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 [2021-03]:

  • 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 [2021-12]:

  • 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 [2022-08].

Minor changes

• Add main and sub arguments to all plots (and deprecate the previous title_lbl argument) [2022-08].

• 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 [2022-08].

• Update URLs in README.md and all vignettes to https://riskyr.org/ [2021-03].

• Increase options and robustness for labeling frequencies and probabilities in plots [2021-03].

• Reduce widths of freq boxes in plot_prism() to reduce overlaps [2021-03].

• Rename labels in txt_TF to avoid confusion, as "True condition" (i.e., X) was FALSE (now "absent") for "True negatives" (TN/cr cases) [2021-03].

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

riskyr 0.3.0

riskyr 0.3.0

riskyr 0.3.0 is published on CRAN on March 23, 2021.

Log of changes since last release:

Major changes

• Added plot_fnet() for plotting frequency nets (Binder et al., 2020) [2020-12].

Minor changes

Changes to existing visualization functions

• Changed default setting of mar_notes in all plotting functions [2021-01]:
  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() [2019-01]:
  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() [2019-01]:
  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() [2019-01]:
  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() [2019-01]:
  Using the new p_lwd and p_scale arguments allows scaling the widths of probability links by current probability values.

Data and functions

• data [2019-07]:
  Removed data files df_scenarios.RData and df_scenarios.csv, as they were redundant to df_scenarios.rda (loaded from \data).

• make_cond_lbl() [2019-01]:
  The condition label now allows for NA or vectors of several values (for prev, sens, and spec).

• is_prob_range() [2019-01]:
  Add utility 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() [2021-02].

• Add color palettes [2019-01]:

  • 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 [2019-01]:
  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

• Added 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() [2019-01]:
  Enforce 2 different symbol types for icon arrays with a binary perspective (by = cd or dc or ac).

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riskyr 0.2.0

riskyr 0.2.0

riskyr 0.2.0 was ready to be released on December 20, 2018, and published on CRAN on January 03, 2019.

Log of changes since last release:

Major changes

Additional resources

• New riskyrApp version [2018-12]:
  To use selected riskyr functions without the need for coding
  an updated version of riskyrApp is available
  at https://github.com/hneth/riskyrApp (R Shiny code) and
  at http://riskyr.org (interactive online version).

• Using pkgdown [2018-12]:
  Provide package documentation online at https://hneth.github.io/riskyr (latest release version) and https://hneth.github.io/riskyr/dev/ (current development version).

Visualization functions

• Retiring obsolete functions [2018-12]:
  The 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 [2018-11]:
  Show a scenario as double frequency tree (by 3 x 2 perspectives) or a frequency tree (in 3 perspectives) with many additional options; replaces the older plot_fnet and plot_tree functions (and removes dependency on the diagram package).

• New plot_area function [2018-10]:
  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 [2018-10]:
  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 [2018-08]:
  Show scenario frequencies as vertical bars (in various configurations).

Under the hood

• Create plot_util.R collection of graphical utility functions [2018-08]:
  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).

• Updated riskyr function [2018-03]:
  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

• Improved plot_icons function [2018-12]:
  Show icons separated into 2 subsets by 3 perspectives (condition, decision, accuracy), using the same by argument as the other plotting functions.

• plot_curve and plot_plane functions [2018-11]:
  Update variable names (to snake_case) and add arguments (e.g., col_pal, lbl_txt mar_notes, etc.) for consistency with newer plotting functions.

• scale argument [2018-10]:
  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.

• plot_fnet [2018-02]:
  Change argument box.cex to cex.lbl to ensure consistency with plot_curves and plot_plane (and use it to scale arrow labels accordingly). Added warning when using deprecated argument.

• plot_mosaic [2018-02]:
  Change Boolean vsplit argument to by = "cd" vs. by = "dc" to ensure consistency with plot_fnet and plot_tree. Added warning when using deprecated argument.

• mar_notes and plot_mar [2018-09]:
  Use consistent plot margins and options for showing margin notes for all plots.

Other changes

• read_popu [2018-11]:
  Read a data frame popu and interpret is as a riskyr scenario, allows creating scenarios from raw data.

• comp_accu.R [2018-08]:
  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).

Default objects (lists and vectors)

• pal and freq [2018-12]:
  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).

• freq [2018-07]:
  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.

• prob [2018-09]:
  Include accuracy metrics in probabilities (in prob and summary functions).

• pal and txt [2018-10]:
  Add multiple color palettes and text labeling schemes (see ?pal and ?txt for details).

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 [2018-03]:
  Bug fix to also swap symbols in legend when the symbol order is changed manually.

• txt_def [2018-02]:
  Simplify some default text labels (e.g., for current population, condition, and decision).

• .onAttach [2018-02]:
  Cast dice to display probabilistic (i.e., risk-related) start-up messages.

riskyr 0.1.0

• Initial release on CRAN: https://CRAN.R-project.org/package=riskyr [2018-02-19]

riskyr initial release

riskyr initial release

A toolbox for rendering risk literacy more transparent

Risk-related information (like the prevalence of conditions and the sensitivity and specificity of decisions or diagnostic tests) can be expressed in terms of probabilities or frequencies. By providing a toolbox of methods and metrics, riskyr computes, translates, and displays risk-related information in a variety of ways. Offering multiple complementary perspectives on the interplay between key parameters renders teaching and training of risk literacy more transparent.