From 57bbef63a8527e7131e817740d9a61f33f3345a5 Mon Sep 17 00:00:00 2001 From: Derek Ogle Date: Tue, 1 Jun 2021 16:51:20 -0500 Subject: [PATCH] Updated webpage --- R/FSAUtils.R | 3 +- R/deprecated_fitPlot.R | 20 +- _pkgdown.yml | 3 +- docs/news/index.html | 56 ++-- docs/pkgdown.yml | 2 +- docs/reference/CodNorwegian.html | 2 +- docs/reference/fitPlot.html | 44 +-- docs/reference/growthModels.html | 352 +++++++++++++--------- docs/reference/index.html | 6 +- docs/reference/nlsTracePlot.html | 6 +- docs/reference/srStarts.html | 6 +- docs/sitemap.xml | 20 +- man/{fitPlot-deprecated.Rd => fitPlot.Rd} | 0 13 files changed, 290 insertions(+), 230 deletions(-) rename man/{fitPlot-deprecated.Rd => fitPlot.Rd} (100%) diff --git a/R/FSAUtils.R b/R/FSAUtils.R index 7384ab0b..01fe82e3 100644 --- a/R/FSAUtils.R +++ b/R/FSAUtils.R @@ -194,7 +194,8 @@ fishR <- function(where=c("home","IFAR","general","books", invisible(tmp) } - +#' @name fsaNews +#' #' @title Read news and changes for the 'FSA' package. #' #' @description Opens up the \href{https://github.com/droglenc/FSA/blob/master/NEWS.md}{News.md GitHub file} for the \sQuote{FSA} package in an external browser. diff --git a/R/deprecated_fitPlot.R b/R/deprecated_fitPlot.R index bd4476d7..2e6b23b6 100644 --- a/R/deprecated_fitPlot.R +++ b/R/deprecated_fitPlot.R @@ -118,7 +118,7 @@ #' fitPlot(glm1) #' fitPlot(glm1,yaxis1.ticks=c(0,1),yaxis1.lbls=c(0,1)) #' -#' @rdname fitPlot-deprecated +#' @rdname fitPlot #' @export fitPlot <- function (object, ...) { if ("lm" %in% class(object)) ## This is a hack so no double deprecation warning @@ -126,7 +126,7 @@ fitPlot <- function (object, ...) { UseMethod("fitPlot") } -#' @rdname fitPlot-deprecated +#' @rdname fitPlot #' @export fitPlot.lm <- function(object, ...) { object <- iTypeoflm(object) @@ -137,7 +137,7 @@ fitPlot.lm <- function(object, ...) { fitPlot(object,...) } -#' @rdname fitPlot-deprecated +#' @rdname fitPlot #' @export fitPlot.SLR <- function(object,plot.pts=TRUE,pch=16,col.pt="black", col.mdl="red",lwd=3,lty=1, @@ -196,7 +196,7 @@ fitPlot.SLR <- function(object,plot.pts=TRUE,pch=16,col.pt="black", } -#' @rdname fitPlot-deprecated +#' @rdname fitPlot #' @export fitPlot.IVR <- function(object,...) { ## Do some checks @@ -369,14 +369,14 @@ iFitPlotIVR2 <- function(object,plot.pts=TRUE,pch=c(16,21,15,22,17,24,c(3:14)), } # nocov end } -#' @rdname fitPlot-deprecated +#' @rdname fitPlot #' @export fitPlot.POLY <- function(object,...) { fitPlot.SLR(object,...) } -#' @rdname fitPlot-deprecated +#' @rdname fitPlot #' @export fitPlot.ONEWAY <- function (object, xlab=object$Enames[1],ylab=object$Rname,main="", @@ -410,7 +410,7 @@ fitPlot.ONEWAY <- function (object, } # nocov end -#' @rdname fitPlot-deprecated +#' @rdname fitPlot #' @export fitPlot.TWOWAY <- function(object,which,change.order=FALSE, xlab=object$Enames[ord[1]],ylab=object$Rname, @@ -465,7 +465,7 @@ fitPlot.TWOWAY <- function(object,which,change.order=FALSE, } -#' @rdname fitPlot-deprecated +#' @rdname fitPlot #' @export fitPlot.nls <- function(object,d, pch=c(19,1),col.pt=c("black","red"),col.mdl=col.pt, @@ -544,7 +544,7 @@ fitPlot.nls <- function(object,d, } } # nocov end -#' @rdname fitPlot-deprecated +#' @rdname fitPlot #' @export fitPlot.glm <- function(object, ...) { if (object$family$family=="binomial" & object$family$link=="logit") @@ -553,7 +553,7 @@ fitPlot.glm <- function(object, ...) { STOP("Currently only logistic regression GLM models are supported by fitPlot.") } -#' @rdname fitPlot-deprecated +#' @rdname fitPlot #' @export fitPlot.logreg <- function(object, xlab=names(object$model)[2],ylab=names(object$model)[1], diff --git a/_pkgdown.yml b/_pkgdown.yml index 57cecefe..44f4ed73 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -90,7 +90,7 @@ reference: - binCI - hyperCI - poiCI - - bootstrap + - boot - dunnTest - extraSS - geomean @@ -100,6 +100,7 @@ reference: - ksTest - logbtcf - lrt + - nlsBoot - nlsTracePlot - pcumsum - rSquared diff --git a/docs/news/index.html b/docs/news/index.html index 1eb26af8..4f200c33 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -137,7 +137,7 @@

