NEWS.md

stressaddition (development version)

• Fixed a bug where the plotting functions printed NULL to the console.
• Changed maintainer e-mail address to ensure long-term maintainability.
• Internal improvements related to package testing.

stressaddition 3.0.1

• Added missing return values in documentation to comply with CRAN repository policy.
• Added a link to the paper in the description file.

stressaddition 3.0.0

Breaking changes

• Renamed all instances of "effect" to "survival".
• Renamed all instances of "ec" to "lc".
• Renamed predict_mixture(), which was a temporary development name, to multi_tox().
• The argument proportion_ca in the mixture model multi_tox() was renamed and its value reversed. It is now called sa_contribution and specifies the proportion of stress addition in the calculation of toxicant stress. To convert your code from the old version use this equation: sa_contribution = 1 - proportion_ca.
• Renamed stress_tox_sam to stress_tox_sa in the output of multi_tox().

Bugfixes

• Fixed a bug where plot_stress() with argument which = NULL would result in an error. Now it correctly draws the axes without data.
• Fixed some errors in the documentation and improved the examples.

New

• Exported function log10_ticks() for calculating tick mark labels and positions on a base 10 logarithmic axis.
• Added example data set multiple_stress for use with multi_tox().
• Various minor changes to prepare for CRAN submission.

stressaddition 2.7.0

• Fixed some spelling mistakes.
• predict_mixture() now also returns the various stresses.

stressaddition 2.6.0

• The curves data frame in the output of ecxsys() now contains a column with the concentrations which are used for the plot functions in this package. This is useful for generating a nicer concentration axis.
• Changes to ec():
  • Renamed response_value to effect in the output list.
  • response_level of 0 or 100 is now allowed. 0 returns the concentration 0 and 100 returns the concentration Inf. Previously this resulted in an error.
  • It is now possible to set the reference to a custom value, for example 100.

stressaddition 2.5.0

• Fixed unintended behaviour in plot_effect() and plot_stress() where supplying an empty vector caused the four standard curves to show. Now setting which to an empty vector or NULL shows just the axes. The default value is NA.
• Renamed the mixture_effect column in the predict_mixture output data frame to effect.
• Remove the restriction that the concentration vectors in predict_mixture() must be the same length. The longer length must be a multiple of the shorter length because the shorter vector gets recycled to the longer length.

stressaddition 2.4.0

• Improved plot_effect() and plot_stress(). You can now control whether the observed values (the points) should be plotted using the which argument.
• Renamed sys_tox_not_fitted and sys_tox_env_not_fitted to sys_tox_observed and sys_tox_env_observed in the output of ecxsys().

stressaddition 2.3.0

• predict_mixture() now accepts multiple values for the concentration of the second toxicant. Both concentration vectors must be the same length.
• predict_mixture() now returns a data frame with the concentrations and effects. Previously it was only a vector of effects.
• predict_mixture() received a new argument "effect_max" which scales the returned effect values.
• Renamed the arguments of predict_mixture() to use underscore letters a and b instad of 1 and 2. For example model_1 is now model_a.

stressaddition 2.2.1

• Improved documentation of predict_mixture() and included example of symmetry.

stressaddition 2.2.0

• ec() now raises an error if the curve does not cross the desired response level.
• ecxsys() gained a new argument curves_concentration_max which allows setting the maximum concentration of the predicted curves.

stressaddition 2.1.1

• Restore the default behaviour of plot_effect() to also show effect_tox and effect_tox_env.

stressaddition 2.1.0

• The functions plot_effect() and plot_stress() gained a which argument that controls which curves are plotted. Consequently, the show_LL5_model argument of plot_effect() was removed.
• Added arguments xlab and ylab to plot_stress.
• Added argument main to both plot functions.
• Changed some colors of the stress curves so they better match with the colors of related effect curves.
• Added predict_mixture() for the prediction of the effects of mixtures of two toxicants.
• Fixed documentation of ecxsys() and predict_ecxsys().

stressaddition 2.0.0

• Changed the order of arguments in ecxsys().
• Removed hormesis_index argument from ecxsys(). Use hormesis_concentration instead.
• New function predict_ecxsys() replaces fn() from the ecxsys() output.
• Renamed the arguments in ec().
• Made ec() more flexible. It now also accepts a data.frame with a concentration column and a column of response values.
• Added LL5 curves to the legend of plot_effect().
• Replaced every occurrence of "simple" in variable names with "LL5".
• Replaced every occurrence of "sys_stress" in variable names with "sys" because the extra "stress" was redundant.
• Renamed plot_system_stress() to plot_stress() because it is planned to plot more stresses with this function in a future update.
• Changed the order of the columns in the output of predict_ecxsys().
• Improved the internal structure of the package.
• Improved the tests.
• Improved the documentation.

stressaddition 1.11.1

• First public version.
• Added a NEWS.md file to track changes to the package.