Merge pull request #3 from Zadchow/testing

version 2.1.0, double y-axis plotting for ggconcurve( )
zadrafi · Sep 19, 2019 · 11fd615 · 11fd615
2 parents 8d3502a + da2935d
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diff --git a/.DS_Store b/.DS_Store
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: concurve
 Type: Package
-Date: 2019-07-10
+Date: 2019-09-18
 Title: Computes and Plots Consonance (Confidence) Intervals, P-Values, and S-Values to Form Consonance and Surprisal Functions
-Version: 2.0.1
+Version: 2.1.0
 Authors@R: c(
     person("Zad R.", "Chow", , "[email protected]", role = c("aut", "cre"),
       comment = c(ORCID = "0000-0003-1545-8199")
@@ -12,7 +12,7 @@ Authors@R: c(
     )
     )
 Maintainer: Zad R. Chow <[email protected]>
-Description: Allows one to compute consonance (confidence) intervals for various statistical tests along with their corresponding P-values and S-values. The intervals can be plotted to create consonance and surprisal functions allowing one to see what effect sizes are compatible with the test model at various consonance levels rather than being limited to one interval estimate such as 95%. These methods are discussed by Poole C. (1987) <doi:10.2105/AJPH.77.2.195>, Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>, Singh K, Xie M, Strawderman WE. (2007) <arXiv:0708.0976>, 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>.
+Description: Allows one to compute consonance (confidence) intervals for various statistical tests along with their corresponding P-values and S-values. The intervals can be plotted to create consonance and surprisal functions allowing one to see what effect sizes are compatible with the test model at various consonance levels rather than being limited to one interval estimate such as 95%. These methods are discussed by Poole C. (1987) <doi:10.2105/AJPH.77.2.195>, Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>, Singh K, Xie M, Strawderman WE. (2007) <arXiv:0708.0976>, Rothman KJ, Greenland S, Lash TL. (2008, ISBN:9781451190052), Amrhein V, Trafimow D, Greenland S. (2019) <doi:10.1080/00031305.2018.1543137>, Greenland S. (2019) <doi:10.1080/00031305.2018.1529625>, Chow ZR, Greenland S. (2019) <arXiv:1909.08579>, and Greenland S, Chow ZR. (2019) <arXiv:1909.08583>.
 Imports: parallel,
          ggplot2,
          metafor,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# concurve 2.1.0
+
+## Major changes 
+* `ggconcurve()` now plots both the P-values and CI level using both y-axes when the type = "consonance". Previously, this was only possible via `plot_concurve()` (which uses base R graphics) because `ggplot2` had a bug in its last few versions, which inhibited proper transformations in the y-axis. 
+
 # concurve 2.0.1
 
 ## Major changes 

diff --git a/R/curve_rev.R b/R/curve_rev.R
@@ -1,6 +1,6 @@
 # Reverse Engineer Consonance Functions Using the Point Estimate and Confidence Limits
 
-curve_rev <- function(point, LL, UL, measure = "default") {
+curve_rev <- function(point, LL, UL, measure = "default", steps = 10000) {
   if (is.numeric(point) != TRUE) {
     stop("Error: 'x' must be a numeric vector")
   }
@@ -14,7 +14,7 @@ curve_rev <- function(point, LL, UL, measure = "default") {
     stop("Error: 'measure' must be a string such as 'default' or 'ratio'")
   }
 
-  intrvls <- (1:10000) / 10000
+  intrvls <- (1:steps) / steps
   z <- qnorm(1 - intrvls / 2)
 
