[Mmsar-commits] r17 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Feb 7 03:32:17 CET 2010
Author: fguilhaumon
Date: 2010-02-07 03:32:16 +0100 (Sun, 07 Feb 2010)
New Revision: 17
Added:
www/doc_nav.php
www/documentation_datasets.php
www/documentation_functions.php
www/documentation_home.php
www/documentation_install.php
www/documentation_models.php
www/documentation_usage.php
www/footer.php
www/head.php
www/header.php
www/nav.php
www/publications.php
Modified:
www/index.php
Log:
Added: www/doc_nav.php
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--- www/doc_nav.php (rev 0)
+++ www/doc_nav.php 2010-02-07 02:32:16 UTC (rev 17)
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+<div class="box">
+
+ <div class="box-title">Documentation</div>
+
+ <div class="box-content">
+ <ul class="nice-list">
+ <li><strong><a href="documentation_home.php">Home</a></strong></li>
+ <li><a href="documentation_install.php">Installation</a></li>
+ <li><a href="documentation_usage.php">Usage</a></li>
+<!--<li><a href="documentation_plots.html">Plots</a></li>-->
+ <li><a href="documentation_datasets.php">Data sets</a></li>
+ <li><a href="documentation_models.php">Models</a></li>
+ <li><a href="documentation_functions.php">Functions</a></li>
+ </ul>
+ </div>
+
+ </div>
+
Property changes on: www/doc_nav.php
___________________________________________________________________
Name: svn:executable
+ *
Added: www/documentation_datasets.php
===================================================================
--- www/documentation_datasets.php (rev 0)
+++ www/documentation_datasets.php 2010-02-07 02:32:16 UTC (rev 17)
@@ -0,0 +1,138 @@
+<?php include('header.php'); ?>
+ <title>mmSAR - Documentation - Home</title>
+</head>
+
+<body id="top">
+
+<?php include('head.php'); ?>
+<?php include('nav.php'); ?>
+
+<div id="content-wrapper">
+ <div class="center-wrapper">
+
+ <div class="content" id="content-two-columns">
+
+ <div id="main-wrapper">
+ <div id="main">
+
+ <div class="post">
+
+ <div class="post-title"><h1>Data sets</h1></div>
+
+<br/>
+ <div class="post-body">
+
+ <p align="center"><img src="doc_datasets.png" alt="" class="bordered" /></p>
+<br/>
+<div class="notice">A description of available example data sets is expected shortly. The example data sets names are :<br/>
+data.arr<br/>
+data.atl<br/>
+data.galap<br/>
+data.glea<br/>
+data.gleas<br/>
+</div>
+ <p class="large">mmSAR handle SAR data sets as list-objects. A data set is a list of 2 elements :
+<br/>
+<ul>
+ <li><b>$name</b> : a character string specifying the name of the data set</li><br/>
+ <li><b>$data</b> : a R data.frame object with 2 columns :<br/><br/>
+ <ul>
+ <li><b>$a</b> : a numeric vector of areas</li><br/>
+ <li><b>$s</b> : a numeric vector of species richness</li>
+ </ul>
+ </li>
+</ul></p>
+<br/>
+<p class="large">mmSAR provide some example data sets, for example to load a species-area dataset describing the plants of the Galapagos Islands (<a href="publications.html">Preston, 1962</a>) use : </p>
+
+<div class="success">load(data.galap)</div>
+
+
+
+ </div>
+
+ </div>
+
+ </div>
+ </div>
+
+ <div id="sidebar-wrapper">
+ <div id="sidebar">
+
+ <?php include('doc_nav.php'); ?>
+ <div class="box">
+
+ <div class="box-title">Screenshots</div>
+
+ <div class="box-content">
+
+ <div class="thumbnails">
+
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+
+ </div>
+
+
+ </div>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+</div>
+
+<div id="footer-wrapper">
+
+ <div class="center-wrapper">
+
+ <div id="footer">
+
+ <div class="left">
