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pkgdown.yaml GitHub action to v2.
Changed action to only run on a release (rather than a push) but it can
be run
manually as well.R-CMD-check.yaml GitHub action to v2.
Note that I had to add the extra code for
dealing with graphics on the Mac version.fishR(), FSA(), and
README.md. Partially address #86._pkgdown.yml to match that of
FSAdata and more closely match fishR.pkgdown
picks up the CRAN release date to add.CITATION (to match that required for next
version of R).alkIndivAge(): Modified. Added a catch for
NAs in the length sample. Also added a test. This addresses
#88.confint.boot(): Modified. Changed hard-coding of
columns that contained the confidence interval values to find those
columns by grep()ing for the % sign. This
fixes an issue related to car::Confint() returning the
coef() results for functions that have a
coef() method but not for those that do not. Also updated
tests to use results from car::Boot() rather than the old
car::bootCase().PSDcalc: Modified. Changed code to allow for missing
species= as long as addLens= is used. This
allows the user to provide length categories for a species for which
Gabelhouse lengths are not defined. Several new tests were added and
some were modified to handle the changing message re: a missing
species=. The documentation was modified accordingly. This
(finally) addresses #58.PSDlit: Modified. Added info for Redbreast Sunfish and
Spotted Sunfish from Bonvecchio et al. (2023). This addresses
#100).wSlit: Modified documentation. Described the
RLP and EmP acronyms and provided references
for them. This addresses #95). Added
info for Redbreast Sunfish and Spotted Sunfish from Bonvecchio et
al. (2023). This addresses #100).dplyr from imports to
suggests (needed because functions were removed in last
version; however it is still used in some examples; partially addresses
#87).sciplot from imports (because
functions were removed in last version; partially addresses #87).ksTest() to handle issues on the CRAN
M1 build machine (per e-mail from Prof. Ripley on 15-Feb-22; partially
addresses #87).droglenc github that were
related to FSA or FSAdata to be to the
fishR-Core-Team github.filterD(): REMOVED (to
FSAmisc).fitPlot(): REMOVED (to
FSAmisc).fsaNews() and FSANews():
Removed.psdAdd(): Modified. Changed the way PSDlit
was loaded into the function environment so that
FSA::psdAdd() will work. Addresses #85.PSDLit: Modified. Added info for Utah Chub (from here;
address #84).psdVal(): Modified. Changed the way PSDlit
was loaded into the function environment so that
FSA::psdVal() will work. Addresses #85.residPlot(): REMOVED (to
FSAmisc).wrAdd(): Modified. Changed the way WSlit
was loaded into the function environment so that
FSA::wrAdd() will work. Addresses #85.WSLit: Modified. Added info for Utah Chub (from here;
address #84).wsVal(): Modified. Changed the way WSlit
was loaded into the function environment so that
FSA::wsVal() will work. Addresses #85.catchCurve() and
chapmanRobson() as directed by CRAN on 17-Jul-21. Issue
likely caused by changes to fishmethods package.AUThor.plyr from Imports to Suggests.alkPlot(): Modified. Removed use of
chooseColors() (see below).binCI(): Modified. Changed to use
iCheckConfLevel() (which addresses #66).bootCase(): REMOVED. Users can use
car::Boot(), which partially addresses #65.
