From 4038b64d8033ca672ab65a8fbcea18ba73535c6c Mon Sep 17 00:00:00 2001
From: rok-cesnovar <rok.cesnovar@fri.uni-lj.si>
Date: Wed, 14 Jul 2021 10:40:38 +0200
Subject: [PATCH 1/2] remove from vignette and readme

---
 README.md                    |   7 ---
 docs/articles/index.html     |   8 +--
 docs/articles/posterior.html | 108 +++++++++++++++++------------------
 vignettes/posterior.Rmd      |   5 +-
 4 files changed, 60 insertions(+), 68 deletions(-)

diff --git a/README.md b/README.md
index e9644306..dc6af9c5 100644
--- a/README.md
+++ b/README.md
@@ -43,13 +43,6 @@ You can install the latest official release version via
 install.packages("posterior")
 ```
 
-Alternatively, you can install binaries of the current development
-version via
-
-``` r
-install.packages("posterior", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
-```
-
 or directly build the package from GitHub via
 
 ``` r
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 44dc78cd..49238b1a 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -79,7 +79,7 @@
       <ul class="nav navbar-nav">
         <li>
   <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -132,19 +132,19 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://twitter.com/mcmc_stan">
-    <span class="fa fa-twitter"></span>
+    <span class="fas fa-twitter"></span>
      
   </a>
 </li>
 <li>
   <a href="https://github.com/stan-dev/posterior">
-    <span class="fa fa-github"></span>
+    <span class="fas fa-github"></span>
      
   </a>
 </li>
 <li>
   <a href="https://discourse.mc-stan.org/">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
      
   </a>
 </li>
diff --git a/docs/articles/posterior.html b/docs/articles/posterior.html
index d604fc08..7867b25b 100644
--- a/docs/articles/posterior.html
+++ b/docs/articles/posterior.html
@@ -39,7 +39,7 @@
       <ul class="nav navbar-nav">
 <li>
   <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -92,19 +92,19 @@
 <ul class="nav navbar-nav navbar-right">
 <li>
   <a href="https://twitter.com/mcmc_stan">
-    <span class="fa fa-twitter"></span>
+    <span class="fas fa-twitter"></span>
      
   </a>
 </li>
 <li>
   <a href="https://github.com/stan-dev/posterior">
-    <span class="fa fa-github"></span>
+    <span class="fas fa-github"></span>
      
   </a>
 </li>
 <li>
   <a href="https://discourse.mc-stan.org/">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
      
   </a>
 </li>
@@ -118,7 +118,7 @@
 
       
 