   if (measure == "default") {

diff --git a/R/ggconcurve.R b/R/ggconcurve.R
@@ -1,9 +1,8 @@
 ggconcurve <- function(type = "consonance", data, measure = "default", nullvalue = "absent", position = "pyramid",
                        title = "Consonance Function",
                        subtitle = "The function contains consonance intervals at every level.",
-                       caption = "Produced with the concurve R package.",
                        xaxis = "Range of Values",
-                       yaxis = "Consonance Level (%)",
+                       yaxis = "P-value",
                        color = "#555555",
                        fill = "#239a98") {
   if (type == "consonance") {
@@ -28,9 +27,6 @@ ggconcurve <- function(type = "consonance", data, measure = "default", nullvalue
     if (is.character(subtitle) != TRUE) {
       stop("Error: 'subtitle' must be a string.")
     }
-    if (is.character(caption) != TRUE) {
-      stop("Error: 'caption' must be a string.")
-    }
     if (is.character(xaxis) != TRUE) {
       stop("Error: 'xaxis' must be a string.")
     }
@@ -41,53 +37,61 @@ ggconcurve <- function(type = "consonance", data, measure = "default", nullvalue
       stop("Error: 'fill' must be a string for the color.")
     }
     ggplot(data = data) +
-      geom_point(aes(x = lower.limit, y = intrvl.level * 100),
+      geom_point(aes(x = lower.limit, y = pvalue),
         color = color, fill = fill, alpha = 0.5, shape = 20, size = 0.1
       ) +
-      geom_point(aes(x = upper.limit, y = intrvl.level * 100),
+      geom_point(aes(x = upper.limit, y = pvalue),
         color = color, fill = fill, alpha = 0.5, shape = 20, size = 0.1
       ) +
-      geom_ribbon(aes(x = lower.limit, ymin = max(intrvl.level * 100), ymax = intrvl.level * 100),
+      geom_ribbon(aes(x = lower.limit, ymin = min(pvalue), ymax = pvalue),
         fill = fill, alpha = 0.30
       ) +
-      geom_ribbon(aes(x = upper.limit, ymin = max(intrvl.level * 100), ymax = intrvl.level * 100),
+      geom_ribbon(aes(x = upper.limit, ymin = min(pvalue), ymax = pvalue),
         fill = fill, alpha = 0.30
       ) +
       labs(
         title = title,
         subtitle = subtitle,
-        caption = caption,
         x = xaxis,
         y = yaxis
       ) +
       theme_light() +
       theme(
-        axis.title.x = element_text(size = 13),
-        axis.title.y = element_text(size = 13)
+        axis.title.x = element_text(size = 12),
+        axis.title.y = element_text(size = 12)
       ) + {
         if (measure == "default") scale_x_continuous(breaks = scales::pretty_breaks(n = 10))
       } + {
         if (measure == "ratio") scale_x_log10(breaks = scales::pretty_breaks(n = 10))
       } + {
-        if (position == "inverted") scale_y_continuous(breaks = seq(0, 100, 5), expand = c(0, 0))
+        if (position == "inverted") {
+          scale_y_reverse(
+            breaks = seq(0, 1, .05),
+            sec.axis = sec_axis(~ (1 - .) * 100, name = "Levels for CI (%)", breaks = seq(0, 100, 5))
+          )
+        }
       } + {
-        if (position == "pyramid") scale_y_continuous(trans = "reverse", breaks = seq(0, 100, 5), expand = c(0, 0))
+        if (position == "pyramid") {
+          scale_y_continuous(
+            breaks = seq(0, 1, .05),
+            sec.axis = sec_axis(~ (1 - .) * 100, name = "Levels for CI (%)", breaks = seq(0, 100, 5))
+          )
+        }
       } +
-      theme(text = element_text(size = 15)) +
+      theme(text = element_text(size = 11)) +
       theme(
-        plot.title = element_text(size = 16),
-        plot.subtitle = element_text(size = 12),
-        plot.caption = element_text(size = 8)
+        plot.title = element_text(size = 12),
+        plot.subtitle = element_text(size = 11)
       ) +
       if (nullvalue == "present") {
         if (measure == "default") {
           annotate("segment",
-            x = 0, xend = 0, y = 0, yend = 100,
+            x = 0, xend = 0, y = 0, yend = 1,
             color = "#990000", alpha = 0.3, size = .6
           )
         } else if (measure == "ratio") {
           annotate("segment",
-            x = 1, xend = 1, y = 0, yend = 100,
+            x = 1, xend = 1, y = 0, yend = 1,
             color = "#990000", alpha = 0.3, size = .6
           )
         }
@@ -110,9 +114,6 @@ ggconcurve <- function(type = "consonance", data, measure = "default", nullvalue
     if (is.character(subtitle) != TRUE) {
       stop("Error: 'subtitle' must be a string.")
     }
-    if (is.character(caption) != TRUE) {
-      stop("Error: 'caption' must be a string.")
-    }
     if (is.character(xaxis) != TRUE) {
       stop("Error: 'xaxis' must be a string.")
     }
@@ -136,27 +137,25 @@ ggconcurve <- function(type = "consonance", data, measure = "default", nullvalue
         fill = fill, alpha = 0.30
       ) +
       labs(
-        title = "Surprisal Function",
+        title = title,
         subtitle = subtitle,
-        caption = caption,
         x = xaxis,
         y = "S-value (bits of information)"
       ) +
       theme_light() +
       theme(
-        axis.title.x = element_text(size = 13),
-        axis.title.y = element_text(size = 13)
+        axis.title.x = element_text(size = 12),
+        axis.title.y = element_text(size = 12)
       ) + {
         if (measure == "default") scale_x_continuous(breaks = scales::pretty_breaks(n = 10))
       } + {
         if (measure == "ratio") scale_x_log10(breaks = scales::pretty_breaks(n = 10))
       } +
       scale_y_continuous(breaks = seq(0, 14, 0.5), expand = c(0, 0)) +
-      theme(text = element_text(size = 15)) +
+      theme(text = element_text(size = 11)) +
       theme(
-        plot.title = element_text(size = 16),
-        plot.subtitle = element_text(size = 12),
-        plot.caption = element_text(size = 8)
+        plot.title = element_text(size = 12),
+        plot.subtitle = element_text(size = 11)
       )
   }
 }

