Merge pull request #50 from zadrafi/testing

release of version 2.7.7
zadrafi · Oct 12, 2020 · d9cce76 · d9cce76
2 parents 339bd29 + 50fec65
commit d9cce76
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -30,3 +30,6 @@
 ^\.github$
 ^Makefile$
 ^concurve\.pdf$
+^R&G2020\.Rmd$
+^supported\.Rmd$
+^~/concurve/vignettes/supported\.Rmd$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ Type: Package
 Package: concurve
 Title: Computes & Plots Compatibility (Confidence),
        Surprisal, & Likelihood Distributions
-Version: 2.7.6
-Date: 2020-10-06
+Version: 2.7.7
+Date: 2020-10-12
 Authors@R: 
     c(person(given = "Zad",
              family = "Rafi",
@@ -24,11 +24,11 @@ Maintainer: Zad Rafi <[email protected]>
 Description: Computes compatibility (confidence) distributions along with their corresponding P-values,
     S-values, and likelihoods. The intervals can be plotted to form the distributions themselves.  
     Functions can be compared to one another to see how much they overlap. Results can be
-    exported to Microsoft Word, Powerpoint, and TeX documents. The
-    package currently supports resampling methods, computing differences,
-    generalized linear models, mixed-effects models, survival analysis,
-    and meta-analysis. These methods are discussed by Schweder T, Hjort NL. (2016, ISBN:9781316445051) 
-    and Rafi Z, Greenland S. (2020) <doi:10.1186/s12874-020-01105-9>.
+    exported to Microsoft Word, Powerpoint, and TeX documents. The package currently supports 
+    resampling methods, computing differences, generalized linear models, mixed-effects models, 
+    survival analysis, and meta-analysis. These methods are discussed 
+    by Schweder T, Hjort NL. (2016, ISBN:9781316445051) and 
+    Rafi Z, Greenland S. (2020) <doi:10.1186/s12874-020-01105-9>.
 License: GPL-3 | file LICENSE
 URL: https://data.lesslikely.com/concurve/,
      https://github.com/zadrafi/concurve

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# concurve 2.7.6
+# concurve 2.7.7
 ## Major changes 
 * `log` option added to `curve_gen()` to exponentiate the coefficients.
   - Thanks to [Isabella Ghement](https://twitter.com/IsabellaGhement) for finding the issue and notifying us about it.

diff --git a/R/concurve-package.R b/R/concurve-package.R
@@ -1,8 +1,8 @@
-#' @title A description of the concurve R package
+#' @title A description of the `concurve` `R` package
 #' @name concurve-package
 #' @aliases concurve
 #' @docType package
-#' @author Zad Rafi, Andrew D. Vigotsky, and Aaron Caldwell
+#' @author [Zad Rafi](<https://twitter.com/dailyzad>), [Andrew D. Vigotsky](<https://www.researchgate.net/profile/Andrew_Vigotsky>)
 #' @description
 #' Allows one to compute compatibility (confidence)
 #' intervals for various statistical tests along with their corresponding
@@ -14,7 +14,7 @@
 #' \tabular{ll}{ Package: \tab concurve\cr
 #'  Logo: \tab \figure{logo.png}{options: width="50px"}\cr
 #'   Type: \tab Package\cr Version: \tab
-#' 2.7.6\cr Date: \tab 2020-10-05\cr License: \tab GLP-3}
+#' 2.7.7\cr Date: \tab 2020-10-07\cr License: \tab GLP-3}
 #' @details
 #' Accepts most modeling functions that produce confidence intervals to construct distributions.
 #' Instructions are also provided on how to construct similar graphs for [Stata](https://data.lesslikely.com/concurve/articles/stata.html).

diff --git a/R/ggcurve.R b/R/ggcurve.R
@@ -141,10 +141,10 @@ ggcurve <- function(data, type = "c", measure = "default", levels = 0.95, nullva
       geom_point(data = interval, mapping = aes(x = limits, y = 1 - levels), size = 1.75, shape = 18) +
       geom_line(data = interval, mapping = aes(x = limits, y = 1 - levels, group = levels), size = .30) +
       geom_ribbon(aes(x = lower.limit, ymin = min(pvalue), ymax = pvalue),
-        fill = fill, alpha = 0.20
+        fill = fill, alpha = 0.10
       ) +
       geom_ribbon(aes(x = upper.limit, ymin = min(pvalue), ymax = pvalue),
-        fill = fill, alpha = 0.20
+        fill = fill, alpha = 0.10
       ) +
       labs(
         title = title,
@@ -234,10 +234,10 @@ ggcurve <- function(data, type = "c", measure = "default", levels = 0.95, nullva
       geom_point(data = interval, mapping = aes(x = limits, y = (-log2(1 - levels))), size = 1.75, shape = 18) +
       geom_line(data = interval, mapping = aes(x = limits, y = (-log2(1 - levels)), group = levels), size = .30) +
       geom_ribbon(aes(x = lower.limit, ymin = max(svalue), ymax = svalue),
-        fill = fill, alpha = 0.20
+        fill = fill, alpha = 0.10
       ) +
       geom_ribbon(aes(x = upper.limit, ymin = max(svalue), ymax = svalue),
-        fill = fill, alpha = 0.20
+        fill = fill, alpha = 0.10
       ) +
       labs(
         title = title,
@@ -386,7 +386,7 @@ ggcurve <- function(data, type = "c", measure = "default", levels = 0.95, nullva
 