+ <a href="index.html">Home</a> <span class="text-separator">|</span> <a href="documentation_home.html">Documentation</a><span class="text-separator">|</span><a href="publications.html">Publications</a><span class="text-separator">|</span>
+ </div>
+
+ <div class="right">
+ <a href="#">Top ^</a>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+
+</div>
+
+<div id="bottom">
+
+ <div class="center-wrapper">
+
+ <div class="left">
+ © 2009 François Guilhaumon - mmSAR is GPL feel free to use it and contribute to it.<span class="text-separator">|</span>
+ </div>
+
+ <div class="right">
+ <a href="http://templates.arcsin.se/">Website template</a> by <a href="http://arcsin.se/">Arcsin</a>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+</div>
+
+</body>
+</html>
Property changes on: www/documentation_datasets.php
___________________________________________________________________
Name: svn:executable
+ *
Added: www/documentation_functions.php
===================================================================
--- www/documentation_functions.php (rev 0)
+++ www/documentation_functions.php 2010-02-07 02:32:16 UTC (rev 17)
@@ -0,0 +1,123 @@
+<?php include('header.php'); ?>
+ <title>mmSAR - Documentation - Home</title>
+</head>
+
+<body id="top">
+
+<?php include('head.php'); ?>
+<?php include('nav.php'); ?>
+
+<div id="content-wrapper">
+ <div class="center-wrapper">
+
+ <div class="content" id="content-two-columns">
+
+ <div id="main-wrapper">
+ <div id="main">
+
+ <div class="post">
+
+ <div class="post-title"><h1>mmSAR Functions</h1></div>
+
+<br/>
+ <div class="post-body">
+
+ <p align="center"><img src="doc_functions.png" alt="" class="bordered" /></p>
+<br/>
+ <h2 class="quiet">model fitting</h2>
+
+ <p class="large"><b>rssoptim</b> : function (model, data, norTest = "lillie", verb = T)</p>
+
+ <h2 class="quiet">multimodel averaging & confidence intervals</h2>
+
+ <p class="large"><b>multiSAR</b> : function (modelList = c("power","expo","weibull"), data = data.galap, nBoot = 1000, verb = T,
+ crit = "Bayes")</p>
+
+ </div>
+
+ </div>
+
+ </div>
+ </div>
+
+ <div id="sidebar-wrapper">
+ <div id="sidebar">
+
+ <?php include('doc_nav.php'); ?>
+
+ <div class="box">
+
+ <div class="box-title">Screenshots</div>
+
+ <div class="box-content">
+
+ <div class="thumbnails">
+
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+
+ </div>
+
+
+ </div>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+</div>
+
+<div id="footer-wrapper">
+
+ <div class="center-wrapper">
+
+ <div id="footer">
+
+ <div class="left">
+ <a href="index.html">Home</a> <span class="text-separator">|</span> <a href="documentation_home.html">Documentation</a><span class="text-separator">|</span><a href="publications.html">Publications</a><span class="text-separator">|</span>
+ </div>
+
+ <div class="right">
+ <a href="#">Top ^</a>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+
+</div>
+
+<div id="bottom">
+
+ <div class="center-wrapper">
+
+ <div class="left">
+ © 2009 François Guilhaumon - mmSAR is GPL feel free to use it and contribute to it.<span class="text-separator">|</span>
+ </div>
+
+ <div class="right">
+ <a href="http://templates.arcsin.se/">Website template</a> by <a href="http://arcsin.se/">Arcsin</a>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+</div>
+
+</body>
+</html>
Property changes on: www/documentation_functions.php
___________________________________________________________________
Name: svn:executable
+ *
Added: www/documentation_home.php
===================================================================
