From 53f23118d303c9959528abb78b11bd29cea4e9f0 Mon Sep 17 00:00:00 2001 From: Derek Ogle Date: Fri, 28 Feb 2020 08:04:21 -0600 Subject: [PATCH] Closing out v0.8.28 --- DESCRIPTION | 2 +- cran-comments/cran-comments-v0_8_28.md | 9 +++ docs/LICENSE-text.html | 2 +- docs/authors.html | 6 +- docs/index.html | 2 +- docs/news/index.html | 16 +++-- docs/reference/BluegillJL.html | 2 +- docs/reference/BrookTroutTH.html | 2 +- docs/reference/ChinookArg.html | 2 +- docs/reference/CodNorwegian.html | 2 +- docs/reference/CutthroatAL.html | 2 +- docs/reference/Ecoli.html | 2 +- docs/reference/FSA-internals.html | 2 +- docs/reference/FSA.html | 2 +- docs/reference/FSAUtils.html | 2 +- docs/reference/Mirex.html | 2 +- docs/reference/PSDlit.html | 2 +- docs/reference/PikeNY.html | 2 +- docs/reference/PikeNYPartial1.html | 2 +- docs/reference/SMBassLS.html | 2 +- docs/reference/SMBassWB.html | 2 +- docs/reference/Schnute.html | 2 +- docs/reference/SpotVA1.html | 2 +- docs/reference/Subset.html | 2 +- docs/reference/Summarize.html | 2 +- docs/reference/WR79.html | 2 +- docs/reference/WSlit.html | 2 +- docs/reference/WhitefishLC.html | 2 +- docs/reference/addZeroCatch.html | 2 +- docs/reference/ageBias.html | 2 +- docs/reference/agePrecision.html | 2 +- docs/reference/alkAgeDist.html | 2 +- docs/reference/alkIndivAge.html | 2 +- docs/reference/alkMeanVar.html | 2 +- docs/reference/alkPlot.html | 2 +- docs/reference/binCI.html | 2 +- docs/reference/bootCase.html | 2 +- docs/reference/capHistConvert.html | 2 +- docs/reference/capHistSum.html | 2 +- docs/reference/catchCurve.html | 2 +- docs/reference/chapmanRobson.html | 2 +- docs/reference/chooseColors.html | 2 +- docs/reference/col2rgbt.html | 2 +- docs/reference/compIntercepts.html | 2 +- docs/reference/compSlopes.html | 2 +- docs/reference/depletion.html | 2 +- docs/reference/diags.html | 2 +- docs/reference/dunnTest.html | 2 +- docs/reference/expandCounts.html | 2 +- docs/reference/expandLenFreq.html | 2 +- docs/reference/extraTests.html | 2 +- docs/reference/fact2num.html | 2 +- docs/reference/fishR.html | 2 +- docs/reference/fitPlot-5.png | Bin 14545 -> 14526 bytes docs/reference/fitPlot.html | 2 +- docs/reference/fsaNews.html | 2 +- docs/reference/geomean.html | 2 +- docs/reference/growthModels.html | 78 ++++++++++++------------- docs/reference/headtail.html | 2 +- docs/reference/hist.formula.html | 2 +- docs/reference/histFromSum.html | 2 +- docs/reference/hoCoef.html | 2 +- docs/reference/hyperCI.html | 2 +- docs/reference/index.html | 2 +- docs/reference/knitUtil.html | 2 +- docs/reference/ksTest.html | 4 +- docs/reference/lagratio.html | 2 +- docs/reference/lencat.html | 2 +- docs/reference/logbtcf.html | 2 +- docs/reference/lwCompPreds.html | 2 +- docs/reference/mapvalues.html | 2 +- docs/reference/metaM.html | 2 +- docs/reference/mrClosed.html | 2 +- docs/reference/mrOpen.html | 2 +- docs/reference/nlsBoot.html | 2 +- docs/reference/nlsTracePlot.html | 2 +- docs/reference/oddeven.html | 2 +- docs/reference/perc.html | 2 +- docs/reference/plotAB.html | 2 +- docs/reference/plotBinResp.html | 2 +- docs/reference/poiCI.html | 2 +- docs/reference/psdAdd.html | 2 +- docs/reference/psdCI.html | 2 +- docs/reference/psdCalc.html | 2 +- docs/reference/psdPlot.html | 2 +- docs/reference/psdVal.html | 2 +- docs/reference/rSquared.html | 2 +- docs/reference/rcumsum.html | 2 +- docs/reference/removal.html | 2 +- docs/reference/residPlot.html | 2 +- docs/reference/se.html | 2 +- docs/reference/srStarts.html | 2 +- docs/reference/stockRecruitment.html | 22 +++---- docs/reference/sumTable.html | 2 +- docs/reference/tictactoe.html | 2 +- docs/reference/validn.html | 2 +- docs/reference/vbStarts.html | 2 +- docs/reference/wrAdd.html | 2 +- docs/reference/wsVal.html | 2 +- 99 files changed, 168 insertions(+), 151 deletions(-) create mode 100644 cran-comments/cran-comments-v0_8_28.md diff --git a/DESCRIPTION b/DESCRIPTION index 0f4c3e85..027dd9ba 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: FSA Version: 0.8.28 -Date: 2020-2-27 +Date: 2020-2-28 Title: Simple Fisheries Stock Assessment Methods Description: A variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website . diff --git a/cran-comments/cran-comments-v0_8_28.md b/cran-comments/cran-comments-v0_8_28.md new file mode 100644 index 00000000..a4d102e6 --- /dev/null +++ b/cran-comments/cran-comments-v0_8_28.md @@ -0,0 +1,9 @@ +* This updates the existing FSA package on CRAN by fixing errors in the documentation and test files related to change in the use of `stringsAsFactors=` in R v4.0.0 (per e-mail from Kurt Hornik on 27-Feb-20). + +## Notes +* There may be a note about "fishR" being misspelled in the description. This is not a misspelling. +* On [CRAN](https://cran.r-project.org/web/checks/check_results_FSA.html), there is a note in the previous version about a missing `RMark` package for the "r-patched-solaris-x86" flavor. Again (as with previous versions), I am not sure what to do about this note. + +## Testing Environments +* My Windows machine. +* Win Builder -- old-release, release, and development. diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 618c0338..2a5954bc 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -76,7 +76,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/authors.html b/docs/authors.html index 4ef00f00..61dab9e2 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -76,7 +76,7 @@ FSA - 0.8.27.9000 + 0.8.28 @@ -121,13 +121,13 @@

