regenerated the manual with minor changes

gnu-octave · Jan 3, 2024 · c23bfb6 · c23bfb6
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diff --git a/README.md b/README.md
@@ -46,7 +46,7 @@ To install (or test) the statistics-resampling package at it's existing location
 
 ### Usage
 
-All help and demos are documented under 'overview.html' in the 'manual' folder. Note that there are two links to the folder containing the manual, one that works in Windows and one that works on Unix-based platforms such as Mac and Linux. For the best experience navigating the manual, please ensure that javascript is enabled in your browser.
+All help and demos are documented on the 'Function Reference' page (overview.html) in the manual. For the best experience navigating the manual, please ensure that javascript is enabled in your browser.
 
 Function help can also be requested from the Octave/MATLAB command prompt, by typing `help function-name`. 
 

diff --git a/man/generate_manual.m b/man/generate_manual.m
@@ -17,7 +17,7 @@
 % Customize the options
 myopt.include_package_news = false;
 myopt.include_alpha = false;
-myopt.include_demos = false;
+myopt.include_demos = true;
 myopt.download_link = "https://gnu-octave.github.io/packages/statistics-resampling/";
 myopt.repository_link = "https://github.com/gnu-octave/statistics-resampling/";
 myopt.older_versions_download = "https://github.com/gnu-octave/statistics-resampling/releases";
@@ -63,7 +63,7 @@
 
 % Add hyperlink to function reference directly in the HTML of the readme file
 % (since the link in the markdown file would fail on the GitHub page) 
-system ('sed -i '''' -e  ''s/overview.html/\<a href\=\"overview\.html\"\>overview.html\<\/a\>/g'' ./man/manual_docs/statistics-resampling/readme.html');
+system ('sed -i '''' -e  ''s/Function Reference/\<a href\=\"overview\.html\"\>Function Reference\<\/a\>/g'' ./man/manual_docs/statistics-resampling/readme.html');
 
 % Update meta information in all html files
 system ('sed -i '''' -e  ''s/\<meta name\=\"author\" content\=\"\(.*\)\" \/\>/\<meta name\=\"author\" content\=\"Andrew Penn\" \/\>/'' ./man/manual_docs/statistics-resampling/*.html');
@@ -79,7 +79,7 @@
 if exist ('./manual', 'dir')
   delete ('./manual')
 end
-system ('ln -s ./man/manual_docs/statistics-resampling manual');
+system ('ln -s ./man/manual_docs/statistics-resampling/ manual');
 
 % Change back to man directory
 cd man

diff --git a/man/manual_docs/Thumbs.db b/man/manual_docs/Thumbs.db
diff --git a/man/manual_docs/Thumbs.db:encryptable b/man/manual_docs/Thumbs.db:encryptable
diff --git a/man/manual_docs/statistics-resampling/COPYING.html b/man/manual_docs/statistics-resampling/COPYING.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
   <head>
   <meta http-equiv="content-type" content="text/html; charset=utf-8" />
-  <meta name="date" content="2024-01-02"/>
+  <meta name="date" content="2024-01-03"/>
   <meta name="generator" content="generate_html 0.3.3" />
   <meta name="author" content="Andrew Penn" />
   <meta name="description" content="A package for statistical analysis using resampling methods." />

diff --git a/man/manual_docs/statistics-resampling/description.json b/man/manual_docs/statistics-resampling/description.json
@@ -1,14 +1,14 @@
 {
   "generator": "generate_html",
   "generator_version": "0.3.3",
-  "date_generated": "2024-01-02",
+  "date_generated": "2024-01-03",
   "package": 
   {
     "name": "statistics-resampling",
-    "version": "5.5.2",
+    "version": "5.5.3",
     "description": "The statistics-resampling package is an Octave  package and Matlab toolbox that can be used to overcome a wide  variety of statistics problems using non-parametric resampling  methods. In particular, the functions included can be used to  estimate bias, uncertainty (standard errors and confidence  intervals), prediction error, and test hypotheses (p-values).  Variations of the resampling methods are included that improve  the accuracy of the statistics for small samples and samples  with complex dependence structures.",
     "shortdescription": "The statistics-resampling package is an Octave  package and Matlab toolbox that can be used to overcome a wide  variety of statistics problems using non-parametric resampling  methods",
-    "date": "2024-01-02",
+    "date": "2024-01-03",
     "title": "A statistics package with a variety of resampling tools",
     "author": "Andrew Penn <[email protected]>",
     "maintainer": "Andrew Penn <[email protected]>",

