Can you search for peer-reviewed journal articles that use spatial point pattern analysis to examine spatial patterns of organisms (i.e., plant or animals) in relation to environmental or stress gradients?

README.md

@@ -1,10 +1,13 @@
 ---
-title: Ecopattern Explorer
-emoji: 🏃
+title: EcoPattern Explorer 🌿
 colorFrom: blue
-colorTo: indigo
+colorTo: purple
+emoji: 🐳
 sdk: static
 pinned: false
+tags:
+  - deepsite-v3
 ---
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+# Welcome to your new DeepSite project!
+This project was created with [DeepSite](https://huggingface.co/deepsite).

components/article-card.js

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+class CustomArticleCard extends HTMLElement {
+    static get observedAttributes() {
+        return ['title', 'authors', 'journal', 'abstract', 'link', 'image'];
+    }
+
+    constructor() {
+        super();
+        this.attachShadow({ mode: 'open' });
+    }
+
+    connectedCallback() {
+        this.render();
+    }
+
+    attributeChangedCallback(name, oldValue, newValue) {
+        if (oldValue !== newValue) {
+            this.render();
+        }
+    }
+
+    render() {
+        const title = this.getAttribute('title') || 'No title provided';
+        const authors = this.getAttribute('authors') || 'Authors not specified';
+        const journal = this.getAttribute('journal') || 'Journal not specified';
+        const abstract = this.getAttribute('abstract') || 'No abstract available.';
+        const link = this.getAttribute('link') || '#';
+        const image = this.getAttribute('image') || 'http://static.photos/nature/640x360/1';
+
+        this.shadowRoot.innerHTML = `
+            <style>
+                .article-card {
+                    transition: transform 0.3s ease, box-shadow 0.3s ease;
+                }
+                .article-card:hover {
+                    transform: translateY(-5px);
+                    box-shadow: 0 10px 25px -5px rgba(0, 0, 0, 0.1);
+                }
+                .abstract {
+                    display: -webkit-box;
+                    -webkit-line-clamp: 3;
+                    -webkit-box-orient: vertical;
+                    overflow: hidden;
+                }
+            </style>
+            <div class="article-card bg-white rounded-xl overflow-hidden shadow-md h-full flex flex-col animate-fade-in">
+                <div class="h-48 overflow-hidden">
+                    <img src="${image}" alt="${title}" class="w-full h-full object-cover">
+                </div>
+                <div class="p-6 flex-grow flex flex-col">
+                    <div class="flex-grow">
+                        <span class="text-xs font-semibold text-emerald-600 uppercase tracking-wider">${journal}</span>
+                        <h3 class="text-xl font-bold mt-1 mb-2 text-gray-800">${title}</h3>
+                        <p class="text-sm text-gray-500 mb-3">${authors}</p>
+                        <p class="text-gray-600 mb-4 abstract">${abstract}</p>
+                    </div>
+                    <a href="${link}" class="mt-auto inline-flex items-center text-emerald-600 font-medium hover:text-emerald-800">
+                        Read more
+                        <i data-feather="arrow-right" class="ml-1 w-4 h-4"></i>
+                    </a>
+                </div>
+            </div>
+        `;
+    }
+}
+
+customElements.define('custom-article-card', CustomArticleCard);

