-The **FSA** package provides R functions to conduct typical introductory fisheries analyses. Example analyses that use **FSA** can be found in the [Introductory Fisheries Analyses with R book](http://derekogle.com/IFAR/) and on [the *Examples* page](http://derekogle.com/fishR/examples/) of the [fishR website](http://derekogle.com/fishR). You can browse documentation for functions in **FSA** under the *References* tab and recent changes under the *News* tab at the top of this page. Please [cite **FSA**](http://derekogle.com/FSA/authors.html) if you use it in a publication (and [send me a note](mailto:derek@derekogle.com)).
+The **FSA** package provides R functions to conduct typical introductory fisheries analyses. Example analyses that use **FSA** can be found in the [Introductory Fisheries Analyses with R book](http://derekogle.com/IFAR/) and on [the *Examples* page](http://derekogle.com/fishR/examples/) of the [fishR website](http://derekogle.com/fishR/). You can browse documentation for functions in **FSA** under the *References* tab and recent changes under the *News* tab at the top of this page. Please [cite **FSA**](http://derekogle.com/FSA/authors.html) if you use it in a publication (and [send me a note](mailto:derek@derekogle.com)).
### Installation
The [most recent stable version (on CRAN)](https://cloud.r-project.org/package=FSA) of **FSA** may be installed with
diff --git a/cran-comments/cran-comments-v0_8_31.md b/cran-comments/cran-comments-v0_8_31.md
new file mode 100644
index 00000000..a3e60794
--- /dev/null
+++ b/cran-comments/cran-comments-v0_8_31.md
@@ -0,0 +1,10 @@
+* This updates the existing FSA package on CRAN by fixing an issue related to upcoming changes to nls (per e-mail from Martin Maechler on 2-Nov-2020).
+
+## Notes
+* There may be a note about "fishR" being misspelled in the description. This is not a misspelling.
+* On [CRAN](https://cran.r-project.org/web/checks/check_results_FSA.html), there is a note in the previous version about a missing `RMark` package for the "r-patched-solaris-x86" flavor. Again (as with previous versions), I am not sure what to do about this note.
+
+## Testing Environments
+* My Windows machine.
+* Win Builder -- old-release, release, and development.
+# R-hub using check_for_cran().
\ No newline at end of file
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index 83b6c527..68d001b8 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -79,7 +79,7 @@
@@ -480,7 +480,7 @@ inst/CITATION
- Ogle, D.H., P. Wheeler, and A. Dinno. 2020. FSA: Fisheries Stock Analysis. R package version 0.8.30.9000, https://github.com/droglenc/FSA.
+Ogle, D.H., P. Wheeler, and A. Dinno. 2020. FSA: Fisheries Stock Analysis. R package version 0.8.31, https://github.com/droglenc/FSA.
@Manual{,
title = {FSA: Fisheries Stock Analysis},
author = {Derek H. Ogle and Powell Wheeler and Alexis Dinno},
year = {2020},
- note = {R package version 0.8.30.9000},
+ note = {R package version 0.8.31},
url = {https://github.com/droglenc/FSA},
}
@@ -162,7 +162,7 @@
The FSA package provides R functions to conduct typical introductory fisheries analyses. Example analyses that use FSA can be found in the Introductory Fisheries Analyses with R book and on the Examples page of the fishR website. You can browse documentation for functions in FSA under the References tab and recent changes under the News tab at the top of this page. Please cite FSA if you use it in a publication (and send me a note).
+The FSA package provides R functions to conduct typical introductory fisheries analyses. Example analyses that use FSA can be found in the Introductory Fisheries Analyses with R book and on the Examples page of the fishR website. You can browse documentation for functions in FSA under the References tab and recent changes under the News tab at the top of this page. Please cite FSA if you use it in a publication (and send me a note).
The most recent stable version (on CRAN) of FSA may be installed with
-install.packages("FSA")
+install.packages("FSA")
The most recent development version (on GitHub) may be installed with
-if (!require('remotes')) install.packages('remotes'); require('remotes') -remotes::install_github('droglenc/FSA')
+if (!require('remotes')) install.packages('remotes'); require('remotes') +remotes::install_github('droglenc/FSA')
You may need to have R Tools installed on your system to install the development version from GitHub. See the instructions for (R Tools for Windows or R Tools for Mac OS X).