Citation

Ogle DH, Wheeler P, Dinno A (2020). FSA: Fisheries Stock Analysis. -R package version 0.8.27.9000, https://github.com/droglenc/FSA. +R package version 0.8.28, https://github.com/droglenc/FSA. 

@Manual{,
   title = {FSA: Fisheries Stock Analysis},
   author = {Derek H. Ogle and Powell Wheeler and Alexis Dinno},
   year = {2020},
-  note = {R package version 0.8.27.9000},
+  note = {R package version 0.8.28},
   url = {https://github.com/droglenc/FSA},
 }
diff --git a/docs/index.html b/docs/index.html index 1968e978..955bd4fb 100644 --- a/docs/index.html +++ b/docs/index.html @@ -39,7 +39,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/news/index.html b/docs/news/index.html index 9708454f..d1066b68 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -76,7 +76,7 @@ FSA - 0.8.27.9000 + 0.8.28 @@ -119,10 +119,18 @@

Changelog

Source: NEWS.md -
+

-FSA 0.8.27 ongoing 2020-02-03 +FSA 0.8.28 ongoing Unreleased

+
    +
  • +fitPlot(): Modified. Changed so that lines are plotted after the points in the IVR versions.
    • +
  • +ksTest(): Modified. Changed documentation examples to handle R’s new way of handling stringsAsFactors= (per request from CRAN on 27-Feb-20).
    • +
  • +psdAdd(): Modified. Changed testing to handle R’s new way of handling stringsAsFactors= (per request from CRAN on 27-Feb-20).
    • +

@@ -3318,7 +3326,7 @@

Contents

    -
  • 0.8.27
    • +
  • 0.8.28
  • 0.8.27
  • 0.8.26
  • 0.8.25
    • diff --git a/docs/reference/BluegillJL.html b/docs/reference/BluegillJL.html index 5c53e82a..8b723d0b 100644 --- a/docs/reference/BluegillJL.html +++ b/docs/reference/BluegillJL.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28
diff --git a/docs/reference/BrookTroutTH.html b/docs/reference/BrookTroutTH.html index 5f3f9c96..9597313a 100644 --- a/docs/reference/BrookTroutTH.html +++ b/docs/reference/BrookTroutTH.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28

