Authors
Ogle, D.H., J.C. Doll, P. Wheeler, and A. Dinno. 2022. FSA: Fisheries Stock Analysis. R package version 0.9.2, https://github.com/droglenc/FSA.
+Ogle, D.H., J.C. Doll, P. Wheeler, and A. Dinno. 2022. FSA: Fisheries Stock Analysis. R package version 0.9.3, https://github.com/fishR-Core-Team/FSA.
@Manual{,
title = {FSA: Fisheries Stock Analysis},
author = {Derek H. Ogle and Jason C. Doll and Powell Wheeler and Alexis Dinno},
year = {2022},
- note = {R package version 0.9.2},
- url = {https://github.com/droglenc/FSA},
+ note = {R package version 0.9.3},
+ url = {https://github.com/fishR-Core-Team/FSA},
}
diff --git a/docs/index.html b/docs/index.html
index 4e492c29..5d83b0b1 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -41,7 +41,7 @@
@@ -94,13 +94,13 @@ Installation
if (!require('remotes')) install.packages('remotes'); require('remotes')
-remotes::install_github('droglenc/FSA')
+remotes::install_github('fishR-Core-Team/FSA')
You may need to have R Tools installed on your system to install the development version from GitHub. See the instructions for (R Tools for Windows or R Tools for Mac OS X).
Questions / Comments / Problems or Contributions
-Report questions, comments, or bug reports on the issues page.
+Report questions, comments, or bug reports on the issues page.
We are always looking for others to contribute to FSA. Please feel free to make a pull request via GitHub or to contact the maintainers.
Please adhere to the Code of Conduct.
@@ -118,8 +118,8 @@ Note
Links
@@ -162,8 +162,8 @@ Dev status
FSA 0.9.2 12-Feb-21
-- Last version maintained by Derek Ogle. Transfering to fishR Core Team for next version.
+FSA 0.9.3 15-Feb-21
+- Moved
dplyr from imports to suggests (needed because functions were removed in last version; however it is still used in some examples; partially addresses #87).
+- Removed
sciplot from imports (because functions were removed in last version; partially addresses #87).
+- Updated tests for
ksTest() to handle issues on the CRAN M1 build machine (per e-mail from Prof. Ripley on 15-Feb-22; partially addresses #87).
+- Updated all links to the
droglenc github that were related to FSA or FSAdata to be to the fishR-Core-Team github.
+
+
+FSA 0.9.2 12-Feb-212022-02-12
+- Last version maintained by Derek Ogle. Transferring to fishR Core Team for next version.
-
filterD(): REMOVED (to FSAmisc).
-
@@ -63,19 +70,19 @@
FSA 0.9.2 1
-
fsaNews() and FSANews(): Removed.
-
-
psdAdd(): Modified. Changed the way PSDlit was loaded into the function environment so that FSA::psdAdd() will work. Addresses #85.
+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).
+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.
+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.
+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).
+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.
+wsVal(): Modified. Changed the way WSlit was loaded into the function environment so that FSA::wsVal() will work. Addresses #85.
FSA 0.9.1 17-Jul-212021-07-17
@@ -89,70 +96,70 @@ FSA 0.9.0 8-
alkPlot(): Modified. Removed use of chooseColors() (see below).
-binCI(): Modified. Changed to use iCheckConfLevel() (which addresses #66).
+binCI(): Modified. Changed to use iCheckConfLevel() (which addresses #66).
-bootCase(): REMOVED. Users can use car::Boot(), which partially addresses #65.
+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).
+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).
+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.
+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.
+compIntercepts(): REMOVED (to FSAmisc). Added to FSA-defunct. Partially addresses #65.
-compSlopes(): 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).
+depletion(): Modified. Changed to use iCheckConfLevel() (which addresses #66).
-filterD(): DEPRECATED (partially addresses #65).
+filterD(): DEPRECATED (partially addresses #65).
-fitPlot(): DEPRECATED (partially addresses #65). Prior to that removed use of chooseColors() (see above).
+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.
+diags(): REMOVED (moved to FSAmisc). Added to FSA-defunct. Partially addresses #65.
-hoCoef(): 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).
+hyperCI(): Modified. Changed to use iCheckConfLevel() (which addresses #66).
-iCheckConfLevel(): Added (internal to address #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.
+mapvalues(): REMOVED. Added to FSA-defunct. Partially addresses #65.
-mrClosed(): Modified. Changed to use iCheckConfLevel() (which addresses #66).
+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).
+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.
+paletteChoices(): REMOVED. See chooseColors() above. Partially addresses #65.
-poiCI(): Modified. Changed to use iCheckConfLevel() (which addresses #66).
+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).
+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).
+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.
+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).
+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).
+residPlot(): DEPRECATED (partially addresses #65). Prior to that removed use of chooseColors() (see above).
-Subset(): REMOVED. Added to FSA-defunct. Partially addresses #65.
+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.
+WSlit: Modified. Addresses #68.
- Corrected capitalization of “Cavedano Chub”, “European Chub”, “Lake Herring” (metric), and “Pursak Chub”.
- Removed “not in Neumann et al. (2012)” notes.
- Added African Sharptooth Catfish, Ankara Nase, Bighead and Silver Carp, Brook Trout (Appalachia), Fourbarbel Scraper, Horse Barbel, Nile Tilapia, Nipple-Lipped Scraper, Shoal Bass, South European Roach, Spotted Bass (Alabama subspecies) (AKA Alabama Bass).
@@ -171,13 +178,13 @@ FSA 0.8.3
- Added a code of conduct for contributors.
- Moved a bunch of plotting examples in the documentation to
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).
+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.
+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.
@@ -262,13 +269,13 @@ FSA 0.8.23
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.
+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.
+SchnuteRichards(): Added. This addresses #54.
FSA 0.8.22 22-Nov-182018-11-22
@@ -285,39 +292,39 @@ FSA 0.8.21
Added Alexis Dinno as an author for their providing the base functionality of dunnTest(). Should have done this long ago.
Removed all data() in examples that referred to data from this package. Included the package= argument in data() that loaded from other packages.
Added seealso, with links to which functions use the data for examples, to docmentation for all data.frames.
-Removed \dontrun()s from the bootCase related examples now that car package is updated. This addresses #45.
+Removed \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.
+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().
+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().
-Bootstrapping functions: Modified. Changed to using withr::local_par() (partially addresses #38).
+Bootstrapping functions: Modified. Changed to using withr::local_par() (partially addresses #38).
-capHistSum(): Modified. Changed to using withr::local_par() (partially addresses #38).
+capHistSum(): Modified. Changed to using withr::local_par() (partially addresses #38).
-chapmanRobson(): Modified. Changed to using withr::local_par() (partially addresses #38).
+chapmanRobson(): Modified. Changed to using withr::local_par() (partially addresses #38).
fishR(): Modified. Changed examples in documentation to not be run (so as not to open an external webpage).
FSAnews(): Modified. Changed examples in documentation to not be run (so as not to open an external webpage).
-Growth models: Modified. Changed to using withr::local_par() (partially addresses #38).
+Growth models: Modified. Changed to using withr::local_par() (partially addresses #38).
-hist.formula(): Modified. Changed to using withr::local_par() (partially addresses #38).
+hist.formula(): Modified. Changed to using withr::local_par() (partially addresses #38).
-lwCompPreds(): Modified. Changed to using withr::local_par() (partially addresses #38).
+lwCompPreds(): Modified. Changed to using withr::local_par() (partially addresses #38).
plotAB(): Modified. Now in its own documentation file (rather than with ageBias()).
-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).
+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.
+removal(): Modified. Added method="Burhnam" via the #51 from Powell Wheeler.
-residPlot(): Modified. Changed to using withr::local_par() (partially addresses #38).
+residPlot(): Modified. Changed to using withr::local_par() (partially addresses #38).
SMBassWB: Modified. Fixed minor data entry error in row 383.
@@ -342,55 +349,55 @@ FSA 0.8.2
FSA 0.8.19 8-Apr-182018-04-08
-
-
addZeroCatch(): Modified. Changed two 1:nrow() structures to seq_len(nrow()) (partially addressing #36).
+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).
+ageBias(): Modified. Changed all 1: structures to seq_len() (partially addressing #36).
-
-
agePrecision(): 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).
+bcFuns(): Modified. Changed three 1:length() structures to seq_along() (partially addressing #36).
-
-
bootCase() methods: Modified. Changed all 1: structures to seq_len() (partially addressing #36).
+bootCase() methods: Modified. Changed all 1: structures to seq_len() (partially addressing #36).
-
-
capHistConvert(): Modified. Changed all 1: structures to seq_len() or seq_along() (partially addressing #36).
+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).
+capHistSum(): Modified. Changed all 1: structures to seq_len() (partially addressing #36).
-
-
chooseColors(): 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).
+compSlopes(): Modified. Changed all 1: structures to seq_len() (partially addressing #36).
-
-
compIntercepts(): 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).
+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).
+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).
+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().
+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).
+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).
+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).
+mrClosed(): Modified. Changed two 1:length() structures to seq_along() (partially addressing #36).
-
-
nlsBoot() methods: Modified. Changed all 1: structures to seq_len() (partially addressing #36).
+nlsBoot() methods: Modified. Changed all 1: structures to seq_len() (partially addressing #36).
-
plot.boot(): Removed (added last version) until I can test more.
-
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).
+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).
+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).
+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).
+wrAdd(): Modified. Changed three 1: structures to seq_len() or seq_along() (partially addressing #36).
FSA 0.8.18 31-Mar-18
@@ -409,7 +416,7 @@ FSA 0.8.1
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).
+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.
@@ -440,9 +447,9 @@ FSA 0.8.15
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.
+removal(): Modified document by merging pull request #33.
-srStarts(): Modified. Added fixed=. Added some catches for poor starting values. Added relevant tests. Addresses #30.
+srStarts(): Modified. Added fixed=. Added some catches for poor starting values. Added relevant tests. Addresses #30.
FSA 0.8.14 27-Jul-172017-07-27
@@ -526,13 +533,13 @@ FSA 0.8.1
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.
+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.
+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.
+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.
@@ -548,9 +555,9 @@ FSA 0.8.1
iHndlCols2use(): Deleted. Changed to iHndlCols2UseIgnore().
-iHndlCols2UseIgnore(): Added. Previously was iHndlCols2use(). Completely reworked to catch more problems including having both positive and negative indices (fixes #24) and choosing variable names that don’t exist (fixes #25).
+iHndlCols2UseIgnore(): Added. Previously was iHndlCols2use(). Completely reworked to catch more problems including having both positive and negative indices (fixes #24) and choosing variable names that don’t exist (fixes #25).
-iHndlFormula(): Modified. Added code to deal with a formula that is a single “variable” sent in an array. Addresses #21 for the simple situation of single “variable.”
+iHndlFormula(): Modified. Added code to deal with a formula that is a single “variable” sent in an array. Addresses #21 for the simple situation of single “variable.”
iHndlMultWhat(): Modified. Added type= to allow use with message() or cat().
@@ -562,7 +569,7 @@ FSA 0.8.1
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.
+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.
@@ -578,7 +585,7 @@ FSA 0.8.1
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.
+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.
@@ -595,7 +602,7 @@ FSA 0.8.1
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.
+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.
@@ -644,8 +651,8 @@ FSA 0.8.8 1
FSA 0.8.7 8-May-162016-05-08
- Compiled under R v3.3.0.
-- Removed
relax from Suggests. See srStarts() and vbStarts() notes below. This addresses #17.
-- Removed
gdata from Imports. See filterD() and Subset() notes below. This addresses #5.
+- Removed
relax from Suggests. See srStarts() and vbStarts() notes below. This addresses #17.
+- Removed
gdata from Imports. See filterD() and Subset() notes below. This addresses #5.
- Added no coverage blocks to
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().
@@ -658,7 +665,7 @@ FSA 0.8.7 8-
-
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.
+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=.
-
@@ -699,9 +706,9 @@
FSA 0.8.6 2
- Fixed problems with tests, and made the tests more explicit, related to PSD and Wr functions. Suppressed some warnings related to
sumTable() in ALK related tests and Summarize() in age comparisons tests. Prompted by forthcoming changes to testthat.
- Removed
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).
+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.
+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.
-
@@ -715,7 +722,7 @@
FSA 0.8.6 2
-
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.
+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.
-
@@ -726,10 +733,10 @@
FSA 0.8.5 1
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.
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).
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.
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 8c674d3c..2590d423 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 2.14.0.3
pkgdown: 2.0.2
pkgdown_sha: ~
articles: {}
-last_built: 2022-02-12T19:10Z
+last_built: 2022-02-16T00:00Z
urls:
reference: http://derekogle.com/FSA/reference
article: http://derekogle.com/FSA/articles
diff --git a/docs/reference/BluegillJL.html b/docs/reference/BluegillJL.html
index d6309185..043fc4dd 100644
--- a/docs/reference/BluegillJL.html
+++ b/docs/reference/BluegillJL.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Capture histories (2 samples) of Bluegill from Jewett Lake, MI.
- Source: R/BluegillJL.R
+ Source: R/BluegillJL.R
BluegillJL.Rd
diff --git a/docs/reference/BrookTroutTH.html b/docs/reference/BrookTroutTH.html
index f483e184..d14b5b57 100644
--- a/docs/reference/BrookTroutTH.html
+++ b/docs/reference/BrookTroutTH.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.
- Source: R/BrookTroutTH.R
+ Source: R/BrookTroutTH.R
BrookTroutTH.Rd
diff --git a/docs/reference/ChinookArg.html b/docs/reference/ChinookArg.html
index 382bf834..2a4f2833 100644
--- a/docs/reference/ChinookArg.html
+++ b/docs/reference/ChinookArg.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Lengths and weights for Chinook Salmon from three locations in Argentina.
- Source: R/ChinookArg.R
+ Source: R/ChinookArg.R
ChinookArg.Rd
diff --git a/docs/reference/CodNorwegian.html b/docs/reference/CodNorwegian.html
index 6f8a1fb0..569e9682 100644
--- a/docs/reference/CodNorwegian.html
+++ b/docs/reference/CodNorwegian.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Stock and recruitment data for Norwegian cod, 1937-1960.
- Source: R/CodNorwegian.R
+ Source: R/CodNorwegian.R
CodNorwegian.Rd
diff --git a/docs/reference/CutthroatAL.html b/docs/reference/CutthroatAL.html
index 1a6f8f73..ff90e0c6 100644
--- a/docs/reference/CutthroatAL.html
+++ b/docs/reference/CutthroatAL.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Capture histories (9 samples) of Cutthroat Trout from Auke Lake.
- Source: R/CutthroatAL.R
+ Source: R/CutthroatAL.R
CutthroatAL.Rd
diff --git a/docs/reference/Ecoli.html b/docs/reference/Ecoli.html
index 2bef4c7b..fefbb3ee 100644
--- a/docs/reference/Ecoli.html
+++ b/docs/reference/Ecoli.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/FSA-internals.html b/docs/reference/FSA-internals.html
index 9a05a1d8..4f5023c2 100644
--- a/docs/reference/FSA-internals.html
+++ b/docs/reference/FSA-internals.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/FSA.html b/docs/reference/FSA.html
index bd96de6b..d80fb633 100644
--- a/docs/reference/FSA.html
+++ b/docs/reference/FSA.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
@@ -62,8 +62,8 @@ Fisheries stock assessment methods and data.
Details
Functions from this package can be used to perform a variety of basic fisheries stock assessment methods. Detailed descriptions for most functions are available in the Introductory Fisheries Analysis with R book (Ogle 2016). Vignettes for the boxed examples in the “Analysis and Interpretation of Freshwater Fisheries Data” book can be viewed with fishR("AIFFD").
-Questions, comments, or suggestions should be given on the GitHub FSA Issues page.
-Packages with related functionality by the same author are
The FSAdata package contains additional data sets.
Questions, comments, or suggestions should be given on the GitHub FSA Issues page.
+Packages with related functionality by the same author are
The FSAdata package contains additional data sets.
The FSAsim package simulation routines for various fisheries methods.
The FSAWs package contains functions for developing and validating standard weight equations.
diff --git a/docs/reference/Mirex.html b/docs/reference/Mirex.html
index e3825d25..0f075183 100644
--- a/docs/reference/Mirex.html
+++ b/docs/reference/Mirex.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/PSDlit.html b/docs/reference/PSDlit.html
index bb11d70f..5e779170 100644
--- a/docs/reference/PSDlit.html
+++ b/docs/reference/PSDlit.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Gabelhouse five-cell length categories for various species.
- Source: R/PSDlit.R
+ Source: R/PSDlit.R
PSDlit.Rd
diff --git a/docs/reference/PikeNY.html b/docs/reference/PikeNY.html
index 9af7c2e4..5144e19b 100644
--- a/docs/reference/PikeNY.html
+++ b/docs/reference/PikeNY.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Summarized multiple mark-recapture data for all Northern Pike from Buckhorn Marsh, NY.
- Source: R/PikeNY.R
+ Source: R/PikeNY.R
PikeNY.Rd
diff --git a/docs/reference/PikeNYPartial1.html b/docs/reference/PikeNYPartial1.html
index 2cea0c7e..8ee11694 100644
--- a/docs/reference/PikeNYPartial1.html
+++ b/docs/reference/PikeNYPartial1.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Capture histories (4 samples), in capture history format, of a subset of Northern Pike from Buckhorn Marsh, NY.
- Source: R/PikeNYPartial1.R
+ Source: R/PikeNYPartial1.R
PikeNYPartial1.Rd
diff --git a/docs/reference/SMBassLS.html b/docs/reference/SMBassLS.html
index 7db1c11b..30b5d2de 100644
--- a/docs/reference/SMBassLS.html
+++ b/docs/reference/SMBassLS.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Catch-effort data for Little Silver Lake (Ont) Smallmouth Bass.
- Source: R/SMBassLS.R
+ Source: R/SMBassLS.R
SMBassLS.Rd
diff --git a/docs/reference/SMBassWB.html b/docs/reference/SMBassWB.html
index 42fdc4b8..6be0c3eb 100644
--- a/docs/reference/SMBassWB.html
+++ b/docs/reference/SMBassWB.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Growth increment data for West Bearskin Lake, MN, Smallmouth Bass.
