Added my new file

Embedding+Vector.ipynb

@@ -0,0 +1,1110 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "id": "408e9000-977d-4f3f-a001-b06c55095c5f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "## Handle secrets either from env vars or streamlit manager\n",
+    "import streamlit as st\n",
+    "import os\n",
+    "api_key = os.getenv(\"LITELLM_KEY\")\n",
+    "if api_key is None:\n",
+    "    api_key = st.secrets[\"LITELLM_KEY\"]\n",
+    "cirrus_key = os.getenv(\"CIRRUS_KEY\")\n",
+    "if cirrus_key is None:\n",
+    "    cirrus_key = st.secrets[\"CIRRUS_KEY\"]        "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "id": "802c676d-98c9-4e1f-b755-9eb6fbc09754",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import requests\n",
+    "import zipfile\n",
+    "\n",
+    "def download_and_unzip(url, output_dir):\n",
+    "    response = requests.get(url)\n",
+    "    zip_file_path = os.path.basename(url)\n",
+    "    with open(zip_file_path, 'wb') as f:\n",
+    "        f.write(response.content)\n",
+    "    with zipfile.ZipFile(zip_file_path, 'r') as zip_ref:\n",
+    "        zip_ref.extractall(output_dir)\n",
+    "    os.remove(zip_file_path)\n",
+    "\n",
+    "download_and_unzip(\"https://minio.carlboettiger.info/public-data/hwc.zip\", \"hwc\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "id": "00e3d915-4803-477f-9c19-db421cf129ac",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pathlib\n",
+    "from langchain_community.document_loaders import PyPDFLoader\n",
+    "\n",
+    "def pdf_loader(path):\n",
+    "    all_documents = []\n",
+    "    docs_dir = pathlib.Path(path)\n",
+    "    for file in docs_dir.iterdir():\n",
+    "        loader = PyPDFLoader(file)\n",
+    "        documents = loader.load()\n",
+    "        all_documents.extend(documents)\n",
+    "    return all_documents\n",
+    "\n",
+    "docs = pdf_loader('hwc/')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "id": "d830b309-c047-491a-8114-ef9ad18dead5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# NRP embedding model tends to throw errors\n",
+    "# embedding = OpenAIEmbeddings(model = \"embed-mistral\", api_key = api_key, base_url = \"https://llm.nrp-nautilus.io\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "id": "4af17831-eb29-44c4-8a02-6d0cc996b70e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "## Use the model on Cirrus instead:\n",
+    "\n",
+    "from langchain_openai import OpenAIEmbeddings\n",
+    "embedding = OpenAIEmbeddings(\n",
+    "                 model = \"cirrus\",\n",
+    "                 api_key =  cirrus_key, \n",
+    "                 base_url = \"https://llm.cirrus.carlboettiger.info/v1\",\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "id": "efc963ed-d20d-49ce-b86c-05beb0947336",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Build a retrival agent\n",
+    "from langchain_text_splitters import RecursiveCharacterTextSplitter\n",
+    "text_splitter = RecursiveCharacterTextSplitter(chunk_size=5000, chunk_overlap=500)\n",
+    "splits = text_splitter.split_documents(docs)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 27,
+   "id": "bb5e99f3-3b58-423d-8945-bddc034c19fb",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# slow part here, runs on remote GPU\n",
+    "from langchain_core.vectorstores import InMemoryVectorStore\n",
+    "vectorstore = InMemoryVectorStore.from_documents(documents = splits, embedding = embedding)\n",
+    "retriever = vectorstore.as_retriever()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 28,
+   "id": "ad666954-aa66-40ac-a54e-2272f77f2d1c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Choose any of the models listed by their short-name:\n",
+    "# see `curl -H \"Authorization: Bearer $OPENAI_API_KEY\" https://llm.nrp-nautilus.io/v1/models`\n",