bootCase(): REMOVED. Users can use car::Boot(), which partially addresses #65.
  • @@ -307,7 +307,7 @@

  • Changed to depending on R >=3.5.0, because that is the latest version required by a package (i.e., car) that FSA imports or suggests. Used the “check_r_versions_of_package_dependencies” shiny app by “ateucher” (on Github) to help determine this.
  • Removed asbio package from suggests as it hung up Travis-CI build (because of the need for the TCLTK package).
  • -capFirst(): Modified. Fixed bug related to an NA item.
    • +capFirst(): Modified. Fixed bug related to an NA item.

  • psdAdd(): Modified. Changed spec= to species= to be consistent with psdCalc() and psdPlot().
  • @@ -471,7 +471,7 @@

  • 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.
    • +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().
  • @@ -483,9 +483,9 @@

  • nlsBoot() methods: Modified. Changed all 1: structures to seq_len() (partially addressing #36).
  • -plot.boot(): Removed (added last version) until I can test more.
    • +plot.boot(): Removed (added last version) until I can test more.

  • -predict.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).
  • @@ -514,11 +514,11 @@

  • hTest.boot(): Added.
  • -plot.boot(): Added.
    • +plot.boot(): Added.

  • plotAB(): Modified. Added col.numbers= to allow users to modify the color of the numbers when what="numbers" is used (addresses #34).
  • -predict.boot(): Added.
    • +predict.boot(): Added.
  • psdPlot(): Modified. Minor changes to documentation and look of the function code.
  • @@ -586,7 +586,7 @@

  • ageBias(): Modified. A complete rebuild of plot. Major changes are to add plotAB() which is primarily used to make the “legacy” age bias plots of Campana, removal of the “sunflower” plot option, new sets of defaults for many of the arguments that reflect my preferences for visualizing age comparisons (which includes defaulting to plotting differences in ages), addition of the ability to add marginal histograms (xHist=, yHist=, col.hist=, and hist.panel.size=), better handling of axis ticks and labels (primarily to show ticks at integers and make sure 0 is included for differences), and allowing the ability to add “summary layers” to the main plot (see allowAdd=). Many examples were added. Some functionality from previous versions will be broken.
  • -capFirst(): Modified. Changed some if()s with class()es to inherits().
    • +capFirst(): Modified. Changed some if()s with class()es to inherits().

  • compIntercepts(): Modified. Replaced two dim() calls with nrow().
  • @@ -831,9 +831,9 @@

  • growthFunShow(): Added.
  • -srFunShow(): Added.
    • +srFunShow(): Added.