- Source: R/SMBassWB.R
+ Source: R/SMBassWB.R
SMBassWB.Rd
diff --git a/docs/reference/Schnute.html b/docs/reference/Schnute.html
index f8e90184..bd811275 100644
--- a/docs/reference/Schnute.html
+++ b/docs/reference/Schnute.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
The four-parameter growth function from Schnute (1981).
- Source: R/growthModels.R
+ Source: R/growthModels.R
Schnute.Rd
diff --git a/docs/reference/SpotVA1.html b/docs/reference/SpotVA1.html
index 17a78714..5ec0379a 100644
--- a/docs/reference/SpotVA1.html
+++ b/docs/reference/SpotVA1.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/Summarize.html b/docs/reference/Summarize.html
index 9510819d..f097047b 100644
--- a/docs/reference/Summarize.html
+++ b/docs/reference/Summarize.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Summary statistics for a numeric variable.
- Source: R/Summarize.R
+ Source: R/Summarize.R
Summarize.Rd
diff --git a/docs/reference/WR79.html b/docs/reference/WR79.html
index d7db0736..8917d28f 100644
--- a/docs/reference/WR79.html
+++ b/docs/reference/WR79.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/WSlit.html b/docs/reference/WSlit.html
index 36f72322..0d32931b 100644
--- a/docs/reference/WSlit.html
+++ b/docs/reference/WSlit.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/WhitefishLC.html b/docs/reference/WhitefishLC.html
index 1b696af9..74cdc1b8 100644
--- a/docs/reference/WhitefishLC.html
+++ b/docs/reference/WhitefishLC.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Assigned ages from two readers on three structures for Lake Whitefish from Lake Champlain.
- Source: R/WhitefishLC.R
+ Source: R/WhitefishLC.R
WhitefishLC.Rd
diff --git a/docs/reference/addZeroCatch.html b/docs/reference/addZeroCatch.html
index d794d440..c873affa 100644
--- a/docs/reference/addZeroCatch.html
+++ b/docs/reference/addZeroCatch.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Adds zeros for catches of species not collected in some sampling events.
- Source: R/addZeroCatch.R
+ Source: R/addZeroCatch.R
addZeroCatch.Rd
diff --git a/docs/reference/ageBias.html b/docs/reference/ageBias.html
index 8f0b2399..96e73b8e 100644
--- a/docs/reference/ageBias.html
+++ b/docs/reference/ageBias.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Compute and view possible differences between paired sets of ages.
- Source: R/ageComparisons.R
+ Source: R/ageComparisons.R
ageBias.Rd
diff --git a/docs/reference/agePrecision.html b/docs/reference/agePrecision.html
index f71a878a..9f97cef3 100644
--- a/docs/reference/agePrecision.html
+++ b/docs/reference/agePrecision.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Compute measures of precision among sets of ages.
- Source: R/ageComparisons.R
+ Source: R/ageComparisons.R
agePrecision.Rd
diff --git a/docs/reference/alkAgeDist.html b/docs/reference/alkAgeDist.html
index 89f6f747..1dfb209f 100644
--- a/docs/reference/alkAgeDist.html
+++ b/docs/reference/alkAgeDist.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Proportions-at-age from an age-length key
- Source: R/alkSummaries.R
+ Source: R/alkSummaries.R
alkAgeDist.Rd
diff --git a/docs/reference/alkIndivAge.html b/docs/reference/alkIndivAge.html
index 8527e579..20898e94 100644
--- a/docs/reference/alkIndivAge.html
+++ b/docs/reference/alkIndivAge.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Use an age-length key to assign age to individuals in the unaged sample.
- Source: R/alkIndivAge.R
+ Source: R/alkIndivAge.R
alkIndivAge.Rd
@@ -191,27 +191,27 @@ Examples
WR1.comb <- rbind(WR1.age, WR1.len)
# mean length-at-age
Summarize(len~age,data=WR1.comb,digits=2)
-#> age n mean sd min Q1 median Q3 max
-#> 1 4 987 51.86 5.14 35 48.00 52.0 56.00 64
-#> 2 5 395 71.80 5.33 60 68.00 72.0 76.00 84
-#> 3 6 270 86.76 4.83 75 83.00 87.0 89.00 99
-#> 4 7 449 97.45 5.17 85 93.00 97.0 101.00 112
-#> 5 8 146 101.29 5.86 90 97.00 101.5 106.75 113
-#> 6 9 78 103.85 3.08 100 102.00 103.0 105.75 112
-#> 7 10 38 105.42 7.08 95 98.25 107.0 109.75 119
-#> 8 11 6 111.67 1.51 110 110.25 112.0 113.00 113
+#> age n mean sd min Q1 median Q3 max
+#> 1 4 987 51.87 5.15 35 48 52.0 56.00 64
+#> 2 5 396 71.79 5.35 60 68 72.0 76.00 84
+#> 3 6 269 86.73 4.66 75 83 87.0 89.00 98
+#> 4 7 447 97.54 5.14 85 93 97.0 102.00 112
+#> 5 8 147 101.21 5.84 90 97 101.0 107.00 114
+#> 6 9 78 103.68 3.43 100 101 103.0 104.75 113
+#> 7 10 39 105.23 7.18 95 98 107.0 109.50 119
+#> 8 11 6 111.67 1.21 110 111 111.5 112.75 113
# age frequency distribution
( af <- xtabs(~age,data=WR1.comb) )
#> age
#> 4 5 6 7 8 9 10 11
-#> 987 395 270 449 146 78 38 6
+#> 987 396 269 447 147 78 39 6
# proportional age distribution
( ap <- prop.table(af) )
#> age
#> 4 5 6 7 8 9
-#> 0.416631490 0.166737020 0.113972140 0.189531448 0.061629379 0.032925285
+#> 0.416631490 0.167159139 0.113550021 0.188687210 0.062051499 0.032925285
#> 10 11
-#> 0.016040523 0.002532714
+#> 0.016462642 0.002532714
## Second Example -- length sample does not have an age variable
WR2 <- WR79
@@ -278,15 +278,15 @@ Examples
# combine orig age & new ages
WR2.comb <- rbind(WR2.age, WR2.len)
Summarize(len~age,data=WR2.comb,digits=2)
-#> age n mean sd min Q1 median Q3 max
-#> 1 4 987 51.85 5.12 35 48.00 52.0 56.0 64
-#> 2 5 395 71.76 5.22 60 68.00 72.0 76.0 84
-#> 3 6 271 86.76 4.59 75 83.00 87.0 89.0 99
-#> 4 7 448 97.60 5.21 85 93.00 97.0 102.0 114
-#> 5 8 145 101.14 5.76 90 96.00 101.0 107.0 113
-#> 6 9 79 103.75 3.10 100 102.00 103.0 105.0 112
-#> 7 10 38 105.13 7.30 95 97.00 106.5 110.5 119
-#> 8 11 6 111.83 0.75 111 111.25 112.0 112.0 113
+#> age n mean sd min Q1 median Q3 max
+#> 1 4 986 51.85 5.14 35 48 52 56.00 64
+#> 2 5 396 71.72 5.29 60 68 72 76.00 84
+#> 3 6 271 86.81 4.67 75 83 87 89.00 98
+#> 4 7 447 97.49 5.21 85 93 97 101.00 113
+#> 5 8 146 101.20 5.85 90 97 101 107.00 113
+#> 6 9 79 103.96 3.02 100 102 103 105.50 114
+#> 7 10 38 105.29 7.00 95 98 107 110.50 119
+#> 8 11 6 111.50 0.84 111 111 111 111.75 113
## Third Example -- Uneven breaks for length categories
WR3 <- WR79
@@ -353,15 +353,15 @@ Examples
#> 8 8 42 4 40
WR3.comb <- rbind(WR3.age, WR3.len)
Summarize(len~age,data=WR3.comb,digits=2)
-#> age n mean sd min Q1 median Q3 max
-#> 1 4 987 51.87 5.15 35 48 52.0 56 64
-#> 2 5 395 71.72 5.25 60 68 72.0 76 84
-#> 3 6 271 86.85 4.71 75 83 87.0 89 99
-#> 4 7 451 97.65 5.34 85 93 97.0 102 113
-#> 5 8 142 100.68 5.44 90 97 101.0 104 113
-#> 6 9 78 104.40 3.20 100 102 103.0 107 113
-#> 7 10 40 104.80 7.14 95 98 103.5 112 119
-#> 8 11 5 112.60 2.70 110 111 112.0 113 117
+#> age n mean sd min Q1 median Q3 max
+#> 1 4 987 51.85 5.12 35 48 52 56.00 64
+#> 2 5 396 71.81 5.28 60 68 72 76.00 84
+#> 3 6 270 86.73 4.61 75 83 87 89.00 98
+#> 4 7 449 97.76 5.33 86 93 97 102.00 114
+#> 5 8 141 100.52 5.61 90 96 101 104.00 113
+#> 6 9 80 104.15 3.21 100 102 103 107.00 113
+#> 7 10 42 104.90 7.19 95 98 102 111.75 119
+#> 8 11 4 112.00 1.15 111 111 112 113.00 113
diff --git a/docs/reference/alkMeanVar.html b/docs/reference/alkMeanVar.html
index 54018324..d08cd0b6 100644
--- a/docs/reference/alkMeanVar.html
+++ b/docs/reference/alkMeanVar.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Mean Values-at-age from an age-length key
- Source: R/alkSummaries.R
+ Source: R/alkSummaries.R
alkMeanVar.Rd
diff --git a/docs/reference/alkPlot.html b/docs/reference/alkPlot.html
index 17121b36..ef945cb2 100644
--- a/docs/reference/alkPlot.html
+++ b/docs/reference/alkPlot.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/binCI.html b/docs/reference/binCI.html
index 9e1bfe06..4b1de2f6 100644
--- a/docs/reference/binCI.html
+++ b/docs/reference/binCI.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Confidence intervals for binomial probability of success.
- Source: R/CIDists.R
+ Source: R/CIDists.R
binCI.Rd
diff --git a/docs/reference/capHistConvert.html b/docs/reference/capHistConvert.html
index 5b67e26c..b1cb2340 100644
--- a/docs/reference/capHistConvert.html
+++ b/docs/reference/capHistConvert.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Convert between capture history data.frame formats.
- Source: R/capHistConvert.R
+ Source: R/capHistConvert.R
capHistConvert.Rd
diff --git a/docs/reference/capHistSum.html b/docs/reference/capHistSum.html
index 56865cd4..30347c39 100644
--- a/docs/reference/capHistSum.html
+++ b/docs/reference/capHistSum.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Summarize capture histories in individual fish format.
- Source: R/capHistSum.R
+ Source: R/capHistSum.R
capHistSum.Rd
diff --git a/docs/reference/catchCurve.html b/docs/reference/catchCurve.html
index e3d808ef..74cd8ecf 100644
--- a/docs/reference/catchCurve.html
+++ b/docs/reference/catchCurve.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Mortality estimates from the descending limb of a catch curve.
- Source: R/catchCurve.R
+ Source: R/catchCurve.R
catchCurve.Rd
diff --git a/docs/reference/chapmanRobson.html b/docs/reference/chapmanRobson.html
index 5eca9713..99a94104 100644
--- a/docs/reference/chapmanRobson.html
+++ b/docs/reference/chapmanRobson.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Computes Chapman-Robson estimates of S and Z.
- Source: R/chapmanRobson.R
+ Source: R/chapmanRobson.R
chapmanRobson.Rd
diff --git a/docs/reference/col2rgbt.html b/docs/reference/col2rgbt.html
index 805c7929..4a0d5d1d 100644
--- a/docs/reference/col2rgbt.html
+++ b/docs/reference/col2rgbt.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Converts an R color to RGB (red/green/blue) including a transparency (alpha channel).
- Source: R/FSAUtils.R
+ Source: R/FSAUtils.R
col2rgbt.Rd
diff --git a/docs/reference/depletion.html b/docs/reference/depletion.html
index 7c753945..3860292a 100644
--- a/docs/reference/depletion.html
+++ b/docs/reference/depletion.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Computes the Leslie or DeLury population estimate from catch and effort data.
- Source: R/depletion.R
+ Source: R/depletion.R
depletion.Rd
diff --git a/docs/reference/dunnTest.html b/docs/reference/dunnTest.html
index 9ac809f6..af4f878c 100644
--- a/docs/reference/dunnTest.html
+++ b/docs/reference/dunnTest.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Dunn's Kruskal-Wallis Multiple Comparisons.
- Source: R/dunnTest.R
+ Source: R/dunnTest.R
dunnTest.Rd
diff --git a/docs/reference/expandCounts.html b/docs/reference/expandCounts.html
index 553c31dd..abed650f 100644
--- a/docs/reference/expandCounts.html
+++ b/docs/reference/expandCounts.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Repeat individual fish data (including lengths) from tallied counts.
- Source: R/expandCounts.R
+ Source: R/expandCounts.R
expandCounts.Rd
@@ -153,22 +153,22 @@ Examples
#> 2 rows had an individual measurement.
#> 4 rows with multiple measurements were expanded to 15 rows of individual measurements.