diff --git a/docs/reference/ChinookArg.html b/docs/reference/ChinookArg.html index 7df3caba..fae2cdcb 100644 --- a/docs/reference/ChinookArg.html +++ b/docs/reference/ChinookArg.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28
diff --git a/docs/reference/CodNorwegian.html b/docs/reference/CodNorwegian.html index 38017b5c..3ae0b95b 100644 --- a/docs/reference/CodNorwegian.html +++ b/docs/reference/CodNorwegian.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/CutthroatAL.html b/docs/reference/CutthroatAL.html index 84fe7f89..9dab797c 100644 --- a/docs/reference/CutthroatAL.html +++ b/docs/reference/CutthroatAL.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/Ecoli.html b/docs/reference/Ecoli.html index 80ac945e..1c6b86f3 100644 --- a/docs/reference/Ecoli.html +++ b/docs/reference/Ecoli.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/FSA-internals.html b/docs/reference/FSA-internals.html index 5aa428c7..194339fc 100644 --- a/docs/reference/FSA-internals.html +++ b/docs/reference/FSA-internals.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/FSA.html b/docs/reference/FSA.html index 156709ac..72036fc9 100644 --- a/docs/reference/FSA.html +++ b/docs/reference/FSA.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/FSAUtils.html b/docs/reference/FSAUtils.html index b42ab6da..e9262108 100644 --- a/docs/reference/FSAUtils.html +++ b/docs/reference/FSAUtils.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/Mirex.html b/docs/reference/Mirex.html index 464f2faa..6854fce5 100644 --- a/docs/reference/Mirex.html +++ b/docs/reference/Mirex.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/PSDlit.html b/docs/reference/PSDlit.html index 686b0637..ed8bc02f 100644 --- a/docs/reference/PSDlit.html +++ b/docs/reference/PSDlit.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/PikeNY.html b/docs/reference/PikeNY.html index 0adad50e..6b56d073 100644 --- a/docs/reference/PikeNY.html +++ b/docs/reference/PikeNY.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/PikeNYPartial1.html b/docs/reference/PikeNYPartial1.html index 7298089f..23dba9c6 100644 --- a/docs/reference/PikeNYPartial1.html +++ b/docs/reference/PikeNYPartial1.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/SMBassLS.html b/docs/reference/SMBassLS.html index 3ba38180..20e353b3 100644 --- a/docs/reference/SMBassLS.html +++ b/docs/reference/SMBassLS.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/SMBassWB.html b/docs/reference/SMBassWB.html index d54acf40..146d733d 100644 --- a/docs/reference/SMBassWB.html +++ b/docs/reference/SMBassWB.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/Schnute.html b/docs/reference/Schnute.html index e64b1945..99e282b0 100644 --- a/docs/reference/Schnute.html +++ b/docs/reference/Schnute.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/SpotVA1.html b/docs/reference/SpotVA1.html index 1281bd53..25016264 100644 --- a/docs/reference/SpotVA1.html +++ b/docs/reference/SpotVA1.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/Subset.html b/docs/reference/Subset.html index 88297ffe..96266c62 100644 --- a/docs/reference/Subset.html +++ b/docs/reference/Subset.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/Summarize.html b/docs/reference/Summarize.html index 0ff35922..0f982f7e 100644 --- a/docs/reference/Summarize.html +++ b/docs/reference/Summarize.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/WR79.html b/docs/reference/WR79.html index 8e042e2b..8694d317 100644 --- a/docs/reference/WR79.html +++ b/docs/reference/WR79.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/WSlit.html b/docs/reference/WSlit.html index 1b92dae4..ba12bb6d 100644 --- a/docs/reference/WSlit.html +++ b/docs/reference/WSlit.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/WhitefishLC.html b/docs/reference/WhitefishLC.html index 0730fed7..05bcc5b8 100644 --- a/docs/reference/WhitefishLC.html +++ b/docs/reference/WhitefishLC.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/addZeroCatch.html b/docs/reference/addZeroCatch.html index b39f8a7e..c1ac97f2 100644 --- a/docs/reference/addZeroCatch.html +++ b/docs/reference/addZeroCatch.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/ageBias.html b/docs/reference/ageBias.html index c2b4df7b..1ed00b88 100644 --- a/docs/reference/ageBias.html +++ b/docs/reference/ageBias.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/agePrecision.html b/docs/reference/agePrecision.html index b3879f2b..d5a02e53 100644 --- a/docs/reference/agePrecision.html +++ b/docs/reference/agePrecision.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/alkAgeDist.html b/docs/reference/alkAgeDist.html index 3e244bd0..fa84a097 100644 --- a/docs/reference/alkAgeDist.html +++ b/docs/reference/alkAgeDist.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/alkIndivAge.html b/docs/reference/alkIndivAge.html index fc20c7e9..34180a4b 100644 --- a/docs/reference/alkIndivAge.html +++ b/docs/reference/alkIndivAge.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/alkMeanVar.html b/docs/reference/alkMeanVar.html index 84be2dd1..d2ae8795 100644 --- a/docs/reference/alkMeanVar.html +++ b/docs/reference/alkMeanVar.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/alkPlot.html b/docs/reference/alkPlot.html index 847426a6..e5725280 100644 --- a/docs/reference/alkPlot.html +++ b/docs/reference/alkPlot.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/binCI.html b/docs/reference/binCI.html index 1dd2080c..7c9a76fa 100644 --- a/docs/reference/binCI.html +++ b/docs/reference/binCI.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/bootCase.html b/docs/reference/bootCase.html index 7e53aec1..512297ef 100644 --- a/docs/reference/bootCase.html +++ b/docs/reference/bootCase.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/capHistConvert.html b/docs/reference/capHistConvert.html index ca766e42..8f8b8ef8 100644 --- a/docs/reference/capHistConvert.html +++ b/docs/reference/capHistConvert.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/capHistSum.html b/docs/reference/capHistSum.html index d15d733e..95f599b3 100644 --- a/docs/reference/capHistSum.html +++ b/docs/reference/capHistSum.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/catchCurve.html b/docs/reference/catchCurve.html index 878c9c1b..9aff92c3 100644 --- a/docs/reference/catchCurve.html +++ b/docs/reference/catchCurve.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/chapmanRobson.html b/docs/reference/chapmanRobson.html index e6d8df1f..290508ae 100644 --- a/docs/reference/chapmanRobson.html +++ b/docs/reference/chapmanRobson.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/chooseColors.html b/docs/reference/chooseColors.html index 63272c88..5cfb4a3e 100644 --- a/docs/reference/chooseColors.html +++ b/docs/reference/chooseColors.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/col2rgbt.html b/docs/reference/col2rgbt.html index 4cca13bd..099555e2 100644 --- a/docs/reference/col2rgbt.html +++ b/docs/reference/col2rgbt.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/compIntercepts.html b/docs/reference/compIntercepts.html index 080b9296..23602790 100644 --- a/docs/reference/compIntercepts.html +++ b/docs/reference/compIntercepts.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/compSlopes.html b/docs/reference/compSlopes.html index 9820b7aa..55453e7c 100644 --- a/docs/reference/compSlopes.html +++ b/docs/reference/compSlopes.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/depletion.html b/docs/reference/depletion.html index 6195359f..8a81311c 100644 --- a/docs/reference/depletion.html +++ b/docs/reference/depletion.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/diags.html b/docs/reference/diags.html index a38fe44d..c3e06215 100644 --- a/docs/reference/diags.html +++ b/docs/reference/diags.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/dunnTest.html b/docs/reference/dunnTest.html index f72ccf8a..86c0fccd 100644 --- a/docs/reference/dunnTest.html +++ b/docs/reference/dunnTest.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/expandCounts.html b/docs/reference/expandCounts.html index 8fe8882e..2e069e1f 100644 --- a/docs/reference/expandCounts.html +++ b/docs/reference/expandCounts.html @@ -77,7 +77,7 @@ FSA - 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z+tV)89l(?cmK28E3VI>UqBy90x=ciM=M|zHU@CzEM^w1$TuJ3TE>l9zDD&>42|>&=3Fw z$mNK9H!+L_E9Gcaia~O&-Y32MCf)3Zbu?AR4Zq?B;<+S%!V2hhczT8LO|0PqIAV#| zp-)y7%-5R$$pdAL>_o~|P;h#>q#LU=)R?sM#fu$?({dASp8oRd^w+n- zknSIp__VJdxYg6@0dtXrx5&FgWb?JeNg1QQvJQcmt|oRMkS&dXd&bU%>yM%MOnbFqjwDU>^pqu{% FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/fsaNews.html b/docs/reference/fsaNews.html index 03c4c0e1..65f2a40a 100644 --- a/docs/reference/fsaNews.html +++ b/docs/reference/fsaNews.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html index a84fa5f8..ecf9bddb 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/growthModels.html b/docs/reference/growthModels.html index 46230613..6a6a6477 100644 --- a/docs/reference/growthModels.html +++ b/docs/reference/growthModels.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 @@ -267,8 +267,8 @@