NEWS.md
- tibble to suggests (see comment about headtail() below).RichardsFuns() (documentation did not change when parameter letters were changed for the Age and Growth book).headtail() to use as_tibble() from tibble package rather than tbl_df() from dplyr package. Required adding tibble to suggests.nlsTracePlot(): Modified. Created a conditional catch depending on the version of R as the results of nls(*,trace=TRUE) are changing in v4.1.0 (per e-mail from Martin Maechler on 2-Nov-20).gplots package as it is now orphaned. Required adding iRichColors() internal function.gplots package as it is now orphaned. Required adding iRichColors() internal function.lwCompPreds(): Removed \dots from arguments as it was not in usage (per request from CRAN on 3-Feb-20).hist.formula(): Modified. Fixed bug related to subsequent calls after a call that used iaxs=FALSE. This addresses #46.iLegendHelp(): Modified. Added a catch if a proper keyword is not supplied.iLegendHelp(): Modified. Added a catch if a proper keyword is not supplied.
nlsTracePlot(): Modified. Moved error catching for improper keyword for legend placement forward.alkIndivAge(): Modified. Replaced an options(warn=-1) with suppressWarnings().alkPlot(): Modified. Changed to using withr::local_par() (partially addresses #38). Replaced an options(warn=-1) with suppressWarnings().alkPlot(): Modified. Changed to using withr::local_par() (partially addresses #38). Replaced an options(warn=-1) with suppressWarnings().
alkSummaries(): Modified. Replaced an options(warn=-1) with suppressWarnings().withr::local_par() (partially addresses #38).withr::local_par() (partially addresses #38).capHistSum(): Modified. Changed to using withr::local_par() (partially addresses #38).capHistSum(): Modified. Changed to using withr::local_par() (partially addresses #38).
chapmanRobson(): Modified. Changed to using withr::local_par() (partially addresses #38).chapmanRobson(): Modified. Changed to using withr::local_par() (partially addresses #38).
fishR(): Modified. Changed examples in documentation to not be run (so as not to open an external webpage).FSAnews(): Modified. Changed examples in documentation to not be run (so as not to open an external webpage).withr::local_par() (partially addresses #38).withr::local_par() (partially addresses #38).hist.formula(): Modified. Changed to using withr::local_par() (partially addresses #38).hist.formula(): Modified. Changed to using withr::local_par() (partially addresses #38).
lwCompPreds(): Modified. Changed to using withr::local_par() (partially addresses #38).lwCompPreds(): Modified. Changed to using withr::local_par() (partially addresses #38).
plotAB(): Modified. Now in its own documentation file (rather than with ageBias()).removal(): Modified. Added method="Burhnam" via the #51 from Powell Wheeler.residPlot(): Modified. Changed to using withr::local_par() (partially addresses #38).residPlot(): Modified. Changed to using withr::local_par() (partially addresses #38).
SMBassWB: Modified. Fixed minor data entry error in row 383.bcFuns(): Modified. Changed three 1:length() structures to seq_along() (partially addressing #36).bootCase() methods: Modified. Changed all 1: structures to seq_len() (partially addressing #36).bootCase() methods: Modified. Changed all 1: structures to seq_len() (partially addressing #36).
capHistConvert(): Modified. Changed all 1: structures to seq_len() or seq_along() (partially addressing #36).htest.boot(): Removed (added last version) until I can test more.iHndlFormula(): Modified. Now categorizes a character variable as a factor variable. This addresses #35) for hist.formula() and Summarize().iHndlFormula(): Modified. Now categorizes a character variable as a factor variable. This addresses #35) for hist.formula() and Summarize().
lrt(): Modified. Changed all 1: structures to seq_len() or seq_along() (partially addressing #36).mrClosed(): Modified. Changed two 1:length() structures to seq_along() (partially addressing #36).nlsBoot() methods: Modified. Changed all 1: structures to seq_len() (partially addressing #36).nlsBoot() methods: Modified. Changed all 1: structures to seq_len() (partially addressing #36).
plot.boot(): Removed (added last version) until I can test more.R >=3.2.0, because that is the latest version required by a package (i.e., car) that FSA imports or suggests. Used the “check_r_versions_of_package_dependencies” shiny app by “ateucher” (on Github) to help determine this.testthat package.bootCase(): Added. This was added because bootCase() will soon be removed from the car package. It was added so that the code in the Introductory Fisheries Analyses with R book will still work. It is largely a wrapper to Boot() in car with method="case". The documentation was updated somewhat.bootCase(): Added. This was added because bootCase() will soon be removed from the car package. It was added so that the code in the Introductory Fisheries Analyses with R book will still work. It is largely a wrapper to Boot() in car with method="case". The documentation was updated somewhat.
