the plot can be created individually. Second, converted to using gslider() instead of slider().
hyperCI(): Modified to use ciLabel().
lencat(): Modified by using the new checkStartcatW() internal function.
lenFreqExpand(): Modified by adding show.summary= argument and using the new checkStartcatW() internal function.
leslieSim(): Modified in a variety of ways. First, combined the code from leslieSim2() into this function. This required deleting the use.rand= argument and adding a type= argument. In addition, the leslieRandRun() internal function was moved to this R document (from FSA-internals). Second, the functions were all streamlined with new internal functions. Third, converted to using gslider() instead of slider(). Fourth, made minor cosmetic changes to each plot (including adding a small legend to the old leslieSim2()).
leslieSim2(): Deleted. See leslieSim().
lwModelSim(): Modified in a variety of ways. First, streamlined the internal functions so that the plot can be created individually (will ultimately allow use of the manipulate package). Second, converted to using gslider() instead of slider().
mrClosed(): Modified by removing numdigs= argument.
mrClosed1Sim(): Modified in a variety of ways. First, streamlined the internal functions so that the plot can be created individually. Second, converted to using gslider() instead of slider().
poiCI(): Modified to use ciLabel().
rlp(): Modified by replacing decimals= argument with digits= argument.
srSim(): Modified in a variety of ways. First, streamlined the internal functions so that the plot can be created individually. Second, converted to using gslider() instead of slider(). Third, removed the S3methods.
Summarize() Modified by removing numdigs= argument.
TroutDietSL: Added for use with dietOverlap().
vbStarts(): Modified by including a catch for negative starting values of K or starting values of Linf that are 50% smallr or larger than the observed maximum length in the data set.
Changed R dependency to >2.14.0.
Added a ImportsFrom for knitr (purl() in swvCode() added below).
Moved gdata to an ImportsFrom from Suggests. Needed for nobs() in ci.fp1() which is used in fitPlot.ONEWAY and drop.levels() used in the example 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 from Simon Urbanek to eliminate a warning on RCMD Check (that showed up on rforge.net, but not locally).
addMargins(): added from NCStats.
addSigLetters(): added from NCStats. Modified to allow the use of a result from sigLetters() in lets=.
bootCase methods: added from NCStats. Needed to import bootCase from car.
hist.formula(): added from NCStats.
lencat(): made some warning messages more concise.
lsmean(): deleted. Functionality is replaced by lsmeans() in the lsmeans package.
psdVal(), rsdCalc(), rsdVal(), rsdPlot(): added code to 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 eventually be replaced by changed to cld() in the multcomp package.
Summarize(): made some warning messages more concise.
swvCounts(), swvPvalue(), swvANOVA(), swvGLHT(), swvREG(), swvHtest(), swvCode(), swvFinish(): added from miscOgle.
view(): added from NCStats.
wsVal(), wrAdd(): added code to 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
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 by a period).
Switched to using roxygen to construct help files.
Set some values =NULL to eliminate "global bindings" warning when performing the RCMD check -- emp(), pos2adj(), psdVal(), simAgeBias(), srStarts(), vbStarts(), and wsValidate(). This did not work for the WSlit and RSDlit problems in rsdCalc(), rsdPlot(), rsdVal() and wsVal().
Added an importFrom for lineplot.CI()) and se() from sciplot (used in fitPlot()).
Added an importFrom for outlierTest() from car for use in residPlot().
Deleted importFrom for alias() from stats (was used in wlgm()).
Deleted importFrom for boxcox() from MASS (was used in wlgm()).
Deleted depends on NCStats (moved many functions here (see below) and then made NCStats depend on FSA).
Deleted suggests for exactRankTests (apparently no longer needed).
Moved nlstools from depends to suggests (only needed for an example in confint.nlsboot that is not run because of the time required).
Moved plotrix from depends to importsFrom for color.scale(), plotCI(), and thigmophobe().
Moved quantreg from depends to importsFrom for rq() (used in emp()).