#> name lwr.bin upr.bin newlen lennote
-#> 1 Frank 17.0 17.5 17.0 Expanded length
-#> 2 Max 17.0 17.5 17.5 Expanded length
-#> 3 Johnson 15.0 15.5 15.3 Expanded length
-#> 4 Johnson 15.0 15.5 15.3 Expanded length
-#> 5 Johnson 15.0 15.5 15.0 Expanded length
-#> 6 Johnson 15.0 15.5 15.3 Expanded length
-#> 7 Johnson 15.0 15.5 15.0 Expanded length
-#> 8 Johnson 15.0 15.5 15.5 Expanded length
-#> 9 Johnson 15.5 16.0 16.0 Expanded length
-#> 10 Johnson 15.5 16.0 15.9 Expanded length
-#> 11 Johnson 15.5 16.0 15.9 Expanded length
-#> 12 Johnson 15.5 16.0 15.5 Expanded length
-#> 13 Jones 16.0 16.5 16.3 Expanded length
-#> 14 Jones 16.0 16.5 16.0 Expanded length
-#> 15 Frank 16.0 16.5 16.3 Expanded length
-#> 16 Frank 16.0 16.5 16.3 Expanded length
+#> 1 Frank 17.0 17.5 17.2 Expanded length
+#> 2 Max 17.0 17.5 17.2 Expanded length
+#> 3 Johnson 15.0 15.5 15.0 Expanded length
+#> 4 Johnson 15.0 15.5 15.0 Expanded length
+#> 5 Johnson 15.0 15.5 15.2 Expanded length
+#> 6 Johnson 15.0 15.5 15.4 Expanded length
+#> 7 Johnson 15.0 15.5 15.3 Expanded length
+#> 8 Johnson 15.0 15.5 15.0 Expanded length
+#> 9 Johnson 15.5 16.0 15.9 Expanded length
+#> 10 Johnson 15.5 16.0 15.5 Expanded length
+#> 11 Johnson 15.5 16.0 15.6 Expanded length
+#> 12 Johnson 15.5 16.0 15.8 Expanded length
+#> 13 Jones 16.0 16.5 16.4 Expanded length
+#> 14 Jones 16.0 16.5 16.5 Expanded length
+#> 15 Frank 16.0 16.5 16.1 Expanded length
+#> 16 Frank 16.0 16.5 16.4 Expanded length
#> 17 Frank 16.0 16.5 16.3 Expanded length
# some need expansion
@@ -213,20 +213,20 @@ Examples
#> 1 Frank 17.1 17.1 17.1 Observed length
#> 2 Max 17.3 17.3 17.3 Observed length
#> 3 Johnson 15.0 15.5 15.4 Expanded length
-#> 4 Johnson 15.0 15.5 15.2 Expanded length
-#> 5 Johnson 15.0 15.5 15.0 Expanded length
-#> 6 Johnson 15.0 15.5 15.3 Expanded length
-#> 7 Johnson 15.0 15.5 15.1 Expanded length
-#> 8 Johnson 15.0 15.5 15.0 Expanded length
+#> 4 Johnson 15.0 15.5 15.1 Expanded length
+#> 5 Johnson 15.0 15.5 15.3 Expanded length
+#> 6 Johnson 15.0 15.5 15.1 Expanded length
+#> 7 Johnson 15.0 15.5 15.0 Expanded length
+#> 8 Johnson 15.0 15.5 15.4 Expanded length
#> 9 Johnson 15.5 16.0 15.7 Expanded length
-#> 10 Johnson 15.5 16.0 16.0 Expanded length
-#> 11 Johnson 15.5 16.0 16.0 Expanded length
-#> 12 Johnson 15.5 16.0 15.7 Expanded length
-#> 13 Jones 16.0 16.5 16.0 Expanded length
-#> 14 Jones 16.0 16.5 16.3 Expanded length
-#> 15 Frank 16.0 16.5 16.3 Expanded length
-#> 16 Frank 16.0 16.5 16.5 Expanded length
-#> 17 Frank 16.0 16.5 16.1 Expanded length
+#> 10 Johnson 15.5 16.0 15.9 Expanded length
+#> 11 Johnson 15.5 16.0 15.7 Expanded length
+#> 12 Johnson 15.5 16.0 15.6 Expanded length
+#> 13 Jones 16.0 16.5 16.3 Expanded length
+#> 14 Jones 16.0 16.5 16.1 Expanded length
+#> 15 Frank 16.0 16.5 16.4 Expanded length
+#> 16 Frank 16.0 16.5 16.2 Expanded length
+#> 17 Frank 16.0 16.5 16.4 Expanded length
# none need expansion
( d3 <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max"),
@@ -326,21 +326,21 @@ Examples
#> name lwr.bin upr.bin newlen lennote
#> 1 Frank 17.1 17.1 17.1 Observed length
#> 2 Max 17.3 17.3 17.3 Observed length
-#> 3 Johnson 15.0 15.5 15.3 Expanded length
-#> 4 Johnson 15.0 15.5 15.5 Expanded length
-#> 5 Johnson 15.0 15.5 15.1 Expanded length
-#> 6 Johnson 15.0 15.5 15.4 Expanded length
-#> 7 Johnson 15.0 15.5 15.0 Expanded length
-#> 8 Johnson 15.0 15.5 15.2 Expanded length
-#> 9 Johnson 15.0 15.9 15.9 Expanded length
-#> 10 Johnson 15.0 15.9 15.4 Expanded length
-#> 11 Johnson 15.0 15.9 15.1 Expanded length
+#> 3 Johnson 15.0 15.5 15.0 Expanded length
+#> 4 Johnson 15.0 15.5 15.2 Expanded length
+#> 5 Johnson 15.0 15.5 15.4 Expanded length
+#> 6 Johnson 15.0 15.5 15.2 Expanded length
+#> 7 Johnson 15.0 15.5 15.2 Expanded length
+#> 8 Johnson 15.0 15.5 15.1 Expanded length
+#> 9 Johnson 15.0 15.9 15.5 Expanded length
+#> 10 Johnson 15.0 15.9 15.3 Expanded length
+#> 11 Johnson 15.0 15.9 15.5 Expanded length
#> 12 Johnson 15.0 15.9 15.3 Expanded length
-#> 13 Jones 16.0 16.5 16.5 Expanded length
-#> 14 Jones 16.0 16.5 16.4 Expanded length
-#> 15 Frank 16.0 16.9 16.8 Expanded length
-#> 16 Frank 16.0 16.9 16.8 Expanded length
-#> 17 Frank 16.0 16.9 16.5 Expanded length
+#> 13 Jones 16.0 16.5 16.0 Expanded length
+#> 14 Jones 16.0 16.5 16.2 Expanded length
+#> 15 Frank 16.0 16.9 16.6 Expanded length
+#> 16 Frank 16.0 16.9 16.4 Expanded length
+#> 17 Frank 16.0 16.9 16.0 Expanded length
# some need expansion but include zeros and NAs for counts
( d2a <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max","Max","Max","Max"),
@@ -368,21 +368,21 @@ Examples
#> 3 Max NA NA NA Observed length
#> 4 Frank 17.1 17.1 17.1 Observed length
#> 5 Max 17.3 17.3 17.3 Observed length
-#> 6 Johnson 15.0 15.5 15.1 Expanded length
-#> 7 Johnson 15.0 15.5 15.2 Expanded length
+#> 6 Johnson 15.0 15.5 15.2 Expanded length
+#> 7 Johnson 15.0 15.5 15.4 Expanded length
#> 8 Johnson 15.0 15.5 15.4 Expanded length
-#> 9 Johnson 15.0 15.5 15.4 Expanded length
+#> 9 Johnson 15.0 15.5 15.2 Expanded length
#> 10 Johnson 15.0 15.5 15.2 Expanded length
-#> 11 Johnson 15.0 15.5 15.2 Expanded length
-#> 12 Johnson 15.5 16.0 16.0 Expanded length
-#> 13 Johnson 15.5 16.0 15.5 Expanded length
-#> 14 Johnson 15.5 16.0 15.8 Expanded length
-#> 15 Johnson 15.5 16.0 16.0 Expanded length
-#> 16 Jones 16.0 16.5 16.3 Expanded length
+#> 11 Johnson 15.0 15.5 15.0 Expanded length
+#> 12 Johnson 15.5 16.0 15.5 Expanded length
+#> 13 Johnson 15.5 16.0 16.0 Expanded length
+#> 14 Johnson 15.5 16.0 15.7 Expanded length
+#> 15 Johnson 15.5 16.0 15.8 Expanded length
+#> 16 Jones 16.0 16.5 16.1 Expanded length
#> 17 Jones 16.0 16.5 16.3 Expanded length
-#> 18 Frank 16.0 16.5 16.3 Expanded length
-#> 19 Frank 16.0 16.5 16.3 Expanded length
-#> 20 Frank 16.0 16.5 16.0 Expanded length
+#> 18 Frank 16.0 16.5 16.4 Expanded length
+#> 19 Frank 16.0 16.5 16.1 Expanded length
+#> 20 Frank 16.0 16.5 16.1 Expanded length
# some need expansion but include NAs for upper values
( d2b <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max"),
@@ -413,11 +413,11 @@ Examples
#> 10 Johnson 15.5 15.5 15.5 Observed length
#> 11 Johnson 15.5 15.5 15.5 Observed length
#> 12 Johnson 15.5 15.5 15.5 Observed length
-#> 13 Jones 16.0 16.5 16.4 Expanded length
-#> 14 Jones 16.0 16.5 16.0 Expanded length
+#> 13 Jones 16.0 16.5 16.5 Expanded length
+#> 14 Jones 16.0 16.5 16.1 Expanded length
#> 15 Frank 16.0 16.5 16.3 Expanded length
-#> 16 Frank 16.0 16.5 16.2 Expanded length
-#> 17 Frank 16.0 16.5 16.2 Expanded length
+#> 16 Frank 16.0 16.5 16.3 Expanded length
+#> 17 Frank 16.0 16.5 16.1 Expanded length
# some need expansion but include NAs for upper values
( d2c <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max"),
@@ -448,10 +448,10 @@ Examples
#> 10 Johnson 15.5 15.5 15.5 Observed length
#> 11 Johnson 15.5 15.5 15.5 Observed length
#> 12 Johnson 15.5 15.5 15.5 Observed length
-#> 13 Jones 16.0 16.5 16.4 Expanded length
-#> 14 Jones 16.0 16.5 16.0 Expanded length
-#> 15 Frank 16.0 16.5 16.2 Expanded length
-#> 16 Frank 16.0 16.5 16.2 Expanded length
+#> 13 Jones 16.0 16.5 16.3 Expanded length
+#> 14 Jones 16.0 16.5 16.4 Expanded length
+#> 15 Frank 16.0 16.5 16.4 Expanded length
+#> 16 Frank 16.0 16.5 16.0 Expanded length
#> 17 Frank 16.0 16.5 16.1 Expanded length
if (FALSE) {
diff --git a/docs/reference/expandLenFreq.html b/docs/reference/expandLenFreq.html
index d91fe0d4..ce7dc936 100644
--- a/docs/reference/expandLenFreq.html
+++ b/docs/reference/expandLenFreq.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Expands a length frequency based on a subsample.
- Source: R/expandLenFreq.R
+ Source: R/expandLenFreq.R
expandLenFreq.Rd
diff --git a/docs/reference/extraTests.html b/docs/reference/extraTests.html
index 6bca8544..1cd4cdb9 100644
--- a/docs/reference/extraTests.html
+++ b/docs/reference/extraTests.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Likelihood ratio and extra sum-of-squares tests.
- Source: R/extraTests.R
+ Source: R/extraTests.R
extraTests.Rd
diff --git a/docs/reference/fact2num.html b/docs/reference/fact2num.html
index be9ccd6b..1aa2f4ad 100644
--- a/docs/reference/fact2num.html
+++ b/docs/reference/fact2num.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Converts "numeric" factor levels to numeric values.
- Source: R/FSAUtils.R
+ Source: R/FSAUtils.R
fact2num.Rd
diff --git a/docs/reference/fishR.html b/docs/reference/fishR.html
index 4766969a..aeb1e170 100644
--- a/docs/reference/fishR.html
+++ b/docs/reference/fishR.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Opens web pages associated with the fishR website.
- Source: R/FSAUtils.R
+ Source: R/FSAUtils.R
fishR.Rd
diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html
index 4163f384..d011cf99 100644
--- a/docs/reference/geomean.html
+++ b/docs/reference/geomean.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Calculates the geometric mean or geometric standard deviation.
- Source: R/FSAUtils.R
+ Source: R/FSAUtils.R
geomean.Rd
diff --git a/docs/reference/growthModels.html b/docs/reference/growthModels.html
index bd36eeb3..1b78e439 100644
--- a/docs/reference/growthModels.html
+++ b/docs/reference/growthModels.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
- Source: R/growthModels.R
+ Source: R/growthModels.R
growthModels.Rd
@@ -187,8 +187,8 @@ Examples
#> Linf <- Linf[[1]] }
#> Linf*(1-exp(-K*(t-t0)))
#> }
-#> <bytecode: 0x000000000972e5e8>
-#> <environment: 0x00000000091f6a88>
+#> <bytecode: 0x0000000007e2f960>
+#> <environment: 0x000000000874f268>
ages <- 0:20
plot(vb1(ages,Linf=20,K=0.3,t0=-0.2)~ages,type="b",pch=19)
@@ -199,8 +199,8 @@ Examples
#> r <- (L3-L2)/(L2-L1)
#> L1+(L3-L1)*((1-r^(2*((t-t1)/(t3-t1))))/(1-r^2))
#> }
-#> <bytecode: 0x00000000079a3778>
-#> <environment: 0x0000000006a39718>
+#> <bytecode: 0x00000000078e0ef8>
+#> <environment: 0x0000000021822dd0>
plot(vb2(ages,L1=10,L2=19,L3=20,t1=2,t3=18)~ages,type="b",pch=19)
( vb2c <- vbFuns("Francis",simple=TRUE) ) # compare to vb2
@@ -208,8 +208,8 @@ Examples
#> r <- (L3-L2)/(L2-L1)
#> L1+(L3-L1)*((1-r^(2*((t-t1)/(t3-t1))))/(1-r^2))
#> }
-#> <bytecode: 0x00000000078092d0>
-#> <environment: 0x00000000226f0b50>
+#> <bytecode: 0x0000000009177920>
+#> <environment: 0x0000000022b530d8>
## Simple Examples -- Gompertz
( gomp1 <- GompertzFuns() )
@@ -219,8 +219,8 @@ Examples
#> Linf <- Linf[[1]] }
#> Linf*exp(-exp(-gi*(t-ti)))
#> }
-#> <bytecode: 0x000000001f7a23b0>
-#> <environment: 0x0000000006f13f10>
+#> <bytecode: 0x000000001f99b7d0>
+#> <environment: 0x0000000023686290>
plot(gomp1(ages,Linf=800,gi=0.5,ti=5)~ages,type="b",pch=19)
( gomp2 <- GompertzFuns("Ricker2") )
@@ -230,24 +230,24 @@ Examples
#> L0 <- L0[[1]] }
#> L0*exp(a*(1-exp(-gi*t)))
#> }
-#> <bytecode: 0x0000000006f926a0>
-#> <environment: 0x00000000227ce5e8>
+#> <bytecode: 0x000000001fa6c8d8>
+#> <environment: 0x0000000022f8e5d0>
plot(gomp2(ages,L0=2,a=6,gi=0.5)~ages,type="b",pch=19)
( gomp2c <- GompertzFuns("Ricker2",simple=TRUE) ) # compare to gomp2
#> function(t,L0,a,gi) {
#> L0*exp(a*(1-exp(-gi*t)))
#> }
-#> <bytecode: 0x0000000022a02240>
-#> <environment: 0x0000000021ac5b38>
+#> <bytecode: 0x0000000020342258>
+#> <environment: 0x000000002330ace8>
( gompT <- GompertzFuns("Troynikov1"))
#> function(Lm,dt,Linf,gi=NULL) {
#> if (length(Linf)==2) { gi <- Linf[2]
#> Linf <- Linf[1] }
#> Linf*((Lm/Linf)^exp(-gi*dt))-Lm
#> }
-#> <bytecode: 0x0000000022120938>
-#> <environment: 0x0000000022101058>
+#> <bytecode: 0x000000002229ccc8>
+#> <environment: 0x0000000022f4ff18>
## Simple Examples -- Richards
( rich1 <- RichardsFuns() )
@@ -258,8 +258,8 @@ Examples
#> Linf <- Linf[[1]] }
#> Linf*(1-a*exp(-k*t))^b
#> }
-#> <bytecode: 0x00000000226a9490>
-#> <environment: 0x0000000021ef8d68>
+#> <bytecode: 0x0000000022cc4680>
+#> <environment: 0x0000000022e77868>
plot(rich1(ages,Linf=800,k=0.5,a=1,b=6)~ages,type="b",pch=19)
( rich2 <- RichardsFuns(2) )
@@ -270,8 +270,8 @@ Examples
#> Linf <- Linf[[1]] }
#> Linf*(1-(1/b)*exp(-k*(t-ti)))^b
#> }
-#> <bytecode: 0x00000000226b31b8>
-#> <environment: 0x000000002242f3b0>
+#> <bytecode: 0x0000000022cce3a8>
+#> <environment: 0x00000000231f5580>
plot(rich2(ages,Linf=800,k=0.5,ti=3,b=6)~ages,type="b",pch=19)
( rich3 <- RichardsFuns(3) )
@@ -282,8 +282,8 @@ Examples
#> Linf <- Linf[[1]] }
#> Linf/((1+b*exp(-k*(t-ti)))^(1/b))
#> }
-#> <bytecode: 0x00000000226bcb60>
-#> <environment: 0x0000000021c9c788>
+#> <bytecode: 0x0000000022cd7d18>
+#> <environment: 0x0000000023378ad0>
plot(rich3(ages,Linf=800,k=0.5,ti=3,b=0.15)~ages,type="b",pch=19)
( rich4 <- RichardsFuns(4) )
@@ -294,8 +294,8 @@ Examples
#> Linf <- Linf[[1]] }
#> Linf*(1+(b-1)*exp(-k*(t-ti)))^(1/(1-b))
#> }
-#> <bytecode: 0x00000000220b0448>
-#> <environment: 0x0000000022535f08>
+#> <bytecode: 0x0000000022e51ac0>
+#> <environment: 0x000000002345b020>
plot(rich4(ages,Linf=800,k=0.5,ti=3,b=0.95)~ages,type="b",pch=19)
lines(rich4(ages,Linf=800,k=0.5,ti=3,b=1.5)~ages,type="b",pch=19,col="blue")
@@ -307,8 +307,8 @@ Examples
#> Linf <- Linf[[1]] }
#> Linf*(1+(((L0/Linf)^(1-b))-1)*exp(-k*t))^(1/(1-b))
#> }
-#> <bytecode: 0x00000000220b98e8>
-#> <environment: 0x00000000221df530>
+#> <bytecode: 0x0000000022e5af98>
+#> <environment: 0x00000000235a22b8>
plot(rich5(ages,Linf=800,k=0.5,L0=50,b=1.5)~ages,type="b",pch=19)
( rich6 <- RichardsFuns(6) )
@@ -320,16 +320,16 @@ Examples
#> Linf <- Linf[[1]] }
#> Lninf+(Linf-Lninf)*(1+(b-1)*exp(-k*(t-ti)))^(1/(1-b))
#> }
-#> <bytecode: 0x00000000220c66b0>
-#> <environment: 0x00000000222d6448>
+#> <bytecode: 0x0000000022e63fd8>
+#> <environment: 0x0000000024982d80>
plot(rich6(ages,Linf=800,k=0.5,ti=3,Lninf=50,b=1.5)~ages,type="b",pch=19)
( rich2c <- RichardsFuns(2,simple=TRUE) ) # compare to rich2
#> function(t,Linf,k,ti,b) {
#> Linf*(1-(1/b)*exp(-k*(t-ti)))^b
#> }
-#> <bytecode: 0x00000000226bb810>
-#> <environment: 0x0000000022a7a248>
+#> <bytecode: 0x0000000022cd6a00>
+#> <environment: 0x0000000024a74ee8>
## Simple Examples -- Logistic
( log1 <- logisticFuns() )
@@ -339,8 +339,8 @@ Examples
#> Linf <- Linf[[1]] }
#> Linf/(1+exp(-gninf*(t-ti)))
#> }
-#> <bytecode: 0x0000000023ace4a8>
-#> <environment: 0x0000000023af7f40>
+#> <bytecode: 0x0000000024af08b0>
+#> <environment: 0x0000000024b21340>
plot(log1(ages,Linf=800,gninf=0.5,ti=5)~ages,type="b",pch=19)
( log2 <- logisticFuns("CJ2") )
@@ -350,16 +350,16 @@ Examples
#> Linf <- Linf[[1]] }
#> Linf/(1+a*exp(-gninf*t))
#> }
-#> <bytecode: 0x0000000023ad6a68>
-#> <environment: 0x0000000023be8b28>
+#> <bytecode: 0x0000000024afb288>
+#> <environment: 0x0000000024c13d18>
plot(log2(ages,Linf=800,gninf=0.5,a=10)~ages,type="b",pch=19)
( log2c <- logisticFuns("CJ2",simple=TRUE) ) # compare to log2
#> function(t,Linf,gninf,a) {
#> Linf/(1+a*exp(-gninf*t))
#> }
-#> <bytecode: 0x0000000023adf7f8>
-#> <environment: 0x0000000023d535e8>
+#> <bytecode: 0x0000000024b00920>
+#> <environment: 0x0000000024d77a48>
( log3 <- logisticFuns("Karkach") )
#> function(t,Linf,L0=NULL,gninf=NULL) {
#> if (length(Linf)==3) { L0 <- Linf[[2]]
@@ -367,8 +367,8 @@ Examples
#> Linf <- Linf[[1]] }
#> L0*Linf/(L0+(Linf-L0)*exp(-gninf*t))
#> }
-#> <bytecode: 0x0000000023ae0e58>
-#> <environment: 0x0000000023da54f0>
+#> <bytecode: 0x0000000024b05db0>
+#> <environment: 0x0000000024dcde10>
plot(log3(ages,L0=10,Linf=800,gninf=0.5)~ages,type="b",pch=19)
( log4 <- logisticFuns("Haddon") )
@@ -378,8 +378,8 @@ Examples
#> dLmax <- dLmax[1] }
#> dLmax/(1+exp(log(19)*((Lm-L50)/(L95-L50))))
#> }
-#> <bytecode: 0x0000000023aeb5c8>
-#> <environment: 0x0000000023eb4390>
+#> <bytecode: 0x0000000024b11e30>
+#> <environment: 0x0000000024edd658>
###########################################################
diff --git a/docs/reference/headtail.html b/docs/reference/headtail.html
index 9b8439af..d880a14d 100644
--- a/docs/reference/headtail.html
+++ b/docs/reference/headtail.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Shows rows from the head and tail of a data frame or matrix.
- Source: R/FSAUtils.R
+ Source: R/FSAUtils.R
headtail.Rd
diff --git a/docs/reference/hist.formula.html b/docs/reference/hist.formula.html
index a350307a..c65c6c14 100644
--- a/docs/reference/hist.formula.html
+++ b/docs/reference/hist.formula.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Creates separate histograms by levels.