-      </header><script src="posterior_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
+      </header><script src="posterior_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>The posterior R package</h1>
@@ -146,9 +146,9 @@ <h2 class="hasAnchor">
 <div id="installation" class="section level2">
 <h2 class="hasAnchor">
 <a href="#installation" class="anchor"></a>Installation</h2>
-<p>The package is not on CRAN yet, but you can install the latest beta release version via</p>
+<p>You can install the latest official release version via</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"posterior"</span>, repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"https://mc-stan.org/r-packages/"</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"posterior"</span><span class="op">)</span></code></pre></div>
 <p>or the latest development version from GitHub via</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># install.packages("remotes")</span>
@@ -285,17 +285,17 @@ <h4 class="hasAnchor">
 <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div>
 <pre><code>## # A draws_matrix: 10 iterations, 1 chains, and 5 variables
 ##     variable
-## draw    V1    V2     V3     V4    V5
-##   1   0.29 -0.80 -0.884 -1.179 -0.34
-##   2  -1.31  1.11  0.364 -1.202 -0.50
-##   3   1.09  0.40  0.298  1.373  0.90
-##   4   0.51 -0.71 -0.023 -0.086 -0.43
-##   5  -0.56 -0.61  0.614 -0.089  1.19
-##   6   0.93 -0.82 -1.254 -1.884 -1.17
-##   7   1.30  1.77  1.318 -0.831  0.81
-##   8  -0.18  1.21 -0.209 -0.756  0.60
-##   9   1.16 -1.22  0.208  0.291 -0.29
-##   10  0.13  0.53  0.468  1.099  1.37</code></pre>
+## draw    V1    V2    V3     V4     V5
+##   1  -2.10 -0.71  1.38  2.183  0.081
+##   2  -0.87 -0.47 -0.28  0.665  1.820
+##   3  -1.09  0.20  0.79 -0.125  2.872
+##   4  -1.94  0.36 -0.29 -0.611  0.389
+##   5  -1.80  1.82 -1.08  1.230 -1.899
+##   6  -0.79  0.93  0.17 -0.338 -0.483
+##   7   0.24 -1.78 -0.43 -0.576 -0.424
+##   8   0.57 -0.41 -0.62  2.449  0.921
+##   9  -0.41 -0.69  0.59  0.072 -0.102
+##   10 -0.78  1.30 -0.69  1.245 -1.106</code></pre>
 <p>Because the matrix was converted to a <code>draws_matrix</code>, all of the methods for working with <code>draws</code> objects described in subsequent sections of this vignette will now be available.</p>
 <p>Instead of <code><a href="../reference/draws_matrix.html">as_draws_matrix()</a></code> we also could have just used <code><a href="../reference/draws.html">as_draws()</a></code>, which attempts to find the closest available format to the input object. In this case the result would be a <code>draws_matrix</code> object either way.</p>
 </div>
@@ -308,17 +308,17 @@ <h4 class="hasAnchor">
 <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div>
 <pre><code>## # A draws_matrix: 50 iterations, 1 chains, and 2 variables
 ##     variable
-## draw alpha  beta
-##   1   1.52  0.59
-##   2  -0.82 -0.51
-##   3   0.19 -0.46
-##   4  -0.89  0.86
-##   5  -0.44 -0.86
-##   6  -1.39  0.35
-##   7   0.26  0.96
-##   8  -0.19 -1.23
-##   9  -0.69 -0.26
-##   10  0.87 -0.23
+## draw alpha   beta
+##   1   0.63 -0.043
+##   2  -0.44 -0.494
+##   3   0.56 -1.099
+##   4  -0.68 -1.160
+##   5  -0.35 -0.860
+##   6  -0.88  1.651
+##   7   0.68  0.814
+##   8  -1.32 -0.556
+##   9   0.56  0.214
+##   10 -1.99 -0.562
 ## # ... with 40 more draws</code></pre>
 <p>Analogous functions exist for the other draws formats and are used similarly.</p>
 </div>
@@ -426,11 +426,11 @@ <h3 class="hasAnchor">
 <pre><code>## # A draws_matrix: 5 iterations, 1 chains, and 3 variables
 ##     variable
 ## draw alpha  beta theta
-##    1 -1.10  0.77  1.21
-##    2  1.36 -0.53  0.56
-##    3  1.14  0.42  0.75
-##    4  2.43  1.16  1.01
-##    5  0.77 -1.58  1.11</code></pre>
+##    1  0.22 -0.93  0.42
+##    2 -0.24  0.11  1.55
+##    3 -1.17 -0.74  0.51
+##    4 -0.95 -0.74  0.35
+##    5  0.28  0.58  0.62</code></pre>
 <p>Because <code>x1</code> and <code>x2</code> have the same variables, we can bind them along the <code>'draw'</code> dimension to create a single <code>draws_matrix</code> with more draws:</p>
 <div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">x5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/bind_draws.html">bind_draws</a></span><span class="op">(</span><span class="va">x1</span>, <span class="va">x2</span>, along <span class="op">=</span> <span class="st">"draw"</span><span class="op">)</span>
@@ -438,16 +438,16 @@ <h3 class="hasAnchor">
 <pre><code>## # A draws_matrix: 10 iterations, 1 chains, and 2 variables
 ##     variable
 ## draw alpha  beta
-##   1  -1.10  0.77
-##   2   1.36 -0.53
-##   3   1.14  0.42
-##   4   2.43  1.16
-##   5   0.77 -1.58
-##   6  -0.87  0.48
-##   7   2.42 -0.48
-##   8  -1.73  1.96
-##   9   1.00  0.58
-##   10 -0.36  0.87</code></pre>
+##   1   0.22 -0.93
+##   2  -0.24  0.11
+##   3  -1.17 -0.74
+##   4  -0.95 -0.74
+##   5   0.28  0.58
+##   6   0.36  1.12
+##   7   1.53  1.60
+##   8   0.79  0.36
+##   9   0.46 -1.08
+##   10 -0.17 -1.22</code></pre>
 <p>As with all posterior methods, <code><a href="../reference/bind_draws.html">bind_draws()</a></code> can be used with all draws formats and depending on the format different dimensions are available to bind on. For example, we can bind <code>draws_array</code> objects together by <code>iteration</code>, <code>chain</code>, or <code>variable</code>, but a 2-D <code>draws_matrix</code> with the chains combined can only by bound by <code>draw</code> and <code>variable</code>.</p>
 </div>
 </div>
@@ -533,16 +533,16 @@ <h3 class="hasAnchor">
 <pre><code>## # A tibble: 10 x 2
 ##    variable weighted_mean
 ##    &lt;chr&gt;            &lt;dbl&gt;
-##  1 mu                4.32
-##  2 tau               4.01
-##  3 theta[1]          6.34
-##  4 theta[2]          5.27
-##  5 theta[3]          2.90
-##  6 theta[4]          4.85
-##  7 theta[5]          3.47
-##  8 theta[6]          4.15
-##  9 theta[7]          6.77
-## 10 theta[8]          5.06</code></pre>
+##  1 mu                4.15
+##  2 tau               4.04
+##  3 theta[1]          6.57
+##  4 theta[2]          5.12
+##  5 theta[3]          2.81
+##  6 theta[4]          4.87
+##  7 theta[5]          3.13
+##  8 theta[6]          4.27
+##  9 theta[7]          6.25
+## 10 theta[8]          4.73</code></pre>
 </div>
 <div id="specifying-functions-using-lambda-like-syntax" class="section level3">
 <h3 class="hasAnchor">
diff --git a/vignettes/posterior.Rmd b/vignettes/posterior.Rmd
index 189e8e44..85584539 100644
--- a/vignettes/posterior.Rmd
+++ b/vignettes/posterior.Rmd
@@ -27,11 +27,10 @@ from Bayesian models. The primary goals of the package are to:
 