Examp #> } #> Linf * (1 - exp(-K * (t - t0))) #> } -#> <bytecode: 0x0000000017888800> -#> <environment: 0x00000000177d00c8>
ages <- 0:20 +#> <bytecode: 0x0000000015e5b5b0> +#> <environment: 0x0000000015def660>
ages <- 0:20 plot(vb1(ages,Linf=20,K=0.3,t0=-0.2)~ages,type="b",pch=19)
( vb2 <- vbFuns("Francis") )
#> function (t, L1, L2 = NULL, L3 = NULL, t1, t3 = NULL) #> { #> if (length(L1) == 3) { @@ -284,15 +284,15 @@

Examp #> L1 + (L3 - L1) * ((1 - r^(2 * ((t - t1)/(t3 - t1))))/(1 - #> r^2)) #> } -#> <bytecode: 0x0000000017862710> -#> <environment: 0x00000000171ebb20>

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
#> function (t, L1, L2, L3, t1, t3) +#> <bytecode: 0x0000000015e3ff10> +#> <environment: 0x000000001593f5b8>
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
#> function (t, L1, L2, L3, t1, t3) #> { #> r <- (L3 - L2)/(L2 - L1) #> L1 + (L3 - L1) * ((1 - r^(2 * ((t - t1)/(t3 - t1))))/(1 - #> r^2)) #> } -#> <bytecode: 0x00000000178606d8> -#> <environment: 0x00000000163b2238>
+#> <bytecode: 0x0000000015e41ff0> +#> <environment: 0x000000001890ae70>
## Simple Examples -- Gompertz ( gomp1 <- GompertzFuns() )
#> function (t, Linf, gi = NULL, ti = NULL) #> { @@ -303,8 +303,8 @@

Examp #> } #> Linf * exp(-exp(-gi * (t - ti))) #> } -#> <bytecode: 0x00000000161cc8d8> -#> <environment: 0x000000001615f4d8>

plot(gomp1(ages,Linf=800,gi=0.5,ti=5)~ages,type="b",pch=19)
( gomp2 <- GompertzFuns("Ricker2") )
#> function (t, L0, a = NULL, gi = NULL) +#> <bytecode: 0x0000000017997dd0> +#> <environment: 0x00000000189f0760>
plot(gomp1(ages,Linf=800,gi=0.5,ti=5)~ages,type="b",pch=19)
( gomp2 <- GompertzFuns("Ricker2") )
#> function (t, L0, a = NULL, gi = NULL) #> { #> if (length(L0) == 3) { #> a <- L0[[2]] @@ -313,13 +313,13 @@

Examp #> } #> L0 * exp(a * (1 - exp(-gi * t))) #> } -#> <bytecode: 0x00000000161c7f70> -#> <environment: 0x0000000015fbfa70>

