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riskyr 0.4.0.9016

riskyr

The current development version (0.4.0.9001+) is available at https://github.com/hneth/riskyr/.

Changes since last release:

Major changes

  • none yet

Minor changes

  • New hexagon version of logo.

Micro changes

  • Package maintenance:
    • Add GitHub action (R-CMD-check standard)
    • Update README and online documentation

riskyr 0.4.0

riskyr 0.4.0 was released on CRAN on August 15, 2022.

Changes since last release:

Major changes

  • Enable sampling when computing freq from prob (i.e., by description, given N and 3 essential probabilities) [2021-03]:

    • add a sample argument to comp_freq(), comp_freq_prob(), and riskyr();
    • add a sample argument to 6 key plots:
      plot_area(), plot_bar(), plot_fnet(), plot_icons(), plot_prism(), and plot_tab().

  • Allow conversions/translations between data and descriptions:

    • write_popu() creates population data from a description (a riskyr scenario);
    • read_popu() creates a description (a riskyr scenario) from population data.

  • Add a function for plotting cumulative risk curves:

    • plot_crisk() plots curves and auxiliary information for visualizing cumulative risks and risk increments;
    • pal_crisk provides a corresponding color palette (as a named vector).
  • Add FFTrees_riskyr() to convert FFTrees objects into corresponding riskyr objects.

Minor changes

  • Add main and sub arguments to all plots (and deprecate the previous title_lbl argument).
  • Add is_matrix() to verify a 2x2 matrix (as a 2x2 numeric contingency table).
  • Add is_integer() to verify integer values.

Micro changes

  • Fix bug in plot_bar() that caused incorrect bar labels.
  • Update URLs in README.md and all vignettes to https://riskyr.org/.
  • Increase options and robustness for labeling frequencies and probabilities in plots.
  • Reduce widths of freq boxes in plot_prism() to reduce overlaps.
  • Rename labels in txt_TF to avoid confusion, as "True condition" (i.e., X) was FALSE (now "absent") for "True negatives" (TN/cr cases).

riskyr 0.3.0

riskyr 0.3.0 was released on CRAN on March\ 23, 2021.

Changes since last release:

Major changes

Minor changes

Changes to existing visualization functions

  • Change default setting of mar_notes in all plotting functions: Using mar_notes = FALSE as those details are not needed and can be distracting in visualizations.

  • Change default arguments for plot_area() and plot_tab():
    Change default settings from f_lbl_hd = "abb" to f_lbl_hd = "nam" (as this makes more sense for riskyrApp).

  • New options for plot_curve():
    Plotting probability curves as a function of prevalence does not require any specific prevalence value. Thus, setting the prev argument to either NA or to a vector of several probabilities is now supported. Setting the new prev_range argument to a range within c(0, 1) allows zooming into more specific ranges of prev values (on x-axis).

  • New options for plot_plane():
    Plotting a probability plane as a function of sensitivity and specificity does not require specifying all values. Thus, setting the sens and spec arguments to either NA or to a vector of several probabilities is now supported. Setting the new sens_range and spec_range arguments to ranges within c(0, 1) allows zooming into more specific ranges of sens values (on x-axis) and spec values (on y-axis).

  • New options for plot_prism():
    Use the new p_lwd and p_scale arguments to allow scaling the widths of probability links by current probability values.

Data and functions

  • In data: Remove data files df_scenarios.RData and df_scenarios.csv, as they were redundant to df_scenarios.rda (loaded from \data).

  • Improve make_cond_lbl() to allow for NA or vectors of several values (for prev, sens, and spec).

  • Add is_prob_range() function to verify a range of two probability values (to check new arguments of plot_curve() and plot_plane()).

Micro changes

Colors

  • Using colors of pal for fill colors of symbols in plot_icon().

  • Add more color palettes:

    • Add pal_bwp (a strict b+w color palette suited for printing purposes) and corresponding special cases to major plotting functions.
    • Add pal_unikn (based on color definitions of the unikn package).

  • Changes to color palettes:

    • Add a background color pal[["bg"]] to all palettes and plots (to preempt different system defaults).
    • Adopt pal_mod -- rather than pal_mbw -- as default color scheme pal (to highlight cond_true and dec_pos cases in default plots).

Details

  • Add reference to article on theoretical background (Neth et al., 2021).

  • Bug fix in plot_prism(): Allow plotting simple trees for nchar(by) == 2.

  • Bug fix in plot_icons(): Enforced 2 different symbol types for icon arrays with a binary perspective (by = cd or dc or ac).

riskyr 0.2.0

riskyr 0.2.0 was released on CRAN on January 03, 2019.

Changes since last release:

Major changes

Additional resources

Visualization functions

  • Retiring obsolete functions:
    The plotting functions plot_fnet() and plot_tree() are replaced by plot_prism(), and plot_mosaic() is replaced by plot_area(). This improves functionality (e.g., by providing more consistent options across different plotting functions) and removes dependencies on external packages.