Attempted to move reshape to importsFrom but had problems with missing 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 now out-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) from NCStats.
mrClosed(): modified by moving the two internal functions -- mrc1() and mrc2() -- to inside mrClosed, moving the two internal functions -- ci.mrc1() and ci.mrc2() -- to inside confint.mrClosed(), removed the "MRC1" and "MRC2" classes, changed the "MRC" class name to "mrClosed", and added a catch to plot.mrClosed() to stop 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 Rd file.
pos2adj(): modified the labels for the positions by including full names for all directions, eliminating the single letters for the four main directions, but also leaving the four "off" directions as abbreviations.
psdVal(), rsdVal(), rsdCalc(), rsdPlot(): modified to use capFirst so that the user does not need to focus on capitalization 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 now out-dated).
wsValidate(): modified the classnames to "willis" from "WILLIS" and "empq" from "EMPQ". Also made minor modification because of class name change in FroeseWs()
ycPlot(): deleted (Weisberg's LGM is now out-dated).
Moved several functions from NCStats that are used quite often for fisheries analyses. Ultimately, I want to remove the dependency to NCStats.
Deleted an importFrom for gtools, created an internal odd() instead.
Added an importFrom for gplots, to get rich.colors() for chooseColors().
Added an importFrom and removed an import for NCStats.
ageComp(): modified to use internal odd(), rather than odd() imported from gtools.
binCI(): moved from NCStats.
chooseColors(): copied from NCStats (i.e., same function still in NCStats).
confint.nlsBoot(): moved from NCStats.
fact2num(): moved from NCStats.
htest(): copied from NCStats (i.e., same function still 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 where substock fish are not present in the data. Thanks to Max Wolter for pointing out this issue.
Subset(): copied from NCStats (i.e., same function still in NCStats).
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 and suggesting gdata in the description file.
fishR(): Added.
simAgeBias(): changed width to widths in layout() to avoid warning on check.
simLenSelectM(): changed width to widths in layout() to avoid warning on check.
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 handle changes to capHistSum().
capHistSum(): Modified. Changed the returned list structure. First, caphist.sum is now caphist. Second, if only two samples are given, then only caphist and sum, where sum is a data frame of the required summaries for the Petersen method, are returned. If more than two samples are given, then caphist, sum, methodB.top, and methodB.bot are returned. Note that there is n* longer an item labeled as schnabel.sum returned.
mrClosed(): Modified. Modifications to handle the changes to capHistSum(). Also modified so that if only two samples were summarized in a CapHist object and that object is supplied as the first argument to mrClosed() then the Petersen method will find the data it needs from the CapHist object.
rsdPlot(): Modified. Modified calls to min() and max() to include na.rm=TRUE. This fixes bug related to vectors with missing values.
updateFSA(): Removed.
vbFuns(): Modified. Added 'Somers2' option to type= argument.
vbStarts(): Modified. Added 'Somers2' option to type= argument.
Modified description file to show my e-mail address.
Added cnvrt.coords() as an ImportFrom TeachingDemos. Needed for simAgeBias() and simLenSelectM().
ageKey(): Modified. Length categories in the length sample, if none are provided in len.breaks=, are constructed from the length categories present in the age-length key rather than guessing at a starting value and width and creating evenly spaced categories. This should fix the bug that occurred when an age-length key was originally created with even length categories but the key is so sparse that the length categories with actual data are uneven. Also, changed the error catching so that the routine is stopped if a length in the length sample is smaller than the smallest length category in the age length key but will only elicit a warning if the largest length is greater than the largest 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 to growthModelSim() 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 of the original model options as models for length. The plots represent the different characteristics (length or weight) modeled as d* the slider bar options. Added a max.wt= argument for use when modeling weights. Removed "vbBevertonHolt" as a model option because it is covered by "vbTypical" and was not actually implemented. Changed order of models so that "vbTypical" rather than "vbOriginal" is the default model used. Made slight cosmetic changes to slider bar options (e.g., "to" became "t_0"). Made changes and some corrections to the .Rd file.
rsdPlot(): Added. Still needs more thorough proofing.
simAgeBias(): Added.
simAges(): Added.
simApplyAgeBias(): Added.
simLenFromAge(): Added.
simLenSelectM(): Added.
simLenSelectP(): Added.
vbComp(): Modified. Streamlined the code. Changed the 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 the maximum age to model to. The ages= argument can be a vector such that each simulation can have a different set of ages over which the model is evaluated. This allows for more realistinc modeling.
Switched to compiling under R version 2.13.0.
vbFuns(): Modified. Modified Wang's formulas to be for length increments. Added a length increments version to Faben's method ("Fabens2").
Updated citation file.
