R News

CHANGES IN FlexParamCurve 1.5-3:

(note FlexParamCurve 1.5-2 was not generally circulated thus changes detailed
 are additions since 1.5-1)

    * Change in default approach to fitting monotonic curves

      Monotonic curves are exemplified by the logistic and Richards curve, and do not
      incorporate a recessional part of the curve. In previous versions, FlexParamCurve
      fixed recessional parameters to the values in the specified pn.options object (see
      ?modpar). However, if data used in modpar supported recessional parameters non-
      intuitive recessional plots were generated using monotonic curve models (modno 12 
      or 32). The new approach implemented in v1.5-3 is to by default ignore recessional
      parameters whenever modno 12 or 32 are optimized or plotted. To access the original 
      approach (for those who wish to optimize pre-recession parameters only but retain 
      fixed recession trajectories) set force.nonmonotonic = TRUE in modpar.
      
      
    * Update of model selection routines (pn.mod.compare and pn.modselect.step) 
      
      The new default for pn.mod.compare is to proceed using variable models (those 
      with a shape parameter, M, for the pre-recessional part of the curve) for subsequent
      model selection if neither of the initial models successfully converge. User preferences
      can be selected using either forcemod = 3 or forcemod = 4; see ?pn.mod.compare. In both
      selection routines the code has been adjusted to make forcemod work appropriately.
      
    * Implementation of required package dependencies 
    
      The new dependency information required by CRAN has been incorporated.


CHANGES IN FlexParamCurve 1.5-1:


    * IMPORTANT: Change in the use of the Global Environment

      In previous versions, FlexParamCurve has automatically written the pn.options 
      file (with fitting estimates and user custom fitting instructions) to the 
      Global Environment. Additionally, the model selection routines outputed all the 
      fitted nlsList models to the Global Environment. To comform to R good practice 
      for packages, the user can now specify that the Global Environment is not
      written to. To make this version back-compatible with previous FlexParamCurve 
      versions, the default is to write to the Global Environment but this can be 
      switched off setting the parameter Envir to a value for an alternative 
      environment to write to. Internal parameters are written to the namespace 
      environment, FlexParamCurve:::FPCEnv. This applies to the following function
      calls: modpar(), SSposnegRichards(), pn.mod.compare(), pn.modselect.step(), 
      posnegRichards.eqn() and change.pnparameters().
      
    * Addition of new function: get.mod(). 
      
      This is mostly used internally but can be
      used by user to copy files from one environment to another. By default this will
      copy files output from model selection routines (pn.mod.compare() and
      pn.modselect.step() ) from the packge namespace to the global environment.
      
    * Correction of faulty examples. 
    
      FlexParamCurve v1.4-3 was archived for reason of failing
      examples. These have been revised accordingly and pass appropriate tests.

    * Addition of a NEWS file

      This file contains news for all recent versions of FlexParamCurve
      that were previously found at https://pennstate.academia.edu/SteveOswald/Posts
      Please check this website for instant updates

    * Use of Lazy Loading for data files

      The package now uses lazyloading for all data files used in examples. Thus all data
      files can be used directly without the need to call data() beforehand.

    * Bug fix for SSposnegRichards

      Correction of a problem for selection routines pn.mod.compare and pn.modselect.step
      that was caused by failing to specify taper.ends values explicitly when initially
      running modpar. These two selection routines will now work alone whether specifying
      taper.ends or not and regardless of previous runs of modpar.


   * Error message update in pn.modselect.step
    
      Addition of informative error message for this selection routine if no nlsList models are
      are successfully fitted - induces safe termination of the routine with appropriate error message.


CHANGES IN FlexParamCurve 1.4-3:

   * FlexParamCurve Documentation available: Paper, Online Tutorial and Introduction to the R package.

        Methods in Ecology and Evolution recently published a showcase paper on FlexParamCurve
        and is hosting two videos on the package, as online extras.

        These include a ~8 min introduction as to the purpose and utility of the package 
        and a 12 min tutorial in R running you through some of the main functions in FlexParamCurve, 
        including curve selection, model plotting and using FlexParamCurve models within mixed effects models.

         Paper is available at: 
          http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2012.00231.x/abstract
          Videos can be found at: http://www.methodsinecologyandevolution.org/view/0/podcasts.html

   * Major code updates have been made to the package in this version

	selfStart (SSposnegRichards) and model selection routines run ~ 10 x faster and are more reliable!

	more user-options to modpar and model selection routines to allow:
	  
	  tapering at either end of the curve (taper.ends) 
          
          custom specification of parameter bounds (width.bounds)
          
          passing arguments to nls and nlsList within modpar
          
          automated bounds expansion for data exhibiting very different curves between     
            different levels


CHANGES IN FlexParamCurve 1.4-0

   * modpar and SSposnegRichards require users to specify the name of a list object to write model
     parameters and fitting options to, so that multiple models can be fitted alternatively within one session.

   * Various inconsistent names of functions have been updated.

   * This new version is showcased in a forthcoming Methods in Ecology and Evolution Application
     paper: http://www.methodsinecologyandevolution.org/view/0/accepted.html

   * Thanks to Timothy Paine for his helpful suggestions that refined this version of FlexParamCurve.


CHANGES IN FlexParamCurve 1.2

   * Significant improvement in the accuracy of optimizations so this version is to be
    prefered over v1.1. As in version 1.1, it can be used for a variety of complex parameteric growth curves
    or any relationships that exhibit multiple S-shaped curves between predictors and response variables. 

   * Added flexibility to model curves that follow a very general double-Richards type
     (not just positive-negative trajectory), e.g. it can now perform double-positive
     (or double-negative formulations), e.g. Meyer, P.(1994) Bi-logistic growth.
     Technological Forecasting and Social Change. 47: 89-102) 

   * Ability to model two component models (where separate curves do not interact) as well as
     the traditional double curves. e.g. of two component models: Ross, J.L. et al. (1994) Age,
     growth, mortality, and reproductive biology of red drums in North Carolina waters. Transactions
     of the American Fisheries Society 124: 37-54. OR Murphy, S. et al. (2009) Importance of biological'
     parameters in assessing the status of Delphinus delphis. Marine Ecology Progress Series 388: 273-291. 

   * It can estimate double-positive richards and double negative richards and should be able to accomodate
     a wide variety of data [if you have a dataset that doesn't fit then let me know and I'll work it in].
     It is slightly slower for more complex datasets: speeding up optimization algorithms is in the pipeline. 

   * Option "verbose" added for use in modpar and SSposnegRichards to allow trouble shooting. 


CHANGES IN FlexParamCurve 1.1	

  *  I am happy to announce that the FlexParamCurve R package is now available
     on CRAN (http://cran.r-project.org/web/packages/FlexParamCurve/index.html). 

  * This package provides a flexible selfStart function and model selection tools for fitting nls, nlsList and nlme models for data that follow positive and negative trajectories. The package was designed with growth analysis (see Huin & Prince 2000. Chick Growth in Albatrosses: Curve Fitting with a Twist. J. Avian Biol. 31(3): 418-425) in mind but provides support for any curve-fitting requiring combined positive-negative trajectories. 

  * It can be downloaded directly from R in the usually way: 
    install.packages("FlexParamCurve") 