+    "\"\"\"\n",
+    "models = {\"llama3\": \"llama3-sdsc\", \n",
+    "          \"deepseek-small\": \"DeepSeek-R1-Distill-Qwen-32B\",\n",
+    "          \"deepseek\": \"deepseek-r1-qwen-qualcomm\",\n",
+    "          \"gemma3\": \"gemma3\",\n",
+    "          \"phi3\": \"phi3\",\n",
+    "          \"olmo\": \"olmo\"\n",
+    "         }\n",
+    "\"\"\"\n",
+    "from langchain_openai import ChatOpenAI\n",
+    "#llm = ChatOpenAI(model = models['gemma3'],\n",
+    "                 #api_key = api_key, \n",
+    "                 #base_url = \"https://llm.nrp-nautilus.io\",  \n",
+    "                 #temperature=0)\n",
+    "\n",
+    "\n",
+    "from langchain.chains import create_retrieval_chain\n",
+    "from langchain.chains.combine_documents import create_stuff_documents_chain\n",
+    "from langchain_core.prompts import ChatPromptTemplate\n",
+    "\n",
+    "system_prompt = (\n",
+    "    \"You are an assistant for question-answering tasks. \"\n",
+    "    \"Use the following scientific articles as the retrieved context to answer \"\n",
+    "    \"the question. Appropriately cite the articles from the context on which your answer is based using (Author, Year) format. \"\n",
+    "    \"Do not attempt to cite articles that are not in the context.\"\n",
+    "    \"If you don't know the answer, say that you don't know.\"\n",
+    "    \"Use up to five sentences maximum and keep the answer concise.\\n\\n\"\n",
+    "    \"{context}\"\n",
+    ")\n",
+    "\"\"\"\n",
+    "prompt = ChatPromptTemplate.from_messages(\n",
+    "    [\n",
+    "        (\"system\", system_prompt),\n",
+    "        (\"human\", \"{input}\"),\n",
+    "    ]\n",
+    ")\n",
+    "question_answer_chain = create_stuff_documents_chain(retriever, prompt)\n",
+    "rag_chain = create_retrieval_chain(retriever, question_answer_chain)\n",
+    "\"\"\"\n",
+    "\n",
+    "#call the retriever by ourselves\n",
+    "def test_retriever_only(query: str, k: int = 5):\n",
+    "    retriever.search_kwargs[\"k\"] = k  \n",
+    "    retrieved_docs = retriever.invoke(query)\n",
+    "    \n",
+    "    print(f\"\\n Query: {query}\")\n",
+    "    print(f\"\\n Top {k} Retrieved Documents:\\n\" + \"-\"*60)\n",
+    "    \n",
+    "    for i, doc in enumerate(retrieved_docs):\n",
+    "        print(f\"\\n--- Document #{i+1} ---\")\n",
+    "        print(doc.page_content[:1000])  \n",
+    "        if hasattr(doc, \"metadata\") and doc.metadata:\n",
+    "            print(\"\\n[Metadata]:\", doc.metadata)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 29,
+   "id": "e59dc0c7-5f40-4994-b925-11e4a6605a7a",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      " Query: I live in Tanzania and am having issues with lions breaking into my boma and preying on cattle. What are a few ways to help me prevent this from happening in the future? Can you check these pdfs to see which ones might help?\n",
+      "\n",
+      " Top 5 Retrieved Documents:\n",
+      "------------------------------------------------------------\n",
+      "\n",
+      "--- Document #1 ---\n",
+      "hypothesis was that index of pre- and post-ban use\n",
+      "was the same for both types of feeding sites.\n",
+      "We calculated the average annual number of\n",
+      "observed bears during pre- and post-ban periods\n",
+      "for each feeding site. We then used these averages\n",
+      "instead of raw data from individual counts. We\n",
+      "calculated an annual index of feeding site use by\n",
+      "pooling data from all feeding sites (average number\n",
+      "of bears counted at feeding sites in post-ban period\n",
+      "divided by average number of bears counted in pre-\n",
+      "ban period). Subsequently, we used bootstrapping\n",
+      "with 1,000 simulations to test for differences between\n",