catchCurve(): Modified. Changed the weighted regression method so that negative weights are set to zero rather than the minimum of the positive values (brought to my attention by Vaskar Nepal KC). Also added an rSquared() method (per request by Vaskar Nepal KC).dunn.test and lmtest to imports to help with portability for workshops.ageBias(): Modified. Fixed bug in plot() so that the tick marks on the marginal histograms match the tick marks on the main plot. Changed the default hist.panel.size= in plot() so that it more reliably prints the values on the axes of the marginal histograms.ageBias(): Modified. Fixed bug in plot() so that the tick marks on the marginal histograms match the tick marks on the main plot. Changed the default hist.panel.size= in plot() so that it more reliably prints the values on the axes of the marginal histograms.removal(): Modified. Added “warnings” for when all catches are zeroes (an object is still returned with all NAs). Thanks to Daniel Hanks for pointing out this issue.lagratio(): Modified. Changed some if()s with class()es to inherits().iHndlCols2UseIgnore(): Modified. Changed some if()s with class()es to inherits().iHndlCols2UseIgnore(): Modified. Changed some if()s with class()es to inherits().
iLegendHelp(): Modified. Changed some if()s with class()es to inherits().iLegendHelp(): Modified. Changed some if()s with class()es to inherits().
iPredictBoot(): Modified. Changed some if()s with class()es to inherits().is.CapHist(): Added.iTypeoflm(): Modified. Added a catch for a linear model that has a character variable (now alerts the user with a warning).iTypeoflm(): Modified. Added a catch for a linear model that has a character variable (now alerts the user with a warning).
mrClosed(): Modified. Changed some if()s with class()es to is.CapHist().mrOpen(): Modified. Changed some if()s with class()es to is.CapHist().mrOpen(): Modified. Changed some if()s with class()es to is.CapHist().
nlsTracePlot(): Modified. Changed some if()s with class()es to inherits().devtools::spell_check().fishmethods and changes to R v3.4.0.metaM(): Modified. Changed T= to Temp= to reduce potential for conflicts with TRUE abbreviation.metaM(): Modified. Changed T= to Temp= to reduce potential for conflicts with TRUE abbreviation.
reproInfo(): Modified. Added ind= to select a CRAN mirror to help with a common problem I have when knitting.reproInfo(): Modified. Added ind= to select a CRAN mirror to help with a common problem I have when knitting.
srStarts(): Modified. Corrected mis-spelling in directive to FSAsim package.stop()s to STOP()s and all warning()s to WARN(). This modified nearly all functions.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..onAttach(): Modified. Streamlined package startup message.addZeroCatch(): Modified. Added more “catches” for bad data types or arguments.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().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().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().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().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).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.”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().iHndlMultWhat(): Modified. Added type= to allow use with message() or cat().
iPlotExists(): Added. Helps with bug fix in hist.formula().iPlotExists(): Added. Helps with bug fix in hist.formula().
is.wholenumber(): Added. Needed for changes to binCI(), hyperCI(), and poiCI().is.wholenumber(): Added. Needed for changes to binCI(), hyperCI(), and poiCI().
kCounts(): Modified. Fixed bug with capitalize= and zero. Streamlined code. Added tests.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.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.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().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.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().predict.nlsBoot(): Modified. See note for predict.bootCase().
psdCalc(): Modified. Fixed bug in output if more than two additional lengths were supplied.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().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".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.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.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.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.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.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().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().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().GompertzModels(): Removed. Replaced with growthFunShow().iGetDecimals(): Modified. Fixed a bug that occured when an integer was provided.iGetDecimals(): Modified. Fixed a bug that occured when an integer was provided.
lenFreqExpand(): Removed. Deprecated since 0.4.32. Use expandLenFreq().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.iCheckStartCatW(): Modified. Now use iGetDecimals() to extract the number of decimals in startcat and w.
iCheckStartcat(): Added.iCheckW(): Added.iGetDecimals(): Added.iGetDecimals(): Added.
lencat(): Modified. Changed order of startcat= and breaks=. Slight modifications to documentation.psdVal(): Modified. Minor changes to documentation.purl2(): Modified. Added delHeader= argument and functionality.purl2(): Modified. Added delHeader= argument and functionality.
