version 1.5.0

cran · Nov 29, 2019 · 2db7578 · 2db7578
1 parent 33dfa71
commit 2db7578
Show file tree

Hide file tree

Showing 11 changed files with 477 additions and 429 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,22 +2,22 @@ Package: pvaluefunctions
 Type: Package
 Title: Creates and Plots P-Value Functions, S-Value Functions,
         Confidence Distributions and Confidence Densities
-Version: 1.4.0
+Version: 1.5.0
 Authors@R: person("Denis", "Infanger", email = "denis.infanger@unibas.ch", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9028-7110"))
 Maintainer: Denis Infanger <denis.infanger@unibas.ch>
 Description: Contains functions to compute and plot confidence distributions, confidence densities, p-value functions and s-value (surprisal) functions for several commonly used estimates. Instead of just calculating one p-value and one confidence interval, p-value functions display p-values and confidence intervals for many levels thereby allowing to gauge the compatibility of several parameter values with the data. These methods are discussed by Infanger D, Schmidt-Trucksäss A. (2019) <doi:10.1002/sim.8293>; Poole C. (1987) <doi:10.2105/AJPH.77.2.195>; Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>; Bender R, Berg G, Zeeb H. (2005) <doi:10.1002/bimj.200410104> ; Singh K, Xie M, Strawderman WE. (2007) <doi:10.1214/074921707000000102>; Rothman KJ, Greenland S, Lash TL. (2008, ISBN:9781451190052); Amrhein V, Trafimow D, Greenland S. (2019) <doi:10.1080/00031305.2018.1543137>; and Greenland S. (2019) <doi:10.1080/00031305.2018.1529625>.
 Depends: R (>= 3.1.0)
-Imports: ggplot2 (>= 3.1.1), scales (>= 1.0.0), zipfR (>= 0.6-10),
+Imports: ggplot2 (>= 3.2.1), scales (>= 1.1.0), zipfR (>= 0.6-66),
         stats
 Suggests: knitr, rmarkdown, devtools
 License: GPL-3
 URL: https://github.com/DInfanger/pvaluefunctions
 VignetteBuilder: knitr
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.1
 NeedsCompilation: no
-Packaged: 2019-07-29 10:11:41 UTC; denis
+Packaged: 2019-11-28 16:18:24 UTC; denis
 Author: Denis Infanger [aut, cre] (<https://orcid.org/0000-0001-9028-7110>)
 Repository: CRAN
-Date/Publication: 2019-07-29 10:30:02 UTC
+Date/Publication: 2019-11-29 19:30:02 UTC
diff --git a/MD5 b/MD5
@@ -1,16 +1,16 @@
-8bac1519d3b70342b71c6da01b161c5a *DESCRIPTION
-f4e77ba3810347894cacc5e5b68da3c0 *NAMESPACE
-432f7c368403a84d8c7eb4cda3c5f4e7 *NEWS.md
-857de638980826a182058eaeb581a529 *R/confidence_distributions.R
-2e00cc6973ec02d032d81f028bf97549 *README.md
+de48818d4f845bdb6bd4aa34b465ede4 *DESCRIPTION
+3409f9c443502b59ae0ad5470176af68 *NAMESPACE
+2c6b403d7ba9c1f151d0d3868912c087 *NEWS.md
+50c765ca454c7ec1275c12a0b7e3128d *R/confidence_distributions.R
+d5a552f9cec9e869a4ada9c7837c653b *README.md
 74eefc761dce35d2d65c8015f7ca0786 *build/vignette.rds
-0f8cd72defecc9bfe64f4f2c90ce1d8f *inst/doc/pvaluefun.R
-e8ca070218f0d915bc92e46cef44a1d2 *inst/doc/pvaluefun.Rmd
-5c84400fcda421accac14043de11e382 *inst/doc/pvaluefun.html
-d07ff02d3da2633b39a22cecc9f899b2 *man/conf_dist.Rd
+154b5bc5c2f4cdf2e7cecdd2553640a2 *inst/doc/pvaluefun.R
+324f4e4961c5f7e5462d3856505411a9 *inst/doc/pvaluefun.Rmd
+c031fdd00e77b223629be8b2515e1862 *inst/doc/pvaluefun.html
+e6633ca7aae7c9fad21342643bfc575d *man/conf_dist.Rd
 980cb17e2b55086ed935ceb30719966c *man/figures/README-benderfig1-1.png
 0f6a5b495f94aac63300fe76cf7ebc60 *man/figures/README-ttest_pval-1.png
 45b1828f89a32887dff20ed1cab87bdf *man/figures/README-ttest_sval-1.png
 70f0280813823dfe841f21813465f121 *man/figures/logo.svg
 f8ad09a83a4bae484432532e94a6c95d *man/figures/logo2.svg
-e8ca070218f0d915bc92e46cef44a1d2 *vignettes/pvaluefun.Rmd
+324f4e4961c5f7e5462d3856505411a9 *vignettes/pvaluefun.Rmd
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,4 +1,4 @@
-# Generated by roxygen2: do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 export(conf_dist)
 import(ggplot2)