+      "SUPPLEMENTAL FEEDING AND BEAR DEPREDATIONS N Kavcˇicˇ et al. 113\n",
+      "Ursus 24(2):111–119 (2013)\n",
+      "\n",
+      "[Metadata]: {'producer': 'GPL Ghostscript 9.26', 'creator': '', 'creationdate': '2022-06-06T23:09:49-07:00', 'moddate': '2022-06-06T23:09:49-07:00', 'title': '', 'author': '', 'subject': '', 'keywords': '', 'source': 'hwc\\\\Kavcic et al. 2013.pdf', 'total_pages': 9, 'page': 2, 'page_label': '3'}\n",
+      "\n",
+      "--- Document #2 ---\n",
+      "ESPINOSA AND JACOBSON 59\n",
+      "TABLE 3\n",
+      "Linear Multiple Regressions Showing the Association of Variables With People’s Attitudes, Behavioral\n",
+      "Intentions and Perceived Program Impacts\n",
+      "A) Attitude B) Attitude C) Behavioral\n",
+      "toward toward intention in a D) Bear Project\n",
+      "bear protection bear presence conflict with a bear support\n",
+      "Explanatory Std. Beta Std. Beta Std. Beta Std. Beta\n",
+      "variables coefficient Sig. coefficient Sig. coefficient Sig. coefficient Sig.\n",
+      "Gender∗ −.137 .182 −.302 .010 −.544 .000 −.339 .002\n",
+      "Age −.154 .076 .001 .995 .016 .855 .026 .778\n",
+      "Monthly income −.108 .180 .081 .367 −.036 .643 .189 .027\n",
+      "Cow predation by\n",
+      "bears∗∗\n",
+      "−.139 .077 −.196 .028 −.024 .754 .001 .994\n",
+      "Environmental\n",
+      "knowledge\n",
+      ".484 .000 .189 .144 .235 .037 .182 .117\n",
+      "Participation in\n",
+      "Bear Project∗∗\n",
+      ".145 .087 .149 .132 .063 .447 .387 .000\n",
+      "Adjusted R2 .266 .081 .159 .232\n",
+      "SE of the estimate .773 1 .108 .916 .850\n",
+      "N 121 121 145 114\n",
+      "∗Male = 1, Female = 0; ∗∗ Yes = 1, No = 0.\n",
+      "each lasting approximately 1.5 hrs, were conducted with teachers (\n",
+      "\n",
+      "[Metadata]: {'producer': 'Acrobat Distiller 6.0.1 (Windows)', 'creator': 'dvips(k) 5.95a Copyright 2005 Radical Eye Software', 'creationdate': '2011-11-09T13:01:02+05:30', 'moddate': '2011-11-09T13:01:23+05:30', 'title': 'Human-Wildlife Conflict and Environmental Education: Evaluating a Community Program to Protect the A', 'source': 'hwc\\\\Espinosa et al. 2011.pdf', 'total_pages': 12, 'page': 5, 'page_label': '59'}\n",
+      "\n",
+      "--- Document #3 ---\n",
+      "KEYWORDS\n",
+      "bio-logging, crop guarding, crop-foraging, fencing, home range, human-wildlife conflict\n",
+      "mitigation, primate, raiding frequency, social sciences, space use\n",
+      "1 | INTRODUCTION\n",
+      "With an expanding human population that is encroach-\n",
+      "ing on natural landscapes, negative interactions between\n",
+      "people and wildlife are increasing. Such interactions are\n",
+      "more marked when wildlife searches for and consumes\n",
+      "food resources in farmlands (Warren et al.,\n",
+      "2007; Webber\n",
+      "et al.,2011) and urban areas (Contesse et al.,2004; Yeo &\n",
+      "Neo, 2010). Crop and urban foraging wildlife can result\n",
+      "in severe economic losses for people because of the dam-\n",
+      "age they cause to crops and infrastructure (Tavolaro\n",
+      "et al., 2022) contributing to negative human –wildlife\n",
+      "interactions and feelings of insecurity by people, espe-\n",
+      "cially when large mammals or carnivore species forage in\n",
+      "human spaces (Soulsbury & White, 2016). For wildlife,\n",
+      "these interactions can pose significant welfare costs and\n",
+      "threaten populations of endangered sp\n",
+      "\n",