plot.boot(): REMOVED. Conflicted with
boot::plot.boot() which caused an error with CRAN. Same
functionality is available with
pairs(<boot object>$t).catchCurve(): Modified. Removed hard-coding of
ylim= for plot.catchCurve() (this addresses #70 … Thanks
to Brendan Runde). Added round.est= so that the user can
control the decimals on mortality estimate values. Changed to use
iCheckConfLevel() (which addresses #66).chapmanRobson(): Modified. Removed hard-coding of
ylim= for plot.chapmanRobson(). Added
round.est= so that the user can control the decimals on
mortality and survival estimate values. Changed to use
iCheckConfLevel() (which addresses #66).chooseColors(): REMOVED. This was an
exported function that should have been internal. Regardless, where it
was used has been removed and the user is now allowed to provide their
own vector of colors. See iCheckMultColors(). Partially
addresses #65.compIntercepts(): REMOVED (to
FSAmisc). Added to FSA-defunct. Partially
addresses #65.compSlopes(): REMOVED (to
FSAmisc). Added to FSA-defunct. Partially
addresses #65.depletion(): Modified. Changed to use
iCheckConfLevel() (which addresses #66).filterD(): DEPRECATED (partially
addresses #65).fitPlot(): DEPRECATED (partially
addresses #65). Prior
to that removed use of chooseColors() (see above).diags(): REMOVED (moved to
FSAmisc). Added to FSA-defunct. Partially
addresses #65.hoCoef(): REMOVED (moved to
FSAmisc). Added to FSA-defunct. Partially
addresses #65.hyperCI(): Modified. Changed to use
iCheckConfLevel() (which addresses #66).iCheckConfLevel(): Added (internal to address #66).iCheckMultColors(): Added (internal). Part of removing
chooseColors() and paletteChoices().iRichColors(): REMOVED (as part of
removing chooseColors()).mapvalues(): REMOVED. Added to
FSA-defunct. Partially addresses #65.mrClosed(): Modified. Changed to use
iCheckConfLevel() (which addresses #66).mrOpen(): Modified. Added a warning for when r==0,
which causes the SE of M and thus N to be Infinity (this
addresses #69). Added
a similar warning for when R==0 (but not the last time period). Added
tests for the warning messages. Changed one use of apply()
to rowSums() for ease of reading. Changed to use
iCheckConfLevel() (which addresses #66).paletteChoices(): REMOVED. See
chooseColors() above. Partially addresses #65.poiCI(): Modified. Changed to use
iCheckConfLevel() (which addresses #66).psdAdd(): Modified. Changed a levels() in
iPSDlitCheck() to unique() because
species is no longer a factor due to updating
PSDlit (i.e., rdata file changed with new
read.csv()).psdCalc(): Modified. Added a catch for when “tibble”s
are sent in data= (addresses #75).
Changed to use iCheckConfLevel() (which addresses #66).psdCI(): Modified. Changed to use
iCheckConfLevel() (which addresses #66).PSDlit: Modified. Added length categories for Shoal
Bass and Pallid Sturgeon. Added Striped Bass (Hybrid) and Striped Bass x
White Bass; though these are the same as the existing Palmetto Bass.
Added “source”s for each entry.psdVal(): Modified. Changed a levels() in
iPSDlitCheck() and iListSpecies() to
unique() because species is no longer a factor
due to updating PSDlit (i.e., rdata file changed with new
read.csv()). Added a showJustSource= argument
that will show the source info (if TRUE) or not (if
FALSE; default), which partially addresses #76.removal(): Modified. Added check and then warning if
non-whole numbers are in catch= (addresses #60). Also
modified checks of data integrity to be more robust (e.g., if a
character vector is sent). Changed to use iCheckConfLevel()
(which addresses #66).residPlot(): DEPRECATED (partially
addresses #65). Prior
to that removed use of chooseColors() (see above).Subset(): REMOVED. Added to
FSA-defunct. Partially addresses #65.wrAdd(): Modified. Changed a levels() in
iwsLitCheck() to unique() because
species is no longer a factor due to updating
WSlit (i.e., rdata file changed with new
read.csv()).WSlit: Modified. Addresses #68.
wsVal(): Modified. Changed a levels() in
iwsLitCheck() to unique() because
species is no longer a factor due to updating
WSlit (i.e., rdata file changed with new
read.csv()).usethis::use_github_action_check_standard()).usethis::use_github_action("pkgdown")).tests\plottests\ to speed up testing. The
tests\plottests\ was added to .Rbuildignore
.hist.formula(): Modified. Fixed bug with y-axes when
freq=FALSE is used (fixes #62; thanks
to @carlostorrescubila).fitPlot(): Modified. Fixed bugs with handling models
that used character rather than factor variables.plotBinResp(): REMOVED. Removed as a user-facing
function, but made as an internal function for continued use in
fitPlot() while fitPlot() is deprecated.psdAdd(): Modified. Fixed bug relate to species that
were NA (fixes #64; thanks
to Dan Shoup). Added more tests and fixed some typos in the
documentation.psdPlot(): Modified. Fixed bug with box around the plot
when add.psd=FALSE. Added 5% expansion to top of y-axis so
that bars did not run into the box.residPlot(): Modified. Fixed bugs with handling models
that used character rather than factor variables.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).rhub::check_for_cran() for checking
before sending to CRAN.Summarize() and ksTest()
that used data.frame(). This should have been done with
v0.8.28.ksTest() that were identified
using R-hub.fishR(): Modified. Changed base URL to