--- www/documentation_home.php (rev 0)
+++ www/documentation_home.php 2010-02-07 02:32:16 UTC (rev 17)
@@ -0,0 +1,127 @@
+<?php include('header.php'); ?>
+ <title>mmSAR - Documentation - Home</title>
+</head>
+
+<body id="top">
+
+<?php include('head.php'); ?>
+<?php include('nav.php'); ?>
+
+<div id="content-wrapper">
+ <div class="center-wrapper">
+
+ <div class="content" id="content-two-columns">
+
+ <div id="main-wrapper">
+ <div id="main">
+
+ <div class="post">
+
+ <div class="post-title"><h1>Documentation Home</h1></div>
+
+<br/>
+ <div class="post-body">
+
+ <p align="center"><img src="doc_home.png" width="640" alt="" class="bordered" /><br/>Objects of the mmSAR package (data sets, models, optimization function and model averagin function).</p>
+<br/>
+ <h2 class="quiet">mmSAR overview</h2>
+
+ <p class="large">mmSAR is a flexible and scalable implementation of the multimodel SAR framework for species-area datasets (<a href="publications.html">Guilhaumon et al. 2008</a>). </p>
+
+ <p class="large">mmSAR implements the basic bricks of the multimodel inference paradigm (<a href="publications.html">Burnham & Anderson, 2002</a>) with simple R list-objects and functions. The package is scalable and users can easily create their own model and data objects.</p>
+
+ <p class="large">If you are new to multimodel inference or non linear SAR fitting, a good start is the <a href="publications.html">Guilhaumon et al. (2008)</a> paper (freely available at the PNAS website), particularly the methods section and the supplementary material <a href="http://www.pnas.org/content/suppl/2008/10/01/0803610105.DCSupplemental/0803610105SI.pdf" target="_blank" title="link to supporting information at the PNAS website"><img src="pdf.png" alt="link to supporting information at the PNAS website" title="link to supporting information at the PNAS website" align="bottom" height="16" width="16"></a>.</p>
+
+
+ <div class="error"><p class="large">In order to use mmSAR, a basic knowledge of R is expected. R and related documentations can be downloaded at
+<a href="http://www.r-project.org/" target="_new">http://www.r-project.org/</a>.<br/>
+Although mmSAR is user friendly, the knowledge of some concepts such as <i>functions</i> and some R objects types such as <i>lists</i> is required.</p></div>
+
+
+ </div>
+
+ </div>
+
+ </div>
+ </div>
+
+ <div id="sidebar-wrapper">
+ <div id="sidebar">
+
+ <?php include('doc_nav.php'); ?>
+ <div class="box">
+
+ <div class="box-title">Screenshots</div>
+
+ <div class="box-content">
+
+ <div class="thumbnails">
+
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+
+ </div>
+
+
+ </div>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+</div>
+
+<div id="footer-wrapper">
+
+ <div class="center-wrapper">
+
+ <div id="footer">
+
+ <div class="left">
+ <a href="index.html">Home</a> <span class="text-separator">|</span> <a href="documentation_home.html">Documentation</a><span class="text-separator">|</span><a href="publications.html">Publications</a><span class="text-separator">|</span>
+ </div>
+
+ <div class="right">
+ <a href="#">Top ^</a>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+
+</div>
+
+<div id="bottom">
+
+ <div class="center-wrapper">
+
+ <div class="left">
+ © 2009 François Guilhaumon - mmSAR is GPL feel free to use it and contribute to it.<span class="text-separator">|</span>
+ </div>
+
+ <div class="right">
+ <a href="http://templates.arcsin.se/">Website template</a> by <a href="http://arcsin.se/">Arcsin</a>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+</div>