+      "[Metadata]: {'producer': 'Acrobat Distiller 11.0 (Windows); modified using iText 4.2.0 by 1T3XT', 'creator': 'Arbortext Advanced Print Publisher 9.1.520/W Unicode', 'creationdate': '2023-06-16T15:56:20+05:30', 'keywords': '', 'moddate': '2025-05-27T12:15:01-07:00', 'subject': 'Conservat Sci and Prac 2023.5:e12948', 'wps-proclevel': '3', 'wps-journaldoi': '10.1111/(ISSN)2578-4854', 'title': 'Using behavioral studies to adapt management decisions and reduce negative interactions between humans and baboons in Cape Town, South Africa', 'wps-articledoi': '10.1111/csp2.12948', 'source': 'hwc\\\\Fehlmann et al. 2022.pdf', 'total_pages': 16, 'page': 1, 'page_label': '2'}\n",
+      "\n",
+      "--- Document #4 ---\n",
+      "and among lethal interventions, 48.6% investigated culling (N =1 7 ) ,\n",
+      "34.3% retaliatory killing (N = 12), and 17.1% trophy-hunting (N =6 ) .\n",
+      "Contrary to the whole body of literature, most of these case studies were\n",
+      "located in the Neartic (63.6%) followed by the Afrotropic (24.5%) and\n",
+      "Paleartic (7.7%) (Fig. 3). Nonetheless, the species included in the case studies\n",
+      "reflected the generalfindings, with most of the management experiments\n",
+      "being conducted on wolves (29.4%) followed by bears (23.8%) and leopards\n",
+      "(16.1%) (Fig. 2). Surprisingly, almost none of the experiments were con-\n",
+      "ducted on tigers, despite their strong presence in the whole literature and\n",
+      "their heavy impact, including attacks on humans (Dhungana et al., 2016).\n",
+      "Fig. 2.Species prevalence in literature (black bars,N = 525) and case studies (gray bars, N = 143).\n",
+      "Fig. 3.Geographic prevalence in literature (black bars, N = 525) and case studies (gray bars,N = 143), with species involved per geographic area. In circles, mean result\n",
+      "\n",
+      "[Metadata]: {'producer': 'PyPDF', 'creator': 'Elsevier', 'creationdate': '2022-06-07T02:40:21+00:00', 'author': 'Charlotte Lorand', 'crossmarkdomains[1]': 'elsevier.com', 'crossmarkdomains[2]': 'sciencedirect.com', 'crossmarkdomainexclusive': 'true', 'crossmarkmajorversiondate': '2010-04-23', 'elsevierwebpdfspecifications': '7.0', 'keywords': 'Human-carnivore coexistence; Lethal control; Non-lethal management; Conservation interventions; Effectiveness; Evidence-based', 'moddate': '2022-06-07T02:40:21+00:00', 'subject': 'Science of the Total Environment, 838 (2022) 156195. doi:10.1016/j.scitotenv.2022.156195', 'title': \"Effectiveness of interventions for managing human-large carnivore conflicts worldwide: Scare them off, don't remove them\", 'doi': '10.1016/j.scitotenv.2022.156195', 'robots': 'noindex', 'source': 'hwc\\\\Lorand et al. 2022.pdf', 'total_pages': 11, 'page': 5, 'page_label': '6'}\n",
+      "\n",
+      "--- Document #5 ---\n",
+      "because they have longer perimeters (Fig. 1B). Finally, 80–85% of\n",
+      "the cost of materials of most fences is in the corner and end systems;\n",
+      "therefore, an effort should be made to minimize these.\n",
+      "We designed a computer model to assist with determining if\n",
+      "fencing is economically feasible for reducing deer damage and, if\n",
+      "so, which fence design would be optimal (VerCauteren et al.\n",
+      "2006). Our interactive model provides economic analyses and\n",
+      "predicts the scenarios associated with fencing relative to area and\n",
+      "perimeter of the protected plot, value and percentage of crop\n",
+      "damaged annually prior to fencing, cost of the fence, and efficacy\n",
+      "of the fence. Users of the model can easily adjust the above\n",
+      "variables to fit their individual situations and needs. By running a\n",
+      "series of simulations, users can answer questions directly related to\n",
+      "the economics associated with different fence designs for their\n",
+      "situation.\n",
+      "Negative Impacts\n",
+      "Fences can effectively protect human commodities; however, they\n",