components/footer.js

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+class CustomFooter extends HTMLElement {
+    connectedCallback() {
+        this.attachShadow({ mode: 'open' });
+        this.shadowRoot.innerHTML = `
+            <style>
+                footer {
+                    background-color: #f8fafc;
+                }
+                .footer-link:hover {
+                    color: #059669;
+                }
+            </style>
+            <footer class="border-t border-gray-200">
+                <div class="container mx-auto px-4 py-12">
+                    <div class="grid grid-cols-1 md:grid-cols-4 gap-8">
+                        <div>
+                            <h3 class="text-lg font-semibold mb-4 text-emerald-700">EcoPattern Explorer</h3>
+                            <p class="text-gray-600 mb-4">
+                                A curated collection of spatial ecology research using point pattern analysis.
+                            </p>
+                            <div class="flex space-x-4">
+                                <a href="#" class="text-gray-500 hover:text-emerald-600">
+                                    <i data-feather="twitter"></i>
+                                </a>
+                                <a href="#" class="text-gray-500 hover:text-emerald-600">
+                                    <i data-feather="github"></i>
+                                </a>
+                                <a href="#" class="text-gray-500 hover:text-emerald-600">
+                                    <i data-feather="linkedin"></i>
+                                </a>
+                            </div>
+                        </div>
+                        
+                        <div>
+                            <h4 class="font-semibold mb-4 text-gray-800">Resources</h4>
+                            <ul class="space-y-2">
+                                <li><a href="#" class="footer-link text-gray-600">Tutorials</a></li>
+                                <li><a href="#" class="footer-link text-gray-600">Software Tools</a></li>
+                                <li><a href="#" class="footer-link text-gray-600">Datasets</a></li>
+                                <li><a href="#" class="footer-link text-gray-600">Methodology Guides</a></li>
+                            </ul>
+                        </div>
+                        
+                        <div>
+                            <h4 class="font-semibold mb-4 text-gray-800">Research Areas</h4>
+                            <ul class="space-y-2">
+                                <li><a href="#" class="footer-link text-gray-600">Plant Ecology</a></li>
+                                <li><a href="#" class="footer-link text-gray-600">Wildlife Ecology</a></li>
+                                <li><a href="#" class="footer-link text-gray-600">Urban Ecology</a></li>
+                                <li><a href="#" class="footer-link text-gray-600">Disease Ecology</a></li>
+                            </ul>
+                        </div>
+                        
+                        <div>
+                            <h4 class="font-semibold mb-4 text-gray-800">Contact</h4>
+                            <ul class="space-y-2">
+                                <li class="flex items-start">
+                                    <i data-feather="mail" class="text-gray-500 mr-2 mt-1"></i>
+                                    <a href="mailto:research@ecopattern.org" class="footer-link text-gray-600">research@ecopattern.org</a>
+                                </li>
+                                <li class="flex items-start">
+                                    <i data-feather="map-pin" class="text-gray-500 mr-2 mt-1"></i>
+                                    <span class="text-gray-600">Ecology Research Institute</span>
+                                </li>
+                            </ul>
+                        </div>
+                    </div>
+                    
+                    <div class="border-t border-gray-200 mt-8 pt-8 text-center text-gray-500 text-sm">
+                        <p>© ${new Date().getFullYear()} EcoPattern Explorer. All rights reserved.</p>
+                    </div>
+                </div>
+            </footer>
+        `;
+    }
+}
+
+customElements.define('custom-footer', CustomFooter);

components/navbar.js

@@ -0,0 +1,66 @@
+class CustomNavbar extends HTMLElement {
+    connectedCallback() {
+        this.attachShadow({ mode: 'open' });
+        this.shadowRoot.innerHTML = `
+            <style>
+                nav {
+                    background-color: white;
+                    box-shadow: 0 2px 4px rgba(0,0,0,0.1);
+                }
+                .nav-link:hover {
+                    color: #059669;
+                }
+                .nav-link.active {
+                    color: #059669;
+                    border-bottom: 2px solid #059669;
+                }
+            </style>
+            <nav class="sticky top-0 z-50">
+                <div class="container mx-auto px-4 py-4 flex justify-between items-center">
+                    <a href="#" class="flex items-center space-x-2">
+                        <i data-feather="map" class="text-emerald-600"></i>
+                        <span class="text-xl font-bold text-emerald-700">EcoPattern Explorer</span>
+                    </a>
+                    
+                    <div class="hidden md:flex space-x-8">
+                        <a href="#" class="nav-link active font-medium">Home</a>
+                        <a href="#" class="nav-link font-medium">Research</a>
+                        <a href="#" class="nav-link font-medium">Methods</a>
+                        <a href="#" class="nav-link font-medium">Resources</a>
+                        <a href="#" class="nav-link font-medium">About</a>
+                    </div>
+                    
+                    <button class="md:hidden focus:outline-none" id="mobile-menu-button">
+                        <i data-feather="menu"></i>
+                    </button>
+                </div>
+                
+                <!-- Mobile menu -->
+                <div class="hidden md:hidden bg-white py-2 px-4" id="mobile-menu">
+                    <a href="#" class="block py-2 nav-link active">Home</a>
+                    <a href="#" class="block py-2 nav-link">Research</a>
+                    <a href="#" class="block py-2 nav-link">Methods</a>
+                    <a href="#" class="block py-2 nav-link">Resources</a>
+                    <a href="#" class="block py-2 nav-link">About</a>
+                </div>
+            </nav>
+        `;
+        
+        // Mobile menu toggle
+        const menuButton = this.shadowRoot.getElementById('mobile-menu-button');
+        const mobileMenu = this.shadowRoot.getElementById('mobile-menu');
+        
+        menuButton.addEventListener('click', () => {
+            mobileMenu.classList.toggle('hidden');
+            const icon = menuButton.querySelector('i');
+            if (mobileMenu.classList.contains('hidden')) {
+                icon.setAttribute('data-feather', 'menu');
+            } else {
+                icon.setAttribute('data-feather', 'x');
+            }
+            feather.replace();
+        });
+    }
+}
+
+customElements.define('custom-navbar', CustomNavbar);

