TropFishR 1.6.3 (2021-09-02)

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’.

TropFishR 1.6.2 (2020-01-27)

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

TropFishR 1.6.1

Bug fixes

  - The LBB functionality was removed from the package.

TropFishR 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

TropFishR 1.2.1

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.

TropFishR 1.2

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