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,13 @@
 ## NEWS and changes for the pvaluefunctions package
 
+
+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
 -------------
 

diff --git a/R/confidence_distributions.R b/R/confidence_distributions.R
@@ -41,13 +41,14 @@ if (getRversion() >= "2.15.1") {
 #' @param ylab_sec (optional) String indicating the title for the secondary (right) y-axis.
 #' @param inverted Logical. Indicating the orientation of the y-axis for the \emph{P}-value function (\code{p_val}), S-value function (\code{s_val}) and the confidence distribution (\code{cdf}). By default (i.e. \code{inverted = FALSE}) small \emph{P}-values are plotted at the bottom and large ones at the top so that the cusp of the \emph{P}-value function is a the top. By setting \code{inverted = TRUE}, the y-axis is inverted. Ignored for confidence densities.
 #' @param x_scale String indicating the scaling of the x-axis. The default is to scale the x-axis logarithmically if the transformation specified in \code{trans} is "exp" (exponential) and linearly otherwise. The option \code{linear} (can be abbreviated) forces a linear scaling and the option \code{logarithm} (can be abbreviated) forces a logarithmic scaling, regardless what has been specified in \code{trans}.
-#'
-#' @return \code{conf_dist} returns four data frames and a ggplot2-plot object: \code{res_frame} (contains parameter values, \emph{p}-values (one- and two-sided), s-values, confidence distribution and density, variable names and type of hypothesis), \code{conf_frame} (contains the specified confidence level(s) and the corresponding lower and upper limits as well as the corresponding variable name), \code{counternull_frame} (contains the counternull and the corresponding null values), \code{point_est} (contains the mean, median and mode point estimates) and \code{plot} (a ggplot2-plot object).
+#' @param plot Logical. Should a plot be created (\code{TRUE}, the default) or not (\code{FALSE}). \code{FALSE} can be useful if users want to create their own plots using the returned data from the function. If \code{FALSE}, no ggplot2 object is returned.
+
+#' @return \code{conf_dist} returns four data frames and if \code{plot = TRUE} was specified, a ggplot2-plot object: \code{res_frame} (contains parameter values (e.g. mean differences, odds ratios etc.), \emph{p}-values (one- and two-sided), s-values, confidence distributions and densities, variable names and type of hypothesis), \code{conf_frame} (contains the specified confidence level(s) and the corresponding lower and upper limits as well as the corresponding variable name), \code{counternull_frame} (contains the counternull and the corresponding null values), \code{point_est} (contains the mean, median and mode point estimates) and if \code{plot = TRUE} was specified, \code{plot} (a ggplot2 object).
 #' @references Bender R, Berg G, Zeeb H. Tutorial: using confidence curves in medical research. \emph{Biom J.} 2005;47(2):237-247.
 #'
 #' Bonett DG, Wright TA. Sample size requirements for estimating Pearson, Kendall and Spearman correlations. \emph{Psychometrika.} 2000;65(1):23-28.
 #'
