- - +
- - + @@ -122,11 +122,20 @@
- Corrected testing issue for
catchCurve()andchapmanRobson()as directed by CRAN on 17-Jul-21. Issue likely caused by changes tofishmethodspackage.
+ - Make note of the several removed (now defunct) and deprecated (soon to be defunct) functions listed below.
- Added Jason Doll as an
AUThor. - Moved
plyrfrom Imports to Suggests. -
@@ -134,10 +143,10 @@
-
binCI(): Modified. Changed to useiCheckConfLevel()(which addresses #66). -
-
bootCase(): REMOVED. Users can usecar::Boot(), which partially addresses #65. +bootCase(): REMOVED. Users can usecar::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>$t).
+
plot.boot(): REMOVED. Conflicted withboot::plot.boot()which caused an error with CRAN. Same functionality is available withpairs(<boot object>$t). -
-
-
@@ -145,21 +154,21 @@
-
chapmanRobson(): Modified. Removed hard-coding ofylim=forplot.chapmanRobson(). Addedround.est=so that the user can control the decimals on mortality and survival estimate values. Changed to useiCheckConfLevel()(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. SeeiCheckMultColors(). Partially addresses #65.
+ -
-
compIntercepts(): REMOVED (toFSAmisc). Added toFSA-defunct. Partially addresses #65.
+ -
-
compSlopes(): REMOVED (toFSAmisc). Added toFSA-defunct. Partially addresses #65.
+ -
depletion(): Modified. Changed to useiCheckConfLevel()(which addresses #66). -
-
filterD(): DEPRECATED (partially addresses #65).
+ -
-
fitPlot(): DEPRECATED (partially addresses #65). Prior to that removed use ofchooseColors()(see above).
+ -
-
diags(): REMOVED (moved toFSAmisc). Added toFSA-defunct. Partially addresses #65.
+ -
-
hoCoef(): REMOVED (moved toFSAmisc). Added toFSA-defunct. Partially addresses #65.
+ -
hyperCI(): Modified. Changed to useiCheckConfLevel()(which addresses #66). -
@@ -167,15 +176,15 @@
-
iCheckMultColors(): Added (internal). Part of removingchooseColors()andpaletteChoices(). -
-
iRichColors(): REMOVED (as part of removingchooseColors()).
+ -
-
mapvalues(): REMOVED. Added toFSA-defunct. Partially addresses #65.
+ -
mrClosed(): Modified. Changed to useiCheckConfLevel()(which addresses #66). -
mrOpen(): Modified. Added a warning for when r==0, which causes the SE of M and thus N to beInfinity(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 ofapply()torowSums()for ease of reading. Changed to useiCheckConfLevel()(which addresses #66). -
-
paletteChoices(): REMOVED. SeechooseColors()above. Partially addresses #65.
+ -
poiCI(): Modified. Changed to useiCheckConfLevel()(which addresses #66). -
@@ -191,9 +200,9 @@
-
removal(): Modified. Added check and then warning if non-whole numbers are incatch=(addresses #60). Also modified checks of data integrity to be more robust (e.g., if a character vector is sent). Changed to useiCheckConfLevel()(which addresses #66). -
-
residPlot(): DEPRECATED (partially addresses #65). Prior to that removed use ofchooseColors()(see above).
+ -
-
Subset(): REMOVED. Added toFSA-defunct. Partially addresses #65.
+ -
wrAdd(): Modified. Changed alevels()iniwsLitCheck()tounique()becausespeciesis no longer a factor due to updatingWSlit(i.e., rdata file changed with newread.csv()). -
@@ -2157,7 +2166,7 @@
-
-
removal(): Modified. Completely modified the code so that the examples withapply()andlapply()would also provide confidence intervals. Also changed the code to reflect that $\sum_{i=1}^{k-1}T_{i}$ from Schnute (1983) is the same as X from Carle and Strub (1978), the $\sum_{i=1}^{k-1}T_{i}-C_{1}$ in Schnute (1983) is the same as X − (k − 1)C1, and q in Schnute (1983) is p in most other resources. These changes allowed some efficiencies and connected the theory behind the methods more firmly. Removed the check for character data. Kept the check for whether catch was a vector or not but if catch is a one row or one column matrix or data.frame then it will be converted to a vector to continue. The latter change allows one to extract one row from a data.frame to send toremoval()without having to useas.numeric(). Modified and added examples of the use ofapply()andlapply().