- Source: R/hist.formula.R
+ Source: R/hist.formula.R
hist.formula.Rd
diff --git a/docs/reference/histFromSum.html b/docs/reference/histFromSum.html
index 4b78f4a5..a6249ce1 100644
--- a/docs/reference/histFromSum.html
+++ b/docs/reference/histFromSum.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Create a histogram from a frequency table.
- Source: R/histFromSum.R
+ Source: R/histFromSum.R
histFromSum.Rd
diff --git a/docs/reference/hyperCI.html b/docs/reference/hyperCI.html
index 57615bc3..98357628 100644
--- a/docs/reference/hyperCI.html
+++ b/docs/reference/hyperCI.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Confidence interval for population size (N) in hypergeometric distribution.
- Source: R/CIDists.R
+ Source: R/CIDists.R
hyperCI.Rd
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 637580d8..cd232d43 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -17,7 +17,7 @@
@@ -442,7 +442,7 @@ Data
All known standard weight equations.
Defunct
- Defunction functions.
+ Defunct functions.
bootCase() chooseColors() compIntercepts() compSlopes() diags() filterD() fitPlot() fsaNews() hoCoef() mapvalues() plotBinResp() residPlot() Subset()
diff --git a/docs/reference/knitUtil.html b/docs/reference/knitUtil.html
index 566e1e8d..f56ebffe 100644
--- a/docs/reference/knitUtil.html
+++ b/docs/reference/knitUtil.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Specific utilities for use in a knitr document.
- Source: R/knitUtil.R
+ Source: R/knitUtil.R
knitUtil.Rd
diff --git a/docs/reference/ksTest.html b/docs/reference/ksTest.html
index 58d92eef..4fa21c9c 100644
--- a/docs/reference/ksTest.html
+++ b/docs/reference/ksTest.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/lagratio.html b/docs/reference/lagratio.html
index dff7a7eb..dfd66ddf 100644
--- a/docs/reference/lagratio.html
+++ b/docs/reference/lagratio.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/lencat.html b/docs/reference/lencat.html
index 8182783f..e69957da 100644
--- a/docs/reference/lencat.html
+++ b/docs/reference/lencat.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/logbtcf.html b/docs/reference/logbtcf.html
index 0b66cc46..1ddd1c31 100644
--- a/docs/reference/logbtcf.html
+++ b/docs/reference/logbtcf.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Constructs the correction-factor used when back-transforming log-transformed values.
- Source: R/FSAUtils.R
+ Source: R/FSAUtils.R
logbtcf.Rd
diff --git a/docs/reference/lwCompPreds.html b/docs/reference/lwCompPreds.html
index d9865efc..6ac0d6e0 100644
--- a/docs/reference/lwCompPreds.html
+++ b/docs/reference/lwCompPreds.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Constructs plots of predicted weights at given lengths among different groups.
- Source: R/lwCompPreds.R
+ Source: R/lwCompPreds.R
lwCompPreds.Rd
diff --git a/docs/reference/metaM.html b/docs/reference/metaM.html
index 2db2b3a3..d4661c14 100644
--- a/docs/reference/metaM.html
+++ b/docs/reference/metaM.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/mrClosed.html b/docs/reference/mrClosed.html
index d89ab6f8..abef6ad6 100644
--- a/docs/reference/mrClosed.html
+++ b/docs/reference/mrClosed.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Estimate initial population size for single or multiple census mark-recapture data.
- Source: R/mrClosed.R
+ Source: R/mrClosed.R
mrClosed.Rd
diff --git a/docs/reference/mrOpen.html b/docs/reference/mrOpen.html
index 938e0360..2f704908 100644
--- a/docs/reference/mrOpen.html
+++ b/docs/reference/mrOpen.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Jolly-Seber analysis from multiple mark-recapture events from an open population.
- Source: R/mrOpen.R
+ Source: R/mrOpen.R
mrOpen.Rd
diff --git a/docs/reference/nlsBoot.html b/docs/reference/nlsBoot.html
index 435aa5ac..fcca8086 100644
--- a/docs/reference/nlsBoot.html
+++ b/docs/reference/nlsBoot.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Associated S3 methods for nlsBoot from nlstools.
- Source: R/bootstrap.R
+ Source: R/bootstrap.R
nlsBoot.Rd
diff --git a/docs/reference/nlsTracePlot.html b/docs/reference/nlsTracePlot.html
index bc5fc3c5..bc57e4b6 100644
--- a/docs/reference/nlsTracePlot.html
+++ b/docs/reference/nlsTracePlot.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Adds model fits from nls iterations to active plot.
- Source: R/nlsTracePlot.R
+ Source: R/nlsTracePlot.R
nlsTracePlot.Rd
diff --git a/docs/reference/perc.html b/docs/reference/perc.html
index fc0db423..16500e7b 100644
--- a/docs/reference/perc.html
+++ b/docs/reference/perc.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Computes the percentage of values in a vector less than or greater than (and equal to) some value.
- Source: R/FSAUtils.R
+ Source: R/FSAUtils.R
perc.Rd
diff --git a/docs/reference/plotAB.html b/docs/reference/plotAB.html
index 0e146366..005043d8 100644
--- a/docs/reference/plotAB.html
+++ b/docs/reference/plotAB.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Construct traditional (Campana-like) age-bias plots.
- Source: R/ageComparisons.R
+ Source: R/ageComparisons.R
plotAB.Rd
diff --git a/docs/reference/poiCI.html b/docs/reference/poiCI.html
index 1afc0813..0bd31bac 100644
--- a/docs/reference/poiCI.html
+++ b/docs/reference/poiCI.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/psdAdd.html b/docs/reference/psdAdd.html
index 09b771fe..825be160 100644
--- a/docs/reference/psdAdd.html
+++ b/docs/reference/psdAdd.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Creates a vector of Gabelhouse lengths for each species in an entire data frame.
- Source: R/psdAdd.R
+ Source: R/psdAdd.R
psdAdd.Rd
diff --git a/docs/reference/psdCI.html b/docs/reference/psdCI.html
index a026841b..a9fab439 100644
--- a/docs/reference/psdCI.html
+++ b/docs/reference/psdCI.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/psdCalc.html b/docs/reference/psdCalc.html
index f7a997cf..9c208ed6 100644
--- a/docs/reference/psdCalc.html
+++ b/docs/reference/psdCalc.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Convenience function for calculating PSD-X and PSD X-Y values.
- Source: R/psdCalc.R
+ Source: R/psdCalc.R
psdCalc.Rd
diff --git a/docs/reference/psdPlot.html b/docs/reference/psdPlot.html
index 3f9919ce..70c4babf 100644
--- a/docs/reference/psdPlot.html
+++ b/docs/reference/psdPlot.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Length-frequency histogram with Gabelhouse lengths highlighted.
- Source: R/psdPlot.R
+ Source: R/psdPlot.R
psdPlot.Rd
diff --git a/docs/reference/psdVal.html b/docs/reference/psdVal.html
index f8320284..68cf152b 100644
--- a/docs/reference/psdVal.html
+++ b/docs/reference/psdVal.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Finds Gabelhouse lengths (for PSD calculations) for a species.
- Source: R/psdVal.R
+ Source: R/psdVal.R
psdVal.Rd
diff --git a/docs/reference/rSquared.html b/docs/reference/rSquared.html
index 9bb050ac..be7ab1fb 100644
--- a/docs/reference/rSquared.html
+++ b/docs/reference/rSquared.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Extract the coefficient of determination from a linear model object.
- Source: R/FSAUtils.R
+ Source: R/FSAUtils.R
rSquared.Rd
diff --git a/docs/reference/rcumsum.html b/docs/reference/rcumsum.html
index 83bc6cce..a8c0c06b 100644
--- a/docs/reference/rcumsum.html
+++ b/docs/reference/rcumsum.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Computes the prior to or reverse cumulative sum of a vector.
- Source: R/FSAUtils.R
+ Source: R/FSAUtils.R
rcumsum.Rd
diff --git a/docs/reference/removal.html b/docs/reference/removal.html
index 8caad71f..47fdb1c8 100644
--- a/docs/reference/removal.html
+++ b/docs/reference/removal.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Population estimates for k-, 3-, or 2-pass removal data.
- Source: R/removal.R
+ Source: R/removal.R
removal.Rd
diff --git a/docs/reference/se.html b/docs/reference/se.html
index ebe12670..87941dc5 100644
--- a/docs/reference/se.html
+++ b/docs/reference/se.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
@@ -75,7 +75,7 @@ Value
See also
- See se in sciplot for similar functionality.
+ See se in sciplot for similar functionality.
@@ -50,7 +50,7 @@
Finds reasonable starting values for parameters in specific parameterizations of common stock-recruitment models.
- Source: R/srStarts.R
+ Source: R/srStarts.R
srStarts.Rd
diff --git a/docs/reference/sumTable.html b/docs/reference/sumTable.html
index 2817021d..4b63b305 100644
--- a/docs/reference/sumTable.html
+++ b/docs/reference/sumTable.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Creates a one- or two-way table of summary statistics.
- Source: R/sumTable.R
+ Source: R/sumTable.R
sumTable.Rd
diff --git a/docs/reference/tictactoe.html b/docs/reference/tictactoe.html
index f388a2d9..ae96ecc2 100644
--- a/docs/reference/tictactoe.html
+++ b/docs/reference/tictactoe.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Construct a base tic-tac-toe plot for presenting predator-prey PSD values.
- Source: R/tictactoe.R
+ Source: R/tictactoe.R
tictactoe.Rd
diff --git a/docs/reference/validn.html b/docs/reference/validn.html
index 3642b7b0..aaa3ac6e 100644
--- a/docs/reference/validn.html
+++ b/docs/reference/validn.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Finds the number of valid (non-NA) values in a vector.
- Source: R/FSAUtils.R
+ Source: R/FSAUtils.R
validn.Rd
diff --git a/docs/reference/vbStarts.html b/docs/reference/vbStarts.html
index aca2392a..ae26879b 100644
--- a/docs/reference/vbStarts.html
+++ b/docs/reference/vbStarts.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Find reasonable starting values for a von Bertalanffy growth function.
- Source: R/vbStarts.R
+ Source: R/vbStarts.R
vbStarts.Rd
diff --git a/docs/reference/wrAdd.html b/docs/reference/wrAdd.html
index 5a954603..9c877514 100644
--- a/docs/reference/wrAdd.html
+++ b/docs/reference/wrAdd.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/wsVal.html b/docs/reference/wsVal.html
index cebe5f56..578fde5a 100644
--- a/docs/reference/wsVal.html
+++ b/docs/reference/wsVal.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Finds standard weight equation coefficients for a particular species.
- Source: R/wsVal.R
+ Source: R/wsVal.R
wsVal.Rd
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 22783efc..bf52b330 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -28,13 +28,13 @@
http://derekogle.com/FSA/reference/agePrecision.html
- http://derekogle.com/FSA/reference/ALKAgeDist.html
+ http://derekogle.com/FSA/reference/alkAgeDist.html
http://derekogle.com/FSA/reference/alkIndivAge.html
- http://derekogle.com/FSA/reference/ALKMeanVar.html
+ http://derekogle.com/FSA/reference/alkMeanVar.html
http://derekogle.com/FSA/reference/alkPlot.html
@@ -114,18 +114,9 @@
http://derekogle.com/FSA/reference/fact2num.html
-
- http://derekogle.com/FSA/reference/filterD-deprecated.html
-
-
- http://derekogle.com/FSA/reference/filterD.html
-
http://derekogle.com/FSA/reference/fishR.html
-
- http://derekogle.com/FSA/reference/fitPlot-deprecated.html
-
http://derekogle.com/FSA/reference/fitPlot.html
diff --git a/inst/helpers/installTester.R b/inst/helpers/installTester.R
index fdcc45d3..e9930b3f 100644
--- a/inst/helpers/installTester.R
+++ b/inst/helpers/installTester.R
@@ -31,9 +31,7 @@ lwCompPreds(lm1,xlab="Location")
## Make sure all dependent and imported packages would load
library(plyr)
-library(dplyr)
library(car)
library(dunn.test)
library(lmtest)
library(plotrix)
-library(sciplot)
diff --git a/man/FSA.Rd b/man/FSA.Rd
index d181531a..8f266482 100644
--- a/man/FSA.Rd
+++ b/man/FSA.Rd
@@ -10,11 +10,11 @@ Functions to support basic fisheries stock assessment methods.
\details{
Functions from this package can be used to perform a variety of basic fisheries stock assessment methods. Detailed descriptions for most functions are available in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analysis with R} book (Ogle 2016). Vignettes for the boxed examples in the \dQuote{Analysis and Interpretation of Freshwater Fisheries Data} book can be viewed with \code{fishR("AIFFD")}.
-Questions, comments, or suggestions should be given on the \href{https://github.com/droglenc/FSA/issues/}{GitHub FSA Issues page}.
+Questions, comments, or suggestions should be given on the \href{https://github.com/fishR-Core-Team/FSA/issues/}{GitHub FSA Issues page}.
Packages with related functionality by the same author are
\itemize{
- \item The \href{https://github.com/droglenc/FSAdata/}{FSAdata package} contains additional data sets.
+ \item The \href{https://github.com/fishR-Core-Team/FSAdata/}{FSAdata package} contains additional data sets.
\item The \href{https://github.com/droglenc/FSAsim/}{FSAsim package} simulation routines for various fisheries methods.
\item The \href{https://github.com/droglenc/FSAWs/}{FSAWs package} contains functions for developing and validating standard weight equations.
}
diff --git a/man/se.Rd b/man/se.Rd
index 7ef1f0e9..9659a586 100644
--- a/man/se.Rd
+++ b/man/se.Rd
@@ -33,7 +33,7 @@ se(x2)
}
\seealso{
-See \code{\link[sciplot]{se}} in \pkg{sciplot} for similar functionality.
+See \code{se} in \pkg{sciplot} for similar functionality.
}
\author{
Derek H. Ogle, \email{derek@derekogle.com}
diff --git a/tests/testthat/testthat_ksTest.R b/tests/testthat/testthat_ksTest.R
index 84bd213a..a0358fc7 100644
--- a/tests/testthat/testthat_ksTest.R
+++ b/tests/testthat/testthat_ksTest.R
@@ -28,29 +28,31 @@ test_that("ksTest() messages",{
## Test Output Types ----
test_that("Does ksTest() match ks.test()",{
- exp_nms <- c("statistic","p.value","alternative","method","data.name")
x <- rnorm(50)
y <- runif(30)
df <- data.frame(dat=c(x,y),grp=factor(rep(c("X","Y"),c(50,30))),
stringsAsFactors=FALSE)
## one-sample (from ks.test) still works
- tmp <- ksTest(x+2,"pgamma",3,2)
- expect_is(tmp,"htest")
- expect_equal(mode(tmp),"list")
- expect_equal(names(tmp),exp_nms)
+ tmp1 <- ksTest(x+2,"pgamma",3,2)
+ tmp1o <- ks.test(x+2,"pgamma",3,2)
+ expect_is(tmp1,"htest")
+ expect_equal(mode(tmp1),"list")
+ expect_equal(names(tmp1),names(tmp1o))
## first two-sample example in ?ks.test
- tmp <- ksTest(x,y)
- expect_is(tmp,"htest")
- expect_equal(mode(tmp),"list")
- expect_equal(names(tmp),exp_nms)
- # using formula notation
- tmp1 <- ksTest(dat~grp,data=df)
+ tmp1 <- ksTest(x,y)
+ tmp1o <- ks.test(x,y)
expect_is(tmp1,"htest")
expect_equal(mode(tmp1),"list")
- expect_equal(names(tmp1),exp_nms)
- expect_identical(tmp,tmp1)
+ expect_equal(names(tmp1),names(tmp1o))
+
+ # using formula notation
+ tmp1f <- ksTest(dat~grp,data=df)
+ expect_is(tmp1f,"htest")
+ expect_equal(mode(tmp1f),"list")
+ expect_equal(names(tmp1f),names(tmp1o))
+ expect_identical(tmp1,tmp1f)
})
@@ -63,15 +65,15 @@ test_that("Does ksTest() match ks.test()",{
## one-sample (from ks.test) still works
tmp1 <- ksTest(x+2, "pgamma", 3, 2)
- tmp2 <- ks.test(x+2, "pgamma", 3, 2)
- expect_equal(tmp1$statistic,tmp2$statistic)
- expect_equal(tmp1$p.value,tmp2$p.value)
+ tmp1o <- ks.test(x+2, "pgamma", 3, 2)
+ expect_equal(tmp1$statistic,tmp1o$statistic)
+ expect_equal(tmp1$p.value,tmp1o$p.value)
## first two-sample example in ?ks.test
tmp1 <- ksTest(x,y)
- tmp2 <- ks.test(x,y)
- tmp3 <- ksTest(dat~grp,data=df)
- expect_equal(tmp1,tmp2)
- expect_equal(tmp3,tmp2)
+ tmp1o <- ks.test(x,y)
+ tmp1f <- ksTest(dat~grp,data=df)
+ expect_equal(tmp1,tmp1o)
+ expect_equal(tmp1f,tmp1o)
})
if (!require('remotes')) install.packages('remotes'); require('remotes')
-remotes::install_github('droglenc/FSA')Questions / Comments / Problems or Contributions
-Report questions, comments, or bug reports on the issues page.
+Report questions, comments, or bug reports on the issues page.
We are always looking for others to contribute to FSA. Please feel free to make a pull request via GitHub or to contact the maintainers.
Please adhere to the Code of Conduct.
Links
@@ -162,8 +162,8 @@Dev status
-
+ FSA 0.9.2 12-Feb-21
-- Last version maintained by Derek Ogle. Transfering to fishR Core Team for next version. +
- Moved
dplyrfromimportstosuggests(needed because functions were removed in last version; however it is still used in some examples; partially addresses #87).
+ - Removed
sciplotfromimports(because functions were removed in last version; partially addresses #87).
+ - Updated tests for
ksTest()to handle issues on the CRAN M1 build machine (per e-mail from Prof. Ripley on 15-Feb-22; partially addresses #87).