 ## Installation
 
-The package is not on CRAN yet, but you can install the latest beta release 
-version via 
+You can install the latest official release version via
 
 ```{r install, eval=FALSE}
-install.packages("posterior", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
+install.packages("posterior")
 ```
 
 or the latest development version from GitHub via 

From acc3054fd806078641e26300456a34280702c2a7 Mon Sep 17 00:00:00 2001
From: Paul Buerkner <paul.buerkner@gmail.com>
Date: Wed, 14 Jul 2021 12:32:45 +0200
Subject: [PATCH 2/2] README: minor cleaning

---
 README.Rmd |  8 +-----
 README.md  | 72 +++++++++++++++++++++++++++---------------------------
 2 files changed, 37 insertions(+), 43 deletions(-)

diff --git a/README.Rmd b/README.Rmd
index ed2518d4..f4a5e4bc 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -58,13 +58,7 @@ You can install the latest official release version via
 install.packages("posterior")
 ```
 
-Alternatively, you can install binaries of the current development version via
-
-```{r install_mc_stan, eval=FALSE}
-install.packages("posterior", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
-```
-
-or directly build the package from GitHub via
+or build the developmental version directly from GitHub via
 
 ```{r install_github, eval=FALSE}
 # install.packages("remotes")
diff --git a/README.md b/README.md
index dc6af9c5..c36943d4 100644
--- a/README.md
+++ b/README.md
@@ -43,7 +43,7 @@ You can install the latest official release version via
 install.packages("posterior")
 ```
 
-or directly build the package from GitHub via
+or build the developmental version directly from GitHub via
 