diff --git a/man/manual_docs/statistics-resampling/function/boot.html b/man/manual_docs/statistics-resampling/function/boot.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
   <head>
   <meta http-equiv="content-type" content="text/html; charset=utf-8" />
-  <meta name="date" content="2024-01-02"/>
+  <meta name="date" content="2024-01-03"/>
   <meta name="generator" content="generate_html 0.3.3" />
   <meta name="author" content="Andrew Penn" />
   <meta name="description" content="A package for statistical analysis using resampling methods." />
@@ -111,9 +111,9 @@ <h2>Demonstration 1</h2>
 <p>Produces the following output</p>
 <pre class="example">ans =
 
-   2   2   3   3   1   1   2   2   3   2   2   3   3   1   3   2   1   2   3   1
-   2   3   3   2   1   1   1   2   3   3   3   1   1   2   3   3   2   1   1   2
-   3   2   3   3   2   2   2   1   3   3   1   1   1   1   2   1   2   1   3   1</pre>
+   3   1   1   2   3   3   2   1   2   2   3   1   3   1   3   1   1   3   3   3
+   2   2   3   3   1   1   3   1   2   1   1   2   2   2   2   2   3   3   2   3
+   1   2   1   3   1   1   1   1   2   2   3   1   3   2   2   2   3   1   2   3</pre>
 </div>
 <h2>Demonstration 2</h2>
 <div class="demo">
@@ -125,9 +125,9 @@ <h2>Demonstration 2</h2>
 <p>Produces the following output</p>
 <pre class="example">ans =
 
-   3   3   2   3   1   2   2   1   1   3   3   1   2   3   2   2   1   2   2   3
-   2   1   1   2   1   1   3   1   1   3   3   2   3   1   1   3   1   2   2   2
-   2   3   1   3   3   2   3   1   1   3   3   1   3   3   1   2   1   2   2   2</pre>
+   3   3   1   2   3   1   2   1   2   2   1   1   3   1   2   2   3   1   1   1
+   3   3   2   3   3   2   2   1   2   2   1   2   3   1   2   3   3   2   3   1
+   3   1   1   2   3   2   3   1   1   3   3   2   3   1   2   3   1   2   1   2</pre>
 </div>
 <h2>Demonstration 3</h2>
 <div class="demo">

diff --git a/man/manual_docs/statistics-resampling/function/boot1way.html b/man/manual_docs/statistics-resampling/function/boot1way.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
   <head>
   <meta http-equiv="content-type" content="text/html; charset=utf-8" />
-  <meta name="date" content="2024-01-02"/>
+  <meta name="date" content="2024-01-03"/>
   <meta name="generator" content="generate_html 0.3.3" />
   <meta name="author" content="Andrew Penn" />
   <meta name="description" content="A package for statistical analysis using resampling methods." />
@@ -472,7 +472,7 @@ <h2>Demonstration 6</h2>
 -----------------------------------------------------------------------------
 | Comparison |     Test # |      Ref # | Difference |          t |        p |
 |------------|------------|------------|------------|------------|----------|
-|          1 |          2 |          1 |    +0.8209 |      +2.12 |     .059 |
+|          1 |          2 |          1 |    +0.4115 |      +0.82 |     .371 |
 