+ - Updated all links to the
droglencgithub that were related toFSAorFSAdatato be to thefishR-Core-Teamgithub.
+
FSA 0.9.3 15-Feb-21
+
+
FSA 0.9.2 12-Feb-212022-02-12
+- Last version maintained by Derek Ogle. Transferring to fishR Core Team for next version.
-
filterD(): REMOVED (toFSAmisc). -
@@ -63,19 +70,19 @@
FSA 0.9.2 1
-
fsaNews()andFSANews(): Removed. -
-
psdAdd(): Modified. Changed the wayPSDlitwas loaded into the function environment so thatFSA::psdAdd()will work. Addresses #85.
+ -
-
PSDLit: Modified. Added info for Utah Chub (from here; address #84).
+ -
-
psdVal(): Modified. Changed the wayPSDlitwas loaded into the function environment so thatFSA::psdVal()will work. Addresses #85.
+ -
residPlot(): REMOVED (toFSAmisc). -
-
wrAdd(): Modified. Changed the wayWSlitwas loaded into the function environment so thatFSA::wrAdd()will work. Addresses #85.
+ -
-
WSLit: Modified. Added info for Utah Chub (from here; address #84).
+ -
-
wsVal(): Modified. Changed the wayWSlitwas loaded into the function environment so thatFSA::wsVal()will work. Addresses #85.
+
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.
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.
FSA 0.9.1 17-Jul-212021-07-17
@@ -89,70 +96,70 @@FSA 0.9.0 8-
alkPlot(): Modified. Removed use of chooseColors() (see below).binCI(): Modified. Changed to use iCheckConfLevel() (which addresses #66).binCI(): Modified. Changed to use iCheckConfLevel() (which addresses #66).
bootCase(): REMOVED. Users can use car::Boot(), which partially addresses #65.
+bootCase(): REMOVED. Users can use car::Boot(), which partially addresses #65.
-
plot.boot(): REMOVED. Conflicted withboot::plot.boot()which caused an error with CRAN. Same functionality is available withpairs(<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).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).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.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.compIntercepts(): REMOVED (to FSAmisc). Added to FSA-defunct. Partially addresses #65.
compSlopes(): 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).depletion(): Modified. Changed to use iCheckConfLevel() (which addresses #66).
filterD(): DEPRECATED (partially addresses #65).filterD(): DEPRECATED (partially addresses #65).
fitPlot(): DEPRECATED (partially addresses #65). Prior to that removed use of chooseColors() (see above).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.diags(): REMOVED (moved to FSAmisc). Added to FSA-defunct. Partially addresses #65.
hoCoef(): 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).hyperCI(): Modified. Changed to use iCheckConfLevel() (which addresses #66).
iCheckConfLevel(): Added (internal to address #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.mapvalues(): REMOVED. Added to FSA-defunct. Partially addresses #65.
mrClosed(): Modified. Changed to use iCheckConfLevel() (which addresses #66).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).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.paletteChoices(): REMOVED. See chooseColors() above. Partially addresses #65.
poiCI(): Modified. Changed to use iCheckConfLevel() (which addresses #66).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).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).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.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).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).residPlot(): DEPRECATED (partially addresses #65). Prior to that removed use of chooseColors() (see above).
Subset(): REMOVED. Added to FSA-defunct. Partially addresses #65.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.
+WSlit: Modified. Addresses #68.
- Corrected capitalization of “Cavedano Chub”, “European Chub”, “Lake Herring” (metric), and “Pursak Chub”.
- Removed “not in Neumann et al. (2012)” notes.
- Added African Sharptooth Catfish, Ankara Nase, Bighead and Silver Carp, Brook Trout (Appalachia), Fourbarbel Scraper, Horse Barbel, Nile Tilapia, Nipple-Lipped Scraper, Shoal Bass, South European Roach, Spotted Bass (Alabama subspecies) (AKA Alabama Bass). @@ -171,13 +178,13 @@
- Added a code of conduct for contributors.
- Moved a bunch of plotting examples in the documentation to
tests\plottests\to speed up testing. Thetests\plottests\was added to.Rbuildignore. -
-
hist.formula(): Modified. Fixed bug with y-axes whenfreq=FALSEis used (fixes #62; thanks to @carlostorrescubila).
+
FSA 0.8.3
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.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.FSA 0.8.23
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.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.SchnuteRichards(): Added. This addresses #54.
FSA 0.8.22 22-Nov-182018-11-22
@@ -285,39 +292,39 @@FSA 0.8.21
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.\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.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().alkPlot(): Modified. Changed to using withr::local_par() (partially addresses #38). Replaced an options(warn=-1) with suppressWarnings().
alkSummaries(): Modified. Replaced an options(warn=-1) with suppressWarnings().withr::local_par() (partially addresses #38).withr::local_par() (partially addresses #38).capHistSum(): Modified. Changed to using withr::local_par() (partially addresses #38).capHistSum(): Modified. Changed to using withr::local_par() (partially addresses #38).
chapmanRobson(): Modified. Changed to using withr::local_par() (partially addresses #38).chapmanRobson(): Modified. Changed to using withr::local_par() (partially addresses #38).
fishR(): Modified. Changed examples in documentation to not be run (so as not to open an external webpage).FSAnews(): Modified. Changed examples in documentation to not be run (so as not to open an external webpage).withr::local_par() (partially addresses #38).withr::local_par() (partially addresses #38).hist.formula(): Modified. Changed to using withr::local_par() (partially addresses #38).hist.formula(): Modified. Changed to using withr::local_par() (partially addresses #38).
lwCompPreds(): Modified. Changed to using withr::local_par() (partially addresses #38).lwCompPreds(): Modified. Changed to using withr::local_par() (partially addresses #38).
plotAB(): Modified. Now in its own documentation file (rather than with ageBias()).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).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.removal(): Modified. Added method="Burhnam" via the #51 from Powell Wheeler.
residPlot(): Modified. Changed to using withr::local_par() (partially addresses #38).residPlot(): Modified. Changed to using withr::local_par() (partially addresses #38).
SMBassWB: Modified. Fixed minor data entry error in row 383.FSA 0.8.2
FSA 0.8.19 8-Apr-182018-04-08
-
-
addZeroCatch(): Modified. Changed two 1:nrow() structures to seq_len(nrow()) (partially addressing #36).
+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).
+ageBias(): Modified. Changed all 1: structures to seq_len() (partially addressing #36).
-
-
agePrecision(): 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).
+bcFuns(): Modified. Changed three 1:length() structures to seq_along() (partially addressing #36).
-
-
bootCase() methods: Modified. Changed all 1: structures to seq_len() (partially addressing #36).
+bootCase() methods: Modified. Changed all 1: structures to seq_len() (partially addressing #36).
-
-
capHistConvert(): Modified. Changed all 1: structures to seq_len() or seq_along() (partially addressing #36).
+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).
+capHistSum(): Modified. Changed all 1: structures to seq_len() (partially addressing #36).
-
-
chooseColors(): 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).
+compSlopes(): Modified. Changed all 1: structures to seq_len() (partially addressing #36).
-
-
compIntercepts(): 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).
+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).
+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).
+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().
+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).
+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).
+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).
+mrClosed(): Modified. Changed two 1:length() structures to seq_along() (partially addressing #36).
-
-
nlsBoot() methods: Modified. Changed all 1: structures to seq_len() (partially addressing #36).
+nlsBoot() methods: Modified. Changed all 1: structures to seq_len() (partially addressing #36).
-
plot.boot(): Removed (added last version) until I can test more.
-
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).
+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).
+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).
+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).
+wrAdd(): Modified. Changed three 1: structures to seq_len() or seq_along() (partially addressing #36).
FSA 0.8.18 31-Mar-18
@@ -409,7 +416,7 @@ FSA 0.8.1
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).
+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.
@@ -440,9 +447,9 @@ FSA 0.8.15
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.
+removal(): Modified document by merging pull request #33.
-srStarts(): Modified. Added fixed=. Added some catches for poor starting values. Added relevant tests. Addresses #30.
+srStarts(): Modified. Added fixed=. Added some catches for poor starting values. Added relevant tests. Addresses #30.
FSA 0.8.14 27-Jul-172017-07-27
@@ -526,13 +533,13 @@ FSA 0.8.1
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.
+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.
+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.
+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.
@@ -548,9 +555,9 @@ FSA 0.8.1
iHndlCols2use(): Deleted. Changed to iHndlCols2UseIgnore().
-iHndlCols2UseIgnore(): Added. Previously was iHndlCols2use(). Completely reworked to catch more problems including having both positive and negative indices (fixes #24) and choosing variable names that don’t exist (fixes #25).
+iHndlCols2UseIgnore(): Added. Previously was iHndlCols2use(). Completely reworked to catch more problems including having both positive and negative indices (fixes #24) and choosing variable names that don’t exist (fixes #25).
-iHndlFormula(): Modified. Added code to deal with a formula that is a single “variable” sent in an array. Addresses #21 for the simple situation of single “variable.”
+iHndlFormula(): Modified. Added code to deal with a formula that is a single “variable” sent in an array. Addresses #21 for the simple situation of single “variable.”
iHndlMultWhat(): Modified. Added type= to allow use with message() or cat().
@@ -562,7 +569,7 @@ FSA 0.8.1
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.
+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.
@@ -578,7 +585,7 @@ FSA 0.8.1
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.
+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.
@@ -595,7 +602,7 @@ FSA 0.8.1
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.
+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.
@@ -644,8 +651,8 @@ FSA 0.8.8 1
FSA 0.8.7 8-May-162016-05-08
- Compiled under R v3.3.0.
-- Removed
relax from Suggests. See srStarts() and vbStarts() notes below. This addresses #17.
-- Removed
gdata from Imports. See filterD() and Subset() notes below. This addresses #5.
+- Removed
relax from Suggests. See srStarts() and vbStarts() notes below. This addresses #17.
+- Removed
gdata from Imports. See filterD() and Subset() notes below. This addresses #5.
- Added no coverage blocks to
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().
@@ -658,7 +665,7 @@ FSA 0.8.7 8-
-
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.
+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=.
-
@@ -699,9 +706,9 @@
FSA 0.8.6 2
- Fixed problems with tests, and made the tests more explicit, related to PSD and Wr functions. Suppressed some warnings related to
sumTable() in ALK related tests and Summarize() in age comparisons tests. Prompted by forthcoming changes to testthat.
- Removed
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).
+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.
+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.
-
@@ -715,7 +722,7 @@
FSA 0.8.6 2
-
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.
+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.
-
@@ -726,10 +733,10 @@
FSA 0.8.5 1
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.
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).
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.
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 8c674d3c..2590d423 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 2.14.0.3
pkgdown: 2.0.2
pkgdown_sha: ~
articles: {}
-last_built: 2022-02-12T19:10Z
+last_built: 2022-02-16T00:00Z
urls:
reference: http://derekogle.com/FSA/reference
article: http://derekogle.com/FSA/articles
diff --git a/docs/reference/BluegillJL.html b/docs/reference/BluegillJL.html
index d6309185..043fc4dd 100644
--- a/docs/reference/BluegillJL.html
+++ b/docs/reference/BluegillJL.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Capture histories (2 samples) of Bluegill from Jewett Lake, MI.
- Source: R/BluegillJL.R
+ Source: R/BluegillJL.R
BluegillJL.Rd
diff --git a/docs/reference/BrookTroutTH.html b/docs/reference/BrookTroutTH.html
index f483e184..d14b5b57 100644
--- a/docs/reference/BrookTroutTH.html
+++ b/docs/reference/BrookTroutTH.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.
- Source: R/BrookTroutTH.R
+ Source: R/BrookTroutTH.R
BrookTroutTH.Rd
diff --git a/docs/reference/ChinookArg.html b/docs/reference/ChinookArg.html
index 382bf834..2a4f2833 100644
--- a/docs/reference/ChinookArg.html
+++ b/docs/reference/ChinookArg.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Lengths and weights for Chinook Salmon from three locations in Argentina.
- Source: R/ChinookArg.R
+ Source: R/ChinookArg.R
ChinookArg.Rd
diff --git a/docs/reference/CodNorwegian.html b/docs/reference/CodNorwegian.html
index 6f8a1fb0..569e9682 100644
--- a/docs/reference/CodNorwegian.html
+++ b/docs/reference/CodNorwegian.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Stock and recruitment data for Norwegian cod, 1937-1960.
- Source: R/CodNorwegian.R
+ Source: R/CodNorwegian.R
CodNorwegian.Rd
diff --git a/docs/reference/CutthroatAL.html b/docs/reference/CutthroatAL.html
index 1a6f8f73..ff90e0c6 100644
--- a/docs/reference/CutthroatAL.html
+++ b/docs/reference/CutthroatAL.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Capture histories (9 samples) of Cutthroat Trout from Auke Lake.
- Source: R/CutthroatAL.R
+ Source: R/CutthroatAL.R
CutthroatAL.Rd
diff --git a/docs/reference/Ecoli.html b/docs/reference/Ecoli.html
index 2bef4c7b..fefbb3ee 100644
--- a/docs/reference/Ecoli.html
+++ b/docs/reference/Ecoli.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/FSA-internals.html b/docs/reference/FSA-internals.html
index 9a05a1d8..4f5023c2 100644
--- a/docs/reference/FSA-internals.html
+++ b/docs/reference/FSA-internals.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/FSA.html b/docs/reference/FSA.html
index bd96de6b..d80fb633 100644
--- a/docs/reference/FSA.html
+++ b/docs/reference/FSA.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
@@ -62,8 +62,8 @@ Fisheries stock assessment methods and data.
Details
Functions from this package can be used to perform a variety of basic fisheries stock assessment methods. Detailed descriptions for most functions are available in the Introductory Fisheries Analysis with R book (Ogle 2016). Vignettes for the boxed examples in the “Analysis and Interpretation of Freshwater Fisheries Data” book can be viewed with fishR("AIFFD").
-Questions, comments, or suggestions should be given on the GitHub FSA Issues page.
-Packages with related functionality by the same author are
The FSAdata package contains additional data sets.
Questions, comments, or suggestions should be given on the GitHub FSA Issues page.
+Packages with related functionality by the same author are
The FSAdata package contains additional data sets.
The FSAsim package simulation routines for various fisheries methods.
The FSAWs package contains functions for developing and validating standard weight equations.
diff --git a/docs/reference/Mirex.html b/docs/reference/Mirex.html
index e3825d25..0f075183 100644
--- a/docs/reference/Mirex.html
+++ b/docs/reference/Mirex.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/PSDlit.html b/docs/reference/PSDlit.html
index bb11d70f..5e779170 100644
--- a/docs/reference/PSDlit.html
+++ b/docs/reference/PSDlit.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Gabelhouse five-cell length categories for various species.
- Source: R/PSDlit.R
+ Source: R/PSDlit.R
PSDlit.Rd
diff --git a/docs/reference/PikeNY.html b/docs/reference/PikeNY.html
index 9af7c2e4..5144e19b 100644
--- a/docs/reference/PikeNY.html
+++ b/docs/reference/PikeNY.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Summarized multiple mark-recapture data for all Northern Pike from Buckhorn Marsh, NY.
- Source: R/PikeNY.R
+ Source: R/PikeNY.R
PikeNY.Rd
diff --git a/docs/reference/PikeNYPartial1.html b/docs/reference/PikeNYPartial1.html
index 2cea0c7e..8ee11694 100644
--- a/docs/reference/PikeNYPartial1.html
+++ b/docs/reference/PikeNYPartial1.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Capture histories (4 samples), in capture history format, of a subset of Northern Pike from Buckhorn Marsh, NY.
- Source: R/PikeNYPartial1.R
+ Source: R/PikeNYPartial1.R
PikeNYPartial1.Rd
diff --git a/docs/reference/SMBassLS.html b/docs/reference/SMBassLS.html
index 7db1c11b..30b5d2de 100644
--- a/docs/reference/SMBassLS.html
+++ b/docs/reference/SMBassLS.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Catch-effort data for Little Silver Lake (Ont) Smallmouth Bass.
- Source: R/SMBassLS.R
+ Source: R/SMBassLS.R
SMBassLS.Rd
diff --git a/docs/reference/SMBassWB.html b/docs/reference/SMBassWB.html
index 42fdc4b8..6be0c3eb 100644
--- a/docs/reference/SMBassWB.html
+++ b/docs/reference/SMBassWB.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Growth increment data for West Bearskin Lake, MN, Smallmouth Bass.
- Source: R/SMBassWB.R
+ Source: R/SMBassWB.R
SMBassWB.Rd
diff --git a/docs/reference/Schnute.html b/docs/reference/Schnute.html
index f8e90184..bd811275 100644
--- a/docs/reference/Schnute.html
+++ b/docs/reference/Schnute.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
The four-parameter growth function from Schnute (1981).
- Source: R/growthModels.R
+ Source: R/growthModels.R
Schnute.Rd
diff --git a/docs/reference/SpotVA1.html b/docs/reference/SpotVA1.html
index 17a78714..5ec0379a 100644
--- a/docs/reference/SpotVA1.html
+++ b/docs/reference/SpotVA1.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/Summarize.html b/docs/reference/Summarize.html
index 9510819d..f097047b 100644
--- a/docs/reference/Summarize.html
+++ b/docs/reference/Summarize.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Summary statistics for a numeric variable.
- Source: R/Summarize.R
+ Source: R/Summarize.R
Summarize.Rd
diff --git a/docs/reference/WR79.html b/docs/reference/WR79.html
index d7db0736..8917d28f 100644
--- a/docs/reference/WR79.html
+++ b/docs/reference/WR79.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/WSlit.html b/docs/reference/WSlit.html
index 36f72322..0d32931b 100644
--- a/docs/reference/WSlit.html
+++ b/docs/reference/WSlit.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/WhitefishLC.html b/docs/reference/WhitefishLC.html
index 1b696af9..74cdc1b8 100644
--- a/docs/reference/WhitefishLC.html
+++ b/docs/reference/WhitefishLC.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Assigned ages from two readers on three structures for Lake Whitefish from Lake Champlain.
- Source: R/WhitefishLC.R
+ Source: R/WhitefishLC.R
WhitefishLC.Rd
diff --git a/docs/reference/addZeroCatch.html b/docs/reference/addZeroCatch.html
index d794d440..c873affa 100644
--- a/docs/reference/addZeroCatch.html
+++ b/docs/reference/addZeroCatch.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Adds zeros for catches of species not collected in some sampling events.
