riskyr 0.4.0 was released on CRAN on August 15, 2022.
Changes since last release:
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).
FFTrees_riskyr() to convert FFTrees
objects into corresponding riskyr objects [2022-08].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.
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 was released on CRAN on March 23, 2021.
Changes since last release:
plot_fnet() for plotting frequency nets
(Binder
et al., 2020) [2020-12].Change 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 [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()).
Using colors of pal for fill colors of symbols in
plot_icon() [2021-02].
Add more 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).
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() [2019-01]: Enforced 2
different symbol types for icon arrays with a binary perspective
(by = cd or dc or ac).
riskyr 0.2.0 was released on CRAN on January 03, 2019.
Changes since last release:
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 https://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).
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).
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).
Update 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).
Improve 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.
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).
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).
More consistent argument and variable names (using snake_case).
Many additions and corrections in documentation, examples, and vignettes.
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 was released on CRAN on February 19, 2018.
References
To cite riskyr in derivations and publications please use:
The following article provides details on the conceptual and theoretical background:
[NEWS.md updated on 2022-08-15 by hn.]