Added importFrom for tools and utils packages.
ageKey(): Modified. Added a len.breaks= argument so that an age-length key with variable widths for the length categories can be used. Added an example to the Rd file to illustrate the use.
confint.MRC(): Modified. Replaced numdigs= argument with digits= argument. Retained numdigs= for backwards compatability.
lwPredsComp.Rd: Modified. Replaced use of lgrep() with grepl() because of change in NCStats.
removal(): Modified. Changed order of items printed in 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) is also included in the returned list.
The first change is cosmetic, the second change was made to help with some
troubleshooting. Added an argument to allow choosing the method of contructing
SE for the CarleStrub method. Created an internal function for computing the
Zippin SE method to allow easier use with the other methods. The help file
was changed to make note of the non-estimable SE when No=T in the CarleStrub
method under certain circumstances. These changes result in a different SE
being reported if the CarleStrub method is used and CS.se="Zippin" (the
default) is used. The "old" results can be obtained by using
CS.se="Alternative". I have yet to find a solid references for this SE.
summary.MRC(): Modified. Replaced numdigs= argument with digits= argument. Retained numdigs= for backwards compatability.
tictactoeAdd(): Modified. Added capability of labeling points.
updateFSA(): Added. Had to add an importFrom from the tools package.
vbFuns(): Modified. Added Wang and Wang2 functions.
moved to compling under 2.12.1 (32-bit)
changed dependency to >2.11.1
ageComp(): modified dramatically. Primarily added the ability to test for bias by comparing the mean of the y-structure to the value of the x-structure with t-tests adjusted for multiple comparisons. Modified the code to allow this to happen more efficiently and to output results in the plot() and summary() methods. Also modified the plot() method so that the default is to just show the confidence intervals rather than showing the CIs and the range of the data (use show.rng=TRUE to see the old plot). Also changed the CI colors so that significant differences are shown in red (default) and non-significant differences are shown in blue (default) (set both col.err= and col.err.sig= to the same color to get the old plot).
lencat(): modified so that vname=NULL is the default. This will default to using "LCat" as the variable name (as in the previous version). However, modified the way the vname is appended to the new data frame so that if vname already exists in the data frame a new name will be used (vname plus some number).
removal(): added just.ests= argument and changed the ests part of the returned value to be a vector rather than a matrix. Both changes allowed for better use of lapply() for computing the removal estimates on more than one group. Changed from an error to a warning for situations where the method could not compute population estimates (i.e., because the population was not depleted). In addition, NAs are returned in situations where population estimates can not be made. An example of computing the removal estimate for more than one group was added to the .rd file. Thanks to Jon Bolland for asking the question that motivated these changes.
completed changing naming convention to "camel" type -- e.g., stockRecruitModels() rather than stock.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 of simulation 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(). This is an internal function.
leslieSim(): renamed from leslie.sim().
leslieSim2(): renamed from leslie.sim2().
limnoProfilePlot(): renamed from limnoprofile.plot().
lwModelSim(): renamed from lwmodel.sim().
lwPredsComp(): renamed from comp.lwpreds().
mrClosed(): renamed from mr.closed(). Modified for name changes 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(). Modified for 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 modified for name changes in NCStats.
ycPlot(): renamed from ycplot().
moved to compiling under 2.11.1.
started changing my naming convention to "camel" type -- e.g., stockRecruitModels() rather than stock.recruit.models(). In this version, I am only changing the functions that I am working on. I will change the rest in the next version.
added an importFrom for nlme as groupedData() was needed for vbDataGen().
age.key(): Modified the way that the length categories in the age-length key is determined. Previously I just used the rownames found in the key, but this allows lengths with a row of all NA or zeroes 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. In addition, I added a warning message if the row sums d* not sum to 1.
caphist.convert(): Modified such that an "RMark" type can be output. 0 chapmanPlot(): Added.
growmodel.sim(): Deleted. Changed to growthModelSim(). See below. 0 growthModelSim(): Added. Initially a renaming of growmodel.sim(). However, the model names were changed to be more consistent with other functions and a method for the Mooij et al. paramaterization was added.
growthModels(): Added.
srFuns(): Added.
srStarts(): Added.
stock.recruit(): Deleted, along with all related generics.
stock.recruit.sim(): Deleted. Changed to stockRecruitSim(). See below.
stockRecruitModels(): Added.
stockRecruitSim(): Initially a renaming of stock.recruit.sim. However, added a "formula" method which required adding generic and default methods. Changed the order of the S and R arguments. Re-ordered, modified, and added models in accordance with the vignette. Updated the Rd file to reflect these changes and made a very slight modification to the examples and added an example to illustrate the use of the formula. Found decent default values for simulations.
stockRecruitSim.default(): Added. See above.
stockRecruitSim.formula(): Added. See above.
vbDataGen(): Added.
vbFuns(): Added.
vbStarts(): Added.
walfordPlot(): Added.
moved to compiling under 2.10.1.