+
+</body>
+</html>
Property changes on: www/documentation_home.php
___________________________________________________________________
Name: svn:executable
+ *
Added: www/documentation_install.php
===================================================================
--- www/documentation_install.php (rev 0)
+++ www/documentation_install.php 2010-02-07 02:32:16 UTC (rev 17)
@@ -0,0 +1,123 @@
+<?php include('header.php'); ?>
+ <title>mmSAR - Documentation - Home</title>
+</head>
+
+<body id="top">
+
+<?php include('head.php'); ?>
+<?php include('nav.php'); ?>
+
+<div id="content-wrapper">
+ <div class="center-wrapper">
+
+ <div class="content" id="content-two-columns">
+
+ <div id="main-wrapper">
+ <div id="main">
+
+ <div class="post">
+
+ <div class="post-title"><h1>Installation</h1></div>
+
+<br/>
+ <div class="post-body">
+
+ <p class="large">To install the mmSAR package directly within R type:</p>
+
+<div class="success">install.packages("mmSAR", repos="http://R-Forge.R-project.org")</div>
+
+ <p class="large">You need an internet connexion and administrators privileges under linux to do this.<br/><br/>Whenever you do not have admin rights on the system you are running R, you can install the package locally.<br/><br/>Assuming you own a directly located at 'myPackagesDirectoryPath', you can install the mmSAR package locally in the 'myPackagesDirectory' directory using the 'lib' argument of the 'install.packages' function :</p>
+
+<div class="success">install.packages("mmSAR", repos="http://R-Forge.R-project.org", lib="myPackagesDirectoryPath")</div>
+
+ <p class="large">After that when loading the mmSAR package, use the 'lib.loc' argument of the 'library' function to find the package :</p>
+
+<div class="success">library(mmSAR, lib.loc="myPackagesDirectoryPath")</div>
+
+ </div>
+
+ </div>
+
+ </div>
+ </div>
+
+ <div id="sidebar-wrapper">
+ <div id="sidebar">
+
+ <?php include('doc_nav.php'); ?>
+ <div class="box">
+
+ <div class="box-title">Screenshots</div>
+
+ <div class="box-content">
+
+ <div class="thumbnails">
+
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+
+ </div>
+
+
+ </div>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+</div>
+
+<div id="footer-wrapper">
+
+ <div class="center-wrapper">
+
+ <div id="footer">
+
+ <div class="left">
+ <a href="index.html">Home</a> <span class="text-separator">|</span> <a href="documentation_home.html">Documentation</a><span class="text-separator">|</span><a href="publications.html">Publications</a><span class="text-separator">|</span>
+ </div>
+
+ <div class="right">
+ <a href="#">Top ^</a>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+
+</div>
+
+<div id="bottom">
+
+ <div class="center-wrapper">
+
+ <div class="left">
+ © 2009 François Guilhaumon - mmSAR is GPL feel free to use it and contribute to it.<span class="text-separator">|</span>
+ </div>
+
+ <div class="right">
+ <a href="http://templates.arcsin.se/">Website template</a> by <a href="http://arcsin.se/">Arcsin</a>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+</div>
+
+</body>
+</html>
Property changes on: www/documentation_install.php
___________________________________________________________________
Name: svn:executable
+ *
Added: www/documentation_models.php
===================================================================
--- www/documentation_models.php (rev 0)
+++ www/documentation_models.php 2010-02-07 02:32:16 UTC (rev 17)
@@ -0,0 +1,205 @@
+<?php include('header.php'); ?>
+ <title>mmSAR - Documentation - Home</title>
+</head>