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) +#> <bytecode: 0x000000001799a968> +#> <environment: 0x0000000017311d38>
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: 0x00000000161c8d38> -#> <environment: 0x0000000015c281c8>
( gompT <- GompertzFuns("Troynikov1"))
#> function (Lm, dt, Linf, gi = NULL) +#> <bytecode: 0x0000000017999c80> +#> <environment: 0x000000000ad61040>
( gompT <- GompertzFuns("Troynikov1"))
#> function (Lm, dt, Linf, gi = NULL) #> { #> if (length(Linf) == 2) { #> gi <- Linf[2] @@ -327,8 +327,8 @@

Examp #> } #> Linf * ((Lm/Linf)^exp(-gi * dt)) - Lm #> } -#> <bytecode: 0x00000000161668b0> -#> <environment: 0x0000000015a348f0>

+#> <bytecode: 0x00000000179a09d8> +#> <environment: 0x0000000017769c58>
## Simple Examples -- Richards ( rich1 <- RichardsFuns() )
#> function (t, Linf, k = NULL, a = NULL, b = NULL) #> { @@ -340,8 +340,8 @@

Examp #> } #> Linf * (1 - a * exp(-k * t))^b #> } -#> <bytecode: 0x000000001594c558> -#> <environment: 0x0000000015931858>

plot(rich1(ages,Linf=800,k=0.5,a=1,b=6)~ages,type="b",pch=19)
( rich2 <- RichardsFuns(2) )
#> function (t, Linf, k = NULL, ti = NULL, b = NULL) +#> <bytecode: 0x0000000018ab78d0> +#> <environment: 0x000000000b7e2880>
plot(rich1(ages,Linf=800,k=0.5,a=1,b=6)~ages,type="b",pch=19)
( rich2 <- RichardsFuns(2) )
#> function (t, Linf, k = NULL, ti = NULL, b = NULL) #> { #> if (length(Linf) == 4) { #> k <- Linf[[2]] @@ -351,8 +351,8 @@

Examp #> } #> Linf * (1 - (1/b) * exp(-k * (t - ti)))^b #> } -#> <bytecode: 0x000000001594a0f8> -#> <environment: 0x000000000bd32a18>

plot(rich2(ages,Linf=800,k=0.5,ti=3,b=6)~ages,type="b",pch=19)
( rich3 <- RichardsFuns(3) )
#> function (t, Linf, k = NULL, ti = NULL, b = NULL) +#> <bytecode: 0x000000001756abe8> +#> <environment: 0x00000000174e8458>
plot(rich2(ages,Linf=800,k=0.5,ti=3,b=6)~ages,type="b",pch=19)
( rich3 <- RichardsFuns(3) )
#> function (t, Linf, k = NULL, ti = NULL, b = NULL) #> { #> if (length(Linf) == 4) { #> k <- Linf[[2]] @@ -362,8 +362,8 @@

Examp #> } #> Linf/((1 + b * exp(-k * (t - ti)))^(1/b)) #> } -#> <bytecode: 0x0000000015947f38> -#> <environment: 0x000000000b94ed00>

plot(rich3(ages,Linf=800,k=0.5,ti=3,b=0.15)~ages,type="b",pch=19)
( rich4 <- RichardsFuns(4) )
#> function (t, Linf, k = NULL, ti = NULL, b = NULL) +#> <bytecode: 0x000000001884d350> +#> <environment: 0x000000000c167108>
plot(rich3(ages,Linf=800,k=0.5,ti=3,b=0.15)~ages,type="b",pch=19)
( rich4 <- RichardsFuns(4) )
#> function (t, Linf, k = NULL, ti = NULL, b = NULL) #> { #> if (length(Linf) == 4) { #> k <- Linf[[2]] @@ -373,8 +373,8 @@

Examp #> } #> Linf * (1 + (b - 1) * exp(-k * (t - ti)))^(1/(1 - b)) #> } -#> <bytecode: 0x0000000015945e58> -#> <environment: 0x000000000b2e9b38>

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")
( rich5 <- RichardsFuns(5) )
#> function (t, Linf, k = NULL, L0 = NULL, b = NULL) +#> <bytecode: 0x0000000009c232d8> +#> <environment: 0x000000000bf39038>
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")
( rich5 <- RichardsFuns(5) )
#> function (t, Linf, k = NULL, L0 = NULL, b = NULL) #> { #> if (length(Linf) == 4) { #> k <- Linf[[2]] @@ -385,8 +385,8 @@

Examp #> Linf * (1 + (((L0/Linf)^(1 - b)) - 1) * exp(-k * t))^(1/(1 - #> b)) #> } -#> <bytecode: 0x0000000015941f48> -#> <environment: 0x000000000aab2d18>

plot(rich5(ages,Linf=800,k=0.5,L0=50,b=1.5)~ages,type="b",pch=19)
( rich6 <- RichardsFuns(6) )
#> function (t, Linf, k = NULL, ti = NULL, Lninf = NULL, b = NULL) +#> <bytecode: 0x0000000017025ed0> +#> <environment: 0x000000000b74c8d0>
plot(rich5(ages,Linf=800,k=0.5,L0=50,b=1.5)~ages,type="b",pch=19)
( rich6 <- RichardsFuns(6) )
#> function (t, Linf, k = NULL, ti = NULL, Lninf = NULL, b = NULL) #> { #> if (length(Linf) == 5) { #> k <- Linf[[2]] @@ -398,13 +398,13 @@