+
removal(): Modified. Completely modified the code so that the examples withapply()andlapply()would also provide confidence intervals. Also changed the code to reflect that $\sum_{i=1}^{k-1}T_{i}$ from Schnute (1983) is the same as X from Carle and Strub (1978), the $\sum_{i=1}^{k-1}T_{i}-C_{1}$ in Schnute (1983) is the same as X − (k−1)C1, and q in Schnute (1983) is p in most other resources. These changes allowed some efficiencies and connected the theory behind the methods more firmly. Removed the check for character data. Kept the check for whether catch was a vector or not but if catch is a one row or one column matrix or data.frame then it will be converted to a vector to continue. The latter change allows one to extract one row from a data.frame to send toremoval()without having to useas.numeric(). Modified and added examples of the use ofapply()andlapply(). -
-
- - +
- - + diff --git a/docs/reference/ChinookArg.html b/docs/reference/ChinookArg.html index 93e83fa3..e0846c61 100644 --- a/docs/reference/ChinookArg.html +++ b/docs/reference/ChinookArg.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/CodNorwegian.html b/docs/reference/CodNorwegian.html index 78c0188f..9e47679b 100644 --- a/docs/reference/CodNorwegian.html +++ b/docs/reference/CodNorwegian.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/CutthroatAL.html b/docs/reference/CutthroatAL.html index 15b733e5..42541640 100644 --- a/docs/reference/CutthroatAL.html +++ b/docs/reference/CutthroatAL.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/Ecoli.html b/docs/reference/Ecoli.html index f3207409..7333e12c 100644 --- a/docs/reference/Ecoli.html +++ b/docs/reference/Ecoli.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/FSA-internals.html b/docs/reference/FSA-internals.html index ae701c42..614d218d 100644 --- a/docs/reference/FSA-internals.html +++ b/docs/reference/FSA-internals.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/FSA.html b/docs/reference/FSA.html index 2d0e04b5..953afd21 100644 --- a/docs/reference/FSA.html +++ b/docs/reference/FSA.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/Mirex.html b/docs/reference/Mirex.html index 9060bfea..d99df27f 100644 --- a/docs/reference/Mirex.html +++ b/docs/reference/Mirex.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/PSDlit.html b/docs/reference/PSDlit.html index 0c09ff06..20107b6c 100644 --- a/docs/reference/PSDlit.html +++ b/docs/reference/PSDlit.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/PikeNY.html b/docs/reference/PikeNY.html index a8176e7f..5e22692c 100644 --- a/docs/reference/PikeNY.html +++ b/docs/reference/PikeNY.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/PikeNYPartial1.html b/docs/reference/PikeNYPartial1.html index f2d053de..661e9318 100644 --- a/docs/reference/PikeNYPartial1.html +++ b/docs/reference/PikeNYPartial1.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/SMBassLS.html b/docs/reference/SMBassLS.html index 1d35b608..c7bffe61 100644 --- a/docs/reference/SMBassLS.html +++ b/docs/reference/SMBassLS.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/SMBassWB.html b/docs/reference/SMBassWB.html index 565ef18d..0e89fdec 100644 --- a/docs/reference/SMBassWB.html +++ b/docs/reference/SMBassWB.