- Source: R/addZeroCatch.R
+ Source: R/addZeroCatch.R
addZeroCatch.Rd
diff --git a/docs/reference/ageBias.html b/docs/reference/ageBias.html
index 8f0b2399..96e73b8e 100644
--- a/docs/reference/ageBias.html
+++ b/docs/reference/ageBias.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Compute and view possible differences between paired sets of ages.
- Source: R/ageComparisons.R
+ Source: R/ageComparisons.R
ageBias.Rd
diff --git a/docs/reference/agePrecision.html b/docs/reference/agePrecision.html
index f71a878a..9f97cef3 100644
--- a/docs/reference/agePrecision.html
+++ b/docs/reference/agePrecision.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Compute measures of precision among sets of ages.
- Source: R/ageComparisons.R
+ Source: R/ageComparisons.R
agePrecision.Rd
diff --git a/docs/reference/alkAgeDist.html b/docs/reference/alkAgeDist.html
index 89f6f747..1dfb209f 100644
--- a/docs/reference/alkAgeDist.html
+++ b/docs/reference/alkAgeDist.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Proportions-at-age from an age-length key
- Source: R/alkSummaries.R
+ Source: R/alkSummaries.R
alkAgeDist.Rd
diff --git a/docs/reference/alkIndivAge.html b/docs/reference/alkIndivAge.html
index 8527e579..20898e94 100644
--- a/docs/reference/alkIndivAge.html
+++ b/docs/reference/alkIndivAge.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Use an age-length key to assign age to individuals in the unaged sample.
- Source: R/alkIndivAge.R
+ Source: R/alkIndivAge.R
alkIndivAge.Rd
@@ -191,27 +191,27 @@ Examples
WR1.comb <- rbind(WR1.age, WR1.len)
# mean length-at-age
Summarize(len~age,data=WR1.comb,digits=2)
-#> age n mean sd min Q1 median Q3 max
-#> 1 4 987 51.86 5.14 35 48.00 52.0 56.00 64
-#> 2 5 395 71.80 5.33 60 68.00 72.0 76.00 84
-#> 3 6 270 86.76 4.83 75 83.00 87.0 89.00 99
-#> 4 7 449 97.45 5.17 85 93.00 97.0 101.00 112
-#> 5 8 146 101.29 5.86 90 97.00 101.5 106.75 113
-#> 6 9 78 103.85 3.08 100 102.00 103.0 105.75 112
-#> 7 10 38 105.42 7.08 95 98.25 107.0 109.75 119
-#> 8 11 6 111.67 1.51 110 110.25 112.0 113.00 113
+#> age n mean sd min Q1 median Q3 max
+#> 1 4 987 51.87 5.15 35 48 52.0 56.00 64
+#> 2 5 396 71.79 5.35 60 68 72.0 76.00 84
+#> 3 6 269 86.73 4.66 75 83 87.0 89.00 98
+#> 4 7 447 97.54 5.14 85 93 97.0 102.00 112
+#> 5 8 147 101.21 5.84 90 97 101.0 107.00 114
+#> 6 9 78 103.68 3.43 100 101 103.0 104.75 113
+#> 7 10 39 105.23 7.18 95 98 107.0 109.50 119
+#> 8 11 6 111.67 1.21 110 111 111.5 112.75 113
# age frequency distribution
( af <- xtabs(~age,data=WR1.comb) )
#> age
#> 4 5 6 7 8 9 10 11
-#> 987 395 270 449 146 78 38 6
+#> 987 396 269 447 147 78 39 6
# proportional age distribution
( ap <- prop.table(af) )
#> age
#> 4 5 6 7 8 9
-#> 0.416631490 0.166737020 0.113972140 0.189531448 0.061629379 0.032925285
+#> 0.416631490 0.167159139 0.113550021 0.188687210 0.062051499 0.032925285
#> 10 11
-#> 0.016040523 0.002532714
+#> 0.016462642 0.002532714
## Second Example -- length sample does not have an age variable
WR2 <- WR79
@@ -278,15 +278,15 @@ Examples
# combine orig age & new ages
WR2.comb <- rbind(WR2.age, WR2.len)
Summarize(len~age,data=WR2.comb,digits=2)
-#> age n mean sd min Q1 median Q3 max
-#> 1 4 987 51.85 5.12 35 48.00 52.0 56.0 64
-#> 2 5 395 71.76 5.22 60 68.00 72.0 76.0 84
-#> 3 6 271 86.76 4.59 75 83.00 87.0 89.0 99
-#> 4 7 448 97.60 5.21 85 93.00 97.0 102.0 114
-#> 5 8 145 101.14 5.76 90 96.00 101.0 107.0 113
-#> 6 9 79 103.75 3.10 100 102.00 103.0 105.0 112
-#> 7 10 38 105.13 7.30 95 97.00 106.5 110.5 119
-#> 8 11 6 111.83 0.75 111 111.25 112.0 112.0 113
+#> age n mean sd min Q1 median Q3 max
+#> 1 4 986 51.85 5.14 35 48 52 56.00 64
+#> 2 5 396 71.72 5.29 60 68 72 76.00 84
+#> 3 6 271 86.81 4.67 75 83 87 89.00 98
+#> 4 7 447 97.49 5.21 85 93 97 101.00 113
+#> 5 8 146 101.20 5.85 90 97 101 107.00 113
+#> 6 9 79 103.96 3.02 100 102 103 105.50 114
+#> 7 10 38 105.29 7.00 95 98 107 110.50 119
+#> 8 11 6 111.50 0.84 111 111 111 111.75 113
## Third Example -- Uneven breaks for length categories
WR3 <- WR79
@@ -353,15 +353,15 @@ Examples
#> 8 8 42 4 40
WR3.comb <- rbind(WR3.age, WR3.len)
Summarize(len~age,data=WR3.comb,digits=2)
-#> age n mean sd min Q1 median Q3 max
-#> 1 4 987 51.87 5.15 35 48 52.0 56 64
-#> 2 5 395 71.72 5.25 60 68 72.0 76 84
-#> 3 6 271 86.85 4.71 75 83 87.0 89 99
-#> 4 7 451 97.65 5.34 85 93 97.0 102 113
-#> 5 8 142 100.68 5.44 90 97 101.0 104 113
-#> 6 9 78 104.40 3.20 100 102 103.0 107 113
-#> 7 10 40 104.80 7.14 95 98 103.5 112 119
-#> 8 11 5 112.60 2.70 110 111 112.0 113 117
+#> age n mean sd min Q1 median Q3 max
+#> 1 4 987 51.85 5.12 35 48 52 56.00 64
+#> 2 5 396 71.81 5.28 60 68 72 76.00 84
+#> 3 6 270 86.73 4.61 75 83 87 89.00 98
+#> 4 7 449 97.76 5.33 86 93 97 102.00 114
+#> 5 8 141 100.52 5.61 90 96 101 104.00 113
+#> 6 9 80 104.15 3.21 100 102 103 107.00 113
+#> 7 10 42 104.90 7.19 95 98 102 111.75 119
+#> 8 11 4 112.00 1.15 111 111 112 113.00 113
FSA 0.8.19 8-Apr-182018-04-08
-
-
addZeroCatch(): Modified. Changed two1:nrow()structures toseq_len(nrow())(partially addressing #36).
+ -
-
ageBias(): Modified. Changed all1:structures toseq_len()(partially addressing #36).
+ -
-
agePrecision(): Modified. Changed all1:structures toseq_len()(partially addressing #36).
+ -
-
bcFuns(): Modified. Changed three1:length()structures toseq_along()(partially addressing #36).
+ -
-
bootCase()methods: Modified. Changed all1:structures toseq_len()(partially addressing #36).
+ -
-
capHistConvert(): Modified. Changed all1:structures toseq_len()orseq_along()(partially addressing #36).
+ -
-
capHistSum(): Modified. Changed all1:structures toseq_len()(partially addressing #36).
+ -
-
chooseColors(): Modified. Changed all1:structures toseq_len()(partially addressing #36).
+ -
-
compSlopes(): Modified. Changed all1:structures toseq_len()(partially addressing #36).
+ -
-
compIntercepts(): Modified. Changed all1:structures toseq_len()(partially addressing #36).
+ -
-
extraSS(): Modified. Changed all1:structures toseq_len()orseq_along()(partially addressing #36).
+ -
-
headtail(): Modified. Changed all1:structures toseq_len()(partially addressing #36).
+ -
-
hist.formula()methods: Modified. Changed all1:structures toseq_len()(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) forhist.formula()andSummarize().
+ -
-
lrt(): Modified. Changed all1:structures toseq_len()orseq_along()(partially addressing #36).
+ -
-
lwCompPreds(): Modified. Changed all1:structures toseq_len()orseq_along()(partially addressing #36).
+ -
-
mrClosed(): Modified. Changed two1:length()structures toseq_along()(partially addressing #36).
+ -
-
nlsBoot()methods: Modified. Changed all1:structures toseq_len()(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 three1:structures toseq_len()orseq_along()(partially addressing #36).
+ -
-
residPlot(): Modified. Changed three1:length()structures toseq_along()(partially addressing #36).
+ -
-
Summarize(): Modified. Changed one1:length()structure toseq_along()(partially addressing #36).
+ -
-
wrAdd(): Modified. Changed three1:structures toseq_len()orseq_along()(partially addressing #36).
+
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).
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).
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).
FSA 0.8.18 31-Mar-18
@@ -409,7 +416,7 @@FSA 0.8.1
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).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.FSA 0.8.15
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.removal(): Modified document by merging pull request #33.
srStarts(): Modified. Added fixed=. Added some catches for poor starting values. Added relevant tests. Addresses #30.srStarts(): Modified. Added fixed=. Added some catches for poor starting values. Added relevant tests. Addresses #30.
FSA 0.8.14 27-Jul-172017-07-27
@@ -526,13 +533,13 @@FSA 0.8.1
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.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.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.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.FSA 0.8.1
iHndlCols2use(): Deleted. Changed to iHndlCols2UseIgnore().iHndlCols2UseIgnore(): Added. Previously was iHndlCols2use(). Completely reworked to catch more problems including having both positive and negative indices (fixes #24) and choosing variable names that don’t exist (fixes #25).iHndlCols2UseIgnore(): Added. Previously was iHndlCols2use(). Completely reworked to catch more problems including having both positive and negative indices (fixes #24) and choosing variable names that don’t exist (fixes #25).
iHndlFormula(): Modified. Added code to deal with a formula that is a single “variable” sent in an array. Addresses #21 for the simple situation of single “variable.”iHndlFormula(): Modified. Added code to deal with a formula that is a single “variable” sent in an array. Addresses #21 for the simple situation of single “variable.”
iHndlMultWhat(): Modified. Added type= to allow use with message() or cat().FSA 0.8.1
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.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.FSA 0.8.1
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.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.FSA 0.8.1
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.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.FSA 0.8.8 1
FSA 0.8.7 8-May-162016-05-08
- Compiled under R v3.3.0.
-- Removed
relax from Suggests. See srStarts() and vbStarts() notes below. This addresses #17.
-- Removed
gdata from Imports. See filterD() and Subset() notes below. This addresses #5.
+- Removed
relax from Suggests. See srStarts() and vbStarts() notes below. This addresses #17.
+- Removed
gdata from Imports. See filterD() and Subset() notes below. This addresses #5.
- Added no coverage blocks to
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().
@@ -658,7 +665,7 @@ FSA 0.8.7 8-
-
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.
+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=.
-
@@ -699,9 +706,9 @@
FSA 0.8.6 2
- Fixed problems with tests, and made the tests more explicit, related to PSD and Wr functions. Suppressed some warnings related to
sumTable() in ALK related tests and Summarize() in age comparisons tests. Prompted by forthcoming changes to testthat.
- Removed
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).
+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.
+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.
-
@@ -715,7 +722,7 @@
FSA 0.8.6 2
-
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.
+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.
-
@@ -726,10 +733,10 @@
FSA 0.8.5 1
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.
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).
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.
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 8c674d3c..2590d423 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 2.14.0.3
pkgdown: 2.0.2
pkgdown_sha: ~
articles: {}
-last_built: 2022-02-12T19:10Z
+last_built: 2022-02-16T00:00Z
urls:
reference: http://derekogle.com/FSA/reference
article: http://derekogle.com/FSA/articles
diff --git a/docs/reference/BluegillJL.html b/docs/reference/BluegillJL.html
index d6309185..043fc4dd 100644
--- a/docs/reference/BluegillJL.html
+++ b/docs/reference/BluegillJL.html
@@ -17,7 +17,7 @@
FSA 0.8.7 8-May-162016-05-08
- Compiled under R v3.3.0. -
- Removed
relaxfromSuggests. SeesrStarts()andvbStarts()notes below. This addresses #17.
- - Removed
gdatafromImports. SeefilterD()andSubset()notes below. This addresses #5.
+ - Removed
relaxfromSuggests. SeesrStarts()andvbStarts()notes below. This addresses #17.
+ - Removed
gdatafromImports. SeefilterD()andSubset()notes below. This addresses #5. - Added no coverage blocks to
ageKeyPlot(),capHistSum(),hist.formula(),histFromSum(),lwCompPreds(),plot.agebias(),plot.CatchCurve(),plot.ChapmanRobson(),plot.Depletion(),plotBinResp(),print.compSlopes(),print.compIntercepts(),print.metaM(),psdPlot(),residPlot(),srModels(),srStarts(), andvbStarts(). -
ageKey(): Removed. Deprecated since 0.4.24. UsealkIndivAge().
@@ -658,7 +665,7 @@ -
filterD(): Modified. Changed to usedroplevels()frombaserather thandrop.levels()fromgdata. Addedexcept=. -
-
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. Changedtype=toparam=. -
@@ -699,9 +706,9 @@
FSA 0.8.6 2
- Fixed problems with tests, and made the tests more explicit, related to PSD and Wr functions. Suppressed some warnings related to
sumTable()in ALK related tests andSummarize()in age comparisons tests. Prompted by forthcoming changes totestthat. - Removed
News.mdfrom.Rbuildignore(apparently now supported by CRAN). -
-
alkPlot(): Modified. Changed so thatxlim=andylim=would work whentype="area"andtype="bar". This fixes #10 (Thanks to Joseph Feldhaus).
+
alkPlot(): Modified. Changed so thatxlim=andylim=would work whentype="area"andtype="bar". This fixes #10 (Thanks to Joseph Feldhaus). - Fixed problems with tests, and made the tests more explicit, related to PSD and Wr functions. Suppressed some warnings related to
-
-
hist.formula(): Modified. Added thebreaks=argument (mostly a pass-through) and thew=argument that allows the user to just set the width of the bins without having to set eachbreakvalue. This should complete #15.
+ -
iCheckStartCatW(): Modified. Now useiGetDecimals()to extract the number of decimals instartcatandw. -
@@ -715,7 +722,7 @@
FSA 0.8.6 2
-
psdAdd(): Modified. Minor changes to documentation. -
-
psdPlot(): Modified. Fixed bug related to PSD values being printed when only PSD-Q existed (needed to adddrop0Est=FALSEto thepsdCalc()call; this fixes #13). Made the histogram bars flush with the x-axis rather than hovering above it (addedyaxis="i"tohist(); this fixes #12). Minor changes to documentation.
+ -
psdVal(): Modified. Minor changes to documentation. -
@@ -726,10 +733,10 @@
FSA 0.8.5 1
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 whenNAvalues were present. There was an inconsistency between whenwhat="precision"andwhat="difference"was used insummary(). The bug fix now properly divides by the “valid sample size” forwhat="precision". This fixes #9 (Thanks to Joseph Feldhaus). Now returnsvalidn. Modifications to the documentation.
-histFromSum(): Added. Addresses #4.
+agePrecision(): Modified. Fixed bug related to computations of percent agreement whenNAvalues were present. There was an inconsistency between whenwhat="precision"andwhat="difference"was used insummary(). The bug fix now properly divides by the “valid sample size” forwhat="precision". This fixes #9 (Thanks to Joseph Feldhaus). Now returnsvalidn. Modifications to the documentation.
+histFromSum(): Added. Addresses #4.metaM(): Modified. Changed order of methods inmethods=. Minor corrections and additions to documentation.
-mrClosed(): Modified. Now sends warning if anNAappears in the first position ofm, the first position ofM, or the last position ofRand 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).
+mrClosed(): Modified. Now sends warning if anNAappears in the first position ofm, the first position ofM, or the last position ofRand 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 toiGetAllDependencis()based on forthcoming changes topackage.dependencies()(as notified by CRAN).vbStarts(): Modified. Fixed bug whendynamicPlot=TRUEwas used.
FSA 0.8.7 8-
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.
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.
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.
Capture histories (2 samples) of Bluegill from Jewett Lake, MI.
- Source:R/BluegillJL.R
+ Source: R/BluegillJL.R
BluegillJL.RdCatch-at-age for Tobin Harbor, Isle Royale Brook Trout.
- Source:R/BrookTroutTH.R
+ Source: R/BrookTroutTH.R
BrookTroutTH.RdLengths and weights for Chinook Salmon from three locations in Argentina.
- Source:R/ChinookArg.R
+ Source: R/ChinookArg.R
ChinookArg.RdStock and recruitment data for Norwegian cod, 1937-1960.
- Source:R/CodNorwegian.R
+ Source: R/CodNorwegian.R
CodNorwegian.RdCapture histories (9 samples) of Cutthroat Trout from Auke Lake.
- Source:R/CutthroatAL.R
+ Source: R/CutthroatAL.R
CutthroatAL.RdFisheries stock assessment methods and data.
Details
Functions from this package can be used to perform a variety of basic fisheries stock assessment methods. Detailed descriptions for most functions are available in the Introductory Fisheries Analysis with R book (Ogle 2016). Vignettes for the boxed examples in the “Analysis and Interpretation of Freshwater Fisheries Data” book can be viewed with fishR("AIFFD").
Questions, comments, or suggestions should be given on the GitHub FSA Issues page.
-Packages with related functionality by the same author are
The FSAdata package contains additional data sets.
