pvaluefunctions

P-value functions

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Accompanying paper

We published an accompanying paper to illustrate the use of p-value functions:

Infanger D, Schmidt-Trucksäss A. (2019): P value functions: An underused method to present research results and to promote quantitative reasoning. Statistics in Medicine, 1-9. doi: 10.1002/sim.8293.

Recreation of the figures in the paper

The code and instructions to reproduce all graphics in our paper can be found in the following GitHub repository: https://github.com/DInfanger/pvalue_functions

Overview

This is the repository for the R-package pvaluefunctions. The package contains R functions to create graphics of p-value functions, confidence distributions, confidence densities, or the Surprisal value (S-value) (Greenland 2019).

Installation

You can install the package directly from CRAN by typing install.packages("pvaluefunctions"). After installation, load it in R using library(pvaluefunctions).

Dependencies

The function depends on the following R packages, which need to be installed beforehand:

Use the command install.packages(c("ggplot2", "scales", "zipfR")) in R to install those packages.

Important information!

The newest version of ggplot2 (3.1.1) has a bug in sec_axis that will lead to the secondary y-axis being labelled wrongly.

It is therefore recommended that you install the developmental version of ggplot2 until the bug has been fixed. You can install the developmental version using the following command (after installing the devtools package): devtools::install_github("tidyverse/ggplot2")

To see what version of ggplot2 has been used to create the plots on this page, see the Session info.

This warning will be deleted upon the release of a new version of ggplot2 that fixes the bug.

Examples

For more examples and code, see the vignette.

References

Bender R, Berg G, Zeeb H. (2005): Tutorial: using confidence curves in medical research. Biom J. 47(2): 237-47.

Fraser D. A. S. (2019): The p-value function and statistical inference. Am Stat, 73:sup1, 135-147.

Greenland S (2019): Valid P-Values Behave Exactly as They Should: Some Misleading Criticisms of P-Values and Their Resolution with S-Values. Am Stat, 73sup1, 106-114.

Infanger D, Schmidt-Trucksäss A. (2019): P value functions: An underused method to present research results and to promote quantitative reasoning. Stat Med, 1-9. doi: 10.1002/sim.8293.

Poole C. (1987a): Beyond the confidence interval. Am J Public Health. 77(2): 195-9.

Poole C. (1987b) Confidence intervals exclude nothing. Am J Public Health. 77(4): 492-3.

Rosenthal R, Rubin DB. (1994): The counternull value of an effect size: A new statistic. Psychol Sci. 5(6): 329-34.

Schweder T, Hjort NL. (2016): Confidence, likelihood, probability: statistical inference with confidence distributions. New York, NY: Cambridge University Press.

Xie M, Singh K, Strawderman WE. (2011): Confidence Distributions and a Unifying Framework for Meta-Analysis. J Am Stat Assoc 106(493): 320-33. doi: 10.1198/jasa.2011.tm09803.

Xie Mg, Singh K. (2013): Confidence distribution, the frequentist distribution estimator of a parameter: A review. Internat Statist Rev. 81(1): 3-39.

Contact

Denis Infanger

Session info

#> R version 3.6.1 (2019-07-05)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 10 x64 (build 17134)
#> 
#> Matrix products: default
#> 
#> locale:
#> [1] LC_COLLATE=German_Switzerland.1252  LC_CTYPE=German_Switzerland.1252   
#> [3] LC_MONETARY=German_Switzerland.1252 LC_NUMERIC=C                       
#> [5] LC_TIME=German_Switzerland.1252    
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] pvaluefunctions_1.4.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_1.0.2         pillar_1.4.2       compiler_3.6.1    
#>  [4] prettyunits_1.0.2  remotes_2.1.0      tools_3.6.1       
#>  [7] testthat_2.2.1     digest_0.6.20      pkgbuild_1.0.3    
#> [10] pkgload_1.0.2      tibble_2.1.3       gtable_0.3.0      
#> [13] evaluate_0.14      memoise_1.1.0      pkgconfig_2.0.2   
#> [16] rlang_0.4.0        cli_1.1.0          curl_4.0          
#> [19] yaml_2.2.0         xfun_0.8           dplyr_0.8.3       
#> [22] withr_2.1.2        stringr_1.4.0      knitr_1.23        
#> [25] desc_1.2.0         fs_1.3.1           devtools_2.1.0    
#> [28] tidyselect_0.2.5   rprojroot_1.3-2    grid_3.6.1        
#> [31] glue_1.3.1         R6_2.4.0           processx_3.4.1    
#> [34] rmarkdown_1.14     sessioninfo_1.1.1  purrr_0.3.2       
#> [37] callr_3.3.1        ggplot2_3.2.0.9000 magrittr_1.5      
#> [40] scales_1.0.0       backports_1.1.4    ps_1.3.0          
#> [43] htmltools_0.3.6    usethis_1.5.1      assertthat_0.2.1  
#> [46] colorspace_1.4-1   stringi_1.4.3      lazyeval_0.2.2    
#> [49] munsell_0.5.0      crayon_1.3.4

License

License: GPL v3