     ggplot(data = data, mapping = aes(x = values, y = support)) +
       geom_line() +
-      geom_ribbon(aes(x = values, ymin = min(support), ymax = support), fill = fill, color = color, alpha = 0.20) +
+      geom_ribbon(aes(x = values, ymin = min(support), ymax = support), fill = fill, color = color, alpha = 0.10) +
       labs(
         title = title,
         subtitle = subtitle,
@@ -433,7 +433,7 @@ ggcurve <- function(data, type = "c", measure = "default", levels = 0.95, nullva
 
     ggplot(data = data, mapping = aes(x = values, y = loglikelihood)) +
       geom_line() +
-      geom_ribbon(aes(x = values, ymin = min(loglikelihood), ymax = loglikelihood), fill = fill, color = color, alpha = 0.20) +
+      geom_ribbon(aes(x = values, ymin = min(loglikelihood), ymax = loglikelihood), fill = fill, color = color, alpha = 0.10) +
       labs(
         title = title,
         subtitle = subtitle,
@@ -481,7 +481,7 @@ ggcurve <- function(data, type = "c", measure = "default", levels = 0.95, nullva
 
     ggplot(data = data, mapping = aes(x = values, y = likelihood)) +
       geom_line() +
-      geom_ribbon(aes(x = values, ymin = min(likelihood), ymax = likelihood), fill = fill, color = color, alpha = 0.20) +
+      geom_ribbon(aes(x = values, ymin = min(likelihood), ymax = likelihood), fill = fill, color = color, alpha = 0.10) +
       labs(
         title = title,
         subtitle = subtitle,
@@ -529,7 +529,7 @@ ggcurve <- function(data, type = "c", measure = "default", levels = 0.95, nullva
 
     ggplot(data = data, mapping = aes(x = values, y = deviancestat)) +
       geom_line() +
-      geom_ribbon(aes(x = values, ymin = deviancestat, ymax = max(deviancestat)), fill = fill, color = color, alpha = 0.20) +
+      geom_ribbon(aes(x = values, ymin = deviancestat, ymax = max(deviancestat)), fill = fill, color = color, alpha = 0.10) +
       labs(
         title = title,
         subtitle = subtitle,

diff --git a/R/plot_compare.R b/R/plot_compare.R
@@ -93,10 +93,10 @@ plot_compare <- function(data1, data2, type = "c", measure = "default", nullvalu
                          xaxis = expression(theta == ~"Range of Values"),
                          yaxis1 = expression(paste(italic(p), "-value")),
                          yaxis2 = "Levels for CI (%)",
-                         color1 = darken("#D55E00", 0.4),
-                         color2 = darken("#009E73", 0.4),
-                         fill1 = "#D55E0050",
-                         fill2 = "#009E7350") {
+                         color1 = darken("#D55E00", 0.2),
+                         color2 = darken("#009E73", 0.2),
+                         fill1 = "#99c7c7",
+                         fill2 = "#d46c5b") {
   cols <- c(fill1, fill2)
 