+The FSAdata package contains additional data sets.
The FSAsim package simulation routines for various fisheries methods.
The FSAWs package contains functions for developing and validating standard weight equations.
Questions, comments, or suggestions should be given on the GitHub FSA Issues page.
+Packages with related functionality by the same author are
Gabelhouse five-cell length categories for various species.
- Source:R/PSDlit.R
+ Source: R/PSDlit.R
PSDlit.RdSummarized multiple mark-recapture data for all Northern Pike from Buckhorn Marsh, NY.
- Source:R/PikeNY.R
+ Source: R/PikeNY.R
PikeNY.RdCapture histories (4 samples), in capture history format, of a subset of Northern Pike from Buckhorn Marsh, NY.
- Source:R/PikeNYPartial1.R
+ Source: R/PikeNYPartial1.R
PikeNYPartial1.RdCatch-effort data for Little Silver Lake (Ont) Smallmouth Bass.
- Source:R/SMBassLS.R
+ Source: R/SMBassLS.R
SMBassLS.RdGrowth increment data for West Bearskin Lake, MN, Smallmouth Bass.
- Source:R/SMBassWB.R
+ Source: R/SMBassWB.R
SMBassWB.RdThe four-parameter growth function from Schnute (1981).
- Source:R/growthModels.R
+ Source: R/growthModels.R
Schnute.RdSummary statistics for a numeric variable.
- Source:R/Summarize.R
+ Source: R/Summarize.R
Summarize.RdAssigned ages from two readers on three structures for Lake Whitefish from Lake Champlain.
- Source:R/WhitefishLC.R
+ Source: R/WhitefishLC.R
WhitefishLC.RdAdds zeros for catches of species not collected in some sampling events.
- Source:R/addZeroCatch.R
+ Source: R/addZeroCatch.R
addZeroCatch.RdCompute and view possible differences between paired sets of ages.
- Source:R/ageComparisons.R
+ Source: R/ageComparisons.R
ageBias.RdCompute measures of precision among sets of ages.
- Source:R/ageComparisons.R
+ Source: R/ageComparisons.R
agePrecision.RdProportions-at-age from an age-length key
- Source:R/alkSummaries.R
+ Source: R/alkSummaries.R
alkAgeDist.RdUse an age-length key to assign age to individuals in the unaged sample.
- Source:R/alkIndivAge.R
+ Source: R/alkIndivAge.R
alkIndivAge.RdExamples
WR1.comb <- rbind(WR1.age, WR1.len) # mean length-at-age Summarize(len~age,data=WR1.comb,digits=2) -#> age n mean sd min Q1 median Q3 max -#> 1 4 987 51.86 5.14 35 48.00 52.0 56.00 64 -#> 2 5 395 71.80 5.33 60 68.00 72.0 76.00 84 -#> 3 6 270 86.76 4.83 75 83.00 87.0 89.00 99 -#> 4 7 449 97.45 5.17 85 93.00 97.0 101.00 112 -#> 5 8 146 101.29 5.86 90 97.00 101.5 106.75 113 -#> 6 9 78 103.85 3.08 100 102.00 103.0 105.75 112 -#> 7 10 38 105.42 7.08 95 98.25 107.0 109.75 119 -#> 8 11 6 111.67 1.51 110 110.25 112.0 113.00 113 +#> age n mean sd min Q1 median Q3 max +#> 1 4 987 51.87 5.15 35 48 52.0 56.00 64 +#> 2 5 396 71.79 5.35 60 68 72.0 76.00 84 +#> 3 6 269 86.73 4.66 75 83 87.0 89.00 98 +#> 4 7 447 97.54 5.14 85 93 97.0 102.00 112 +#> 5 8 147 101.21 5.84 90 97 101.0 107.00 114 +#> 6 9 78 103.68 3.43 100 101 103.0 104.75 113 +#> 7 10 39 105.23 7.18 95 98 107.0 109.50 119 +#> 8 11 6 111.67 1.21 110 111 111.5 112.75 113 # age frequency distribution ( af <- xtabs(~age,data=WR1.comb) ) #> age #> 4 5 6 7 8 9 10 11 -#> 987 395 270 449 146 78 38 6 +#> 987 396 269 447 147 78 39 6 # proportional age distribution ( ap <- prop.table(af) ) #> age #> 4 5 6 7 8 9 -#> 0.416631490 0.166737020 0.113972140 0.189531448 0.061629379 0.032925285 +#> 0.416631490 0.167159139 0.113550021 0.188687210 0.062051499 0.032925285 #> 10 11 -#> 0.016040523 0.002532714 +#> 0.016462642 0.002532714 ## Second Example -- length sample does not have an age variable WR2 <- WR79 @@ -278,15 +278,15 @@Examples
# combine orig age & new ages WR2.comb <- rbind(WR2.age, WR2.len) Summarize(len~age,data=WR2.comb,digits=2) -#> age n mean sd min Q1 median Q3 max -#> 1 4 987 51.85 5.12 35 48.00 52.0 56.0 64 -#> 2 5 395 71.76 5.22 60 68.00 72.0 76.0 84 -#> 3 6 271 86.76 4.59 75 83.00 87.0 89.0 99 -#> 4 7 448 97.60 5.21 85 93.00 97.0 102.0 114 -#> 5 8 145 101.14 5.76 90 96.00 101.0 107.0 113 -#> 6 9 79 103.75 3.10 100 102.00 103.0 105.0 112 -#> 7 10 38 105.13 7.30 95 97.00 106.5 110.5 119 -#> 8 11 6 111.83 0.75 111 111.25 112.0 112.0 113 +#> age n mean sd min Q1 median Q3 max +#> 1 4 986 51.85 5.14 35 48 52 56.00 64 +#> 2 5 396 71.72 5.29 60 68 72 76.00 84 +#> 3 6 271 86.81 4.67 75 83 87 89.00 98 +#> 4 7 447 97.49 5.21 85 93 97 101.00 113 +#> 5 8 146 101.20 5.85 90 97 101 107.00 113 +#> 6 9 79 103.96 3.02 100 102 103 105.50 114 +#> 7 10 38 105.29 7.00 95 98 107 110.50 119 +#> 8 11 6 111.50 0.84 111 111 111 111.75 113 ## Third Example -- Uneven breaks for length categories WR3 <- WR79 @@ -353,15 +353,15 @@Examples
#> 8 8 42 4 40 WR3.comb <- rbind(WR3.age, WR3.len) Summarize(len~age,data=WR3.comb,digits=2) -#> age n mean sd min Q1 median Q3 max -#> 1 4 987 51.87 5.15 35 48 52.0 56 64 -#> 2 5 395 71.72 5.25 60 68 72.0 76 84 -#> 3 6 271 86.85 4.71 75 83 87.0 89 99 -#> 4 7 451 97.65 5.34 85 93 97.0 102 113 -#> 5 8 142 100.68 5.44 90 97 101.0 104 113 -#> 6 9 78 104.40 3.20 100 102 103.0 107 113 -#> 7 10 40 104.80 7.14 95 98 103.5 112 119 -#> 8 11 5 112.60 2.70 110 111 112.0 113 117 +#> age n mean sd min Q1 median Q3 max +#> 1 4 987 51.85 5.12 35 48 52 56.00 64 +#> 2 5 396 71.81 5.28 60 68 72 76.00 84 +#> 3 6 270 86.73 4.61 75 83 87 89.00 98 +#> 4 7 449 97.76 5.33 86 93 97 102.00 114 +#> 5 8 141 100.52 5.61 90 96 101 104.00 113 +#> 6 9 80 104.15 3.21 100 102 103 107.00 113 +#> 7 10 42 104.90 7.19 95 98 102 111.75 119 +#> 8 11 4 112.00 1.15 111 111 112 113.00 113Mean Values-at-age from an age-length key
- Source:R/alkSummaries.R
+ Source: R/alkSummaries.R
alkMeanVar.RdConfidence intervals for binomial probability of success.
- Source:R/CIDists.R
+ Source: R/CIDists.R
binCI.RdConvert between capture history data.frame formats.
- Source:R/capHistConvert.R
+ Source: R/capHistConvert.R
capHistConvert.RdSummarize capture histories in individual fish format.
- Source:R/capHistSum.R
+ Source: R/capHistSum.R
capHistSum.RdMortality estimates from the descending limb of a catch curve.
- Source:R/catchCurve.R
+ Source: R/catchCurve.R
catchCurve.RdComputes Chapman-Robson estimates of S and Z.
- Source:R/chapmanRobson.R
+ Source: R/chapmanRobson.R
chapmanRobson.RdConverts an R color to RGB (red/green/blue) including a transparency (alpha channel).
- Source:R/FSAUtils.R
+ Source: R/FSAUtils.R
col2rgbt.RdComputes the Leslie or DeLury population estimate from catch and effort data.
- Source:R/depletion.R
+ Source: R/depletion.R
depletion.RdDunn's Kruskal-Wallis Multiple Comparisons.
- Source:R/dunnTest.R
+ Source: R/dunnTest.R
dunnTest.RdRepeat individual fish data (including lengths) from tallied counts.
- Source:R/expandCounts.R
+ Source: R/expandCounts.R
expandCounts.RdExamples
#> 2 rows had an individual measurement. #> 4 rows with multiple measurements were expanded to 15 rows of individual measurements. #> name lwr.bin upr.bin newlen lennote -#> 1 Frank 17.0 17.5 17.0 Expanded length -#> 2 Max 17.0 17.5 17.5 Expanded length -#> 3 Johnson 15.0 15.5 15.3 Expanded length -#> 4 Johnson 15.0 15.5 15.3 Expanded length -#> 5 Johnson 15.0 15.5 15.0 Expanded length -#> 6 Johnson 15.0 15.5 15.3 Expanded length -#> 7 Johnson 15.0 15.5 15.0 Expanded length -#> 8 Johnson 15.0 15.5 15.5 Expanded length -#> 9 Johnson 15.5 16.0 16.0 Expanded length -#> 10 Johnson 15.5 16.0 15.9 Expanded length -#> 11 Johnson 15.5 16.0 15.9 Expanded length -#> 12 Johnson 15.5 16.0 15.5 Expanded length -#> 13 Jones 16.0 16.5 16.3 Expanded length -#> 14 Jones 16.0 16.5 16.0 Expanded length -#> 15 Frank 16.0 16.5 16.3 Expanded length -#> 16 Frank 16.0 16.5 16.3 Expanded length +#> 1 Frank 17.0 17.5 17.2 Expanded length +#> 2 Max 17.0 17.5 17.2 Expanded length +#> 3 Johnson 15.0 15.5 15.0 Expanded length +#> 4 Johnson 15.0 15.5 15.0 Expanded length +#> 5 Johnson 15.0 15.5 15.2 Expanded length +#> 6 Johnson 15.0 15.5 15.4 Expanded length +#> 7 Johnson 15.0 15.5 15.3 Expanded length +#> 8 Johnson 15.0 15.5 15.0 Expanded length +#> 9 Johnson 15.5 16.0 15.9 Expanded length +#> 10 Johnson 15.5 16.0 15.5 Expanded length +#> 11 Johnson 15.5 16.0 15.6 Expanded length +#> 12 Johnson 15.5 16.0 15.8 Expanded length +#> 13 Jones 16.0 16.5 16.4 Expanded length +#> 14 Jones 16.0 16.5 16.5 Expanded length +#> 15 Frank 16.0 16.5 16.1 Expanded length +#> 16 Frank 16.0 16.5 16.4 Expanded length #> 17 Frank 16.0 16.5 16.3 Expanded length # some need expansion @@ -213,20 +213,20 @@Examples
#> 1 Frank 17.1 17.1 17.1 Observed length #> 2 Max 17.3 17.3 17.3 Observed length #> 3 Johnson 15.0 15.5 15.4 Expanded length -#> 4 Johnson 15.0 15.5 15.2 Expanded length -#> 5 Johnson 15.0 15.5 15.0 Expanded length -#> 6 Johnson 15.0 15.5 15.3 Expanded length -#> 7 Johnson 15.0 15.5 15.1 Expanded length -#> 8 Johnson 15.0 15.5 15.0 Expanded length +#> 4 Johnson 15.0 15.5 15.1 Expanded length +#> 5 Johnson 15.0 15.5 15.3 Expanded length +#> 6 Johnson 15.0 15.5 15.1 Expanded length +#> 7 Johnson 15.0 15.5 15.0 Expanded length +#> 8 Johnson 15.0 15.5 15.4 Expanded length #> 9 Johnson 15.5 16.0 15.7 Expanded length -#> 10 Johnson 15.5 16.0 16.0 Expanded length -#> 11 Johnson 15.5 16.0 16.0 Expanded length -#> 12 Johnson 15.5 16.0 15.7 Expanded length -#> 13 Jones 16.0 16.5 16.0 Expanded length -#> 14 Jones 16.0 16.5 16.3 Expanded length -#> 15 Frank 16.0 16.5 16.3 Expanded length -#> 16 Frank 16.0 16.5 16.5 Expanded length -#> 17 Frank 16.0 16.5 16.1 Expanded length +#> 10 Johnson 15.5 16.0 15.9 Expanded length +#> 11 Johnson 15.5 16.0 15.7 Expanded length +#> 12 Johnson 15.5 16.0 15.6 Expanded length +#> 13 Jones 16.0 16.5 16.3 Expanded length +#> 14 Jones 16.0 16.5 16.1 Expanded length +#> 15 Frank 16.0 16.5 16.4 Expanded length +#> 16 Frank 16.0 16.5 16.2 Expanded length +#> 17 Frank 16.0 16.5 16.4 Expanded length # none need expansion ( d3 <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max"), @@ -326,21 +326,21 @@Examples
#> name lwr.bin upr.bin newlen lennote #> 1 Frank 17.1 17.1 17.1 Observed length #> 2 Max 17.3 17.3 17.3 Observed length -#> 3 Johnson 15.0 15.5 15.3 Expanded length -#> 4 Johnson 15.0 15.5 15.5 Expanded length -#> 5 Johnson 15.0 15.5 15.1 Expanded length -#> 6 Johnson 15.0 15.5 15.4 Expanded length -#> 7 Johnson 15.0 15.5 15.0 Expanded length -#> 8 Johnson 15.0 15.5 15.2 Expanded length -#> 9 Johnson 15.0 15.9 15.9 Expanded length -#> 10 Johnson 15.0 15.9 15.4 Expanded length -#> 11 Johnson 15.0 15.9 15.1 Expanded length +#> 3 Johnson 15.0 15.5 15.0 Expanded length +#> 4 Johnson 15.0 15.5 15.2 Expanded length +#> 5 Johnson 15.0 15.5 15.4 Expanded length +#> 6 Johnson 15.0 15.5 15.2 Expanded length +#> 7 Johnson 15.0 15.5 15.2 Expanded length +#> 8 Johnson 15.0 15.5 15.1 Expanded length +#> 9 Johnson 15.0 15.9 15.5 Expanded length +#> 10 Johnson 15.0 15.9 15.3 Expanded length +#> 11 Johnson 15.0 15.9 15.5 Expanded length #> 12 Johnson 15.0 15.9 15.3 Expanded length -#> 13 Jones 16.0 16.5 16.5 Expanded length -#> 14 Jones 16.0 16.5 16.4 Expanded length -#> 15 Frank 16.0 16.9 16.8 Expanded length -#> 16 Frank 16.0 16.9 16.8 Expanded length -#> 17 Frank 16.0 16.9 16.5 Expanded length +#> 13 Jones 16.0 16.5 16.0 Expanded length +#> 14 Jones 16.0 16.5 16.2 Expanded length +#> 15 Frank 16.0 16.9 16.6 Expanded length +#> 16 Frank 16.0 16.9 16.4 Expanded length +#> 17 Frank 16.0 16.9 16.0 Expanded length # some need expansion but include zeros and NAs for counts ( d2a <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max","Max","Max","Max"), @@ -368,21 +368,21 @@Examples
#> 3 Max NA NA NA Observed length #> 4 Frank 17.1 17.1 17.1 Observed length #> 5 Max 17.3 17.3 17.3 Observed length -#> 6 Johnson 15.0 15.5 15.1 Expanded length -#> 7 Johnson 15.0 15.5 15.2 Expanded length +#> 6 Johnson 15.0 15.5 15.2 Expanded length +#> 7 Johnson 15.0 15.5 15.4 Expanded length #> 8 Johnson 15.0 15.5 15.4 Expanded length -#> 9 Johnson 15.0 15.5 15.4 Expanded length +#> 9 Johnson 15.0 15.5 15.2 Expanded length #> 10 Johnson 15.0 15.5 15.2 Expanded length -#> 11 Johnson 15.0 15.5 15.2 Expanded length -#> 12 Johnson 15.5 16.0 16.0 Expanded length -#> 13 Johnson 15.5 16.0 15.5 Expanded length -#> 14 Johnson 15.5 16.0 15.8 Expanded length -#> 15 Johnson 15.5 16.0 16.0 Expanded length -#> 16 Jones 16.0 16.5 16.3 Expanded length +#> 11 Johnson 15.0 15.5 15.0 Expanded length +#> 12 Johnson 15.5 16.0 15.5 Expanded length +#> 13 Johnson 15.5 16.0 16.0 Expanded length +#> 14 Johnson 15.5 16.0 15.7 Expanded length +#> 15 Johnson 15.5 16.0 15.8 Expanded length +#> 16 Jones 16.0 16.5 16.1 Expanded length #> 17 Jones 16.0 16.5 16.3 Expanded length -#> 18 Frank 16.0 16.5 16.3 Expanded length -#> 19 Frank 16.0 16.5 16.3 Expanded length -#> 20 Frank 16.0 16.5 16.0 Expanded length +#> 18 Frank 16.0 16.5 16.4 Expanded length +#> 19 Frank 16.0 16.5 16.1 Expanded length +#> 20 Frank 16.0 16.5 16.1 Expanded length # some need expansion but include NAs for upper values ( d2b <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max"), @@ -413,11 +413,11 @@Examples
#> 10 Johnson 15.5 15.5 15.5 Observed length #> 11 Johnson 15.5 15.5 15.5 Observed length #> 12 Johnson 15.5 15.5 15.5 Observed length -#> 13 Jones 16.0 16.5 16.4 Expanded length -#> 14 Jones 16.0 16.5 16.0 Expanded length +#> 13 Jones 16.0 16.5 16.5 Expanded length +#> 14 Jones 16.0 16.5 16.1 Expanded length #> 15 Frank 16.0 16.5 16.3 Expanded length -#> 16 Frank 16.0 16.5 16.2 Expanded length -#> 17 Frank 16.0 16.5 16.2 Expanded length +#> 16 Frank 16.0 16.5 16.3 Expanded length +#> 17 Frank 16.0 16.5 16.1 Expanded length # some need expansion but include NAs for upper values ( d2c <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max"), @@ -448,10 +448,10 @@Examples
#> 10 Johnson 15.5 15.5 15.5 Observed length #> 11 Johnson 15.5 15.5 15.5 Observed length #> 12 Johnson 15.5 15.5 15.5 Observed length -#> 13 Jones 16.0 16.5 16.4 Expanded length -#> 14 Jones 16.0 16.5 16.0 Expanded length -#> 15 Frank 16.0 16.5 16.2 Expanded length -#> 16 Frank 16.0 16.5 16.2 Expanded length +#> 13 Jones 16.0 16.5 16.3 Expanded length +#> 14 Jones 16.0 16.5 16.4 Expanded length +#> 15 Frank 16.0 16.5 16.4 Expanded length +#> 16 Frank 16.0 16.5 16.0 Expanded length #> 17 Frank 16.0 16.5 16.1 Expanded length if (FALSE) { diff --git a/docs/reference/expandLenFreq.html b/docs/reference/expandLenFreq.html index d91fe0d4..ce7dc936 100644 --- a/docs/reference/expandLenFreq.html +++ b/docs/reference/expandLenFreq.html @@ -17,7 +17,7 @@Expands a length frequency based on a subsample.