diff --git a/R/plot_concurve.R b/R/plot_concurve.R
@@ -1,18 +1,21 @@
 plot_concurve <- function(type = "consonance",
                           data,
                           measure = "default",
+                          intervals = FALSE,
                           title = "Consonance Function",
                           xlab = "Theta",
                           ylab1 = "P-value",
                           ylab2 = "Confidence Level (%)",
+                          fontsize = 12,
                           fill = "#239a9880") {
 
   # Overall graph parameters
   par(
+    ps = fontsize,
     mar = c(4.5, 5, 3, 5),
     font.main = 1,
-    cex.main = 1.3,
-    cex.lab = 1.15
+    cex.main = 1,
+    cex.lab = 1
   )
 
   # Consonance function
@@ -86,8 +89,11 @@ plot_concurve <- function(type = "consonance",
       side = 4, at = c(seq(from = 0, to = 100, by = 10)),
       tck = 1, lty = 2, col = "grey", las = 1
     )
-    text(par("usr") + 0.95, 28,
-      srt = -90, adj = 0, labels = "Consonance Level (%)", cex = 1.05,
+
+    # 0.95, 28
+
+    text(par("usr") + 1, 15,
+      srt = -90, adj = 0, labels = ylab2, cex = 1,
       xpd = TRUE
     )
     par(new = T)
@@ -97,7 +103,7 @@ plot_concurve <- function(type = "consonance",
     )
 
     # Labels for interval estimates and maximum likelihood
-
+    if (intervals == TRUE) {
     text(
       x = 1.27, y = 3,
       paste(
@@ -142,6 +148,7 @@ plot_concurve <- function(type = "consonance",
       ),
       cex = 0.93, col = "black"
     )
+    }
   }
 
   # Surprisal function
@@ -154,9 +161,9 @@ plot_concurve <- function(type = "consonance",
           xlim = c(min(lower.limit), max(upper.limit)),
           panel.first = grid(),
           type = "l",
-          xlab = "Theta",
-          ylab = "S-value",
-          main = "Surpisal Function",
+          xlab = xlab,
+          ylab = "S-value (bits of information)",
+          main = title,
           yaxt = "n",
           las = 1
         )
@@ -166,9 +173,9 @@ plot_concurve <- function(type = "consonance",
           xlim = c(min(lower.limit), max(upper.limit)),
           panel.first = grid(),
           type = "l",
-          xlab = "Theta",
-          ylab = "S-value",
-          main = "Surpisal Function",
+          xlab = xlab,
+          ylab = "S-value (bits of information)",
+          main = title,
           yaxt = "n",
           las = 1,
           log = "x"

diff --git a/README.Rmd b/README.Rmd
@@ -18,8 +18,8 @@ concurve | Graph Interval Functions <img src="man/figures/logo.svg" align="right
 
 # Examples 
 
-<img src = "https://res.cloudinary.com/less-likely/image/upload/v1562705215/Site/Figure1.png" align="center" width ="400">
-<img src = "https://res.cloudinary.com/less-likely/image/upload/v1562705215/Site/Figure2.png" align="center" width="400">
+<img src = "https://res.cloudinary.com/less-likely/image/upload/v1568855498/Site/Figure1.png" align="center" width ="400">
+<img src = "https://res.cloudinary.com/less-likely/image/upload/v1568855498/Site/Figure2.png" align="center" width="400">
 
