Changes in version 1.6.3 (2021-10-04)                  

New features

  - Exclude NA in VBGF function with argument na.rm = TRUE (default is
    FALSE)
  - SPR calculation in Thompson and Bell yield per recruit model +
    SPR-based reference points

Bug fixes

  - Correct separation index calculation in Bhattacharya's method
    (correct = (L1 - L2) / (sd1 + sd2)/2)
  - Correct standard deviation calculation in Bhattacharya's method
    (correct = sqrt(-dL/b)
  - Correct equations of Heincke and Robson & Chapman methods in the
    Z_CPUE function
  - Return score_mat in ELEFAN function

Minor changes

  - Updated vignettes
  - LazyData = false which implies that data("...") has to be used to
    load a package into the R environment, e.g. data("snyLFQ7")
  - Argument plots_refs in plot.predict_mod function to select which
    reference points in the prediction models should be plotted. By
    default all reference points are plotted: plot_refs =
    c("F01","Fmax","F05","F04").
  - Argument cols_refs in plot.predict_mod function to select the colour
    for the reference points in the prediction models. Default colours
    are cols_refs = c("goldenrod2","darkred","darkgreen","darkorange").
  - Change naming from 'Fmsy' in prediction models to 'Fmax'.

                 Changes in version 1.6.2 (2020-01-28)                  

Bug fixes

  - Use of matrices was adjusted to comply with new R matrix classes
      - ELEFAN_GA was adjusted to use new arguments of the underlying
        GA::ga function

                 Changes in version 1.6.1 (2019-01-17)                  

Bug fixes

  - The LBB functionality was removed from the package.

                         Changes in version 1.6                         

New features

  - The Length-based Bayesian biomass estimator method (LBB) by Froese
    et al. (2018) has been added to the package.
      - Improved implementation of compilation of length-frequency data
        allowing for faster compilation of lfq data with lfqCreate and
        lfqModify (with argument bin_size) and allowing compilation of
        large data sets
      - New possibilities to easily modify length-frequency data objects
        by means of "lfqModify", including aggregating catch matrix per
        year, per quarter, or per month, subsetting lfq data with range
        of length classes or sampling dates

Documentation

  - A new vignette "LBBmanual" with the introduction and demonstration
    of LBB within TropFishR has been added.

Bug fixes

  - Seasonal growth parameters are now added correctly to the lfq object
    in lfqModify

                 Changes in version 1.2.1 (2018-01-08)                  

Documentation

  - A new vignette has been added to the package. The vignette
    "ELEFANTutorial" outlines all ELEFAN functions available in
    TropFishR in detail.

Bug fixes

  - The ELEFAN functions did not overwrite any element of the lfq object
    but instead concatinated parameters onto the object. This can have
    unintended side effects, e.g. if several growth parameters are saved
    in the lfq object and the plotting functions are called. Now, the
    application of ELEFAN functions overwrites any growth parameters in
    the lfq object.

                  Changes in version 1.2 (2017-12-13)                   

New features

  - Due to more efficient matrix computations ELEFAN is 2-4 times faster
    as before
      - missing seed values were added in ELEFAN_GA()
      - plot.lfq() allows plotting relative frequencies, this is in
        particular useful in cases where one sampling time has a large
        number of samples
      - plot.catchCurve() allows plotting results according to length
        rather than relative age. This can be done with the argument
        xaxis.
      - lfq plot can be used to plot 2 different lfq data sets; this
        allows to visually compare the two data sets
      - lfqModfiy() allows combining two different lfq data sets. This
        might be interesting when different fleets are investigated
        separately
      - possible to define and plot multiple regression lines in the
        catch curve analysis
      - length converted catch curve can account for the seasonalized
        VBGF

User-visible changes

  - better control over graphical devices with par(), when par() defined
    the default settings are not used
      - growth parameters can now be added to lfq lists as "par"
        elements, this is convenient as it is in line with the results
        of the ELEFAN methods

Documentation

  - new vignette with a short description of lfq data and how to import
    lfq data into R
      - updated tutorial vignette
      - more informative error and warning messages for many functions
      - document with news and changes about package version was added

Bug fixes

  - crash report of ELEFAN_GA with interactive sessions (Rstudio) fixed
    and more stable on windows
      - plot.catchCurve() was not displaying the regression line, but a
        straight line from the first to last point of the chosen
        interval
      - restructering of lfq data was not in line with FiSAT
        implementation
      - fixing bug in handling of leap years
      - when merging lfq data with another list using c() one has to
        reassign the class "lfq" to the merged object, this has been
        added in the tutorial
      - beep sound was causing R crashes on windows computers and was
        therefore removed