+
+<body id="top">
+
+<?php include('head.php'); ?>
+<?php include('nav.php'); ?>
+
+<div id="content-wrapper">
+ <div class="center-wrapper">
+
+ <div class="content" id="content-two-columns">
+
+ <div id="main-wrapper">
+ <div id="main">
+
+ <div class="post">
+
+ <div class="post-title"><h1>Models</h1></div>
+
+<br/>
+ <div class="post-body">
+<p align="center"><img src="doc_models.png" alt="" class="bordered" /></p>
+<br/>
+
+
+<p class="large">Currently, mmSAR handles 8 non linear SAR models such as the power SAR model and others :<br/>
+<table class="data-table">
+ <tr>
+ <th>Name</td>
+ <th>Formula</td>
+ <th>Parameters</td>
+ <th>Shape</td>
+ <th>Asymptotic</td>
+ </tr>
+ <tr>
+ <td>power</td>
+ <td>S = cA<SUP>z</SUP></td>
+ <td>2</td>
+ <td>convex</td>
+ <td>no</td>
+ </tr>
+ <tr>
+ <td>exponential</td>
+ <td>S = c + zlog(A)</td>
+ <td>2</td>
+ <td>convex</td>
+ <td>no</td>
+ </tr>
+ <tr>
+ <td>negative
+ exponential</td>
+ <td>S = c(1 -
+ exp(-zA))</td>
+ <td>2</td>
+ <td>convex</td>
+ <td>yes</td>
+ </tr>
+ <tr>
+ <td>Monod</td>
+ <td>S = (cA) / (z + A)</td>
+ <td>2</td>
+ <td>convex</td>
+ <td>yes</td>
+ </tr>
+ <tr>
+ <td>rational
+ function</td>
+ <td>S = (c + zA) / (1 + fA)</td>
+ <td>3</td>
+ <td>convex</td>
+ <td>yes</td>
+ </tr>
+ <tr>
+ <td>logistic</td>
+ <td>S = c / (1 + exp(-zA+f)</td>
+ <td>3</td>
+ <td>sigmoid</td>
+ <td>yes</td>
+ </tr>
+ <tr>
+ <td>Lomolino</td>
+ <td>S = c / 1 + (z<SUP>log(f/A)</SUP>)</td>
+ <td>3</td>
+ <td>sigmoid</td>
+ <td>yes</td>
+ </tr>
+ <tr>
+ <td>cumulative
+ Weibull</td>
+ <td>S = c(1 - exp(-zA<SUP>f</SUP>))
+
+ </td>
+ <td>3</td>
+ <td>sigmoid</td>
+ <td>yes</td>
+ </tr>
+</table>
+</p>
+
+
+ <p class="large">mmSAR handle SAR models as list-objects. A model is a list of 8 elements (examples ar given for the exponential model) :<br/>
+<br/>
+<ul>
+ <li><b>$name</b> : a character string specifying the name of the model (ex: "expo")</li><br/>
+ <li><b>$formula </b>: an R expression with named parameters (ex: expression(s == z * log(a) + c) )</li><br/>
+ <li><b>$paramnumber</b> : a numeric specifying the numbers of parameters in the function (ex: 2)</li><br/>
+ <li><b>$paramnames</b> : a vector of character string of length $paramnumber specifying the parameters names, as in $formula (ex: c("c","z") )</li><br/>
+ <li><b>$parLim </b>: a vector of character string of length $paramnumber specifying the parameters limits from 'R' for (-∞;+∞), 'Rplus' for [0;+∞) or 'unif' for [0;1] (ex: c("R","Rplus")) </li><br/>
+ <li><b>$fun</b> : an R function corresponding to the model function (ex : function(par,data){if(length(data)>1) d=data[[1]] else d=data; s = par[2] * log(d) + par[1]; names(s)=c("s.expo"); as.vector(s)} )</li><br/>
+ <li><b>$rssfun </b> : an R function corresponding to the model Residual Sum of Squares function (ex : function(par,data,opt){if(opt)par=backLink(par,expo$parLim) ; sum( (data[[2]] - (par[2] * log(data[[1]]) + par[1]) ) ^2 ) } )</li><br/>
+ <li><b>$init </b> : an R function corresponding to an initial values calculation for the fitting algorithm, this is a model specific function as $fun adn $rssfun (ex: function(data){semilog.data = data.frame(log(data[[1]]),data[[2]]) ; names(semilog.data)=c("a","s") ; par=lm(s~a,semilog.data)$coefficients ; names(par)=c("c","z") ; par } )</li><br/>
+</ul>
+</p>
+
+ <p class="large">To load a model, for example the exponential model use :</p>
+ <div class="success">load(expo)</div>
+ </div>
+
+ </div>
+
+ </div>
+ </div>
+
+ <div id="sidebar-wrapper">
+ <div id="sidebar">
+
+ <?php include('doc_nav.php'); ?>