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/Schnute.html b/docs/reference/Schnute.html index 6e2389e7..2061385a 100644 --- a/docs/reference/Schnute.html +++ b/docs/reference/Schnute.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/SpotVA1.html b/docs/reference/SpotVA1.html index 90f9c48f..9d3720b3 100644 --- a/docs/reference/SpotVA1.html +++ b/docs/reference/SpotVA1.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/Summarize.html b/docs/reference/Summarize.html index 19dc0b8a..b3247a9d 100644 --- a/docs/reference/Summarize.html +++ b/docs/reference/Summarize.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/WR79.html b/docs/reference/WR79.html index 3a30acec..2c72716a 100644 --- a/docs/reference/WR79.html +++ b/docs/reference/WR79.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/WSlit.html b/docs/reference/WSlit.html index 108a60af..63f32314 100644 --- a/docs/reference/WSlit.html +++ b/docs/reference/WSlit.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/WhitefishLC.html b/docs/reference/WhitefishLC.html index 619e157e..41b894a6 100644 --- a/docs/reference/WhitefishLC.html +++ b/docs/reference/WhitefishLC.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/addZeroCatch.html b/docs/reference/addZeroCatch.html index 98b1df63..9c6f9246 100644 --- a/docs/reference/addZeroCatch.html +++ b/docs/reference/addZeroCatch.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/ageBias.html b/docs/reference/ageBias.html index ba0b066e..cf76784a 100644 --- a/docs/reference/ageBias.html +++ b/docs/reference/ageBias.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/agePrecision.html b/docs/reference/agePrecision.html index d2c23601..9df49d56 100644 --- a/docs/reference/agePrecision.html +++ b/docs/reference/agePrecision.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/alkAgeDist.html b/docs/reference/alkAgeDist.html index cfe10933..3e1dd6e2 100644 --- a/docs/reference/alkAgeDist.html +++ b/docs/reference/alkAgeDist.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/alkIndivAge.html b/docs/reference/alkIndivAge.html index fa406e4d..d628cacf 100644 --- a/docs/reference/alkIndivAge.html +++ b/docs/reference/alkIndivAge.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/alkMeanVar.html b/docs/reference/alkMeanVar.html index c65a5bb8..9ee31b23 100644 --- a/docs/reference/alkMeanVar.html +++ b/docs/reference/alkMeanVar.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/alkPlot.html b/docs/reference/alkPlot.html index adfc10b9..04bb9520 100644 --- a/docs/reference/alkPlot.html +++ b/docs/reference/alkPlot.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/binCI.html b/docs/reference/binCI.html index b462fdb9..e1676f00 100644 --- a/docs/reference/binCI.html +++ b/docs/reference/binCI.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/capHistConvert.html b/docs/reference/capHistConvert.html index 87dee295..635b8bb1 100644 --- a/docs/reference/capHistConvert.html +++ b/docs/reference/capHistConvert.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/capHistSum.html b/docs/reference/capHistSum.html index c147fa39..39f6a704 100644 --- a/docs/reference/capHistSum.html +++ b/docs/reference/capHistSum.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/catchCurve.html b/docs/reference/catchCurve.html index f86d91c3..fc1400ac 100644 --- a/docs/reference/catchCurve.html +++ b/docs/reference/catchCurve.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/chapmanRobson.html b/docs/reference/chapmanRobson.html index 2a2ac179..82e19c72 100644 --- a/docs/reference/chapmanRobson.html +++ b/docs/reference/chapmanRobson.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/col2rgbt.html b/docs/reference/col2rgbt.html index c2e9f26a..b8c1dc2e 100644 --- a/docs/reference/col2rgbt.html +++ b/docs/reference/col2rgbt.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/depletion.html b/docs/reference/depletion.html index 3bc29f08..7b44d095 100644 --- a/docs/reference/depletion.html +++ b/docs/reference/depletion.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/dunnTest.html b/docs/reference/dunnTest.html index b096a83b..91c51544 100644 --- a/docs/reference/dunnTest.html +++ b/docs/reference/dunnTest.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/expandCounts.html b/docs/reference/expandCounts.html index 9ea45d12..40ad72db 100644 --- a/docs/reference/expandCounts.html +++ b/docs/reference/expandCounts.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/expandLenFreq.html b/docs/reference/expandLenFreq.html index 455004ca..ac81e1e5 100644 --- a/docs/reference/expandLenFreq.html +++ b/docs/reference/expandLenFreq.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/extraTests.html b/docs/reference/extraTests.html index 6271f01a..534683ce 100644 --- a/docs/reference/extraTests.html +++ b/docs/reference/extraTests.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/fact2num.html b/docs/reference/fact2num.html index 669ceb00..8c8c4157 100644 --- a/docs/reference/fact2num.html +++ b/docs/reference/fact2num.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/fishR.html b/docs/reference/fishR.html index f0447eb7..fcd399a4 100644 --- a/docs/reference/fishR.html +++ b/docs/reference/fishR.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/fitPlot.html b/docs/reference/fitPlot.html index 17d7a0a6..7176554f 100644 --- a/docs/reference/fitPlot.html +++ b/docs/reference/fitPlot.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/fsaNews.html b/docs/reference/fsaNews.html index 4fea641e..34f0950c 100644 --- a/docs/reference/fsaNews.html +++ b/docs/reference/fsaNews.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html index 75659385..3872d244 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + diff --git a/docs/reference/growthModels.html b/docs/reference/growthModels.html index 471ca0b1..b6a86033 100644 --- a/docs/reference/growthModels.html +++ b/docs/reference/growthModels.html @@ -80,7 +80,7 @@ @@ -96,13 +96,13 @@
- - +
- - + @@ -271,8 +271,8 @@
Changelog
Source:NEWS.md
-
+
@@ -96,13 +96,13 @@
+
+ +FSA 0.9.1 17-Jul-21 Unreleased +
+-
+
-FSA 0.9.0 ongoing Unreleased +FSA 0.9.0 8-Jun-21 2021-06-09
-
+
chooseColors(): REMOVED. This was an exported function that should have been internal. Regardless, where it was used has been removed and the user is now allowed to provide their own vector of colors. See iCheckMultColors(). Partially addresses #65.
compIntercepts(): REMOVED (to FSAmisc). Added to FSA-defunct. Partially addresses #65.
compSlopes(): REMOVED (to FSAmisc). Added to FSA-defunct. Partially addresses #65.
filterD(): DEPRECATED (partially addresses #65).
fitPlot(): DEPRECATED (partially addresses #65). Prior to that removed use of chooseColors() (see above).
diags(): REMOVED (moved to FSAmisc). Added to FSA-defunct. Partially addresses #65.
hoCoef(): REMOVED (moved to FSAmisc). Added to FSA-defunct. Partially addresses #65.
iRichColors(): REMOVED (as part of removing chooseColors()).
mapvalues(): REMOVED. Added to FSA-defunct. Partially addresses #65.
paletteChoices(): REMOVED. See chooseColors() above. Partially addresses #65.
residPlot(): DEPRECATED (partially addresses #65). Prior to that removed use of chooseColors() (see above).
Subset(): REMOVED. Added to FSA-defunct. Partially addresses #65.
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index a6c5c154..8f69eaa4 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,8 +1,8 @@
-pandoc: 2.11.4
+pandoc: 2.14.0.2
pkgdown: 1.6.1
pkgdown_sha: ~
articles: {}
-last_built: 2021-06-09T14:46Z
+last_built: 2021-07-17T14:30Z
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 7b6f8e84..8e53f30f 100644
--- a/docs/reference/BluegillJL.html
+++ b/docs/reference/BluegillJL.html
@@ -80,7 +80,7 @@
@@ -96,13 +96,13 @@
Examp
#> Linf <- Linf[[1]] }
#> Linf*(1-exp(-K*(t-t0)))
#> }
-#> <bytecode: 0x000000001eb6d9b8>
-#> <environment: 0x000000001f64bb58>ages <- 0:20
+#> <bytecode: 0x0000000021b84418>
+#> <environment: 0x0000000021a4dc08>
( vb2 <- vbFuns("Francis") )
#> function(t,L1,L2=NULL,L3=NULL,t1,t3=NULL) {
@@ -281,15 +281,15 @@ Examp
#> r <- (L3-L2)/(L2-L1)
#> L1+(L3-L1)*((1-r^(2*((t-t1)/(t3-t1))))/(1-r^2))
#> }
-#> <bytecode: 0x000000001e796f88>
-#> <environment: 0x000000001c6d4438>
plot(vb2(ages,L1=10,L2=19,L3=20,t1=2,t3=18)~ages,type="b",pch=19)
+#> <bytecode: 0x0000000021b3d170>
+#> <environment: 0x000000001e243b48>
( 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: 0x000000001e8bcda8>
-#> <environment: 0x000000001ceed520>
+#> <bytecode: 0x0000000021b346e0>
+#> <environment: 0x000000001e13bdb8>
## Simple Examples -- Gompertz
( gomp1 <- GompertzFuns() )
#> function(t,Linf,gi=NULL,ti=NULL) {
@@ -298,8 +298,8 @@ Examp
#> Linf <- Linf[[1]] }
#> Linf*exp(-exp(-gi*(t-ti)))
#> }
-#> <bytecode: 0x000000001cc7c828>
-#> <environment: 0x000000001cb3c060>
plot(gomp1(ages,Linf=800,gi=0.5,ti=5)~ages,type="b",pch=19)
+#> <bytecode: 0x000000001e0405d0>
+#> <environment: 0x000000001e002dd8>
( gomp2 <- GompertzFuns("Ricker2") )
#> function(t,L0,a=NULL,gi=NULL) {
#> if (length(L0)==3) { a <- L0[[2]]
@@ -307,21 +307,21 @@ Examp
#> L0 <- L0[[1]] }
#> L0*exp(a*(1-exp(-gi*t)))
#> }
-#> <bytecode: 0x000000001cc5dab8>
-#> <environment: 0x000000001c917b00>
plot(gomp2(ages,L0=2,a=6,gi=0.5)~ages,type="b",pch=19)
+#> <bytecode: 0x000000001e03a0b8>
+#> <environment: 0x000000001e592690>
( gomp2c <- GompertzFuns("Ricker2",simple=TRUE) ) # compare to gomp2
#> function(t,L0,a,gi) {
#> L0*exp(a*(1-exp(-gi*t)))
#> }
-#> <bytecode: 0x000000001cc254c8>
-#> <environment: 0x000000001c6f7440>( gompT <- GompertzFuns("Troynikov1"))
+#> <bytecode: 0x000000001e031168>
+#> <environment: 0x000000001e490d88>( 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: 0x000000001cbb0d38>
-#> <environment: 0x000000001c606308>
+#> <bytecode: 0x000000001e01bfa0>
+#> <environment: 0x000000001e435e18>