FSA-package(): updated.
added a dependency to tcltk so that simulators would work properly upon load of FSA.
age.comp(): added xlim= and ylim= arguments so user can control x- and y-axis limits if desired. Changed code so that better choices for axis limits are selected automatically if xlim and ylim are both NULL. Changed code so that the "extra" vertical space added when show.n=TRUE AND ylim is NLL is 10 percent of the y-axis range rather than just an extra one unit. Allowed function to work better with xaxt="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 labeled if the column did not already exist in the data frame. Was also indirectly modified with lencat() modification. Also modified to stop and warn the user if the length sample has fish whose lengths are not present in the length-age key (previously there was a warning, but then ultimately there was an error).
catch.curve(): added a use.weights= argument to allow using weights in the catch curve regression as proposed by Maceina and Bettoli (1998).
chapman.robson(): changed S result from a proportion to a percentage (i.e., * 100).
comp.lwpreds(): added center.value= argument to allow centering in the regressions. Added an example to the .rd file.
fsa.news(): added to show user the NEWS file.
growmodel.sim(): added the ability to use a formula and data= argument. Made the model argument not have a default value. Corrected an error when both x and y were NULL. Corrected errors in the Rd file. Thanks to Jacek Szlakowski for pointing out these problems.
lencat(): modified so that an "extra" last length category (with no fish in it) was not included when as.fact=TRUE and drop.levels=FALSE is used. This should correct the "problem" of an extra all-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 of bin.ci() from NCStats.
added a namespace
removed dependencies and changed to imports ... left plotrix and quantreg as dependencies (they d* not have a namespaces). left reshape as a dependency because of it's dependency on plyr.
.FirstLib(): removed (changed to .onLoad() because of namespace).
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 function converted increments to radii.
growrad.plot(): added. Exported in namespace.
mr.closed(): modified by changing library(Rcapture) to require(Rcapture) in help page.
plot.EMPQ(): modified by changing object$prob to x$prob.
emp.rd: fixed an incorrect use of Summary() (changed to summary()).
validateWs(): converted sign.slope variable in the Willis method to a factor to deal with situations where all results were positive or negative.
wlgm.rd: fixed the summarization example (cast() did not work with Summarize().
added a dependency to quantreg (for rq() in emp()).
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 when converting from a capture-by-event type. This is particulary useful if the event names are things like 'first', 'second', 'third', 'fourth' because R orders these alphabetically which adversely effects the correctness of the capture histories.
compute.Ws(): moved this internal function out of validateWs() to be a stand-alone internal function. This allows usage with 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 a method= argument that allows choice of using linear regression or quantile regression to find the Ws equation. Modified objects in the return list (added rawdata component) and added the back-transformed Wq value in regdata (for comparison with Gerow's Excel tool). Changed code for finding summarized dataframes inside the function by using cast() from the reshape package -- this resulted in a 3x reduction in system.time().
mr.closed(): modified by correcting error in the multiple census methods if M, n, and m (but not R) were supplied. Also corrected 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 species name so that the user can just type PSDval() to get the list of possible species names. Also added a check to see if RSDlit was already loaded.
validateWs(): added probs= argument result to return list. Corrected ylab in plotting methods. Added a predict method. Modified EmpQ() internal function to use predict() methods for emp and rlp objects. Streamlined some of the code by including a compute.Ws() internal function and using the update() function. Changed code for finding summarized dataframes inside the function by using cast() from the reshape package -- this resulted in a 1.5x reduction in system.time().
wetperim(),summary.WetPerim(),plot.WetPerim(): added.
wlgm(): major changes included moving some internal functions outside of wlgm(), adding the ability to use the data= argument, and adding the ability to fit weighted regressions on the summary statistics. Other minor changes were also made. Updated the .Rd file.
WSval(),WRval(): added a check for missing species name so that the user can just type WSval() to get the list of possible species names. Also added a check to see if WSlit was already loaded.