  • New plot_prism() function:
    Show a scenario as double frequency tree (by 3 x 2 perspectives) or a frequency tree (in 3 perspectives) with many additional options; combines and replaces the older plot_fnet() and plot_tree() functions (and removes dependency on the diagram package).

  • New plot_area() function:
    Show a scenario as a mosaic plot of relative proportions (in 3 x 2 x 2 possible versions, with many additional options); replaces the older plot_mosaic() function (and removes dependencies on the grid and vcd packages).

  • New plot_tab() function:
    Show a scenario as contingency table of frequencies (with row and column sums, and options for showing probabilities); a variant of plot_area() that does not scale area sizes.

  • New plot_bar() function:
    Show scenario frequencies as vertical bars (in various configurations).

Under the hood

  • Create plot_util.R collection of graphical utility functions:
    Define a new box object type and various functions for plotting, labeling, and linking them in graphs (to remove dependencies on and limitations imposed by other packages).

  • Update riskyr() function:
    As an alternative to providing 3 essential frequencies, it is now possible to define a scenario from 4 essential frequencies (and check for consistency with given probabilities).

Minor changes

Changes to existing visualization functions

  • Improve plot_icons() function:
    Show icons separated into 2 subsets by 3 perspectives (condition, decision, accuracy), using the same by argument as the other plotting functions.

  • Improve plot_curve() and plot_plane() functions:
    Update variable names (to snake_case) and add arguments (e.g., col_pal, lbl_txt mar_notes, etc.) for consistency with newer plotting functions.

  • Add scale argument:
    The new plotting functions feature a scale argument that allows scaling the size or areas of boxes either by (exact) probability or by (possibly rounded) frequency. When using scale = "f", the probabilities shown are also re-computed from (possibly rounded) frequencies.

  • Improve plot_fnet() function:
    Change argument box.cex to cex.lbl to ensure consistency with plot_curves() and plot_plane() (and use it to scale arrow labels accordingly). Add a warning when using deprecated argument.

  • Improve plot_mosaic() function:
    Change Boolean vsplit argument to by = "cd" vs. by = "dc" to ensure consistency with plot_fnet() and plot_tree(). Add a warning when using deprecated argument.

  • Improve mar_notes and plot_mar arguments:
    Use consistent plot margins and options for showing margin notes for all plots.

Default objects (lists and vectors)

  • Improve pal and freq arguments:
    Use more consistent color and frequency names (e.g., cond_true, dec_pos, and dec_cor are now names of frequencies and the colors corresponding to these frequencies).

  • Improve freq object:
    Add a 3rd perspective (by accuracy or by correspondence of decision to condition) and corresponding frequency pair of dec.cor and dec.err (i.e., hi + cr vs. mi + fa as the diagonal of 4 SDT cases). This increases the number of frequencies in freq from 9 to 11. Also added corresponding labels in init_txt.R and colors in init_pal.R.

  • Improve prob object:
    Include accuracy metrics in probabilities (in prob and summary functions).

  • Improve pal and txt objects:
    Add multiple color palettes and text labeling schemes (see ?pal and ?txt for details).

Other changes

  • Improve read_popu() function:
    Read a data frame popu and interpret is as a riskyr scenario, allows creating scenarios from raw data.

  • Add comp_accu.R file:
    Compute exact accuracy values (not approximations, when using comp_accu_freq on rounded freq values) by using the new function comp_accu_prob() to compute the list accu from probabilities. Signal rounding when showing accuracy based on rounded frequencies in plots (when show.accu == TRUE and round == TRUE).

Micro changes

General changes

  • More consistent argument and variable names (using snake_case).

  • Many additions and corrections in documentation, examples, and vignettes.

Details

  • plot_icons(): Bug fix to also swap symbols in legend when the symbol order is changed manually.

  • txt_def: Simplify some default text labels (e.g., for current population, condition, and decision).

  • .onAttach: Cast dice to display probabilistic (i.e., risk-related) start-up messages.

riskyr 0.1.0

riskyr 0.1.0 was released on CRAN on February 19, 2018.

References

To cite riskyr in derivations and publications please use:

  • Neth, H., Gaisbauer, F., Gradwohl, N., & Gaissmaier, W. (2022). riskyr: Rendering Risk Literacy more Transparent.
    Social Psychology and Decision Sciences, University of Konstanz, Germany. Computer software (R package version 0.4.0, Aug. 15, 2022). Retrieved from https://CRAN.R-project.org/package=riskyr.

The following article provides details on the conceptual and theoretical background:

  • Neth, H., Gradwohl, N., Streeb, D., Keim, D.A., & Gaissmaier, W. (2021). Perspectives on the 2x2 matrix: Solving semantically distinct problems based on a shared structure of binary contingencies.
    Frontiers in Psychology, 11, 567817. doi: 10.3389/fpsyg.2020.567817

[NEWS.md updated on 2024-02-16.]