Examp #> Lninf + (Linf - Lninf) * (1 + (b - 1) * exp(-k * (t - ti)))^(1/(1 - #> b)) #> } -#> <bytecode: 0x00000000159386c8> -#> <environment: 0x000000000a8ba570>

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) +#> <bytecode: 0x000000001655b0a8> +#> <environment: 0x000000000b440e40>
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: 0x0000000015947598> -#> <environment: 0x000000000a73f2e8>
+#> <bytecode: 0x00000000160e1e58> +#> <environment: 0x000000000b1ee3e8>
## Simple Examples -- Logistic ( log1 <- logisticFuns() )
#> function (t, Linf, gninf = NULL, ti = NULL) #> { @@ -415,8 +415,8 @@

Examp #> } #> Linf/(1 + exp(-gninf * (t - ti))) #> } -#> <bytecode: 0x000000000a690a98> -#> <environment: 0x000000000a685470>

plot(log1(ages,Linf=800,gninf=0.5,ti=5)~ages,type="b",pch=19)
( log2 <- logisticFuns("CJ2") )
#> function (t, Linf, gninf = NULL, a = NULL) +#> <bytecode: 0x000000000b1299a8> +#> <environment: 0x000000000b1220e0>
plot(log1(ages,Linf=800,gninf=0.5,ti=5)~ages,type="b",pch=19)
( log2 <- logisticFuns("CJ2") )
#> function (t, Linf, gninf = NULL, a = NULL) #> { #> if (length(Linf) == 3) { #> gninf <- Linf[[2]] @@ -425,13 +425,13 @@

Examp #> } #> Linf/(1 + a * exp(-gninf * t)) #> } -#> <bytecode: 0x000000000a6889b8> -#> <environment: 0x000000000a14c988>

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) +#> <bytecode: 0x000000000b128bd0> +#> <environment: 0x000000000ae6c698>
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: 0x000000000a689630> -#> <environment: 0x00000000097faa70>
( log3 <- logisticFuns("Karkach") )
#> function (t, Linf, L0 = NULL, gninf = NULL) +#> <bytecode: 0x000000000b125c48> +#> <environment: 0x000000000ab400a0>
( log3 <- logisticFuns("Karkach") )
#> function (t, Linf, L0 = NULL, gninf = NULL) #> { #> if (length(Linf) == 3) { #> L0 <- Linf[[2]] @@ -440,8 +440,8 @@

Examp #> } #> L0 * Linf/(L0 + (Linf - L0) * exp(-gninf * t)) #> } -#> <bytecode: 0x000000000a686050> -#> <environment: 0x000000000974a920>

plot(log3(ages,L0=10,Linf=800,gninf=0.5)~ages,type="b",pch=19)
( log4 <- logisticFuns("Haddon") )
#> function (Lm, dLmax, L50 = NULL, L95 = NULL) +#> <bytecode: 0x000000000b1261f8> +#> <environment: 0x000000000aa95430>
plot(log3(ages,L0=10,Linf=800,gninf=0.5)~ages,type="b",pch=19)
( log4 <- logisticFuns("Haddon") )
#> function (Lm, dLmax, L50 = NULL, L95 = NULL) #> { #> if (length(dLmax) == 3) { #> L50 <- dLmax[2] @@ -450,8 +450,8 @@

Examp #> } #> dLmax/(1 + exp(log(19) * ((Lm - L50)/(L95 - L50)))) #> } -#> <bytecode: 0x000000000a687630> -#> <environment: 0x0000000007fb79e8>

+#> <bytecode: 0x000000000b1239a8> +#> <environment: 0x0000000009d865a0>
########################################################### ## Examples of fitting diff --git a/docs/reference/headtail.html b/docs/reference/headtail.html index 90119ff0..2c68137f 100644 --- a/docs/reference/headtail.html +++ b/docs/reference/headtail.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28
diff --git a/docs/reference/hist.formula.html b/docs/reference/hist.formula.html index 01a83a8a..45ec176e 100644 --- a/docs/reference/hist.formula.html +++ b/docs/reference/hist.formula.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/histFromSum.html b/docs/reference/histFromSum.html index a8ed1445..5cc487e0 100644 --- a/docs/reference/histFromSum.html +++ b/docs/reference/histFromSum.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/hoCoef.html b/docs/reference/hoCoef.html index 0790584c..d7136726 100644 --- a/docs/reference/hoCoef.html +++ b/docs/reference/hoCoef.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/hyperCI.html b/docs/reference/hyperCI.html index 1b6b6453..5bfe1a1f 100644 --- a/docs/reference/hyperCI.html +++ b/docs/reference/hyperCI.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/index.html b/docs/reference/index.html index a550be2d..7aeeb367 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -76,7 +76,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/knitUtil.html b/docs/reference/knitUtil.html index fff67e3e..69d41a8b 100644 --- a/docs/reference/knitUtil.html +++ b/docs/reference/knitUtil.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 diff --git a/docs/reference/ksTest.html b/docs/reference/ksTest.html index a786189a..1e9ee07a 100644 --- a/docs/reference/ksTest.html +++ b/docs/reference/ksTest.html @@ -77,7 +77,7 @@ FSA - 0.8.27.9000 + 0.8.28 @@ -188,7 +188,7 @@