## Simple Examples -- Richards
( rich1 <- RichardsFuns() )
#> function(t,Linf,k=NULL,a=NULL,b=NULL) {
@@ -331,8 +331,8 @@ Examp
#> Linf <- Linf[[1]] }
#> Linf*(1-a*exp(-k*t))^b
#> }
-#> <bytecode: 0x000000001c1ff7a0>
-#> <environment: 0x000000001bf9ef38>
plot(rich1(ages,Linf=800,k=0.5,a=1,b=6)~ages,type="b",pch=19)
+#> <bytecode: 0x000000001e318040>
+#> <environment: 0x0000000007079320>
( rich2 <- RichardsFuns(2) )
#> function(t,Linf,k=NULL,ti=NULL,b=NULL) {
#> if (length(Linf)==4) { k <- Linf[[2]]
@@ -341,8 +341,8 @@ Examp
#> Linf <- Linf[[1]] }
#> Linf*(1-(1/b)*exp(-k*(t-ti)))^b
#> }
-#> <bytecode: 0x000000001c1cfb28>
-#> <environment: 0x000000001b49bb30>
plot(rich2(ages,Linf=800,k=0.5,ti=3,b=6)~ages,type="b",pch=19)
+#> <bytecode: 0x000000001e30e468>
+#> <environment: 0x000000001d343700>
( rich3 <- RichardsFuns(3) )
#> function(t,Linf,k=NULL,ti=NULL,b=NULL) {
#> if (length(Linf)==4) { k <- Linf[[2]]
@@ -351,8 +351,8 @@ Examp
#> Linf <- Linf[[1]] }
#> Linf/((1+b*exp(-k*(t-ti)))^(1/b))
#> }
-#> <bytecode: 0x000000001c0dc800>
-#> <environment: 0x000000001b30ad00>
plot(rich3(ages,Linf=800,k=0.5,ti=3,b=0.15)~ages,type="b",pch=19)
+#> <bytecode: 0x000000001e302858>
+#> <environment: 0x000000001cfa4628>
( rich4 <- RichardsFuns(4) )
#> function(t,Linf,k=NULL,ti=NULL,b=NULL) {
#> if (length(Linf)==4) { k <- Linf[[2]]
@@ -361,8 +361,8 @@ Examp
#> Linf <- Linf[[1]] }
#> Linf*(1+(b-1)*exp(-k*(t-ti)))^(1/(1-b))
#> }
-#> <bytecode: 0x000000001c0773a8>
-#> <environment: 0x0000000009ae8090>
plot(rich4(ages,Linf=800,k=0.5,ti=3,b=0.95)~ages,type="b",pch=19)
+#> <bytecode: 0x0000000006ee6be8>
+#> <environment: 0x000000001c4af280>
( rich5 <- RichardsFuns(5) )
#> function(t,Linf,k=NULL,L0=NULL,b=NULL) {
@@ -372,8 +372,8 @@ Examp
#> Linf <- Linf[[1]] }
#> Linf*(1+(((L0/Linf)^(1-b))-1)*exp(-k*t))^(1/(1-b))
#> }
-#> <bytecode: 0x000000001c0416b8>
-#> <environment: 0x0000000007e376e0>
plot(rich5(ages,Linf=800,k=0.5,L0=50,b=1.5)~ages,type="b",pch=19)
+#> <bytecode: 0x0000000006edbf98>
+#> <environment: 0x000000001bd493c0>
( rich6 <- RichardsFuns(6) )
#> function(t,Linf,k=NULL,ti=NULL,Lninf=NULL,b=NULL) {
#> if (length(Linf)==5) { k <- Linf[[2]]
@@ -383,14 +383,14 @@ Examp
#> Linf <- Linf[[1]] }
#> Lninf+(Linf-Lninf)*(1+(b-1)*exp(-k*(t-ti)))^(1/(1-b))
#> }
-#> <bytecode: 0x000000001bfe3918>
-#> <environment: 0x0000000009182490>
plot(rich6(ages,Linf=800,k=0.5,ti=3,Lninf=50,b=1.5)~ages,type="b",pch=19)
+#> <bytecode: 0x000000000710fc68>
+#> <environment: 0x000000001ba477a8>
( rich2c <- RichardsFuns(2,simple=TRUE) ) # compare to rich2
#> function(t,Linf,k,ti,b) {
#> Linf*(1-(1/b)*exp(-k*(t-ti)))^b
#> }
-#> <bytecode: 0x000000001c0f3428>
-#> <environment: 0x00000000061322e8>
+#> <bytecode: 0x000000001e3036a0>
+#> <environment: 0x000000001b8b30f0>
## Simple Examples -- Logistic
( log1 <- logisticFuns() )
#> function(t,Linf,gninf=NULL,ti=NULL) {
@@ -399,8 +399,8 @@ Examp
#> Linf <- Linf[[1]] }
#> Linf/(1+exp(-gninf*(t-ti)))
#> }
-#> <bytecode: 0x0000000021e33728>
-#> <environment: 0x0000000021c21e98>
plot(log1(ages,Linf=800,gninf=0.5,ti=5)~ages,type="b",pch=19)
+#> <bytecode: 0x000000001b7a14b0>
+#> <environment: 0x000000001b738428>
( log2 <- logisticFuns("CJ2") )
#> function(t,Linf,gninf=NULL,a=NULL) {
#> if (length(Linf)==3) { gninf <- Linf[[2]]