  • -srModels(): Removed. Replaced with srFunShow().
    • +srModels(): Removed. Replaced with srFunShow().
  • srStarts(): Modified. Removed dynamicPlot=TRUE option. Moved it to FSAsim package. Modified plot when plot=TRUE by adding “STARTING VALUES” to title and moving starting values to within the plot. Added cex.main= and col.main=.
  • @@ -1437,7 +1437,7 @@

  • removal(): Modified. Changed all cat() to message()s.
  • -srFuns(): Modified. Changed all cat() to message()s. Created some tests.
    • +srFuns(): Modified. Changed all cat() to message()s. Created some tests.

    • @@ -1516,7 +1516,7 @@

  • mapvalues(): Deleted. Deleted the function from FSA but imported it from plyr and then exported it from FSA so that it would be available to fisheries users without having to load plyr.
  • -oddeven(): Modified. Added some checks with error messages. Added suite of tests.
    • +oddeven(): Modified. Added some checks with error messages. Added suite of tests.
  • perc(): Modified. Added ability to use “and equals” or not to the items in dir= (i.e., there are now four items in dir=). Fixed a bug related to using na.rm=FALSE and a “less than” situation. Added some checks with error messages. Added suite of tests.
  • @@ -1677,7 +1677,7 @@

  • updated DESCRIPTION file (following this – http://r-pkgs.had.co.nz/description.html
  • -srFuns(): Modified. Changed function returned when simplify=FALSE so that if the parameters are named that the name is dropped. Thus, when the function is used, the returned result will not be annoyingly named as the first parameter. Added functionality for the “density-independence” model.
    • +srFuns(): Modified. Changed function returned when simplify=FALSE so that if the parameters are named that the name is dropped. Thus, when the function is used, the returned result will not be annoyingly named as the first parameter. Added functionality for the “density-independence” model.

  • srStarts(): Modified. Added functionality for the “density-independence” model.
  • @@ -1692,7 +1692,7 @@

  • growthModelSim(): Deleted. The simulation functionality was moved to the FSAsim package. The functionality related to finding starting values for the von Bertalanffy modesl was moved to vbStarts().
  • -srFuns(): Modified. A complete rebuild to make similar to vbFuns(). Added simple=. Added type='Shepherd' for the Shepherd (1982) three parameter model and type='SailaLorda' for the “Saila-Lorda” three parameter model from Iles (1994). Added tests for error messages.
    • +srFuns(): Modified. A complete rebuild to make similar to vbFuns(). Added simple=. Added type='Shepherd' for the Shepherd (1982) three parameter model and type='SailaLorda' for the “Saila-Lorda” three parameter model from Iles (1994). Added tests for error messages.

  • srModels(): Modified. A complete rebuild to make similar to growthModels(). Added “Shepherd” and “Saila-Lorda” models.
  • @@ -1738,7 +1738,7 @@

    • -capFirst(): Modified. Added a check to make sure the inputted object was either a character or factor class. Added code to return the object as the same class of the original object.
      • +capFirst(): Modified. Added a check to make sure the inputted object was either a character or factor class. Added code to return the object as the same class of the original object.
    • lencat(): Modified. Added a catch for bad choices of arguments. Added a catch to send a warning if the vector contains all NA values (this happens when lencat() is used within a loop or as part of psdAdd()). Added tests for error and warning messages. Changed how the formula was handled in the formula method.
    • @@ -2025,13 +2025,13 @@

    • Added a suggests for dplyr.
    • Added an external file in inst/extdata for testing PSD and Wr calculations.
    • -capFirst(): Modified. Changed words= to which=.
      • +capFirst(): Modified. Changed words= to which=.