-#' Infanger D, Schmidt-Trucksäss A. \emph{P} value functions: An underused method to present research results and to promote quantitative reasoning. \emph{Stat Med.} 2019;1-9.
+#' Infanger D, Schmidt-Trucksäss A. \emph{P} value functions: An underused method to present research results and to promote quantitative reasoning. \emph{Stat Med.} 2019;38:4189-4197.
 #'
 #' Newcombe RG. Interval estimation for the difference between independent proportions: comparison of eleven methods. \emph{Stat Med.} 1998;17:873-890.
 #'
@@ -94,6 +95,7 @@ if (getRversion() >= "2.15.1") {
 #'   , ylab_sec = NULL
 #'   , inverted = FALSE
 #'   , x_scale = "default"
+#'   , plot = TRUE
 #' )
 #'
 #' #======================================================================================
@@ -125,6 +127,7 @@ if (getRversion() >= "2.15.1") {
 #'   , ylab_sec = NULL
 #'   , inverted = FALSE
 #'   , x_scale = "default"
+#'   , plot = TRUE
 #' )
 #'
 #' #=======================================================================================
@@ -154,6 +157,7 @@ if (getRversion() >= "2.15.1") {
 #'   , ylab_sec = NULL
 #'   , inverted = TRUE
 #'   , x_scale = "default"
+#'   , plot = TRUE
 #' )
 #'
 #' #======================================================================================
@@ -181,6 +185,7 @@ if (getRversion() >= "2.15.1") {
 #'   , ylab_sec = NULL
 #'   , inverted = FALSE
 #'   , x_scale = "default"
+#'   , plot = TRUE
 #' )
 #'
 #' #======================================================================================
@@ -228,6 +233,7 @@ if (getRversion() >= "2.15.1") {
 #'   , ylab_sec = NULL
 #'   , inverted = FALSE
 #'   , x_scale = "default"
+#'   , plot = TRUE
 #' )
 #'
 #' #========================================================================================
@@ -266,6 +272,7 @@ if (getRversion() >= "2.15.1") {
 #'   , inverted = TRUE
 #'   , title = "Figure 1 in Bender et al. (2005)"
 #'   , x_scale = "default"
+#'   , plot = TRUE
 #' )
 #'
 #' @seealso \code{\link[concurve]{ggconcurve}}
@@ -303,6 +310,7 @@ conf_dist <- function(
   , ylab_sec = NULL
   , inverted = FALSE
   , x_scale = c("default", "linear", "logarithm")
+  , plot = TRUE
 ) {
 
   #-----------------------------------------------------------------------------
@@ -851,6 +859,8 @@ conf_dist <- function(
   # Plot using ggplot2
   #-----------------------------------------------------------------------------
 
+
+
   # Create custom y-axis scale (mixed linear and logarithmic)
 
   # Transform cutoff for log-y-axis if applicable
@@ -1314,9 +1324,11 @@ conf_dist <- function(
     p <- p + ggtitle(title)
   }
 
-  res$plot <- p
-
-  suppressWarnings(print(p))
+  # Only print and return the plot object if requested
+  if (isTRUE(plot)) {
+    res$plot <- p
+    suppressWarnings(print(p))
+  }
 
   return(res)
 

diff --git a/README.md b/README.md
@@ -9,7 +9,6 @@ pvaluefunctions
       - [Overview](#overview)
       - [Installation](#installation)
       - [Dependencies](#dependencies)
-          - [Important information\!](#important-information)
       - [Examples](#examples)
       - [References](#references)
       - [Contact](#contact)
@@ -33,7 +32,8 @@ 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.
+reasoning. *Statistics in Medicine.* **38**: 4189-4197. doi:
+10.1002/sim.8293.
 