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.
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).
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.
headtail(): Modified. Changed head() to utils::head() and tail() to utils::tail().hist.bootCase(): Modified. Changed hist() to hist.formula().hist.bootCase(): Modified. Changed hist() to hist.formula().
iAgeBiasPlot(): Modified. Changed grconvertY() to graphics::grconvertY().iHistResids(): Modified. Removed graphics::hist() and changed to hist.formula().iHndlFormula(): Modified. Changed terms() to stats::terms().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().iMakeColor(): Modified. Changed rgb() to grdevices::rgb().
iMakeModelHeading(): Modified. Changed formula() to stats::formula() (within an lapply()).iSchnute(): Modified. Changed optimize() to grdevices::optimize().iTypeoflm(): Modified. Changed formula() to stats::formula().iTypeoflm(): Modified. Changed formula() to stats::formula().
plot.AgeBias(): Modified. Changed rgb() to grdevices::rgb().psdVal(): Modified. Changed data() to utils::data().reproInfo(): Modified. Changed graphics.off() to grdevices::graphics.off().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.reproInfo(): Added markdown to the out= types.reproInfo(): Added markdown to the out= types.
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.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.sumTable(): Modified. Converted to using iHndlFormula(). Added tests.
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.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.importFrom() directives and went to hard-wiring to packages with ::. Added imports() directives for stats, graphics, tools, and grDevices. Removed imports() directive for multcomp().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.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.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().confint.nlsBoot(): Modified. Created a common internal function for use with confint.bootCase().
GompertzFuns(): Moved into growthModels file. Did not change behavior.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.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().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.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.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().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.hist.formula(): Modified. Rebuilt to use iHndlFormula(). Modified how xlab= is used (result is the same). Added some tests.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().ksTest(): Modified. Rebuilt to use iHndlFormula(). Added some tests for messages and to make sure results matched ks.test().
alkIndivAge(): Modified. Switched to using iHndlFormula() at the beginning. Added more checks and tests.alkIndivAge(): Modified. Switched to using iHndlFormula() at the beginning. Added more checks and tests.
expandLenFreq(): Modified. Added more checks. Added some tests.ks2d2p(): Modified. Rewrote the print() method. This removed a number of cat()s.metaM(): Modified. Changed all cat() to message()s.metaM(): Modified. Changed all cat() to message()s.
mrOpen(): Modified. Changed all cat() to message()s.mrOpen(): Modified. Changed all cat() to message()s.
removal(): Modified. Changed all cat() to message()s.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.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.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.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.
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.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().kCounts(): Added. Was swvCounts().
kPvalue(): Added. Was swvPvalue().kPvalue(): Added. Was swvPvalue().
purl2(): Added. Was swvCode(). Added timestamp= argument for adding a timestamp to the created script.purl2(): Added. Was swvCode(). Added timestamp= argument for adding a timestamp to the created script.
reproInfo(): Added. Was swvFinish().reproInfo(): Added. Was swvFinish().
swvANOVA(): Deleted. Moved to NCStats.swvCode(): Deleted. Changed to purl2().swvCode(): Deleted. Changed to purl2().
swvCounts(): Deleted. Changed to kCounts().swvCounts(): Deleted. Changed to kCounts().
swvFinish(): Deleted. Changed to reproInfo().swvFinish(): Deleted. Changed to reproInfo().
swvGLHT(): Deleted. Moved to NCStats.swvHtest(): Deleted. Moved to NCStats.swvPvalue(): Deleted. Changed to kPvalue().swvPvalue(): Deleted. Changed to kPvalue().
swvREG(): Deleted. Moved to NCStats.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.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..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.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.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.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.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'.catchCurve(): Modified. Removed the use of larger points in the plot().catchCurve(): Modified. Removed the use of larger points in the plot().
chapmanRobson(): 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.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.Mmethods(): Added. Added as a function and removed as a vector.
alkPlot(): Modified. Changed behavior for adding a legend to alleviate a bug.metaM(): Added.metaM(): Added.
confint.nlsBoot(): Modified. Changed default for err.col= to black from red. Fixed example due to changes in nlsBoot package.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.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.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.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().tictactoe(): Modfied.tictactoeAdd(): Removed. Directed user to use plotCI() from plotrix instead.tictactoeAdd(): Removed. Directed user to use plotCI() from plotrix instead.
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.summary.mrOpen(): Modified. Removed “Estimates” heading if verbose=FALSE.