https: (from http:). Added open=,
primarily to allow not opening a browser during testing.epitools package as it may soon
be orphaned. See changes to binCI() and
poiCI() outlined below.binCI(): Modified. Added internal functions that are
based on (but not identical to) functions in the epitools
package which will possibly be deprecated soon (per note from CRAN on
7-Mar-20).poiCI(): Modified. Added internal functions that are
based on (but not identical to) functions in the epitools
package which will possibly be deprecated soon (per note from CRAN on
7-Mar-20).fitPlot(): Modified. Changed so that lines are plotted
after the points in the IVR versions.ksTest(): Modified. Changed documentation examples to
handle R’s new way of handling stringsAsFactors= (per
request from CRAN on 27-Feb-20).psdAdd(): Modified. Changed testing to handle R’s new
way of handling stringsAsFactors= (per request from CRAN on
27-Feb-20).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).repeatedRows2Keep(): Modified. Now makes comparisons as
if NAs are regular values.R >=3.5.0, 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.asbio package from suggests as it hung up
Travis-CI build (because of the need for the TCLTK package).capFirst(): Modified. Fixed bug related to an
NA item.psdAdd(): Modified. Changed spec= to
species= to be consistent with psdCalc() and
psdPlot().peek(): Added.repeatedRows2Keep(): Modified. Added a catch if the
data.frame only contains one row (it then returns TRUE so
that that row is kept).agePrecision(): Modified. Changed so that PE2 and CV2
use the median in the entire calculation rather than just in the
denominator.iHndlColsUseIgnore(): Modified. Changed so that a 0
indice returns an error.repeatedRows2Keep(): Added.vbStarts(): Modified. Corrected bug related to point
transparenty when plot=TRUE and there is no age/length
combination repeats (i.e., all age/length combinations are unique).
Corrected bug of col.main= being ignored when
plot=TRUE.\concept in Rd files per CRAN
request.testthat folder as suggested in
testthat release notes.Subset() (replaced with
filterD()).fitPlot(): Modified. Fixed bug related to y-axis limits
not extending to contain the data, confidence bands, or prediction bands
(in fitPlot.slr()). This addresses #3 listed for
NCStats).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.nlsTracePlot(): Modified. Moved error catching for
improper keyword for legend placement forward.SchnuteRichards(): Added. This addresses #54.fishmethods package
(vblrt() replaced with growthlrt() and
T= replaced with TC= in
M.empirical()) per CRAN request.withr to Imports (see usages below).Encoding: UTF-8 to DESCRIPTION.method="Burnham" to removal().dunnTest(). Should have done this long
ago.data() in examples that referred to data
from this package. Included the package= argument in
data() that loaded from other packages.seealso, with links to which functions use the
data for examples, to docmentation for all data.frames.\dontrun()s from the bootCase
related examples now that car package is updated. This
addresses #45.addZeroCatch(): Modified. Added a catch that turns a
“tibble” into a regular data.frame (which obviates some errors that
occur with tibbles). Minor changes to documentation and comments in the
code.agePrecision(): Modified. Added intermediate and
summary calculations for median and modal age; average absolute
deviation and standard deviation; APE and CV with the median rather than
the mean as the divisor; and index of precision (D). Added
show.prec2=. Updated tests and examples. Other minor
modifications to the function code. Addresses #41 and #49.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().alkSummaries(): Modified. Replaced an
options(warn=-1) with suppressWarnings().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).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).hist.formula(): 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()).psdCalc(): Modified. Better handled the situation where
the user asks for summaries with some fish greater than stock size but
no fish greater than quality size (addresses #50; thanks
to Timothy Spier for the bug report).removal(): Modified. Added
method="Burhnam" via the #51 from
Powell Wheeler.residPlot(): Modified. Changed to using
withr::local_par() (partially addresses #38).SMBassWB: Modified. Fixed minor data entry error in row
383.vbFuns(): Modified. Added Francis3 to the
list of models.asbio, DescTools, nlme,
and psych packages to Suggests because they are used in
tests (and as will soon be required by CRAN … per an e-mail from CRAN on
17-May-18).addRadCap(): Removed. Moved to RFishBC
package.bcFuns(): Removed. Moved to RFishBC
package.gConvert(): Removed. Moved to RFishBC
package.mrClosed(): Modified. Fixed a bug that was related to
poiCI() returning results from all four types. Now
mrClosed() will use only one type. Thanks to Timothy Spiers
for pointing out this bug.SMBassWB: Modified. Fixed minor data entry error in row
404. Changed link in documentation from alr3 to
alr4 package.addZeroCatch(): Modified. Changed two
1:nrow() structures to seq_len(nrow())
(partially addressing #36).ageBias(): Modified. Changed all 1:
structures to seq_len() (partially addressing #36).agePrecision(): Modified. Changed all 1:
structures to seq_len() (partially addressing #36).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).capHistConvert(): Modified. Changed all 1:
structures to seq_len() or seq_along()
(partially addressing #36).capHistSum(): Modified. Changed all 1:
structures to seq_len() (partially addressing #36).chooseColors(): Modified. Changed all 1:
structures to seq_len() (partially addressing #36).compSlopes(): Modified. Changed all 1:
structures to seq_len() (partially addressing #36).compIntercepts(): Modified. Changed all 1:
structures to seq_len() (partially addressing #36).extraSS(): Modified. Changed all 1:
structures to seq_len() or seq_along()
(partially addressing #36).headtail(): Modified. Changed all 1:
structures to seq_len() (partially addressing #36).hist.formula() methods: Modified. Changed all
1: structures to seq_len() (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().lrt(): Modified. Changed all 1: structures
to seq_len() or seq_along() (partially
addressing #36).lwCompPreds(): 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).plot.boot(): Removed (added last version) until I can
test more.predict.boot(): Removed (added last version) until I
can test more.psdAdd(): Modified. Changed three 1:
structures to seq_len() or seq_along()
(partially addressing #36).residPlot(): Modified. Changed three
1:length() structures to seq_along()
(partially addressing #36).Summarize(): Modified. Changed one
1:length() structure to seq_along() (partially
addressing #36).wrAdd(): Modified. Changed three 1:
structures to seq_len() or seq_along()
(partially addressing #36).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.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).depletion(): Modified. Added an rSquared()
method.expandCounts(): Modified. Minor changes to
documentation.hTest.boot(): Added.plot.boot(): Added.plotAB(): Modified. Added col.numbers= to
allow users to modify the color of the numbers when
what="numbers" is used (addresses #34).predict.boot(): Added.psdPlot(): Modified. Minor changes to documentation and
look of the function code.rSquared(): Added from NCStats, but
including a generic method so that it can be used for other models
(e.g., catchCurve()).vbFuns(): Modified. Switched Fabens and
Fabens2 parameterizations to better match Wang
(i.e., increment model first). Added Francis2
parameterization for tag-recapture data.vbStarts(): Modified. Fixed some spacing issues with
the warnings when starting values for Linf was poorly estimated. Added
an argument to ivbStarts.LinfK() to suppress checking the
value of Linf. This argument reduces the change of double-printing the
warning message when there are bad estimates of starting values for Linf
and K.dunnTest(): Modified. Adjusted code to handle the
addition of altp= to and modified output from
dunn.test() in dunn.test. Added additional
tests and corrected some issues in the documentation.GompertzFuns(): Modified. Fixed error in message (i.e.,
msg=TRUE) for param="Ricker2".growthFunShow(): Modified. Fixed error in expression
for type="Logistic" and
param="CampanaJones1".helpers directory that will test
that all required packages are installed.iAddOutlierTestResults(): Modified. Fixed bug related
to point labels in residPlot() when the data.frame for the
original model had NA values.removal(): Modified document by merging pull request #33.srStarts(): Modified. Added fixed=. Added
some catches for poor starting values. Added relevant tests. Addresses
#30.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.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.Summarize(): Modified. Fixed bug when
percZero!="always" and there are no valid values such that
the calculated percent of zeroes is NA.ageBias(): Modified. A complete rebuild of
plot. Major changes are to add plotAB() which
is primarily used to make the “legacy” age bias plots of Campana,
removal of the “sunflower” plot option, new sets of defaults for many of
the arguments that reflect my preferences for visualizing age
comparisons (which includes defaulting to plotting differences in ages),
addition of the ability to add marginal histograms (xHist=,
yHist=, col.hist=, and
hist.panel.size=), better handling of axis ticks and labels
(primarily to show ticks at integers and make sure 0 is included for
differences), and allowing the ability to add “summary layers” to the
main plot (see allowAdd=). Many examples were added. Some
functionality from previous versions will be broken.capFirst(): Modified. Changed some if()s
with class()es to inherits().compIntercepts(): Modified. Replaced two
dim() calls with nrow().fact2num(): Modified. Changed some if()s
with class()es to inherits().lagratio(): 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().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).mrClosed(): 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().perc(): Modified. Changed some if()s with
class()es to inherits().plotAB(): Added. See description above for
ageBias().plotBinResp(): Modified. Changed how default
transparency level is calculated and set the maximum transparency to 50
(changed from 500). Fixed bug in how the width of the proportions
windows were calculated by default. These changes will affect
fitPlot() for logistic regression models.psdAdd(): Modified. Changed some if()s
with class()es to inherits().residPlot(): Modified. Changed default for
loess= from TRUE to FALSE.