 -----------------------------------------------------------------------------
 |    GROUP # |                                       GROUP label |        N |
@@ -517,7 +517,7 @@ <h2>Demonstration 7</h2>
 -----------------------------------------------------------------------------
 | Comparison |     Test # |      Ref # | Difference |          t |        p |
 |------------|------------|------------|------------|------------|----------|
-|          1 |          2 |          1 |    +0.1060 |      +0.14 |     .869 |
+|          1 |          2 |          1 |   -0.01201 |      -0.02 |     .975 |
 
 -----------------------------------------------------------------------------
 |    GROUP # |                                       GROUP label |        N |

diff --git a/man/manual_docs/statistics-resampling/function/bootbayes.html b/man/manual_docs/statistics-resampling/function/bootbayes.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
   <head>
   <meta http-equiv="content-type" content="text/html; charset=utf-8" />
-  <meta name="date" content="2024-01-02"/>
+  <meta name="date" content="2024-01-03"/>
   <meta name="generator" content="generate_html 0.3.3" />
   <meta name="author" content="Andrew Penn" />
   <meta name="description" content="A package for statistical analysis using resampling methods." />
@@ -185,7 +185,7 @@ <h2>Demonstration 1</h2>
 
 Posterior Statistics: 
  original     bias         median       stdev       CI_lower      CI_upper
- +184.5       +0.001564    +184.5       1.297       +181.9        +186.9</pre>
+ +184.5       +0.04851     +184.5       1.332       +181.9        +187.1</pre>
 </div>
 <h2>Demonstration 2</h2>
 <div class="demo">
@@ -221,8 +221,8 @@ <h2>Demonstration 2</h2>
 
 Posterior Statistics: 
  original     bias         median       stdev       CI_lower      CI_upper
- +175.5       +0.007876    +175.5       2.448       +171.0        +180.6    
- +0.1904      -0.001330    +0.1895      0.08048     +0.02760      +0.3412</pre>
+ +175.5       +0.03707     +175.5       2.396       +171.2        +180.6    
+ +0.1904      -0.001122    +0.1924      0.08038     +0.02220      +0.3359</pre>
 </div>
 
 <p>Package: <a href="../index.html">statistics-resampling</a></p>

diff --git a/man/manual_docs/statistics-resampling/function/bootcdf.html b/man/manual_docs/statistics-resampling/function/bootcdf.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
   <head>
   <meta http-equiv="content-type" content="text/html; charset=utf-8" />
-  <meta name="date" content="2024-01-02"/>
+  <meta name="date" content="2024-01-03"/>
   <meta name="generator" content="generate_html 0.3.3" />
   <meta name="author" content="Andrew Penn" />
   <meta name="description" content="A package for statistical analysis using resampling methods." />

diff --git a/man/manual_docs/statistics-resampling/function/bootci.html b/man/manual_docs/statistics-resampling/function/bootci.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
   <head>
   <meta http-equiv="content-type" content="text/html; charset=utf-8" />
-  <meta name="date" content="2024-01-02"/>
+  <meta name="date" content="2024-01-03"/>
   <meta name="generator" content="generate_html 0.3.3" />
   <meta name="author" content="Andrew Penn" />
   <meta name="description" content="A package for statistical analysis using resampling methods." />
@@ -182,8 +182,8 @@ <h2>Demonstration 1</h2>
 <p>Produces the following output</p>
 <pre class="example">ci =
 
-   23.825
-   34.411</pre>
+   23.616
+   34.358</pre>
 </div>
 <h2>Demonstration 2</h2>
 <div class="demo">
@@ -201,8 +201,8 @@ <h2>Demonstration 2</h2>
 <p>Produces the following output</p>
 <pre class="example">ci =
 
-   23.462
-   34.651</pre>
+   23.975
+   34.269</pre>
 </div>
 <h2>Demonstration 3</h2>
 <div class="demo">
@@ -221,8 +221,8 @@ <h2>Demonstration 3</h2>
 <p>Produces the following output</p>
 <pre class="example">ci =
 