+ <div class="box">
+
+ <div class="box-title">Screenshots</div>
+
+ <div class="box-content">
+
+ <div class="thumbnails">
+
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+
+ </div>
+
+
+ </div>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+</div>
+
+<div id="footer-wrapper">
+
+ <div class="center-wrapper">
+
+ <div id="footer">
+
+ <div class="left">
+ <a href="index.html">Home</a> <span class="text-separator">|</span> <a href="documentation_home.html">Documentation</a><span class="text-separator">|</span><a href="publications.html">Publications</a><span class="text-separator">|</span>
+ </div>
+
+ <div class="right">
+ <a href="#">Top ^</a>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+
+</div>
+
+<div id="bottom">
+
+ <div class="center-wrapper">
+
+ <div class="left">
+ © 2009 François Guilhaumon - mmSAR is GPL feel free to use it and contribute to it.<span class="text-separator">|</span>
+ </div>
+
+ <div class="right">
+ <a href="http://templates.arcsin.se/">Website template</a> by <a href="http://arcsin.se/">Arcsin</a>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+</div>
+
+</body>
+</html>
Property changes on: www/documentation_models.php
___________________________________________________________________
Name: svn:executable
+ *
Added: www/documentation_usage.php
===================================================================
--- www/documentation_usage.php (rev 0)
+++ www/documentation_usage.php 2010-02-07 02:32:16 UTC (rev 17)
@@ -0,0 +1,146 @@
+<?php include('header.php'); ?>
+ <title>mmSAR - Documentation - Home</title>
+</head>
+
+<body id="top">
+
+<?php include('head.php'); ?>
+<?php include('nav.php'); ?>
+
+<div id="content-wrapper">
+ <div class="center-wrapper">
+
+ <div class="content" id="content-two-columns">
+
+ <div id="main-wrapper">
+ <div id="main">
+
+ <div class="post">
+
+ <div class="post-title"><h1>mmSAR usage</h1></div>
+
+<br/>
+ <div class="post-body">
+
+ <h2 class="quiet">Loading mmSAR</h2>
+
+ <p class="large">After <a href="documentation_install.html">installation</a>, load mmSAR with :</p>
+
+<div class="success">library(mmSAR)</div><br/>
+
+ <h2 class="quiet">Use case 1 : the simple case.</h2><br/>
+
+<p align="center"><img src="doc_use1.png" alt="" class="bordered" /></p>
+
+ <p class="large">Basic non linear SAR model fits are obtained with the <a href="documentation_functions.html">rssoptim</a> function, this function takes for arguments a <a href="documentation_models.html">model object</a> and a <a href="documentation_datasets.html">data set object</a>. Further arguments are available (see <a href="documentation_functions.html">'Functions'</a>). A basic run :</p>
+
+<div class="success">#loading the exponential model<br/>
+data(expo)<br/><br/>
+#loading the Galapagos Islands plants data set (<a href="publications.html">Preston, 1962</a>)<br/>
+data(data.glap)<br/><br/>
+#fitting the exponential model to the Galapagos dataset<br/>
+res <- rssoptim(expo,data.galap)<br/> </div><br/>
+
+ <h2 class="quiet">Use case 2 : multimodel SARs.</h2><br/>
+
+<p align="center"><img src="doc_use2.png" alt="" class="bordered" /></p>
+
+ <p class="large">Multimodel SAR fits are obtained with the <a href="documentation_functions.html">multiSAR</a> function, this function takes for arguments a vector of character strings for model names and a <a href="documentation_datasets.html">data set object</a>. Further arguments are available (see <a href="documentation_functions.html">'Functions'</a>). A basic run :</p>
+
