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.]
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