NEWS and
changes for the pvaluefunctions package
1.6.2
- The calculations for Pearson’s correlation coefficient now use the
exact distribution described in a preprint by Gunnar Taraldsen (2020).
This makes the use of the gsl package necessary because the calculations
involve the Gaussian hypergeometric function (2F1). Warning: This can
make the calculations drastically longer if a high value of
n_values is used.
- The function
conf_dist now also calculates the
proportion of the AUCC that lies above any specified null values.
- Small changes in the help page for
conf_dist.
1.6.1
- Fixed a bug concerning the calculation of Newcombe’s Wilson score
interval with continuity correction for the difference of two
proportions.
- Removed the “cairo” device from pngs in the vignette.
1.6.0
- The returned data frame is now sorted for convenience; this is
purely cosmetic.
- Dependence on R increased to R version 3.5.0
- Added an option
same_color to specify whether curves
should be distinguished by colors or not if they are plotted together in
the same graph. Can be useful if there are many curves plotted
together.
- Added an option
plot_legend to specify whether a legend
should be drawn if multiple curves are plotted together and
distinguished by color (i.e. same_color = FALSE and
together = TRUE).
- Added an option
col to specify the color of the curves
if they are not to be distinguished by color
(i.e. same_color = FALSE).
- Areas under the confidence curves (AUCC) according to Berrar (2017)
are now calculated and returned. They offer a way to compare multiple
estimates with respect to their precision. The AUCC is calculated on the
untransformed scale using numerical integration (trapezoidal
integration) implemented in the
pracma package which is now
imported.
- Removed data link to external data (UCLA) in an example (odds
ratio). Certificates for this site apparently expired.
1.5.0
- Vignette, README and DESCRIPTION updated to reflect that the newest
version of ggplot2 (3.2.1) fixes the former bug with
sec_axis.
- Added an option
plot to conf_dist that
controls whether a plot is created or not. If users want to create their
own plots, they can set this option to FALSE and use the
returned data (res_frame) which is the basis for the plots
to create them.
1.4.0
- Added option
inverted which allows users to plot
p-value functions, s-value functions and confidence distributions with
the y-axis inverted.
- Added a new example showing a p-value function for an odds
ratio with an inverted y-axis (cf. Bender et al. 2005).
- The option
xlim is now strictly enforced: Any null
values that are outside of the specified x-axis-limits are not plotted
and a corresponding message is printed out as information.
- Added new option
x_scale to manually force the scaling
of the x-axis.
- Added two more examples in the vignette replicating Figure 1 and
Figure 2 from Bender et al. (2005).
- Various smaller bug fixes and improvements: Fixed some checks, fixed
plotting vertical lines for null values.
1.3.0
- NEWS file was converted to an .md file.
- Users can now provide a title for the plot (option
title).
- Users can now provide titles for the primary and secondary y-axis
(options
ylab and ylab_sec).
- Users can now specify the number of rows
nrow and
columns ncol to be used in facet_wrap
(ggplot2) when multiple estimates are plotted separately (option
together = FALSE).
- Changed some of the examples: Changed option
log_yaxis = TRUE to log_yaxis = FALSE.
- Code: Changed logical checks
x == TRUE and
x == FALSE to isTRUE(x) and to
isFALSE(x).
- Code: Checked and improved/fixed some of the initial
consistency/input checks that are performed at the beginning of the
function.
1.2.0
- Added option
plot_counternull to plot the counternull
value(s) on the graphics if applicable and possible.
- Effect sizes on the log-scale (e.g. Odds ratio, Hazard ratio,
Incidence rate ratio) are now plotted on a logarithmic x-axis so that
the p-value function is symmetric around the point estimate.
- The default is now to omit a logarithmic part of the y-axis.
- Warnings from ggplot2 are now suppressed during the function
call.
- Not interesting for practitioners: Source code for creating the
plots was cleaned up and more comments were added.
1.1.0
- Improved vignette with reduced figure size and several orthographic
errors fixed. Added a new example (difference between proportions)
- New estimate type implemented: Difference between two independent
proportions (
type = "propdiff") based on Wilson’s interval
(see Newcombe (1998) for details)
1.0.0