 ``` r
 # install.packages("remotes")
@@ -293,12 +293,12 @@ x4 <- bind_draws(x1, x3, along = "variable")
 print(x4)
 #> # A draws_matrix: 5 iterations, 1 chains, and 3 variables
 #>     variable
-#> draw  alpha beta theta
-#>    1  0.240    1  0.59
-#>    2  0.232    1  0.25
-#>    3 -1.234    1  0.70
-#>    4  0.479    1  1.41
-#>    5  0.013    1  1.28
+#> draw alpha beta theta
+#>    1 -0.82    1  0.54
+#>    2  0.53    1  0.54
+#>    3 -0.79    1  0.38
+#>    4  0.92    1  0.58
+#>    5 -0.17    1  0.17
 ```
 
 Or, we can bind `x1` and `x2` together along the `'draw'` dimension:
@@ -308,17 +308,17 @@ x5 <- bind_draws(x1, x2, along = "draw")
 print(x5)
 #> # A draws_matrix: 10 iterations, 1 chains, and 2 variables
 #>     variable
-#> draw   alpha beta
-#>   1   0.2400    1
-#>   2   0.2319    1
-#>   3  -1.2345    1
-#>   4   0.4795    1
-#>   5   0.0134    1
-#>   6  -1.0251    2
-#>   7  -1.9515    2
-#>   8  -0.0013    2
-#>   9   1.6684    2
-#>   10  0.2678    2
+#> draw  alpha beta
+#>   1  -0.820    1
+#>   2   0.527    1
+#>   3  -0.789    1
+#>   4   0.925    1
+#>   5  -0.169    1
+#>   6  -0.193    2
+#>   7   1.535    2
+#>   8   0.502    2
+#>   9  -0.207    2
+#>   10 -0.085    2
 ```
 
 As with all **posterior** methods, `bind_draws` can be used with all
@@ -337,27 +337,27 @@ x <- as_draws_matrix(x)
 print(x)
 #> # A draws_matrix: 10 iterations, 1 chains, and 5 variables
 #>     variable
-#> draw     V1     V2      V3     V4    V5
-#>   1  -0.382 -0.429  0.1463  0.762  2.33
-#>   2  -0.160 -0.211  0.9480 -0.760  1.11
-#>   3  -0.048  0.085  0.5779 -0.627 -0.88
-#>   4   0.513  1.053 -0.7525  1.033 -1.09
-#>   5   1.455 -0.779  1.4205 -1.766  0.16
-#>   6   0.019 -1.131  0.0088 -0.094  0.54
-#>   7   0.767 -1.511  0.7245  0.843  0.28
-#>   8  -0.953 -0.200  1.9397  0.520 -0.58
-#>   9   1.173 -0.325 -0.4821  0.948  1.14
-#>   10  0.873  0.486  1.4913 -0.693  1.02
+#> draw     V1     V2     V3      V4     V5
+#>   1  -0.203  0.616 -1.770 -0.4751 -0.931
+#>   2   0.077  1.060  0.664  0.3097  1.492
+#>   3  -1.733 -0.511  0.215 -0.4082  0.478
+#>   4  -1.127 -0.084  0.039 -0.0935  1.517
+#>   5  -2.102 -0.152  2.204  0.1133 -0.815
+#>   6  -0.304  0.502 -0.090 -0.1632  1.528
+#>   7  -0.802 -1.780  0.416  0.0023  0.265
+#>   8  -0.459  0.804  0.350 -0.2718  1.313
+#>   9   1.116 -2.127 -1.598 -0.7790  0.038
+#>   10 -1.033 -0.694  0.673 -0.0686 -1.437
 
 summarise_draws(x, "mean", "sd", "median", "mad")
 #> # A tibble: 5 x 5
-#>   variable    mean    sd median   mad
-#>   <chr>      <dbl> <dbl>  <dbl> <dbl>
-#> 1 V1        0.326  0.755  0.266 0.822
-#> 2 V2       -0.296  0.747 -0.268 0.641
-#> 3 V3        0.602  0.879  0.651 1.05 
-#> 4 V4        0.0166 0.949  0.213 1.15 
-#> 5 V5        0.403  1.06   0.412 1.06
+#>   variable   mean    sd median   mad
+#>   <chr>     <dbl> <dbl>  <dbl> <dbl>
+#> 1 V1       -0.657 0.924 -0.631 0.685
+#> 2 V2       -0.237 1.07  -0.118 1.00 
+#> 3 V3        0.110 1.14   0.283 0.559
+#> 4 V4       -0.183 0.314 -0.128 0.285
+#> 5 V5        0.345 1.12   0.371 1.68
 ```
 
 Instead of `as_draws_matrix()` we also could have just used