Moved to RForge.net.
changed to R2.7.0.
added a dependency to Rcapture (for the example in caphist.convert).
anova.RLP(): added this function to produce the anova table for the standard weight equation.
caphist.convert(): added this function convert between various capture history formats (FSA,event,MARK,Rcapture).
emp(): added this function, and its generics, to perform Gerow's EmP method for obtaining a standard weight equation.
fit.plot.RLP(): added this function.
plot.RLP(): modified so that color palette with a gradient rather than only a solid color can be used for the populations. In addition, added order.pop= argument that will order the populations from smallest to largest predicted with in the first length interval. When used with the color gradients this will make it easier to see which populations cross over other populations.
rlp(): modified function so that the user can choose to use any-mm length intervals rather than having 10-mm hardwired. Modified output in list somewhat to more closely match the output of emp().
changed some \items to \tabular in RD files. Changed most hard-wired quotes to \sQuote or \dQuote in RD files. Changed some text-based equations to more latex-based equations in \eqn or \deqn markups. This fixed the Latex compilation problems that I was having when using RCMD check.
age.comp(): Removed single-letter values from the what= argument. Will rely on partial matching.
age.key(): Changed default name for new column with ages from "Age" to "age". Added example.
coefplot.WLGM(): Changed to use plotCI() from the plotrix package. This removed the for loop that I had programmed. This also added the sfrac= and gap= arguments. Updated the RD.
depletion(): Removed single-letter and lower-case values 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 the ci.type and phi.type arguments.
plot.RLP(): Added "object <- x" to allow x to be used inside the curve() function without confusion.
removal(): Removed abbreviated values from the type= argument. Will rely on partial matching.
rlp(): Added examples from Murphy et al. (1990)
stock.recruit(): Removed abbreviated values from the type= argument -- will rely on partial matching. Changed sumtype argument to what.
stock.recruit.sim(): Changed model argument to type and added param argument (to make compatible with stock.recruit). Moved R and S arguments to beginning of argument string (more compatible with stock.recruit). STILL NEED to ADD SECOND RICKER MODEL.
vb.comp(): Changed d argument to df.
wlgm.RD(): Added example code. Added some details.
changed to compiling under R 2.6.1.
added FSA.R file that loads the required librarys.
now depends on MASS package because of the creation of the boxcox.WLGM() function and on the plotrix package for elements of ycplot().
add.radcap(): Created this function to add the radius-at-capture to a one-fish-per-line data frame of increments.
age.comp(): Added a match.arg() call for the what argument.
age.key(): Corrected =T or =F to =TRUE or =FALSE.
cc.sim(): Corrected the use of z.param with correct use of Z.param.
coefplot(): A new generic function for plotting coefficients from a Weisberg Linear Growth Model analysis.
g.convert(): Changed arguments from data and measure.var to df and in.var. Included match.arg() for the type argument. Moved type argument as it now has a default. Added the in.pre argument that allows the user to identify all input variables by a common prefix rather than having to list them out in in.var. Added the out.pre argument that allows the user to control the prefix for the newly created variables in the output data frame. Updated help file.
g.reshape(): Changed arguments from data and prefix to df and in.pre. Deleted the measure.var argument. Moved new in.pre argument forward and na.rm argument backward in the argument list. Used in.pre to identify the measure.var variables to send to the melt function. If id.var is left blank (and in.pre is not) then id.var is the remaining variables not identified by in.pre. The val.name argument was set equal to in.pre as the default.
leslie.sim(): Corrected call to old leslie() function with a correct call to depletion() function with type="Leslie".
leslie.sim2(): Corrected two calls to old leslie() function with correct calls to depletion() function with type="Leslie".
leslie.rand.run(): Moved R Documentation alias to FSA-internal.RD.
mr.closed2(): Forced the function to use the lowess() function in the stats rather than the gplots package (which is loaded from NCStats). Also changed the loess.f argument to f and added the iter argument for sending to lowess().
confint.MRO(): Put in a logical catch when printing the confidence intervals because if ci.type="Manly" then CIs for B are not computed.
summary.MRO(): Put in a logical catch when printing the estimates because if ci.type="Manly" then SEs are not computed.
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 performing the Weisberg Linear Growth Model.
ycplot(): A new generic function for creating a year-class plot for the Weisberg Linear Growth Model analysis.