Examp 
## see ks.test for other examples
 x <- rnorm(50)
 y <- runif(30)
-df <- data.frame(dat=c(x,y),grp=rep(c("X","Y"),c(50,30)))
+df <- data.frame(dat=c(x,y),grp=factor(rep(c("x","y"),c(50,30))))
 
 ## one-sample (from ks.test) still works
 ksTest(x+2, "pgamma", 3, 2)
#> 
diff --git a/docs/reference/lagratio.html b/docs/reference/lagratio.html
index dada2911..59b6a278 100644
--- a/docs/reference/lagratio.html
+++ b/docs/reference/lagratio.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     

 
diff --git a/docs/reference/lencat.html b/docs/reference/lencat.html
index 4a4f4ddb..b1504ff0 100644
--- a/docs/reference/lencat.html
+++ b/docs/reference/lencat.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/logbtcf.html b/docs/reference/logbtcf.html
index 4c03cba8..3e3957d9 100644
--- a/docs/reference/logbtcf.html
+++ b/docs/reference/logbtcf.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/lwCompPreds.html b/docs/reference/lwCompPreds.html
index 61b987be..b17dcd89 100644
--- a/docs/reference/lwCompPreds.html
+++ b/docs/reference/lwCompPreds.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/mapvalues.html b/docs/reference/mapvalues.html
index 74bcaacf..eb9bcfeb 100644
--- a/docs/reference/mapvalues.html
+++ b/docs/reference/mapvalues.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/metaM.html b/docs/reference/metaM.html
index d9838a29..1c21b770 100644
--- a/docs/reference/metaM.html
+++ b/docs/reference/metaM.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/mrClosed.html b/docs/reference/mrClosed.html
index 1cf8490c..20471377 100644
--- a/docs/reference/mrClosed.html
+++ b/docs/reference/mrClosed.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/mrOpen.html b/docs/reference/mrOpen.html
index 6d8a2079..39b7ac09 100644
--- a/docs/reference/mrOpen.html
+++ b/docs/reference/mrOpen.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/nlsBoot.html b/docs/reference/nlsBoot.html
index 8b7709a5..3e9674eb 100644
--- a/docs/reference/nlsBoot.html
+++ b/docs/reference/nlsBoot.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/nlsTracePlot.html b/docs/reference/nlsTracePlot.html
index c79e31ae..a806ea6e 100644
--- a/docs/reference/nlsTracePlot.html
+++ b/docs/reference/nlsTracePlot.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/oddeven.html b/docs/reference/oddeven.html
index d1efb482..f2117f19 100644
--- a/docs/reference/oddeven.html
+++ b/docs/reference/oddeven.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/perc.html b/docs/reference/perc.html
index 748d7b1a..9d756fde 100644
--- a/docs/reference/perc.html
+++ b/docs/reference/perc.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/plotAB.html b/docs/reference/plotAB.html
index 8dff0aa5..6887dd1c 100644
--- a/docs/reference/plotAB.html
+++ b/docs/reference/plotAB.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/plotBinResp.html b/docs/reference/plotBinResp.html
index 609d1579..601042e5 100644
--- a/docs/reference/plotBinResp.html
+++ b/docs/reference/plotBinResp.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/poiCI.html b/docs/reference/poiCI.html
index c7367ad5..a4c400be 100644
--- a/docs/reference/poiCI.html
+++ b/docs/reference/poiCI.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/psdAdd.html b/docs/reference/psdAdd.html
index 88e1b92e..15db98a3 100644
--- a/docs/reference/psdAdd.html
+++ b/docs/reference/psdAdd.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/psdCI.html b/docs/reference/psdCI.html
index 1fb64b9d..e74e37a6 100644
--- a/docs/reference/psdCI.html
+++ b/docs/reference/psdCI.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/psdCalc.html b/docs/reference/psdCalc.html
index 31a5b3e2..d3f50564 100644
--- a/docs/reference/psdCalc.html
+++ b/docs/reference/psdCalc.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/psdPlot.html b/docs/reference/psdPlot.html
index beb290c1..910fb9bf 100644
--- a/docs/reference/psdPlot.html
+++ b/docs/reference/psdPlot.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/psdVal.html b/docs/reference/psdVal.html
index dc4d5ec4..cc739b22 100644
--- a/docs/reference/psdVal.html
+++ b/docs/reference/psdVal.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/rSquared.html b/docs/reference/rSquared.html
index d4b7ce15..de02eacc 100644
--- a/docs/reference/rSquared.html
+++ b/docs/reference/rSquared.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/rcumsum.html b/docs/reference/rcumsum.html
index 53ddc989..ff3c46d1 100644
--- a/docs/reference/rcumsum.html
+++ b/docs/reference/rcumsum.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/removal.html b/docs/reference/removal.html
index 47e45712..c92c18d1 100644
--- a/docs/reference/removal.html
+++ b/docs/reference/removal.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/residPlot.html b/docs/reference/residPlot.html
index 24d4285d..df7f6fbc 100644
--- a/docs/reference/residPlot.html
+++ b/docs/reference/residPlot.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/se.html b/docs/reference/se.html
index 667048b2..a726bc42 100644
--- a/docs/reference/se.html
+++ b/docs/reference/se.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/srStarts.html b/docs/reference/srStarts.html
index 242f25cc..22bf1b75 100644
--- a/docs/reference/srStarts.html
+++ b/docs/reference/srStarts.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/stockRecruitment.html b/docs/reference/stockRecruitment.html
index 1a574b53..6c9af62a 100644
--- a/docs/reference/stockRecruitment.html
+++ b/docs/reference/stockRecruitment.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
@@ -205,8 +205,8 @@ 
Examp
 #>     }
 #>     a * S * exp(-b * S)
 #> }
-#> <bytecode: 0x0000000015c95168>
-#> <environment: 0x00000000186196c8>