Changed some if()s with class()es to
inherits().wrAdd(): 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.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.vbStarts(): Modified. Added a catch that Linf cannot be
automatically estimated with fewer than three ages. Corrected
mis-spelling in directive to FSAsim package.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 include all of the information returned 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
returning 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 unlikely 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 FSAsim 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 FSAsim 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 zeros 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.Date: Jun14
added testthat files for error checking of
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.
Date: May14
added Suggests for testthat,
fishmethods, FSAdata for testing and
popbio for an example that was made “interactive” from
“dont run”(see below).
added testthat files for 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().
Date: May14
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 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.
Date: May14
Added Roxygen directives to DESCRIPTION.
Updated to Roxygen2 4.0.0 which modified several help files.
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.
Date: May14
Removed nlme dependencies (with removal of
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.Date: Apr14
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.
Date: Apr14
Changed to compiling under R 3.1.0
Imported stackpoly() from plotrix for use in
ageKeyPlot().
Added concepts (that largely match those in the FSAdata pacakge) to most of the data files.
Made some grammatical changes and added author sections to Rd files.
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).
Date: Apr14
Converted to using github as a repository.
Changed NEWS to NEWS.md
Added ImportFrom for relax package (see below).
ageBias(): Modified. Added a plot that shows 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.Date: Dec13
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().
Date: Oct13
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()).
Date: Jun13
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 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).
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 zeros 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%.
Date: Jan13
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).
Date: 21Dec12
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 usinggslider()instead ofslider()`.
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%
smaller or larger than the observed maximum length in the data
set.
Date: 1Dec12
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
Date: 25Nov12
Switched to using the Project mode in RStudio.
Switched to using semantic versioning for the version number (which means that the hyphen before the last number has been replaced 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).
Date: 8-Nov-12
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).
Date: 21Jun12
Switched to compiling under R version 2.14.1 (64-bit).
Changed license specification from “GPL version 2 or newer” to “GPL (>= 2)” to avoid warning on check.
Added a suggestion for gdata to fix warning with capHistConver.rd (see below).
`capHistConvert.rd: Modified the examples to not use “gdata::combine” by adding a “require(gdata)” in the examples 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.
.onLoad(): Modified. Moved the startup message into
packageStartupMessage() in hopes of eliminating the warning when
checking the package.catchCurveSim(): Modified. Changed max.age= to 15 (from
10). Slightly changed the labels related to ‘Z Steady’ and ‘N*
`Steady’.chapmanRobson(): Modified. Corrected a bug for when the
ages2use= argument contains ages that are not found in the data. Thanks
to Eric Berglund for finding this bug.psdVal(): Modified. As described for rsdVal().rsdCalc(): Added.rsdPlot(): Modified. Modified to reflect changes in
rsdVal().rsdVal(): Modified. Removed the metric= and mm=
arguments in favor of a new argument, units=, where the user chooses the
units as a string. This streamlines, for example, the selection of mm.
The modifications also resulted in mm being the default. Also, removed
the appended units names from the names attribute – i.e., “stock” rather
than “stock.mm” or “stock.in”.wrAdd(): Added.wrVal(): Modified. As described for wsVal().wsVal(): Modified. Removed the justcoef= argument.
Added the ab= and comment= arguments. Also, removed the appended units
names from the names attribute – i.e., “int” rather than “int.E” or
“int.mm”.Date: 1Oct11
Switched to compiling under R version 2.13.1 (32-bit).
Removed importFroms that were required for updateFSA().
Removed splines package from imports list (not needed).
capHistConvert(): Modified. Modifications to 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.
Date: 19Aug11
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. 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.
Date: 15Jun11
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”).
Date: 18Apr11
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.