+<div class="success">#loading all available models<br/>
+data(power)<br/>data(expo)<br/>data(negexpo)<br/>data(monod)<br/>data(ratio)<br/>data(logistic)<br/>data(lomolino)<br/>data(weibull)<br/><br/>
+#loading the Galapagos Islands plants data set (<a href="publications.html">Preston, 1962</a>)<br/>
+data(data.glap)<br/><br/>
+#creating a vector of model names<br/>
+mods = c("power","expo","negexpo","monod","logist","ratio","lomolino","weibull")<br/><br/>
+#fitting all the models to the Galapagos dataset and perform multimodel averaging<br/>
+resAverage <- multiSAR(modelList=mods,data.galap)<br/> </div><br/>
+
+ </div>
+
+ </div>
+
+ </div>
+ </div>
+
+ <div id="sidebar-wrapper">
+ <div id="sidebar">
+
+ <?php include('doc_nav.php'); ?>
+
+ <div class="box">
+
+ <div class="box-title">Screenshots</div>
+
+ <div class="box-content">
+
+ <div class="thumbnails">
+
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+ <a href="#" class="thumb"><img src="sample-thumbnail.jpg" width="64" height="64" alt="" /></a>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+
+ </div>
+
+
+ </div>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+</div>
+
+<div id="footer-wrapper">
+
+ <div class="center-wrapper">
+
+ <div id="footer">
+
+ <div class="left">
+ <a href="index.html">Home</a> <span class="text-separator">|</span> <a href="documentation_home.html">Documentation</a><span class="text-separator">|</span><a href="publications.html">Publications</a><span class="text-separator">|</span>
+ </div>
+
+ <div class="right">
+ <a href="#">Top ^</a>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+ </div>
+
+</div>
+
+<div id="bottom">
+
+ <div class="center-wrapper">
+
+ <div class="left">
+ © 2009 François Guilhaumon - mmSAR is GPL feel free to use it and contribute to it.<span class="text-separator">|</span>
+ </div>
+
+ <div class="right">
+ <a href="http://templates.arcsin.se/">Website template</a> by <a href="http://arcsin.se/">Arcsin</a>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+</div>
+
+</body>
+</html>
Property changes on: www/documentation_usage.php
___________________________________________________________________
Name: svn:executable
+ *
Added: www/footer.php
===================================================================
--- www/footer.php (rev 0)
+++ www/footer.php 2010-02-07 02:32:16 UTC (rev 17)
@@ -0,0 +1,20 @@
+<div id="bottom">
+
+ <div class="center-wrapper">
+
+ <div class="left">
+ © 2009 François Guilhaumon - mmSAR is GPL feel free to use it and contribute to it.<span class="text-separator">|</span>
+ </div>
+
+ <div class="right">
+ <a href="http://templates.arcsin.se/">Website template</a> by <a href="http://arcsin.se/">Arcsin</a>
+ </div>
+
+ <div class="clearer"> </div>
+
+ </div>
+
+</div>
+
+</body>
+</html>
Property changes on: www/footer.php
___________________________________________________________________
Name: svn:executable
+ *
Added: www/head.php
===================================================================
--- www/head.php (rev 0)
+++ www/head.php 2010-02-07 02:32:16 UTC (rev 17)
@@ -0,0 +1,27 @@
+<div id="header-wrapper">
+ <div id="header-wrapper-2">
+ <div class="center-wrapper">
+
+ <div id="header">
+
+ <div id="logo">
+ <h1 id="site-title"><a href="#">mmSAR <span>R-package</span></a></h1>
+ <h2 id="site-slogan">multimodel Species-Area Relationships</h2>
+ </div>
+
+ <div id="help-wrapper">
+ <div id="help">
+
+ <a href="http://r-forge.r-project.org/projects/mmsar/">project summary at the R-forge</a>
+
+ </div>
+ </div>
+
+ </div>
+
+ </div>
+ </div>