-   24.811
-   36.698</pre>
+   25.040
+   36.477</pre>
 </div>
 <h2>Demonstration 4</h2>
 <div class="demo">
@@ -238,8 +238,8 @@ <h2>Demonstration 4</h2>
 <p>Produces the following output</p>
 <pre class="example">ci =
 
-   100.29
-   233.90</pre>
+    96.629
+   235.910</pre>
 </div>
 <h2>Demonstration 5</h2>
 <div class="demo">
@@ -255,8 +255,8 @@ <h2>Demonstration 5</h2>
 <p>Produces the following output</p>
 <pre class="example">ci =
 
-   116.40
-   265.89</pre>
+   117.01
+   260.73</pre>
 </div>
 <h2>Demonstration 6</h2>
 <div class="demo">
@@ -275,8 +275,8 @@ <h2>Demonstration 6</h2>
 <p>Produces the following output</p>
 <pre class="example">ci =
 
-   106.75
-   290.95</pre>
+   108.55
+   297.71</pre>
 </div>
 <h2>Demonstration 7</h2>
 <div class="demo">
@@ -295,8 +295,8 @@ <h2>Demonstration 7</h2>
 <p>Produces the following output</p>
 <pre class="example">ci =
 
-   115.81
-   278.35</pre>
+   111.53
+   268.13</pre>
 </div>
 <h2>Demonstration 8</h2>
 <div class="demo">
@@ -316,8 +316,8 @@ <h2>Demonstration 8</h2>
 <p>Produces the following output</p>
 <pre class="example">ci =
 
-   0.5167
-   0.8730</pre>
+   0.5050
+   0.8633</pre>
 </div>
 <h2>Demonstration 9</h2>
 <div class="demo">

diff --git a/man/manual_docs/statistics-resampling/function/bootclust.html b/man/manual_docs/statistics-resampling/function/bootclust.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
   <head>
   <meta http-equiv="content-type" content="text/html; charset=utf-8" />
-  <meta name="date" content="2024-01-02"/>
+  <meta name="date" content="2024-01-03"/>
   <meta name="generator" content="generate_html 0.3.3" />
   <meta name="author" content="Andrew Penn" />
   <meta name="description" content="A package for statistical analysis using resampling methods." />
@@ -168,11 +168,11 @@ <h2>Demonstration 1</h2>
  Resampling method: Balanced, bootstrap cluster resampling 
  Number of resamples: 1999 
  Confidence interval (CI) type: Expanded bias-corrected and accelerated (BCa) 
- Nominal coverage (and the percentiles used): 95% (1.1%, 97.3%)
+ Nominal coverage (and the percentiles used): 95% (1.2%, 97.5%)
 
 Bootstrap Statistics: 
  original     bias         std_error    CI_lower     CI_upper  
- +29.65       -4.263e-14   +2.546       +23.68       +34.36</pre>
+ +29.65       -3.197e-14   +2.518       +23.91       +34.42</pre>
 </div>
 <h2>Demonstration 2</h2>
 <div class="demo">
@@ -197,11 +197,11 @@ <h2>Demonstration 2</h2>
  Resampling method: Balanced, bootstrap cluster resampling 
  Number of resamples: 1999 
  Confidence interval (CI) type: Expanded bias-corrected and accelerated (BCa) 
- Nominal coverage (and the percentiles used): 95% (1.2%, 98.9%)
+ Nominal coverage (and the percentiles used): 95% (1.0%, 98.7%)
 
 Bootstrap Statistics: 
  original     bias         std_error    CI_lower     CI_upper  
- +29.65       -0.03856     +2.929       +22.93       +35.81</pre>
+ +29.65       -0.04059     +2.946       +22.64       +35.77</pre>
 </div>
 <h2>Demonstration 3</h2>
 <div class="demo">
@@ -228,7 +228,7 @@ <h2>Demonstration 3</h2>
 