Date: 3Mar11
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.
catchCurve(): Modified by adding a formula method. This
required moving the original code into a default method and changing the
age= argument to x=.lenFreqExpand(): Modified by adding the additional=
argument (which required modifying the total= argument and adding an
error check for the situation where the total fish to assign lengths is
not greater than the number of fish in the measured subsample)..onLoad(): modified. Changed to include version number
of loaded version.vbFuns(): Modified by adding simple= argument. Added a
‘Somers’ seasonal growth oscillations model and ‘Fabens’ model for
tag-recapture data. Also added, but did not check, a ‘Laslett’ ‘double
von Bertalanffy’ model.vbStarts(): Modified by setting a catch to return a
single root for st0 or sL0 if the polynomial root found a double root.
Thanks to Giacom* `Tavecchia for identifying this error. Added a
‘Somers’ seasonal growth oscillations model.bcFuns(): Added. Still needs to be thoroughly
proofed.FSAsims(): Modified to reflect srSim() change described
below.listSpecies(): Moved internal function out of being
within RSDval() and WSval() and then added an argument for the data
frame containing the species names. The hope was that this would correct
the “n* `visible binding” warnings when performing RCMD check but it did
not.srModels(): Renamed from stockRecruitModels() to be
more consistent with the rest of the stock-recruitment functions.srSim(): Renamed from stockRecruitSim() to be more
consistent with the rest of the stock-recruitment functions.vbDataGen(): Modified use of minAge argument – will now
always back-calculate to age-1 but minAge denotes the minimum
age-at-capture that will be modeled. Deleted use of cfAge variable in
code.vbModels(): Added.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().Date: 20Aug10
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 zeros to be considered as a length found in the age length key.
Now the row sums are found and the sums with NaN or 0 are removed. 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.
growmodel.sim(): added an option to fit the “original”
von Bertalanffy function. Also added more “mis-spelling” options to the
other model names.Date: 17Dec09
moved to compiling under 2.10.1.
`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.
FSA-package(): updated.
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.
.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.validateWs(): converted sign.slope variable in the
Willis method to a factor to deal with situations where all results were
positive or negative.age.comp(): streamlined code (put bias and difference
plots in same function, used grconvertY for show.n, used plotCI for
range intervals, caught and corrected CI problems when n=1 or SD=0). N*
`functionality difference, just improved code.growmodel.sim(): modified by determining some of the
slider values from the data when x= and y= arguments are not null. This
makes the graph more useful for determining starting values in nls()
modeling.Date: 6Dec08
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.
.First.lib: Addedadd.zerocatch(): added this function to add zeros to
catch records where a species of fish was not caught.limnoprofile.plot(): added this function to simplify
constructing plots of depth versus limnological measure with the depth
decreasing from top to bottom.rlp(): changed default qtype= to 8 (from 7). Added a
probs= argument to allow other than 75th percentile calculations.emp(): updated the help page. Added a logical for if
p.n.low does not exist when using cutoff.tail. Renamed items in the
output list. Added a table of number of individuals per length category
to output list. Added a probs= argument to allow other than 75th
percentile calculations. Added its own generics – rather than relying on
the rlp() generics.FroeseWs(): added this function, and its generics, to
perform the standard weight equation calculation as proposed by Froese
(2006).validateWs(): added this function, and its generics, to
perform the Willis and EmpQ methods for assessing length bias in the
standard weight equations. Added a probs= argument to allow other than
75th percentile calculations. Added a mean= argument to allow use of
means rather than quantiles. Modified to accept an object of class
FROESE.Date: 15May08
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().
lencat(): Modified by adding an as.fact= argument that
allows the user to decide if the resulting variable should be returned
as a factor variable or not. The default is set to return as a factor
variable. This allows tables of the new variable to include zeros for
levels of the new variable that contain no individuals. This makes some
RSD/PSD (and likely age-length key) calculations simpler. Also added a
drop.levels= argument to allow the user to drop unused levels if so
desired.mr.closed(): This function is a combination of the old
mr.closed1() and mr.closed2(). It also allows the user to compute single
census estimates with multiple sub-groups in the data (i.e., length- or
age-classes). The function also allows the user to compute an overall
population esitmate of multiple sub-groups are present and an overall SE
if the incl.SE=TRUE is used. It also corrects the SE computations
implemented in version 0.0-9. This change caused the construction of our
internal functions – mrc1, mrc2, ci.mrc1, and ci.mrc2.mr.closed1(): removed this function. Use mr.closed()
instead.mr.closed2(): removed this function. Use mr.closed()
instead.PSDval(): Added mm= argument so that metric result can
be returned in mm. Also added incl.zero= argument that will include a
zer* `value in the first position in the vector; this is useful for when
creating PSD/RSD values.rcumsum(): Added this function (from NCStats).RSDval(): See PSDval description.age.comp(): Corrected SE calculation used to construct
the CIs. Changed the CI plotting routine to use plotCI in plotrix
package – this puts lines rather than points on the ends of the CIs.