+</div>
+
+
+
Property changes on: www/head.php
___________________________________________________________________
Name: svn:executable
+ *
Added: www/header.php
===================================================================
--- www/header.php (rev 0)
+++ www/header.php 2010-02-07 02:32:16 UTC (rev 17)
@@ -0,0 +1,18 @@
+<?php
+
+$domain=ereg_replace('[^\.]*\.(.*)$','\1',$_SERVER['HTTP_HOST']);
+$group_name=ereg_replace('([^\.]*)\..*$','\1',$_SERVER['HTTP_HOST']);
+$themeroot='http://r-forge.r-project.org/themes/rforge/';
+
+echo '<?xml version="1.0" encoding="UTF-8"?>';
+?>
+
+<!DOCTYPE html
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en ">
+
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+ <meta name="author" content="francois Guilhaumon" />
+ <link rel="stylesheet" type="text/css" href="style.css" media="screen" />
Property changes on: www/header.php
___________________________________________________________________
Name: svn:executable
+ *
Modified: www/index.php
===================================================================
--- www/index.php 2010-02-07 01:46:49 UTC (rev 16)
+++ www/index.php 2010-02-07 02:32:16 UTC (rev 17)
@@ -1,252 +1,90 @@
+<?php include('header.php'); ?>
+ <title>mmSAR - an R package for the modelling of the Species-Area Relationship</title>
+</head>
-<!-- This is the project specific website template -->
-<!-- It can be changed as liked or replaced by other content -->
+<body id="top">
-<?php
+<?php include('head.php'); ?>
+<?php include('nav.php'); ?>
-$domain=ereg_replace('[^\.]*\.(.*)$','\1',$_SERVER['HTTP_HOST']);
-$group_name=ereg_replace('([^\.]*)\..*$','\1',$_SERVER['HTTP_HOST']);
-$themeroot='http://r-forge.r-project.org/themes/rforge/';
+<div id="content-wrapper">
+ <div class="center-wrapper">
+
+ <div class="content">
-echo '<?xml version="1.0" encoding="UTF-8"?>';
-?>
-<!DOCTYPE html
- PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en ">
+ <div id="featured-wrapper">
+ <div id="featured">
- <head>
- <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
- <title><?php echo $group_name; ?></title>
- <link href="<?php echo $themeroot; ?>styles/estilo1.css" rel="stylesheet" type="text/css" />
- </head>
+ <div class="left" style="width: 370px">
+
+ <h2>mm<span>SAR</span></h2>
-<body>
+ <p class="large">mmSAR is an R package for the modelling of the Species-Area Relationship (SAR).</p>
-<!-- R-Forge Logo -->
-<table border="0" width="100%" cellspacing="0" cellpadding="0">
-<tr><td>
-<a href="/"><img src="<?php echo $themeroot; ?>/images/logo.png" border="0" alt="R-Forge Logo" /> </a> </td> </tr>
-</table>
+ <p algn="justify">The mmSAR package implements the multimodel SAR paradigm and provides ecologists with user friendly functions fit SAR models and calculate multimodel SAR inference.</p>
+ <p class="large text-center"><a href="documentation_home.html">browse the online documentation</a> <span class="text-separator">|</span> <a href="http://r-forge.r-project.org/R/?group_id=514">Download</a> </p>
-<!-- get project title -->
-<!-- own website starts here, the following may be changed as you like -->
+ </div>
-<?php if ($handle=fopen('http://'.$domain.'/export/projtitl.php?group_name='.$group_name,'r')){
-$contents = '';
-while (!feof($handle)) {
- $contents .= fread($handle, 8192);
-}
-fclose($handle);
-echo $contents; } ?>
+ <div class="right">
+ <img src="fig_home.png" alt="example multimodelSAR" class="bordered"/>
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/mmsar -r 17
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