 Bootstrap Statistics: 
  original     bias         std_error    CI_lower     CI_upper  
- +171.5       -6.371       +40.29       +100.4       +233.2</pre>
+ +171.5       -6.896       +42.17       +97.64       +236.2</pre>
 </div>
 <h2>Demonstration 4</h2>
 <div class="demo">
@@ -257,7 +257,7 @@ <h2>Demonstration 4</h2>
 
 Bootstrap Statistics: 
  original     bias         std_error    CI_lower     CI_upper  
- +171.5       -8.998       +32.89       +106.2       +214.7</pre>
+ +171.5       -9.648       +33.55       +105.4       +215.7</pre>
 </div>
 <h2>Demonstration 5</h2>
 <div class="demo">
@@ -279,11 +279,11 @@ <h2>Demonstration 5</h2>
  Resampling method: Balanced, bootstrap cluster resampling 
  Number of resamples: 1999 
  Confidence interval (CI) type: Bias-corrected and accelerated (BCa) 
- Nominal coverage (and the percentiles used): 90% (11.9%, 98.7%)
+ Nominal coverage (and the percentiles used): 90% (12.1%, 98.7%)
 
 Bootstrap Statistics: 
  original     bias         std_error    CI_lower     CI_upper  
- +171.5       -6.692       +42.45       +114.8       +259.5</pre>
+ +171.5       -6.468       +41.43       +116.5       +260.9</pre>
 </div>
 <h2>Demonstration 6</h2>
 <div class="demo">
@@ -307,11 +307,11 @@ <h2>Demonstration 6</h2>
  Resampling method: Balanced, bootstrap cluster resampling 
  Number of resamples: 1999 
  Confidence interval (CI) type: Bias-corrected and accelerated (BCa) 
- Nominal coverage (and the percentiles used): 90% (13.1%, 98.7%)
+ Nominal coverage (and the percentiles used): 90% (12.9%, 98.7%)
 
 Bootstrap Statistics: 
  original     bias         std_error    CI_lower     CI_upper  
- +171.5       -9.478       +32.76       +124.0       +229.0</pre>
+ +171.5       -9.204       +33.35       +123.6       +231.5</pre>
 </div>
 <h2>Demonstration 7</h2>
 <div class="demo">
@@ -336,8 +336,8 @@ <h2>Demonstration 7</h2>
 
 Bootstrap Statistics: 
  original     bias         std_error    CI_lower     CI_upper  
- -0.007298    +0.01763     +0.2486      -0.4421      +0.3812    
- -0.4191      +0.002007    +0.3974      -1.037       +0.2626</pre>
+ +0.004343    +0.03624     +0.2375      -0.3956      +0.3770    
+ +0.05687     +0.008261    +0.2293      -0.2890      +0.4664</pre>
 </div>
 <h2>Demonstration 8</h2>
 <div class="demo">
@@ -363,8 +363,8 @@ <h2>Demonstration 8</h2>
 
 Bootstrap Statistics: 
  original     bias         std_error    CI_lower     CI_upper  
- -0.09344     +0.05494     +0.1620      -0.3285      +0.09462   
- +0.1050      -0.04273     +0.4558      -0.4873      +0.7260</pre>
+ +0.008699    -0.02703     +0.1878      -0.2563      +0.3820    
+ +0.1477      -0.04895     +0.2856      -0.4463      +0.4918</pre>
 </div>
 <h2>Demonstration 9</h2>
 <div class="demo">
@@ -394,7 +394,7 @@ <h2>Demonstration 9</h2>
 
 Bootstrap Statistics: 
  original     bias         std_error    CI_lower     CI_upper  
- +0.7764      -0.02417     +0.1438      +0.3894      +0.9917</pre>
+ +0.7764      -0.02512     +0.1479      +0.3828      +0.9978</pre>
 </div>
 
 <p>Package: <a href="../index.html">statistics-resampling</a></p>