+#> <bytecode: 0x0000000017c3a248>
+#> <environment: 0x00000000169377e8>

 # create some dummy stock data
 stock <- seq(0.01,1000,length.out=199)
 
@@ -219,8 +219,8 @@ 
Examp
 #>     }
 #>     a * S/(1 + b * S)
 #> }
-#> <bytecode: 0x000000001712f088>
-#> <environment: 0x00000000169f67d8>
plot(bh1(stock,a=0.5,b=0.01)~stock,type="l",lwd=2,ylab="Recruits",xlab="Spawners",ylim=c(0,50))

+#> <bytecode: 0x00000000183094c0>
+#> <environment: 0x0000000016ccb580>
plot(bh1(stock,a=0.5,b=0.01)~stock,type="l",lwd=2,ylab="Recruits",xlab="Spawners",ylim=c(0,50))

 # Ricker #1 parameterization
 ( r1 <- srFuns("Ricker") )
#> function (S, a, b = NULL) 
 #> {
@@ -230,8 +230,8 @@ 
Examp
 #>     }
 #>     a * S * exp(-b * S)
 #> }
-#> <bytecode: 0x0000000015c95168>
-#> <environment: 0x000000001891b820>
lines(r1(stock,a=0.5,b=0.005)~stock,lwd=2,col="red")

+#> <bytecode: 0x0000000017c3a248>
+#> <environment: 0x0000000015d32cc0>
lines(r1(stock,a=0.5,b=0.005)~stock,lwd=2,col="red")

 # Shephered parameterization
 ( s1 <- srFuns("Shepherd") )
#> function (S, a, b = NULL, c = NULL) 
 #> {
@@ -242,8 +242,8 @@ 
Examp
 #>     }
 #>     a * S/(1 + (b * S)^c)
 #> }
-#> <bytecode: 0x0000000016626b88>
-#> <environment: 0x0000000016390930>
lines(s1(stock,a=0.5,b=0.005,c=2.5)~stock,lwd=2,col="blue")

+#> <bytecode: 0x0000000015e58590>
+#> <environment: 0x0000000015f82950>
lines(s1(stock,a=0.5,b=0.005,c=2.5)~stock,lwd=2,col="blue")

 # Saila-Lorda parameterization
 ( sl1 <- srFuns("SailaLorda") )
#> function (S, a, b = NULL, c = NULL) 
 #> {
@@ -254,8 +254,8 @@ 
Examp
 #>     }
 #>     a * (S^c) * exp(-b * S)
 #> }
-#> <bytecode: 0x00000000166239f8>
-#> <environment: 0x0000000017363718>
lines(sl1(stock,a=0.5,b=0.005,c=1.05)~stock,lwd=2,col="salmon")

+#> <bytecode: 0x0000000015e59a90>
+#> <environment: 0x000000001654b068>
lines(sl1(stock,a=0.5,b=0.005,c=1.05)~stock,lwd=2,col="salmon")

 ## Examples of fitting stock-recruitment functions
 # Fitting the Beverton-Holt #1 parameterization with multiplicative errors
 bh1s <- srStarts(recruits~stock,data=CodNorwegian)
diff --git a/docs/reference/sumTable.html b/docs/reference/sumTable.html
index 201807e8..05bffbf0 100644
--- a/docs/reference/sumTable.html
+++ b/docs/reference/sumTable.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     

 
diff --git a/docs/reference/tictactoe.html b/docs/reference/tictactoe.html
index 95d3bac7..3c19b29a 100644
--- a/docs/reference/tictactoe.html
+++ b/docs/reference/tictactoe.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/validn.html b/docs/reference/validn.html
index 4ac98ab4..1ee4988a 100644
--- a/docs/reference/validn.html
+++ b/docs/reference/validn.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/vbStarts.html b/docs/reference/vbStarts.html
index 595f3795..e65afa67 100644
--- a/docs/reference/vbStarts.html
+++ b/docs/reference/vbStarts.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/wrAdd.html b/docs/reference/wrAdd.html
index 680abc18..90c5a563 100644
--- a/docs/reference/wrAdd.html
+++ b/docs/reference/wrAdd.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28
       
     
 
diff --git a/docs/reference/wsVal.html b/docs/reference/wsVal.html
index 648dee23..93a370f7 100644
--- a/docs/reference/wsVal.html
+++ b/docs/reference/wsVal.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.27.9000
+        0.8.28