   # Consonance Curve -----------------------------------------------------
@@ -143,10 +143,10 @@ plot_compare <- function(data1, data2, type = "c", measure = "default", nullvalu
         color = color2
       ) +
       geom_ribbon(aes(x = lower.limit, ymin = min(pvalue), ymax = pvalue, fill = fill1),
-        alpha = 0.20
+        alpha = 0.10
       ) +
       geom_ribbon(aes(x = upper.limit, ymin = min(pvalue), ymax = pvalue, fill = fill1),
-        alpha = 0.20
+        alpha = 0.10
       ) +
       geom_line(
         data = data2, aes(x = lower.limit, y = pvalue),
@@ -158,11 +158,11 @@ plot_compare <- function(data1, data2, type = "c", measure = "default", nullvalu
       ) +
       geom_ribbon(
         data = data2, aes(x = lower.limit, ymin = min(pvalue), ymax = pvalue, fill = fill2),
-        alpha = 0.20
+        alpha = 0.10
       ) +
       geom_ribbon(
         data = data2, aes(x = upper.limit, ymin = min(pvalue), ymax = pvalue, fill = fill2),
-        alpha = 0.20
+        alpha = 0.10
       ) +
       theme_minimal() +
       labs(
@@ -276,10 +276,10 @@ plot_compare <- function(data1, data2, type = "c", measure = "default", nullvalu
         color = color2
       ) +
       geom_ribbon(aes(x = lower.limit, ymin = max(svalue), ymax = svalue, fill = fill1),
-        alpha = 0.20
+        alpha = 0.10
       ) +
       geom_ribbon(aes(x = upper.limit, ymin = max(svalue), ymax = svalue, fill = fill1),
-        alpha = 0.20
+        alpha = 0.10
       ) +
       geom_line(
         data = data2, aes(x = lower.limit, y = svalue),
@@ -291,11 +291,11 @@ plot_compare <- function(data1, data2, type = "c", measure = "default", nullvalu
       ) +
       geom_ribbon(
         data = data2, aes(x = lower.limit, ymin = max(svalue), ymax = svalue, fill = fill2),
-        alpha = 0.20
+        alpha = 0.10
       ) +
       geom_ribbon(
         data = data2, aes(x = upper.limit, ymin = max(svalue), ymax = svalue, fill = fill2),
-        alpha = 0.20
+        alpha = 0.10
       ) +
       labs(
         title = "Surprisal Functions",
@@ -369,9 +369,9 @@ plot_compare <- function(data1, data2, type = "c", measure = "default", nullvalu
 
     ggplot(data = data1, mapping = aes(x = values, y = support)) +
       geom_line(color = color2) +
-      geom_ribbon(aes(x = values, ymin = min(support), ymax = support, fill = fill1), alpha = 0.20) +
+      geom_ribbon(aes(x = values, ymin = min(support), ymax = support, fill = fill1), alpha = 0.10) +
       geom_line(data = data2, color = color1) +
-      geom_ribbon(data = data2, aes(x = values, ymin = min(support), ymax = support, fill = fill2), alpha = 0.20) +
+      geom_ribbon(data = data2, aes(x = values, ymin = min(support), ymax = support, fill = fill2), alpha = 0.10) +
       labs(
         title = "Relative Likelihood Functions",
         subtitle = subtitle,
@@ -454,9 +454,9 @@ plot_compare <- function(data1, data2, type = "c", measure = "default", nullvalu
 
     ggplot(data = data1, mapping = aes(x = values, y = loglikelihood)) +
       geom_line(color = color1) +
-      geom_ribbon(aes(x = values, ymin = min(loglikelihood), ymax = loglikelihood, fill = fill1), alpha = 0.20) +
+      geom_ribbon(aes(x = values, ymin = min(loglikelihood), ymax = loglikelihood, fill = fill1), alpha = 0.10) +
       geom_line(data = data2, color = color2) +
-      geom_ribbon(data = data2, aes(x = values, ymin = min(loglikelihood), ymax = loglikelihood, fill = fill2), alpha = 0.20) +
+      geom_ribbon(data = data2, aes(x = values, ymin = min(loglikelihood), ymax = loglikelihood, fill = fill2), alpha = 0.10) +
       labs(
         title = "Log-Likelihood Function",
         subtitle = subtitle,
@@ -539,9 +539,9 @@ plot_compare <- function(data1, data2, type = "c", measure = "default", nullvalu
 
     ggplot(data = data1, mapping = aes(x = values, y = likelihood)) +
       geom_line(color = color1) +
-      geom_ribbon(aes(x = values, ymin = min(likelihood), ymax = likelihood, fill = fill1), alpha = 0.20) +
+      geom_ribbon(aes(x = values, ymin = min(likelihood), ymax = likelihood, fill = fill1), alpha = 0.10) +
       geom_line(data = data2, color = color2) +
-      geom_ribbon(data = data2, aes(x = values, ymin = min(likelihood), ymax = likelihood, fill = fill2), alpha = 0.20) +
+      geom_ribbon(data = data2, aes(x = values, ymin = min(likelihood), ymax = likelihood, fill = fill2), alpha = 0.10) +
       labs(
         title = "Likelihood Function",
         subtitle = subtitle,
@@ -623,9 +623,9 @@ plot_compare <- function(data1, data2, type = "c", measure = "default", nullvalu
 