- Source:R/expandLenFreq.R
+ Source: R/expandLenFreq.R
expandLenFreq.RdLikelihood ratio and extra sum-of-squares tests.
- Source:R/extraTests.R
+ Source: R/extraTests.R
extraTests.RdConverts "numeric" factor levels to numeric values.
- Source:R/FSAUtils.R
+ Source: R/FSAUtils.R
fact2num.RdOpens web pages associated with the fishR website.
- Source:R/FSAUtils.R
+ Source: R/FSAUtils.R
fishR.RdCalculates the geometric mean or geometric standard deviation.
- Source:R/FSAUtils.R
+ Source: R/FSAUtils.R
geomean.RdCreates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
- Source:R/growthModels.R
+ Source: R/growthModels.R
growthModels.RdExamples
#> Linf <- Linf[[1]] } #> Linf*(1-exp(-K*(t-t0))) #> } -#> <bytecode: 0x000000000972e5e8> -#> <environment: 0x00000000091f6a88> +#> <bytecode: 0x0000000007e2f960> +#> <environment: 0x000000000874f268> ages <- 0:20 plot(vb1(ages,Linf=20,K=0.3,t0=-0.2)~ages,type="b",pch=19)
@@ -199,8 +199,8 @@ Examples
#> r <- (L3-L2)/(L2-L1) #> L1+(L3-L1)*((1-r^(2*((t-t1)/(t3-t1))))/(1-r^2)) #> } -#> <bytecode: 0x00000000079a3778> -#> <environment: 0x0000000006a39718> +#> <bytecode: 0x00000000078e0ef8> +#> <environment: 0x0000000021822dd0> plot(vb2(ages,L1=10,L2=19,L3=20,t1=2,t3=18)~ages,type="b",pch=19)
( vb2c <- vbFuns("Francis",simple=TRUE) ) # compare to vb2
@@ -208,8 +208,8 @@ Examples
#> r <- (L3-L2)/(L2-L1) #> L1+(L3-L1)*((1-r^(2*((t-t1)/(t3-t1))))/(1-r^2)) #> } -#> <bytecode: 0x00000000078092d0> -#> <environment: 0x00000000226f0b50> +#> <bytecode: 0x0000000009177920> +#> <environment: 0x0000000022b530d8> ## Simple Examples -- Gompertz ( gomp1 <- GompertzFuns() ) @@ -219,8 +219,8 @@Examples
#> Linf <- Linf[[1]] } #> Linf*exp(-exp(-gi*(t-ti))) #> } -#> <bytecode: 0x000000001f7a23b0> -#> <environment: 0x0000000006f13f10> +#> <bytecode: 0x000000001f99b7d0> +#> <environment: 0x0000000023686290> plot(gomp1(ages,Linf=800,gi=0.5,ti=5)~ages,type="b",pch=19)
( gomp2 <- GompertzFuns("Ricker2") )
@@ -230,24 +230,24 @@ Examples
#> L0 <- L0[[1]] } #> L0*exp(a*(1-exp(-gi*t))) #> } -#> <bytecode: 0x0000000006f926a0> -#> <environment: 0x00000000227ce5e8> +#> <bytecode: 0x000000001fa6c8d8> +#> <environment: 0x0000000022f8e5d0> plot(gomp2(ages,L0=2,a=6,gi=0.5)~ages,type="b",pch=19)
( gomp2c <- GompertzFuns("Ricker2",simple=TRUE) ) # compare to gomp2
#> function(t,L0,a,gi) {
#> L0*exp(a*(1-exp(-gi*t)))
#> }
-#> <bytecode: 0x0000000022a02240>
-#> <environment: 0x0000000021ac5b38>
+#> <bytecode: 0x0000000020342258>
+#> <environment: 0x000000002330ace8>
( gompT <- GompertzFuns("Troynikov1"))
#> function(Lm,dt,Linf,gi=NULL) {
#> if (length(Linf)==2) { gi <- Linf[2]
#> Linf <- Linf[1] }
#> Linf*((Lm/Linf)^exp(-gi*dt))-Lm
#> }
-#> <bytecode: 0x0000000022120938>
-#> <environment: 0x0000000022101058>
+#> <bytecode: 0x000000002229ccc8>
+#> <environment: 0x0000000022f4ff18>
## Simple Examples -- Richards
( rich1 <- RichardsFuns() )
@@ -258,8 +258,8 @@ Examples
#> Linf <- Linf[[1]] } #> Linf*(1-a*exp(-k*t))^b #> } -#> <bytecode: 0x00000000226a9490> -#> <environment: 0x0000000021ef8d68> +#> <bytecode: 0x0000000022cc4680> +#> <environment: 0x0000000022e77868> plot(rich1(ages,Linf=800,k=0.5,a=1,b=6)~ages,type="b",pch=19)
( rich2 <- RichardsFuns(2) )
@@ -270,8 +270,8 @@ Examples
#> Linf <- Linf[[1]] } #> Linf*(1-(1/b)*exp(-k*(t-ti)))^b #> } -#> <bytecode: 0x00000000226b31b8> -#> <environment: 0x000000002242f3b0> +#> <bytecode: 0x0000000022cce3a8> +#> <environment: 0x00000000231f5580> plot(rich2(ages,Linf=800,k=0.5,ti=3,b=6)~ages,type="b",pch=19)
( rich3 <- RichardsFuns(3) )
@@ -282,8 +282,8 @@ Examples
#> Linf <- Linf[[1]] } #> Linf/((1+b*exp(-k*(t-ti)))^(1/b)) #> } -#> <bytecode: 0x00000000226bcb60> -#> <environment: 0x0000000021c9c788> +#> <bytecode: 0x0000000022cd7d18> +#> <environment: 0x0000000023378ad0> plot(rich3(ages,Linf=800,k=0.5,ti=3,b=0.15)~ages,type="b",pch=19)
( rich4 <- RichardsFuns(4) )
@@ -294,8 +294,8 @@ Examples
#> Linf <- Linf[[1]] } #> Linf*(1+(b-1)*exp(-k*(t-ti)))^(1/(1-b)) #> } -#> <bytecode: 0x00000000220b0448> -#> <environment: 0x0000000022535f08> +#> <bytecode: 0x0000000022e51ac0> +#> <environment: 0x000000002345b020> plot(rich4(ages,Linf=800,k=0.5,ti=3,b=0.95)~ages,type="b",pch=19) lines(rich4(ages,Linf=800,k=0.5,ti=3,b=1.5)~ages,type="b",pch=19,col="blue")
@@ -307,8 +307,8 @@ Examples
#> Linf <- Linf[[1]] } #> Linf*(1+(((L0/Linf)^(1-b))-1)*exp(-k*t))^(1/(1-b)) #> } -#> <bytecode: 0x00000000220b98e8> -#> <environment: 0x00000000221df530> +#> <bytecode: 0x0000000022e5af98> +#> <environment: 0x00000000235a22b8> plot(rich5(ages,Linf=800,k=0.5,L0=50,b=1.5)~ages,type="b",pch=19)
( rich6 <- RichardsFuns(6) )
@@ -320,16 +320,16 @@ Examples
#> Linf <- Linf[[1]] } #> Lninf+(Linf-Lninf)*(1+(b-1)*exp(-k*(t-ti)))^(1/(1-b)) #> } -#> <bytecode: 0x00000000220c66b0> -#> <environment: 0x00000000222d6448> +#> <bytecode: 0x0000000022e63fd8> +#> <environment: 0x0000000024982d80> plot(rich6(ages,Linf=800,k=0.5,ti=3,Lninf=50,b=1.5)~ages,type="b",pch=19)
( rich2c <- RichardsFuns(2,simple=TRUE) ) # compare to rich2
#> function(t,Linf,k,ti,b) {
#> Linf*(1-(1/b)*exp(-k*(t-ti)))^b
#> }
-#> <bytecode: 0x00000000226bb810>
-#> <environment: 0x0000000022a7a248>
+#> <bytecode: 0x0000000022cd6a00>
+#> <environment: 0x0000000024a74ee8>
## Simple Examples -- Logistic
( log1 <- logisticFuns() )
@@ -339,8 +339,8 @@ Examples
#> Linf <- Linf[[1]] } #> Linf/(1+exp(-gninf*(t-ti))) #> } -#> <bytecode: 0x0000000023ace4a8> -#> <environment: 0x0000000023af7f40> +#> <bytecode: 0x0000000024af08b0> +#> <environment: 0x0000000024b21340> plot(log1(ages,Linf=800,gninf=0.5,ti=5)~ages,type="b",pch=19)
( log2 <- logisticFuns("CJ2") )
@@ -350,16 +350,16 @@ Examples
#> Linf <- Linf[[1]] } #> Linf/(1+a*exp(-gninf*t)) #> } -#> <bytecode: 0x0000000023ad6a68> -#> <environment: 0x0000000023be8b28> +#> <bytecode: 0x0000000024afb288> +#> <environment: 0x0000000024c13d18> plot(log2(ages,Linf=800,gninf=0.5,a=10)~ages,type="b",pch=19)
( log2c <- logisticFuns("CJ2",simple=TRUE) ) # compare to log2
#> function(t,Linf,gninf,a) {
#> Linf/(1+a*exp(-gninf*t))
#> }
-#> <bytecode: 0x0000000023adf7f8>
-#> <environment: 0x0000000023d535e8>
+#> <bytecode: 0x0000000024b00920>
+#> <environment: 0x0000000024d77a48>
( log3 <- logisticFuns("Karkach") )
#> function(t,Linf,L0=NULL,gninf=NULL) {
#> if (length(Linf)==3) { L0 <- Linf[[2]]
@@ -367,8 +367,8 @@ Examples
#> Linf <- Linf[[1]] } #> L0*Linf/(L0+(Linf-L0)*exp(-gninf*t)) #> } -#> <bytecode: 0x0000000023ae0e58> -#> <environment: 0x0000000023da54f0> +#> <bytecode: 0x0000000024b05db0> +#> <environment: 0x0000000024dcde10> plot(log3(ages,L0=10,Linf=800,gninf=0.5)~ages,type="b",pch=19)
( log4 <- logisticFuns("Haddon") )
@@ -378,8 +378,8 @@ Examples
#> dLmax <- dLmax[1] } #> dLmax/(1+exp(log(19)*((Lm-L50)/(L95-L50)))) #> } -#> <bytecode: 0x0000000023aeb5c8> -#> <environment: 0x0000000023eb4390> +#> <bytecode: 0x0000000024b11e30> +#> <environment: 0x0000000024edd658> ########################################################### diff --git a/docs/reference/headtail.html b/docs/reference/headtail.html index 9b8439af..d880a14d 100644 --- a/docs/reference/headtail.html +++ b/docs/reference/headtail.html @@ -17,7 +17,7 @@Shows rows from the head and tail of a data frame or matrix.
- Source:R/FSAUtils.R
+ Source: R/FSAUtils.R
headtail.RdCreates separate histograms by levels.
- Source:R/hist.formula.R
+ Source: R/hist.formula.R
hist.formula.RdCreate a histogram from a frequency table.
- Source:R/histFromSum.R
+ Source: R/histFromSum.R
histFromSum.RdConfidence interval for population size (N) in hypergeometric distribution.
- Source:R/CIDists.R
+ Source: R/CIDists.R
hyperCI.RdAll known standard weight equations.
Defunct
-Defunction functions.
+Defunct functions.
bootCase() chooseColors() compIntercepts() compSlopes() diags() filterD() fitPlot() fsaNews() hoCoef() mapvalues() plotBinResp() residPlot() Subset()
Specific utilities for use in a knitr document.
- Source:R/knitUtil.R
+ Source: R/knitUtil.R
knitUtil.Rd
diff --git a/docs/reference/lagratio.html b/docs/reference/lagratio.html
index dff7a7eb..dfd66ddf 100644
--- a/docs/reference/lagratio.html
+++ b/docs/reference/lagratio.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/lencat.html b/docs/reference/lencat.html
index 8182783f..e69957da 100644
--- a/docs/reference/lencat.html
+++ b/docs/reference/lencat.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
diff --git a/docs/reference/logbtcf.html b/docs/reference/logbtcf.html
index 0b66cc46..1ddd1c31 100644
--- a/docs/reference/logbtcf.html
+++ b/docs/reference/logbtcf.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Constructs the correction-factor used when back-transforming log-transformed values.
- Source:R/FSAUtils.R
+ Source: R/FSAUtils.R
logbtcf.RdConstructs plots of predicted weights at given lengths among different groups.
- Source:R/lwCompPreds.R
+ Source: R/lwCompPreds.R
lwCompPreds.Rd
diff --git a/docs/reference/mrClosed.html b/docs/reference/mrClosed.html
index d89ab6f8..abef6ad6 100644
--- a/docs/reference/mrClosed.html
+++ b/docs/reference/mrClosed.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Estimate initial population size for single or multiple census mark-recapture data.
- Source:R/mrClosed.R
+ Source: R/mrClosed.R
mrClosed.RdJolly-Seber analysis from multiple mark-recapture events from an open population.
- Source:R/mrOpen.R
+ Source: R/mrOpen.R
mrOpen.RdAssociated S3 methods for nlsBoot from nlstools.
- Source:R/bootstrap.R
+ Source: R/bootstrap.R
nlsBoot.RdAdds model fits from nls iterations to active plot.
- Source:R/nlsTracePlot.R
+ Source: R/nlsTracePlot.R
nlsTracePlot.RdComputes the percentage of values in a vector less than or greater than (and equal to) some value.
- Source:R/FSAUtils.R
+ Source: R/FSAUtils.R
perc.RdConstruct traditional (Campana-like) age-bias plots.
- Source:R/ageComparisons.R
+ Source: R/ageComparisons.R
plotAB.Rd
diff --git a/docs/reference/psdAdd.html b/docs/reference/psdAdd.html
index 09b771fe..825be160 100644
--- a/docs/reference/psdAdd.html
+++ b/docs/reference/psdAdd.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Creates a vector of Gabelhouse lengths for each species in an entire data frame.
- Source:R/psdAdd.R
+ Source: R/psdAdd.R
psdAdd.Rd
diff --git a/docs/reference/psdCalc.html b/docs/reference/psdCalc.html
index f7a997cf..9c208ed6 100644
--- a/docs/reference/psdCalc.html
+++ b/docs/reference/psdCalc.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Convenience function for calculating PSD-X and PSD X-Y values.
- Source:R/psdCalc.R
+ Source: R/psdCalc.R
psdCalc.RdLength-frequency histogram with Gabelhouse lengths highlighted.
- Source:R/psdPlot.R
+ Source: R/psdPlot.R
psdPlot.RdFinds Gabelhouse lengths (for PSD calculations) for a species.
- Source:R/psdVal.R
+ Source: R/psdVal.R
psdVal.RdExtract the coefficient of determination from a linear model object.
- Source:R/FSAUtils.R
+ Source: R/FSAUtils.R
rSquared.RdComputes the prior to or reverse cumulative sum of a vector.
- Source:R/FSAUtils.R
+ Source: R/FSAUtils.R
rcumsum.RdPopulation estimates for k-, 3-, or 2-pass removal data.
- Source:R/removal.R
+ Source: R/removal.R
removal.Rd
@@ -75,7 +75,7 @@
Value
See also
-See se in sciplot for similar functionality.
See se in sciplot for similar functionality.
Finds reasonable starting values for parameters in specific parameterizations of common stock-recruitment models.
- Source:R/srStarts.R
+ Source: R/srStarts.R
srStarts.RdCreates a one- or two-way table of summary statistics.
- Source:R/sumTable.R
+ Source: R/sumTable.R
sumTable.RdConstruct a base tic-tac-toe plot for presenting predator-prey PSD values.
- Source:R/tictactoe.R
+ Source: R/tictactoe.R
tictactoe.RdFinds the number of valid (non-NA) values in a vector.
- Source:R/FSAUtils.R
+ Source: R/FSAUtils.R
validn.RdFind reasonable starting values for a von Bertalanffy growth function.
- Source:R/vbStarts.R
+ Source: R/vbStarts.R
vbStarts.Rd
diff --git a/docs/reference/wsVal.html b/docs/reference/wsVal.html
index cebe5f56..578fde5a 100644
--- a/docs/reference/wsVal.html
+++ b/docs/reference/wsVal.html
@@ -17,7 +17,7 @@
@@ -50,7 +50,7 @@
Finds standard weight equation coefficients for a particular species.
- Source:R/wsVal.R
+ Source: R/wsVal.R
wsVal.Rd