components/search-card.js

@@ -0,0 +1,60 @@
+class CustomSearchCard extends HTMLElement {
+    connectedCallback() {
+        this.attachShadow({ mode: 'open' });
+        this.shadowRoot.innerHTML = `
+            <style>
+                .search-box {
+                    box-shadow: 0 4px 6px -1px rgba(0, 0, 0, 0.1), 0 2px 4px -1px rgba(0, 0, 0, 0.06);
+                }
+                .search-button {
+                    transition: all 0.2s ease;
+                }
+                .search-button:hover {
+                    background-color: #059669;
+                }
+            </style>
+            <div class="bg-white rounded-xl shadow-md p-6 search-box max-w-2xl mx-auto animate-fade-in">
+                <h3 class="text-xl font-semibold mb-4 text-gray-700">Search Research Articles</h3>
+                <form id="searchForm" class="flex flex-col sm:flex-row gap-4">
+                    <input 
+                        type="text" 
+                        placeholder="e.g., 'spatial patterns plants elevation gradient'" 
+                        class="flex-grow px-4 py-2 border border-gray-300 rounded-lg focus:ring-2 focus:ring-emerald-500 focus:border-emerald-500 outline-none"
+                        id="searchInput"
+                        required>
+                    <button type="submit" class="search-button bg-emerald-600 text-white px-6 py-2 rounded-lg font-medium flex items-center justify-center">
+                        <i data-feather="search" class="mr-2"></i>
+                        Search
+                    </button>
+                </form>
+                <div class="mt-4 flex flex-wrap gap-2">
+                    <span class="text-sm text-gray-500">Try:</span>
+                    <button class="tag-button text-xs bg-gray-100 hover:bg-gray-200 px-3 py-1 rounded-full">Ripley's K</button>
+                    <button class="tag-button text-xs bg-gray-100 hover:bg-gray-200 px-3 py-1 rounded-full">Environmental gradients</button>
+                    <button class="tag-button text-xs bg-gray-100 hover:bg-gray-200 px-3 py-1 rounded-full">Marked point processes</button>
+                </div>
+            </div>
+        `;
+
+        const form = this.shadowRoot.getElementById('searchForm');
+        form.addEventListener('submit', (e) => {
+            e.preventDefault();
+            const searchTerm = this.shadowRoot.getElementById('searchInput').value;
+            this.dispatchEvent(new CustomEvent('submit', { 
+                detail: { searchTerm },
+                bubbles: true,
+                composed: true 
+            }));
+        });
+
+        // Tag buttons
+        const tagButtons = this.shadowRoot.querySelectorAll('.tag-button');
+        tagButtons.forEach(button => {
+            button.addEventListener('click', () => {
+                this.shadowRoot.getElementById('searchInput').value = button.textContent.trim();
+            });
+        });
+    }
+}
+
+customElements.define('custom-search-card', CustomSearchCard);

