[Mmsar-commits] r28 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Feb 7 05:35:14 CET 2010
Author: fguilhaumon
Date: 2010-02-07 05:35:13 +0100 (Sun, 07 Feb 2010)
New Revision: 28
Removed:
www/documentation_datasets.html
www/documentation_functions.html
www/documentation_home.html
www/documentation_install.html
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www/publications.html
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Deleted: www/documentation_datasets.html
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- <link rel="stylesheet" type="text/css" href="style.css" media="screen" />
- <title>mmSAR - Documentation - Home</title>
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- <h1 id="site-title"><a href="#">mmSAR <span>R-package</span></a></h1>
- <h2 id="site-slogan">multimodel Species-Area Relationships</h2>
- </div>
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- <div id="help-wrapper">
- <div id="help">
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- <li><a href="publications.html">Publications</a></li>
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- <div class="post-title"><h1>Data sets</h1></div>
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-<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>
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- <li><a href="documentation_usage.html">Usage</a></li>
-<!--<li><a href="documentation_plots.html">Plots</a></li>-->
- <li><a href="documentation_datasets.html">Data sets</a></li>
- <li><a href="documentation_models.html">Models</a></li>
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- <meta http-equiv="content-type" content="text/html; charset=UTF-8"/>
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- <meta name="keywords" content="" />
- <meta name="author" content="francois Guilhaumon" />
- <link rel="stylesheet" type="text/css" href="style.css" media="screen" />
- <title>mmSAR - Documentation - Home</title>
-</head>
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-<body id="top">
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-<div id="header-wrapper">
- <div id="header-wrapper-2">
- <div class="center-wrapper">
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- <div id="header">
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- <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 page at the R-forge</a>
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- </div>
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- <li class="current_page_item current_page_parent"><a href="documentation_home.html">Documentation</a></li>
- <li><a href="publications.html">Publications</a></li>
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-<br/>
- <div class="post-body">
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- <p align="center"><img src="doc_functions.png" alt="" class="bordered" /></p>
-<br/>
- <h2 class="quiet">model fitting</h2>
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- <p class="large"><b>rssoptim</b> : function (model, data, norTest = "lillie", verb = T)</p>
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- <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>
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- <li><strong><a href="documentation_home.html">Home</a></strong></li>
- <li><a href="documentation_install.html">Installation</a></li>
- <li><a href="documentation_usage.html">Usage</a></li>
- <li><a href="documentation_datasets.html">Data sets</a></li>
- <li><a href="documentation_models.html">Models</a></li>
- <li><a href="documentation_functions.html">Functions</a></li>
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- <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>
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- <meta name="author" content="francois Guilhaumon" />
- <link rel="stylesheet" type="text/css" href="style.css" media="screen" />
- <title>mmSAR - Documentation - Home</title>
-</head>
-
-<body id="top">
-
-<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 page at the R-forge</a>
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- <li><a href="publications.html">Publications</a></li>
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-<br/>
- <div class="post-body">
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- <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>
-
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- <ul class="nice-list">
- <li><strong><a href="documentation_home.html">Home</a></strong></li>
- <li><a href="documentation_install.html">Installation</a></li>
- <li><a href="documentation_usage.html">Usage</a></li>
-<!--<li><a href="documentation_plots.html">Plots</a></li>-->
- <li><a href="documentation_datasets.html">Data sets</a></li>
- <li><a href="documentation_models.html">Models</a></li>
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- <link rel="stylesheet" type="text/css" href="style.css" media="screen" />
- <title>mmSAR - Documentation - Home</title>
-</head>
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-<body id="top">
-
-<div id="header-wrapper">
- <div id="header-wrapper-2">
- <div class="center-wrapper">
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- <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 page at the R-forge</a>
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- <div class="post-title"><h1>Installation</h1></div>
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- <div class="post-body">
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- <p class="large">To install the mmSAR package directly within R type:</p>
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-<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>
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- <p class="large">After that when loading the mmSAR package, use the 'lib.loc' argument of the 'library' function to find the package :</p>
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Deleted: www/documentation_models.html
===================================================================
--- www/documentation_models.html 2010-02-07 04:31:53 UTC (rev 27)
+++ www/documentation_models.html 2010-02-07 04:35:13 UTC (rev 28)
@@ -1,271 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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- <h2 id="site-slogan">multimodel Species-Area Relationships</h2>
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-
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- <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>
-
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Deleted: www/documentation_usage.html
===================================================================
--- www/documentation_usage.html 2010-02-07 04:31:53 UTC (rev 27)
+++ www/documentation_usage.html 2010-02-07 04:35:13 UTC (rev 28)
@@ -1,211 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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-
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- <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>
-
[TRUNCATED]
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