 ### Recreation of the figures in the paper
 
@@ -62,31 +62,22 @@ using `library(pvaluefunctions)`.
 The function depends on the following R packages, which need to be
 installed beforehand:
 
-  - ggplot2
+  - ggplot2 (at least version 3.2.1)
   - scales
   - zipfR
 
 Use the command `install.packages(c("ggplot2", "scales", "zipfR"))` in R
 to install those packages.
 
-### Important information\!
+<!-- ### Important information! -->
 
-The newest version of [ggplot2
-(3.1.1)](https://CRAN.R-project.org/package=ggplot2) has a
-[bug](https://github.com/tidyverse/ggplot2/issues/2978) in `sec_axis`
-that will lead to the secondary y-axis being labelled wrongly.
+<!-- The newest version of [ggplot2 (3.1.1)](https://CRAN.R-project.org/package=ggplot2) has a [bug](https://github.com/tidyverse/ggplot2/issues/2978) 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`](https://CRAN.R-project.org/package=devtools) package):
-`devtools::install_github("tidyverse/ggplot2")`
+<!-- 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`](https://CRAN.R-project.org/package=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](#session-info).
+<!-- 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.
+<!-- This warning will be deleted upon the release of a new version of ggplot2 that fixes the bug. -->
 
 ## Examples
 
@@ -113,7 +104,7 @@ Misleading Criticisms of *P*-Values and Their Resolution with
 
 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.
+reasoning. *Stat Med,* 38, 4189-4197. doi: 10.1002/sim.8293.
 
 Poole C. (1987a): Beyond the confidence interval. *Am J Public Health.*
 77(2): 195-9.
@@ -157,26 +148,26 @@ distribution estimator of a parameter: A review. *Internat Statist Rev.*
     #> [1] stats     graphics  grDevices utils     datasets  methods   base     
     #> 
     #> other attached packages:
-    #> [1] pvaluefunctions_1.4.0
+    #> [1] pvaluefunctions_1.5.0
     #> 
     #> 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
+    #>  [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_1.0.4   
+    #> [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_1.24       
+    #> [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_3.2.1     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
 

diff --git a/inst/doc/pvaluefun.R b/inst/doc/pvaluefun.R
@@ -1,4 +1,4 @@
-## ----setup, include = FALSE, echo = FALSE--------------------------------
+## ----setup, include = FALSE, echo = FALSE-------------------------------------
 knitr::opts_chunk$set(
   collapse = TRUE
   , comment = "#>"
@@ -45,8 +45,10 @@ res <- conf_dist(
   , plot_p_limit = 1 - 0.999
   , plot_counternull = TRUE
   , x_scale = "line"
+  , plot = TRUE
 )
 
+
 ## ----linreg_single_pval, message = FALSE, warning = FALSE, fig.width = 9, fig.height = 7, out.width = "80%", fig.align='center', dev = "png", dev.args = list(type = "cairo-png"), dpi = 200----
 #-----------------------------------------------------------------------------
 # Model
@@ -79,6 +81,7 @@ res <- conf_dist(
   , together = FALSE
   , plot_p_limit = 1 - 0.999
   , plot_counternull = FALSE
+  , plot = TRUE
 )
 
 ## ----linreg_single_cdf, message = FALSE, warning = FALSE, fig.width = 9, fig.height = 7, out.width = "80%", fig.align='center', dev = "png", dev.args = list(type = "cairo-png"), dpi = 200----
@@ -408,6 +411,6 @@ res <- conf_dist(
 rm(rse_fun, rse_fun_inv)
 
 
-## ----session_info, include=TRUE, echo=FALSE------------------------------
+## ----session_info, include=TRUE, echo=FALSE-----------------------------------
 sessionInfo()