    • psdAdd(): Modified. Added a default and a formula version to allow efficiency with dplyr. Added examples. Updated tests.
    • recodeF(): Added.
    • -recodeSpecies(): Deleted. Functionality replaced by recodeF() in combination with capFirst().
      • +recodeSpecies(): Deleted. Functionality replaced by recodeF() in combination with capFirst().
    • wrAdd(): Modified. Added a default and a formula version to allow efficiency with dplyr. Added examples. Updated tests.
    • @@ -2082,7 +2082,7 @@

      • -capFirst() Modified. Added an option to handle a vector of strings rather than just a single string.
        • +capFirst() Modified. Added an option to handle a vector of strings rather than just a single string.
      • lencat(): Modified. Fixed bug with category names when use.names=TRUE. Moved all internal functions outside of lencat() environment (and renamed them). Cleaned up code.
      • @@ -2096,7 +2096,7 @@

      • psdPlot(): Modified. Completely redone (fixed several bugs and overall sloppy code). Added psd.add=. Changed legend.pos= and legend.cex= to psd.pos= and psd.cex=.
      • -recodeSpecies(): Modified. Made changes to reflect new capFirst() functionality.
        • +recodeSpecies(): Modified. Made changes to reflect new capFirst() functionality.

      • tictactoe(): Modfied.
      • @@ -2365,9 +2365,9 @@

      • iPSDLitCheck(): Added. Was psdLitCheck().
      • -is.even(): Added.
        • +is.even(): Added.

      • -is.odd(): Added. Was odd().
        • +is.odd(): Added. Was odd().
      • iTypeoflm(): Added. Was typeoflm().
      • @@ -2384,7 +2384,7 @@

      • makeItemsToRemove(): Deleted. Moved functionality to iMakeItemsToRemove() and moved code to swvUtils file.
      • -odd(): Deleted. Moved functionality to is.odd().
        • +odd(): Deleted. Moved functionality to is.odd().

      • predict.nlsBoot(): Added an interactive() to the nlstools example in the help file.
      • @@ -2629,7 +2629,7 @@

      • agePrecision(): Added. Extracted age precision related material from ageComp(). Modified the code to allow for calculations across more than two structures. Code was streamlined dramatically from what was in ageComp(). Added an example using WhitefishLC as it allows for demonstrating more than two age assignments.
      • -capFirst(): Modified. Added functionality, controlled by the new words= parameter, to allow all words, rather than just the first word, to be capitalized.
        • +capFirst(): Modified. Added functionality, controlled by the new words= parameter, to allow all words, rather than just the first word, to be capitalized.

      • capHistConvert(): Modified the help file by commenting out the example that depends on the RCapture package. This is needed for the RForge site for the time being.
      • @@ -2677,7 +2677,7 @@

      • rsdVal(): Deleted.
      • -recodeSpecies(): Modified. Changed capFirst= to doCapFirst= to minimize confusion with capFirst(). Change doCapFirst= to a character that behaves like words= in capFirst(), rather than as a logical.
        • +recodeSpecies(): Modified. Changed capFirst= to doCapFirst= to minimize confusion with capFirst(). Change doCapFirst= to a character that behaves like words= in capFirst(), rather than as a logical.

      • SpotVA1: Modified. Removed link to source documents because it caused a problem when making the PDF manual.
      • @@ -2772,7 +2772,7 @@

      • ageComp(): Modified some of the code to adjust for name changes in Summarize(). Modified to use a formula notation.

      • ageKey(): Modified to using a formula notation. This removed the dl=, cl=, and ca= arguments. Made minor adjustments to the help pages (in addition to changes related to the argument modifications).

      • bcFuns(): Removed use of %nin%.

        • -

      • capFirst(): Modified so that ONLY the first letter is capitalized (previous version would de-capitalize the first letter in the second word but leave the rest of the letters capitalized).

        • +

      • capFirst(): Modified so that ONLY the first letter is capitalized (previous version would de-capitalize the first letter in the second word but leave the rest of the letters capitalized).

      • capHistSum(): Modified to correct an error that occurred when computing the Method B table when a capture history occurred only once or not at all.

      • chapmanRobson(): Modified by adding the Hoenig et al. (1983) bias correction formula for the estimate of Z as the default option.

      • confint.nlsBoot(): Removed use of %nin%.

        • @@ -2805,7 +2805,7 @@

      • tictactoeAdd(): Modified by changing PSD labels to PSS.

      • vbStarts(): Removed use of %nin%.

      • wetPerim(): Deleted, moved to NCStats (to reduce overhead here).

        • -

      • wrAdd(): Modified. Major modifications to account for changes to WSlit. Added the capFirst() check for species name. Changed subNA= to remove.submin= to make consistent with wrDataPrep().