@@ -408,22 +408,22 @@ Examp
#> Linf <- Linf[[1]] }
#> Linf/(1+a*exp(-gninf*t))
#> }
-#> <bytecode: 0x0000000021e0d798>
-#> <environment: 0x0000000006a86c60>
plot(log2(ages,Linf=800,gninf=0.5,a=10)~ages,type="b",pch=19)
+#> <bytecode: 0x000000001b7804a8>
+#> <environment: 0x000000001b5bfb00>
( log2c <- logisticFuns("CJ2",simple=TRUE) ) # compare to log2
#> function(t,Linf,gninf,a) {
#> Linf/(1+a*exp(-gninf*t))
#> }
-#> <bytecode: 0x0000000021d80f78>
-#> <environment: 0x00000000242952c0>( log3 <- logisticFuns("Karkach") )
+#> <bytecode: 0x000000001b75e850>
+#> <environment: 0x000000001b4610a0>( log3 <- logisticFuns("Karkach") )
#> function(t,Linf,L0=NULL,gninf=NULL) {
#> if (length(Linf)==3) { L0 <- Linf[[2]]
#> gninf <- Linf[[3]]
#> Linf <- Linf[[1]] }
#> L0*Linf/(L0+(Linf-L0)*exp(-gninf*t))
#> }
-#> <bytecode: 0x0000000021cf83b0>
-#> <environment: 0x0000000021bbefc0>plot(log3(ages,L0=10,Linf=800,gninf=0.5)~ages,type="b",pch=19)
+#> <bytecode: 0x000000001b7593f8>
+#> <environment: 0x000000000a912418>
( log4 <- logisticFuns("Haddon") )
#> function(Lm,dLmax,L50=NULL,L95=NULL) {
#> if (length(dLmax)==3) { L50 <- dLmax[2]
@@ -431,8 +431,8 @@ Examp
#> dLmax <- dLmax[1] }
#> dLmax/(1+exp(log(19)*((Lm-L50)/(L95-L50))))
#> }
-#> <bytecode: 0x0000000021c98318>
-#> <environment: 0x0000000021c30ec0>
+#> <bytecode: 0x000000001b7511f0>
+#> <environment: 0x0000000009c382c0>
###########################################################
## Examples of fitting
diff --git a/docs/reference/headtail.html b/docs/reference/headtail.html
index 5890e410..f9dcd555 100644
--- a/docs/reference/headtail.html
+++ b/docs/reference/headtail.html
@@ -80,7 +80,7 @@
@@ -96,13 +96,13 @@
Examp #> r <- (L3-L2)/(L2-L1) #> L1+(L3-L1)*((1-r^(2*((t-t1)/(t3-t1))))/(1-r^2)) #> } -#> <bytecode: 0x000000001e796f88> -#> <environment: 0x000000001c6d4438>
Examp #> Linf <- Linf[[1]] } #> Linf*exp(-exp(-gi*(t-ti))) #> } -#> <bytecode: 0x000000001cc7c828> -#> <environment: 0x000000001cb3c060>
Examp #> L0 <- L0[[1]] } #> L0*exp(a*(1-exp(-gi*t))) #> } -#> <bytecode: 0x000000001cc5dab8> -#> <environment: 0x000000001c917b00>
Examp #> Linf <- Linf[[1]] } #> Linf*(1-a*exp(-k*t))^b #> } -#> <bytecode: 0x000000001c1ff7a0> -#> <environment: 0x000000001bf9ef38>
Examp #> Linf <- Linf[[1]] } #> Linf*(1-(1/b)*exp(-k*(t-ti)))^b #> } -#> <bytecode: 0x000000001c1cfb28> -#> <environment: 0x000000001b49bb30>
Examp #> Linf <- Linf[[1]] } #> Linf/((1+b*exp(-k*(t-ti)))^(1/b)) #> } -#> <bytecode: 0x000000001c0dc800> -#> <environment: 0x000000001b30ad00>
Examp #> Linf <- Linf[[1]] } #> Linf*(1+(b-1)*exp(-k*(t-ti)))^(1/(1-b)) #> } -#> <bytecode: 0x000000001c0773a8> -#> <environment: 0x0000000009ae8090>
Examp #> Linf <- Linf[[1]] } #> Linf*(1+(((L0/Linf)^(1-b))-1)*exp(-k*t))^(1/(1-b)) #> } -#> <bytecode: 0x000000001c0416b8> -#> <environment: 0x0000000007e376e0>
Examp #> Linf <- Linf[[1]] } #> Lninf+(Linf-Lninf)*(1+(b-1)*exp(-k*(t-ti)))^(1/(1-b)) #> } -#> <bytecode: 0x000000001bfe3918> -#> <environment: 0x0000000009182490>
Examp #> Linf <- Linf[[1]] } #> Linf/(1+exp(-gninf*(t-ti))) #> } -#> <bytecode: 0x0000000021e33728> -#> <environment: 0x0000000021c21e98>
Examp #> Linf <- Linf[[1]] } #> Linf/(1+a*exp(-gninf*t)) #> } -#> <bytecode: 0x0000000021e0d798> -#> <environment: 0x0000000006a86c60>