 * * * 
 
@@ -96,3 +96,5 @@ install_github("zadchow/concurve")
 7.  Amrhein V, Trafimow D, Greenland S. Inferential Statistics as Descriptive Statistics: There is No Replication     Crisis if We Don't Expect Replication. _Am Stat_. 2019
 8.  Greenland S. Valid P-values Behave Exactly As They Should. Some misleading criticisms of P-values and their      resolution with S-values. _Am Stat_. 2019;18(136).
 9.  Fraser DAS. The p-value Function and Statistical Inference. _Am Stat_. 2019
+10. Chow ZR, Greenland S. Semantic and Cognitive Tools to Aid Statistical Inference: Replace Confidence and Significance by Compatibility and Surprise. _arXiv:1909.08579 [stat.ME]_. 2019
+11. Greenland S, Chow ZR. To Aid Statistical Inference, Emphasize Unconditional Descriptions of Statistics. _arXiv:1909.08583 [stat.ME]_. 2019
diff --git a/README.md b/README.md
@@ -31,8 +31,8 @@ status](https://ci.appveyor.com/api/projects/status/v8sp9x96dap2om9s?svg=true)](
 
 # Examples
 
-<img src = "https://res.cloudinary.com/less-likely/image/upload/v1562705215/Site/Figure1.png" align="center" width ="400">
-<img src = "https://res.cloudinary.com/less-likely/image/upload/v1562705215/Site/Figure2.png" align="center" width="400">
+<img src = "https://res.cloudinary.com/less-likely/image/upload/v1568855498/Site/Figure1.png" align="center" width ="400">
+<img src = "https://res.cloudinary.com/less-likely/image/upload/v1568855498/Site/Figure2.png" align="center" width="400">
 
 -----
 
@@ -114,3 +114,9 @@ install_github("zadchow/concurve")
     S-values. *Am Stat*. 2019;18(136).
 9.  Fraser DAS. The p-value Function and Statistical Inference. *Am
     Stat*. 2019
+10. Chow ZR, Greenland S. Semantic and Cognitive Tools to Aid
+    Statistical Inference: Replace Confidence and Significance by
+    Compatibility and Surprise. *arXiv:1909.08579 \[stat.ME\]*. 2019
+11. Greenland S, Chow ZR. To Aid Statistical Inference, Emphasize
+    Unconditional Descriptions of Statistics. *arXiv:1909.08583
+    \[stat.ME\]*. 2019
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -33,8 +33,10 @@ navbar:
     articles:
       text: Articles
       menu:
-      - text: Examples With Simulated Data
+      - text: Examples in R
         href: articles/examples.html
+      - text: Using Stata
+        href: articles/stata.html
     news:
       text: News
       href: news/index.html

diff --git a/codemeta.json b/codemeta.json
@@ -5,7 +5,7 @@
   ],
   "@type": "SoftwareSourceCode",
   "identifier": "concurve",
-  "description": "Allows one to compute consonance (confidence) intervals for various statistical tests along with their corresponding P-values and S-values. The intervals can be plotted to create consonance and surprisal functions allowing one to see what effect sizes are compatible with the test model at various consonance levels rather than being limited to one interval estimate such as 95%. These methods are discussed by Poole C. (1987) <doi:10.2105/AJPH.77.2.195>, Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>, Singh K, Xie M, Strawderman WE. (2007) <arXiv:0708.0976>, 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>.",
+  "description": "Allows one to compute consonance (confidence) intervals for various statistical tests along with their corresponding P-values and S-values. The intervals can be plotted to create consonance and surprisal functions allowing one to see what effect sizes are compatible with the test model at various consonance levels rather than being limited to one interval estimate such as 95%. These methods are discussed by Poole C. (1987) <doi:10.2105/AJPH.77.2.195>, Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>, Singh K, Xie M, Strawderman WE. (2007) <arXiv:0708.0976>, Rothman KJ, Greenland S, Lash TL. (2008, ISBN:9781451190052), Amrhein V, Trafimow D, Greenland S. (2019) <doi:10.1080/00031305.2018.1543137>, Greenland S. (2019) <doi:10.1080/00031305.2018.1529625>, Chow ZR, Greenland S. (2019) <arXiv:1909.08579>, and Greenland S, Chow ZR. (2019) <arXiv:1909.08583>.",
   "name": "concurve: Computes and Plots Consonance (Confidence) Intervals, P-Values, and S-Values to Form Consonance and Surprisal Functions",
   "date": "2019-05-10",
   "codeRepository": "https://github.com/Zadchow/concurve",
@@ -16,7 +16,7 @@
   ],
   "issueTracker": "https://github.com/Zadchow/concurve/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "2.0.1",
+  "version": "2.1.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -184,7 +184,7 @@
     }
   ],
   "keywords": ["confidence", "compatibility", "consonance", "surprisal", "interval", "function", "curve"],
-  "fileSize": "3936.013KB",
+  "fileSize": "3833.993KB",
   "contIntegration": [
     "https://travis-ci.org/Zadchow/concurve",
     "https://ci.appveyor.com/project/Zadchow/concurve",