Added a check for computing SDs and CIs for when n=1 or when all
measurements are the same. This reduces (eliminates?) the number of
warnings that are given.catch.curve(): added na.rm=TRUE arguments to min() and
max() in plot.CC(). Changed type= argument so that “params” is the
default rather than “lm”. This makes it more consistent with other
simulation programs.cc.sim(): Put in catch for situations where the CV for
No and Z were equal to zero. Originally, the program attempted to
computed a random number from a normal distribution with a standard
deviation of zero. This corrected the problem of n* `lines appearing
unless the CVs were greater than zero.ch.convert(): STARTED A FUNCTION to CONVERT B/W CAPTURE
HISTORY FORMATS. N* `RD FILE YET.depletion(): Moved type= argument to third position.
Will more easily allow type=“Leslie” as a default (i.e., can just enter
catch and effort vector.FSAsims(): Added a “mark-recap” menu section. Added a
chapman 1-sample M-R item to the menu.leslie.sim(): corrected the conditionals on p.surv and
r.prop so that it asks if any not the first value is less than 1. This
corrects the problem of R returning a large number of warnings.leslie.sim2(): corrected the call to depletion() so
that the type of model (“Leslie”) was the third rather than the first
argument. This was caused by a change in the usage of depletion in
previous version changes.mr.closed1(): Modified output list to include an
estimate of the variance as described in Ricker(1975).summary.MRC1(): Modified output so that (1) the given
information is a little easier to read, (2) the population estimate is
returned in a matrix, (3) the SE from Ricker(1975) can be included in
the outputm, and (4) a label can be placed on row for the matrix output.
The purpose of these changes was to allow the SE to be computed and to
allow future functions to more flexibly use the output.Date: unknown
changed some to in RD files. Changed most hard-wired quotes to or in RD files. Changed some text-based equations to more latex-based equations in or 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.
Date: unknown
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.
agebias.plot(): deleted and replaced with agecomp and
plot.AgeComp functions.agesunflower.plot(): deleted and replaced with agecomp
and plot.AgeComp functions.agecomp(): a new function that, along with its
extractor functions, combines all of the functionality of the old
age.tests(), age.symmetry(),
agebias.plot(), and agesunflower.plot().
Allows for a more seamless comparison of ageing reads.plot.AgeComp(): an extractor function for objects saved
from the agecomp() function. This replaces the old
agebias.plot() and agesunflower.plot()
functions.summary.Agecomp(): an extractor function for objects
saved from the agecomp() function. This replaces the old
age.tests() and age.symmetry() functions.age.symmetry(): deleted and replaced with
agecomp() and summary.AgeComp()
functions.age.tests(): deleted and replaced with
agecomp() and summary.AgeComp()
functions.cc.sim(): modified graphic to (1) include assumption
violation labels on top of the graph and (2) label y-axis with
“log(Catch)” rather than “ln(Catch)”.delury(): deleted and replaced with
depletion() function. See notes for
depletion() function.depletion(): created a new function that performs the
Leslie or Delury method as determined by a user-defined argument to
type. This function replaces the old leslie() and
delury() functions. All extractor functions for the class
“LeslieDelury” have now been changed to class “Depletion”.plot.Depletion(): correct xlab so that it defaults to
“Cumulative Effort” for the Delury method.leslie(): deleted and replaced with depletion function.
See notes for depletion function.leslie.sim(): modified graphic to include assumption
violation labels on top of the graph.mr.open(): modified est.N() internal
function so that N is set equal to n if N<n. In other words, if the
sample size at time i is larger than the estimated population size at
time i then the estimated population size is set equal to the observed
sample size. This corrects the problem of the N.se
calculation attempting to take the square root of a negative number
causing the mr.open() function to shut down.pass.removal(): changed name to removal.removal(): new name for old pass.removal function.rlp(): new name for old (upper-case) RLP.RLP(): changed name to (lower-case) rlp.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.