Summarize(): Modified. Moved all internal functions outside of Summarize() environment (and renamed them).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.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.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.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.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().iAddLoessLine(): Modified. See residPlot().
iHndlFormula(): Modified. COrrected the positioning of the explanatory variables when the model has a response variable.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.)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.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.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..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().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().ciLabel(): Deleted. Moved functionality to iCILabel().
getAllDependencies(): Deleted. Moved functionality to iGetAllDependencies() and moved code to swvUtils file.getMainTitle(): Deleted. Moved functionality to iGetMainTitle() and moved code to residPlot() file.getVarFromFormula(): Deleted. Moved functionality to iGetVarFromFormula().getVarFromFormula(): Deleted. Moved functionality to iGetVarFromFormula().
hndlFormula(): Deleted. Moved functionality to iHndlFormula().hndlFormula(): Deleted. Moved functionality to iHndlFormula().
hndlMultWhat(): Deleted. Moved functionality to iHndlMultWhat().hndlMultWhat(): Deleted. Moved functionality to iHndlMultWhat().
iAddLoessLine(): Added. Was addLoessLine().iAddLoessLine(): Added. Was addLoessLine().
iAddOutlierTestResults(): Added. Was addOutlierTestResults().iCheckStartcatW(): Added. Was checkStartcatW().iCheckStartcatW(): Added. Was checkStartcatW().
iCIfp(): Added. Was ci.fp().iCIfp1(): Added. Was ci.fp.1().iCILabel(): Added. Was ciLabel().iCILabel(): Added. Was ciLabel().
iGetAllDependencies(): Added. Was getAllDependencies().iGetMainTitle(): Added. Was getMainTitle().iGetVarFromFormula(): Added. Was getVarFromFormula().iGetVarFromFormula(): Added. Was getVarFromFormula().
iHndlFormula(): Added. Was hndlFormula().iHndlFormula(): Added. Was hndlFormula().
iHndlMultWhat(): Added. Was hndlMultWhat().iHndlMultWhat(): Added. Was hndlMultWhat().
iLegendHelp(): Added. Was legendHelp().iLegendHelp(): Added. Was legendHelp().
iMakeColor(): Added. Was makeColor().iMakeColor(): Added. Was makeColor().
iMakeFilename(): Added. Was makeFilename().is.odd(): Added. Was odd().iTypeoflm(): Added. Was typeoflm().iTypeoflm(): Added. Was typeoflm().
iwsLitCheck(): Added. Was wsLitCheck()
legendHelp(): Deleted. Moved functionality to iLegendHelp().legendHelp(): Deleted. Moved functionality to iLegendHelp().
listSpecies(): Deleted. Moved functionality to iListSpecies().listSpecies(): Deleted. Moved functionality to iListSpecies().
makeColor(): Deleted. Moved functionality to iMakeColor().makeColor(): Deleted. Moved functionality to iMakeColor().
makeFilename(): Deleted. Moved functionality to iMakeFilename() 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.predict.nlsBoot(): Added an interactive() to the nlstools example in the help file.
printProgressMsg(): Deleted. Not used anywhere.pssVal(): Deleted. Was deprecated several versions ago. See psdVal().typeoflm(): Deleted. Moved functionality to iTypeoflm().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.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.agePrecision(): Modified. Removed deprecated what="agreement".confint.nlsBoot(): Modified. Changed example from “dont run” to “interactive.”confint.nlsBoot(): Modified. Changed example from “dont run” to “interactive.”
fact2num(): Modified. 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.”htest.nlsBoot(): Modified. Changed example from “dont run” to “interactive.”
lagratio(): Modified. Changed example from “dont run” to “interactive.”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.
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 zeros 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 zeros 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.
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. 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.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().stackpoly() from plotrix for use in ageKeyPlot().stackpoly() from plotrix for use in ageKeyPlot().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.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()).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.
histStack(): Deleted, moved to plotrix package. Arguments were changed there.
ks2d(): Deleted, changed to ks2d2().
ks2d1(): Added.
ks2d2(): Added, was ks2d().
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.
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().
.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 zeros. 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).
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%.
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%.
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.
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().
A data frame with 277 observations on the following 2 variables.
A data frame with 277 observations on the following 2 variables.
a numeric vector of indicator variables for the first sample (1=captured)
a numeric vector of indicator variables for the second sample (1=captured)
Used in mrClosed examples.