index.html

@@ -1,19 +1,122 @@
-<!doctype html>
-<html>
-	<head>
-		<meta charset="utf-8" />
-		<meta name="viewport" content="width=device-width" />
-		<title>My static Space</title>
-		<link rel="stylesheet" href="style.css" />
-	</head>
-	<body>
-		<div class="card">
-			<h1>Welcome to your static Space!</h1>
-			<p>You can modify this app directly by editing <i>index.html</i> in the Files and versions tab.</p>
-			<p>
-				Also don't forget to check the
-				<a href="https://huggingface.co/docs/hub/spaces" target="_blank">Spaces documentation</a>.
-			</p>
-		</div>
-	</body>
-</html>
+<!DOCTYPE html>
+<html lang="en" class="scroll-smooth">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>EcoPattern Explorer | Spatial Ecology Research</title>
+    <link rel="stylesheet" href="style.css">
+    <script src="https://cdn.tailwindcss.com"></script>
+    <script src="https://cdn.jsdelivr.net/npm/feather-icons/dist/feather.min.js"></script>
+    <script src="https://unpkg.com/feather-icons"></script>
+    <script src="components/navbar.js"></script>
+    <script src="components/search-card.js"></script>
+    <script src="components/article-card.js"></script>
+    <script src="components/footer.js"></script>
+</head>
+<body class="bg-gray-50 text-gray-800 font-sans">
+    <custom-navbar></custom-navbar>
+
+    <main class="container mx-auto px-4 py-12">
+        <!-- Hero Section -->
+        <section class="mb-20">
+            <div class="max-w-4xl mx-auto text-center">
+                <h1 class="text-4xl md:text-5xl font-bold mb-6 text-emerald-700">Explore Spatial Ecology Research</h1>
+                <p class="text-xl text-gray-600 mb-8">
+                    Discover peer-reviewed journal articles using spatial point pattern analysis to examine organism distributions across environmental gradients.
+                </p>
+                <custom-search-card></custom-search-card>
+            </div>
+        </section>
+
+        <!-- Featured Articles -->
+        <section class="mb-20">
+            <h2 class="text-3xl font-bold mb-8 text-emerald-700 border-b pb-2">Featured Research</h2>
+            <div class="grid grid-cols-1 md:grid-cols-2 lg:grid-cols-3 gap-8">
+                <custom-article-card 
+                    title="Spatial patterns of tree species in response to drought gradients"
+                    authors="Smith et al. (2022)"
+                    journal="Journal of Ecology"
+                    abstract="Examined how drought stress influences spatial distribution patterns of Mediterranean oak species using Ripley's K-function."
+                    link="#"
+                    image="http://static.photos/nature/640x360/42">
+                </custom-article-card>
+                
+                <custom-article-card 
+                    title="Animal movement patterns along urbanization gradients"
+                    authors="Johnson & Lee (2021)"
+                    journal="Landscape Ecology"
+                    abstract="Used point pattern analysis to quantify changes in wildlife spatial distributions across urban-rural gradients."
+                    link="#"
+                    image="http://static.photos/cityscape/640x360/23">
+                </custom-article-card>
+                
+                <custom-article-card 
+                    title="Plant-soil feedbacks drive spatial patterns in alpine ecosystems"
+                    authors="Chen et al. (2023)"
+                    journal="Ecography"
+                    abstract="Investigated spatial associations between plant species and soil properties using marked point processes."
+                    link="#"
+                    image="http://static.photos/aerial/640x360/87">
+                </custom-article-card>
+            </div>
+        </section>
+
+        <!-- Methodology Section -->
+        <section class="mb-20 bg-white rounded-xl shadow-md p-8">
+            <h2 class="text-3xl font-bold mb-6 text-emerald-700">About Spatial Point Pattern Analysis</h2>
+            <div class="grid md:grid-cols-2 gap-8">
+                <div>
+                    <h3 class="text-xl font-semibold mb-4 text-emerald-600">Key Techniques</h3>
+                    <ul class="space-y-3">
+                        <li class="flex items-start">
+                            <i data-feather="check-circle" class="text-emerald-500 mr-2 mt-1"></i>
+                            <span>Ripley's K-function and pair correlation functions</span>
+                        </li>
+                        <li class="flex items-start">
+                            <i data-feather="check-circle" class="text-emerald-500 mr-2 mt-1"></i>
+                            <span>Marked point processes for environmental covariates</span>
+                        </li>
+                        <li class="flex items-start">
+                            <i data-feather="check-circle" class="text-emerald-500 mr-2 mt-1"></i>
+                            <span>Inhomogeneous Poisson processes for gradient analysis</span>
+                        </li>
+                        <li class="flex items-start">
+                            <i data-feather="check-circle" class="text-emerald-500 mr-2 mt-1"></i>
+                            <span>Null model comparisons for pattern significance</span>
+                        </li>
+                    </ul>
+                </div>
+                <div>
+                    <h3 class="text-xl font-semibold mb-4 text-emerald-600">Common Applications</h3>
+                    <ul class="space-y-3">
+                        <li class="flex items-start">
+                            <i data-feather="zap" class="text-amber-500 mr-2 mt-1"></i>
+                            <span>Plant distributions along elevation gradients</span>
+                        </li>
+                        <li class="flex items-start">
+                            <i data-feather="zap" class="text-amber-500 mr-2 mt-1"></i>
+                            <span>Wildlife responses to habitat fragmentation</span>
+                        </li>
+                        <li class="flex items-start">
+                            <i data-feather="zap" class="text-amber-500 mr-2 mt-1"></i>
+                            <span>Disease spread patterns in relation to environmental factors</span>
+                        </li>
+                        <li class="flex items-start">
+                            <i data-feather="zap" class="text-amber-500 mr-2 mt-1"></i>
+                            <span>Invasive species spread dynamics</span>
+                        </li>
+                    </ul>
+                </div>
+            </div>
+        </section>
+    </main>
+
+    <custom-footer></custom-footer>
+
+    <script>
+        feather.replace();
+    </script>
+    <script src="script.js"></script>
+<script src="https://huggingface.co/deepsite/deepsite-badge.js"></script>
+</body>
+</html>