        • +

      • wrAdd(): Modified. Major modifications to account for changes to WSlit. Added the capFirst() check for species name. Changed subNA= to remove.submin= to make consistent with wrDataPrep().

      • wrDataPrep(): Added.

      • wrVal(): Deleted.

      • WSlit: Modified. Completely rebuilt so that quadratic equation using EmP could be incorporated into the database. Also added equations for several new species.

        • @@ -2924,7 +2924,7 @@

      • Moved quantreg from depends to importsFrom for rq() (used in emp()).

      • Attempted to move reshape to importsFrom but had problems with missing is.formula() from plyr.

      • ageComp(): modified class name to “ageComp” from “AgeComp”.

        • -

      • capFirst(): added.

        • +

      • capFirst(): added.

      • catchCurve(): modified class name to “catchCurve” from “CC”.

      • chapmanRobson(): modified class name to “chapmanRobson” from “CR”.

      • coefPlot(): deleted (Weisberg’s LGM is now out-dated).

        • @@ -3238,7 +3238,7 @@

      • caphist.convert(): Modified such that an “RMark” type can be output. 0 chapmanPlot()`: Added.

      • growmodel.sim(): Deleted. Changed to growthModelSim(). See below. 0 growthModelSim()`: Added. Initially a renaming of growmodel.sim(). However, the model names were changed to be more consistent with other functions and a method for the Mooij et al. paramaterization was added.

      • growthModels(): Added.

        • -

      • srFuns(): Added.

        • +

      • srFuns(): Added.

      • srStarts(): Added.

      • stock.recruit(): Deleted, along with all related generics.

      • stock.recruit.sim(): Deleted. Changed to stockRecruitSim(). See below.

        • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 1ae0ca0e..a3a7d21a 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.11.4 pkgdown: 1.6.1 pkgdown_sha: ~ articles: {} -last_built: 2021-06-01T13:23Z +last_built: 2021-06-01T21:47Z urls: reference: http://derekogle.com/FSA/reference article: http://derekogle.com/FSA/articles diff --git a/docs/reference/CodNorwegian.html b/docs/reference/CodNorwegian.html index 2a9921e0..8db8f9c8 100644 --- a/docs/reference/CodNorwegian.html +++ b/docs/reference/CodNorwegian.html @@ -153,7 +153,7 @@

        Topic

        See also

        -

        Used in srStarts, srFuns, and nlsTracePlot examples.

        +

        Used in srStarts, srFuns, and nlsTracePlot examples.

        Examples

        str(CodNorwegian)
diff --git a/docs/reference/fitPlot.html b/docs/reference/fitPlot.html
index 42140adf..c1319026 100644
--- a/docs/reference/fitPlot.html
+++ b/docs/reference/fitPlot.html
@@ -6,7 +6,7 @@
 
 
 
-Fitted model plot for an lm, glm, or nls object. — fitPlot • FSA
+DEPRECATED -- Fitted model plot for an lm, glm, or nls object. — fitPlot • FSA
 
 
 
@@ -46,7 +46,7 @@
 
 
 
-
+
 
 
 
@@ -119,8 +119,8 @@
 
        
   
        
     
        
-    
        Fitted model plot for an lm, glm, or nls object.
        
-    Source: R/fitPlot.R
+    
        DEPRECATED -- Fitted model plot for an lm, glm, or nls object.
        
+    Source: R/deprecated_fitPlot.R
     
     
        
 
@@ -421,7 +421,7 @@ 
        Note
        
     
        This function is meant to allow newbie students the ability to visualize the most common linear models found in an introductory or intermediate level undergraduate statistics course without getting “bogged-down” in the gritty details of a wide variety of functions. This generic function and it's S3 functions allow the student to visualize the means plot of a one-way anova, the main effects and interaction plots of a two-way ANOVA, the fit of a simple linear regression, the fits of many lines in an indicator variable regression, and the fit of a non-linear model with a simple and mostly common set of arguments -- generally, all that is required is a fitted linear model of the type mentioned here as the first argument. This function thus allows newbie students to interact with and visualize moderately complex linear models in a fairly easy and efficient manner. THIS IS NOT A RESEARCH GRADE FUNCTION and the user should learn how to use the functions that this function is based on, build plots from “scratch”, or use more sophisticated plotting packages (e.g., ggplot2 or lattice).
        
     
        See also
        
 
-    
        See abline, regLine in car, error.bars in psych, interaction.plot, and lineplot.CI in sciplot for similar functionality. See residPlot for related functionality.
        
+    
        See abline, regLine in car, error.bars in psych, interaction.plot, and lineplot.CI in sciplot for similar functionality.
        
     
        Author
        
 
     
        Derek H. Ogle, derek@derekogle.com
        
@@ -430,45 +430,45 @@ 
        Examp
     
        # create year as a factor variable
 Mirex$fyear <- factor(Mirex$year)
 # reduce number of years for visual simplicity for iVRs
-Mirex2 <- filterD(Mirex,fyear %in% c(1977,1992))
+Mirex2 <- droplevels(subset(Mirex,fyear %in% c(1977,1992)))
 
 ## One-way ANOVA
 aov1 <- lm(mirex~fyear,data=Mirex)
 fitPlot(aov1)
-
        
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        
 ## Two-way ANOVA
 aov2 <- lm(mirex~fyear*species,data=Mirex)
 # interaction plots and a color change
 fitPlot(aov2,legend="bottomleft")
-
        fitPlot(aov2,change.order=TRUE)
-
        # main effects plots
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        fitPlot(aov2,change.order=TRUE)
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        # main effects plots
 fitPlot(aov2,which="species")
-
        fitPlot(aov2,which="fyear")
-
        
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        fitPlot(aov2,which="fyear")
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        
 ## Simple linear regression (show color change and confidence/prediction bands)
 slr1 <- lm(mirex~weight,data=Mirex)
 fitPlot(slr1)
-
        fitPlot(slr1,interval="both")
-
        
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        fitPlot(slr1,interval="both")
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        
 ## Indicator variable regression with one factor (also showing confidence bands)
 ivr1 <- lm(mirex~weight*fyear,data=Mirex2)
 fitPlot(ivr1,legend="topleft")
-
        fitPlot(ivr1,legend="topleft",interval="confidence")
-
        fitPlot(ivr1,legend="topleft",interval="confidence",col="Dark 2")
-
        
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        fitPlot(ivr1,legend="topleft",interval="confidence")
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        fitPlot(ivr1,legend="topleft",interval="confidence",col="Dark 2")
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        
 ## Indicator variable regression with one factor (assuming parallel lines)
 ivr2 <- lm(mirex~weight+species,data=Mirex2)
 fitPlot(ivr2,legend="topleft")
-
        
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        
 ## Indicator variable regression with two factors
 ivr3 <- lm(mirex~weight*fyear*species,data=Mirex2)
 fitPlot(ivr3,ylim=c(0,0.8),legend="topleft")
-
        fitPlot(ivr3,ylim=c(0,0.8),legend="topleft",col="Spectral")
-
        
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        fitPlot(ivr3,ylim=c(0,0.8),legend="topleft",col="Spectral")
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        
 ## Polynomial regression
 poly1 <- lm(mirex~weight+I(weight^2),data=Mirex)
 fitPlot(poly1,interval="both")
-
        
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        
 ## Non-linear model example
 lr.sv <- list(B1=6,B2=7.2,B3=-1.5)
 nl1 <- nls(cells~B1/(1+exp(B2+B3*days)),start=lr.sv,data=Ecoli)
@@ -482,8 +482,8 @@ 
        Examp
                                  72,73,75,75,76,76,78,79,81))
 glm1 <- glm(fail~temperature,data=d,family="binomial")
 fitPlot(glm1)
-
        fitPlot(glm1,yaxis1.ticks=c(0,1),yaxis1.lbls=c(0,1))
-
        
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.
        fitPlot(glm1,yaxis1.ticks=c(0,1),yaxis1.lbls=c(0,1))
+
        #> Warning: 'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.