Merge pull request #2 from Zadchow/testing

v2.0.1
zadrafi · Jul 10, 2019 · 8d3502a · 8d3502a
2 parents 3bb67c2 + 779a83b
commit 8d3502a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: concurve
 Type: Package
 Date: 2019-07-10
 Title: Computes and Plots Consonance (Confidence) Intervals, P-Values, and S-Values to Form Consonance and Surprisal Functions
-Version: 2.0
+Version: 2.0.1
 Authors@R: c(
     person("Zad R.", "Chow", , "[email protected]", role = c("aut", "cre"),
       comment = c(ORCID = "0000-0003-1545-8199")

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+# concurve 2.0.1
+
+## Major changes 
+
+* `plot_concurve()` now has "measure" as an item which allows for ratio measures to be logarithmically scaled on the x axis. There are two options, "default", which is set as the default option and is for mean differences, and "ratio", which will result in the axis being logarithmically scaled. 
+* `plot_concurve()` also now has a "fill" option which will allow users to choose the color of the plot.
+
+
 # concurve 2.0
 
 ## Major changes 

diff --git a/R/plot_concurve.R b/R/plot_concurve.R
@@ -1,41 +1,63 @@
 plot_concurve <- function(type = "consonance",
                           data,
+                          measure = "default",
                           title = "Consonance Function",
                           xlab = "Theta",
                           ylab1 = "P-value",
-                          ylab2 = "Confidence Level (%)") {
+                          ylab2 = "Confidence Level (%)",
+                          fill = "#239a9880") {
+
+  # Overall graph parameters
   par(
-    mar = c(4.9, 5, 3.5, 5),
+    mar = c(4.5, 5, 3, 5),
     font.main = 1,
     cex.main = 1.3,
     cex.lab = 1.15
   )
 
+  # Consonance function
+
   if (type == "consonance") {
     with(
       data = data,
-      plot(lower.limit, pvalue,
-        xlim = c(min(lower.limit), max(upper.limit)),
-        panel.first = grid(ny = 0),
-        type = "l",
-        xlab = xlab,
-        ylab = ylab1,
-        main = title,
-        yaxt = "n",
-        las = 1
-      )
+      if (measure == "default") {
+        plot(lower.limit, pvalue,
+          xlim = c(min(lower.limit), max(upper.limit)),
+          panel.first = grid(ny = 0),
+          type = "l",
+          xlab = xlab,
+          ylab = ylab1,
+          main = title,
+          yaxt = "n",
+          las = 1
+        )
+      }
+      else if (measure == "ratio") {
+        plot(lower.limit, pvalue,
+          xlim = c(min(lower.limit), max(upper.limit)),
+          panel.first = grid(ny = 0),
+          type = "l",
+          xlab = xlab,
+          ylab = ylab1,
+          main = title,
+          yaxt = "n",
+          las = 1,
+          log = "x"
+        )
+      }
     )
+
     with(data = data, lines(upper.limit, pvalue))
 
     # Shade in area under the curve
 
     polygon(c(max(data$lower.limit), data$lower.limit),
       c(min(data$pvalue), data$pvalue),
-      col = "#239a9880", border = NA
+      col = fill, border = NA
     )
     polygon(c(min(data$upper.limit), data$upper.limit),
       c(min(data$pvalue), data$pvalue),
-      col = "#239a9880", border = NA
+      col = fill, border = NA
     )
     axis(
       side = 2, at = c(seq(from = 0, to = 1, by = .10)),
@@ -120,28 +142,48 @@ plot_concurve <- function(type = "consonance",
       ),
       cex = 0.93, col = "black"
     )
-  } else if (type == "surprisal") {
+  }
+
+  # Surprisal function
+
+  if (type == "surprisal") {
     with(
       data,
-      plot(lower.limit, svalue,
-        xlim = c(min(lower.limit), max(upper.limit)),
-        panel.first = grid(),
-        type = "l",
-        xlab = "Theta",
-        ylab = "S-value",
-        main = "Surpisal Function",
-        yaxt = "n",
-        las = 1
-      )
+      if (measure == "default") {
+        plot(lower.limit, svalue,
+          xlim = c(min(lower.limit), max(upper.limit)),
+          panel.first = grid(),
+          type = "l",
+          xlab = "Theta",
+          ylab = "S-value",
+          main = "Surpisal Function",
+          yaxt = "n",
+          las = 1
+        )
+      }
+      else if (measure == "ratio") {
+        plot(lower.limit, svalue,
+          xlim = c(min(lower.limit), max(upper.limit)),
+          panel.first = grid(),
+          type = "l",
+          xlab = "Theta",
+          ylab = "S-value",
+          main = "Surpisal Function",
+          yaxt = "n",
+          las = 1,
+          log = "x"
+        )
+      }
     )
+
     with(data, lines(upper.limit, svalue))
     polygon(c(max(data$lower.limit), data$lower.limit),
       c(max(data$svalue), data$svalue),
-      col = "#239a9880", border = NA
+      col = fill, border = NA
     )
     polygon(c(min(data$upper.limit), data$upper.limit),
       c(max(data$svalue), data$svalue),
-      col = "#239a9880", border = NA
+      col = fill, border = NA
     )
     axis(side = 2, lty = 2, col = "grey", las = 1)
     par(new = T)

diff --git a/codemeta.json b/codemeta.json
@@ -16,7 +16,7 @@
   ],
   "issueTracker": "https://github.com/Zadchow/concurve/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "2.0",
+  "version": "2.0.1",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -184,7 +184,7 @@
     }
   ],
   "keywords": ["confidence", "compatibility", "consonance", "surprisal", "interval", "function", "curve"],
-  "fileSize": "3935.732KB",
+  "fileSize": "3936.013KB",
   "contIntegration": [
     "https://travis-ci.org/Zadchow/concurve",
     "https://ci.appveyor.com/project/Zadchow/concurve",

diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/examples.html b/docs/articles/examples.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/stata.html b/docs/articles/stata.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/reference/curve_corr.html b/docs/reference/curve_corr.html
diff --git a/docs/reference/curve_gen.html b/docs/reference/curve_gen.html
diff --git a/docs/reference/curve_mean.html b/docs/reference/curve_mean.html
diff --git a/docs/reference/curve_meta.html b/docs/reference/curve_meta.html
diff --git a/docs/reference/curve_rev.html b/docs/reference/curve_rev.html
diff --git a/docs/reference/curve_surv.html b/docs/reference/curve_surv.html
diff --git a/docs/reference/defunct.html b/docs/reference/defunct.html