     ggplot(data = data1, mapping = aes(x = values, y = deviancestat)) +
       geom_line(color = color1) +
-      geom_ribbon(aes(x = values, ymin = deviancestat, ymax = max(deviancestat), fill = fill1), alpha = 0.20) +
+      geom_ribbon(aes(x = values, ymin = deviancestat, ymax = max(deviancestat), fill = fill1), alpha = 0.10) +
       geom_line(data = data2, color = color2) +
-      geom_ribbon(data = data2, aes(x = values, ymin = deviancestat, ymax = max(deviancestat), fill = fill2), alpha = 0.20) +
+      geom_ribbon(data = data2, aes(x = values, ymin = deviancestat, ymax = max(deviancestat), fill = fill2), alpha = 0.10) +
       labs(
         title = "Deviance Functions",
         subtitle = subtitle,

diff --git a/README.Rmd b/README.Rmd
@@ -2,7 +2,7 @@
 output: github_document
 ---
 
-### <span style="color:#000; font-weight: 400;">concurve</span> | Graph Interval Functions </strong> <img src="man/figures/logo.svg" align="right" width="70"/>
+### <span style="color:#000; font-weight: 400;">`concurve`</span> | Graph Frequentist Distributions of Parameters </strong> <img src="man/figures/logo.svg" align="right" width="70"/>
 
 * * * 
 
@@ -58,6 +58,14 @@ Try the following script if you run into any installation issues:
 install.packages("concurve", repos = "https://cloud.r-project.org/", dep = TRUE)
 ```
 
+Install the developer version from [GitHub](https://github.com/zadrafi/concurve/) using the following: 
+
+```{r eval=FALSE}
+remotes::install_github("zadrafi/concurve@master", dependencies = TRUE)
+```
+
+See which versions of the package are currently [supported here](articles/supported.html). 
+
 * * * 
 
 #### Articles

diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 
-### <span style="color:#000; font-weight: 400;">concurve</span> \| Graph Interval Functions </strong> <img src="man/figures/logo.svg" align="right" width="70"/>
+### <span style="color:#000; font-weight: 400;">`concurve`</span> \| Graph Frequentist Distributions of Parameters </strong> <img src="man/figures/logo.svg" align="right" width="70"/>
 
 ------------------------------------------------------------------------
 
@@ -66,6 +66,14 @@ Try the following script if you run into any installation issues:
 
     install.packages("concurve", repos = "https://cloud.r-project.org/", dep = TRUE)
 
+Install the developer version from
+[GitHub](https://github.com/zadrafi/concurve/) using the following:
+
+    remotes::install_github("zadrafi/concurve@master", dependencies = TRUE)
+
+See which versions of the package are currently [supported
+here](articles/supported.html).
+
 ------------------------------------------------------------------------
 
 #### Articles
@@ -143,9 +151,8 @@ The package was currently run on:
     ## [1] stats     graphics  grDevices utils     datasets  methods   base     
     ## 
     ## loaded via a namespace (and not attached):
-    ##  [1] compiler_4.0.2  magrittr_1.5    tools_4.0.2     htmltools_0.5.0
-    ##  [5] yaml_2.2.1      stringi_1.5.3   rmarkdown_2.4   knitr_1.30     
-    ##  [9] stringr_1.4.0   xfun_0.18       digest_0.6.25   rlang_0.4.7    
-    ## [13] evaluate_0.14
+    ##  [1] compiler_4.0.2    magrittr_1.5      credentials_1.3.0 htmltools_0.5.0   tools_4.0.2       yaml_2.2.1        stringi_1.5.3    
+    ##  [8] rmarkdown_2.4     knitr_1.30        stringr_1.4.0     xfun_0.18         digest_0.6.25     rlang_0.4.7       openssl_1.4.3    
+    ## [15] sys_3.4           evaluate_0.14     askpass_1.1
 
 ------------------------------------------------------------------------
diff --git a/SECURITY.md b/SECURITY.md
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -34,7 +34,7 @@ development:
 
 navbar:
   structure:
-    left:  [home, intro, reference, articles, literature, tools, news]
+    left:  [home, intro, reference, articles, misc, literature, tools, news]
     right: [github, twitter]
 
   components:
@@ -71,19 +71,21 @@ navbar:
         href: articles/tables.html  
       - text: Troubleshooting
         href: articles/troubleshooting.html
+    misc:
+      text: Misc
+      menu:
+      - text: Surprisal values
+        href: articles/svalues.html  
     literature:
       text: Literature
       href: articles/literature.html
-    tools:
-      text: S-values
-      href: articles/svalues.html
     news:
       text: News
       menu:
       - text: Package Updates
         href: news/index.html
       - text: Supported Versions
-        href: SECURITY.html
+        href: articles/supported.html
       - text: Feature Wish List
         href: articles/wishlist.html
     github: