riskyr 0.2.0.9008+ Unreleased

Log of changes since last release:

Major changes

  • none so far

Minor changes

Changes to existing visualization functions

  • 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.

Other changes

  • 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]: Utility function to verify a range of 2 probability values (to check new arguments of plot_curve and plot_plane).

Micro changes

New functionality

  • 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.

General changes

  • 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).

  • 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

  • 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).

riskyr 0.2.0 2019-01-03

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

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.

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).

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).

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 2018-02-19