script.js

@@ -0,0 +1,24 @@
+document.addEventListener('DOMContentLoaded', () => {
+    // Initialize animations
+    const cards = document.querySelectorAll('.animate-fade-in');
+    cards.forEach((card, index) => {
+        card.style.animationDelay = `${index * 0.1}s`;
+    });
+
+    // Simulate search functionality
+    const searchForm = document.querySelector('custom-search-card');
+    if (searchForm) {
+        searchForm.addEventListener('submit', (e) => {
+            e.preventDefault();
+            const searchTerm = e.detail.searchTerm;
+            alert(`Searching for: ${searchTerm}\nThis would connect to a real API in production`);
+        });
+    }
+});
+
+// API integration would go here
+async function fetchArticles(query = 'spatial point pattern analysis environmental gradient') {
+    // In a real implementation, this would connect to CrossRef, PubMed, or other academic APIs
+    console.log(`Would fetch articles for query: ${query}`);
+    return [];
+}

style.css

@@ -1,28 +1,47 @@
+@import url('https://fonts.googleapis.com/css2?family=Inter:wght@300;400;500;600;700&display=swap');
+
 body {
-	padding: 2rem;
-	font-family: -apple-system, BlinkMacSystemFont, "Arial", sans-serif;
+    font-family: 'Inter', sans-serif;
+    line-height: 1.6;
+}
+
+/* Custom scrollbar */
+::-webkit-scrollbar {
+    width: 8px;
+    height: 8px;
+}
+
+::-webkit-scrollbar-track {
+    background: #f1f1f1;
 }
 
-h1 {
-	font-size: 16px;
-	margin-top: 0;
+::-webkit-scrollbar-thumb {
+    background: #10b981;
+    border-radius: 4px;
 }
 
-p {
-	color: rgb(107, 114, 128);
-	font-size: 15px;
-	margin-bottom: 10px;
-	margin-top: 5px;
+::-webkit-scrollbar-thumb:hover {
+    background: #059669;
 }
 
-.card {
-	max-width: 620px;
-	margin: 0 auto;
-	padding: 16px;
-	border: 1px solid lightgray;
-	border-radius: 16px;
+/* Animation for cards */
+@keyframes fadeIn {
+    from { opacity: 0; transform: translateY(20px); }
+    to { opacity: 1; transform: translateY(0); }
 }
 
-.card p:last-child {
-	margin-bottom: 0;
+.animate-fade-in {
+    animation: fadeIn 0.6s ease-out forwards;
 }
+
+.delay-100 {
+    animation-delay: 0.1s;
+}
+
+.delay-200 {
+    animation-delay: 0.2s;
+}
+
+.delay-300 {
+    animation-delay: 0.3s;
+}