+      "can have neg\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDFlib PLOP 2.0.0p6 (SunOS)/Acrobat Distiller 6.0 (Windows); modified using iText 4.2.0 by 1T3XT', 'creator': '3B2 Total Publishing System 8.07c/W', 'creationdate': '2006-04-19T19:41:41-05:00', 'moddate': '2025-05-27T12:08:26-07:00', 'subject': 'Wildlife Society Bulletin 2006.34:191-200', 'wps-proclevel': '2', 'wps-journaldoi': '10.1111/wsb4.2006.34.issue-1', 'title': 'From the Field: Fences and Deer‐Damage Management: A Review of Designs and Efficacy', 'wps-articledoi': '10.2193/0091-7648(2006)34[191:FADMAR]2.0.CO;2', 'source': 'hwc\\\\VerCauteren et al. 2006.pdf', 'total_pages': 10, 'page': 3, 'page_label': '4'}\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<function __main__.test_retriever_only(query: str, k: int = 5)>"
+      ]
+     },
+     "execution_count": 29,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "test_query = \"I live in Tanzania and am having issues with lions breaking into my boma and preying on cattle. What are a few ways to help me prevent this from happening in the future? Can you check these pdfs to see which ones might help?\"\n",
+    "test_retriever_only(test_query, k=5)\n",
+    "test_retriever_only"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 30,
+   "id": "968cd90b-0bc6-42f9-a097-97d3f347d93e",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      " Query: What should I do if elephants are destroying my crops? And what are the most cost-effective prevention methods, if there are any you know of? Can you check these pdfs to see which ones might help?\n",
+      "\n",
+      " Top 5 Retrieved Documents:\n",
+      "------------------------------------------------------------\n",
+      "\n",
+      "--- Document #1 ---\n",
+      "hypothesis was that index of pre- and post-ban use\n",
+      "was the same for both types of feeding sites.\n",
+      "We calculated the average annual number of\n",
+      "observed bears during pre- and post-ban periods\n",
+      "for each feeding site. We then used these averages\n",
+      "instead of raw data from individual counts. We\n",
+      "calculated an annual index of feeding site use by\n",
+      "pooling data from all feeding sites (average number\n",
+      "of bears counted at feeding sites in post-ban period\n",
+      "divided by average number of bears counted in pre-\n",
+      "ban period). Subsequently, we used bootstrapping\n",
+      "with 1,000 simulations to test for differences between\n",
+      "SUPPLEMENTAL FEEDING AND BEAR DEPREDATIONS N Kavcˇicˇ et al. 113\n",
+      "Ursus 24(2):111–119 (2013)\n",
+      "\n",
+      "[Metadata]: {'producer': 'GPL Ghostscript 9.26', 'creator': '', 'creationdate': '2022-06-06T23:09:49-07:00', 'moddate': '2022-06-06T23:09:49-07:00', 'title': '', 'author': '', 'subject': '', 'keywords': '', 'source': 'hwc\\\\Kavcic et al. 2013.pdf', 'total_pages': 9, 'page': 2, 'page_label': '3'}\n",
+      "\n",
+      "--- Document #2 ---\n",
+      "ESPINOSA AND JACOBSON 59\n",
+      "TABLE 3\n",
+      "Linear Multiple Regressions Showing the Association of Variables With People’s Attitudes, Behavioral\n",
+      "Intentions and Perceived Program Impacts\n",
+      "A) Attitude B) Attitude C) Behavioral\n",
+      "toward toward intention in a D) Bear Project\n",
+      "bear protection bear presence conflict with a bear support\n",
+      "Explanatory Std. Beta Std. Beta Std. Beta Std. Beta\n",
+      "variables coefficient Sig. coefficient Sig. coefficient Sig. coefficient Sig.\n",
+      "Gender∗ −.137 .182 −.302 .010 −.544 .000 −.339 .002\n",
+      "Age −.154 .076 .001 .995 .016 .855 .026 .778\n",
+      "Monthly income −.108 .180 .081 .367 −.036 .643 .189 .027\n",
+      "Cow predation by\n",
+      "bears∗∗\n",
+      "−.139 .077 −.196 .028 −.024 .754 .001 .994\n",
+      "Environmental\n",
+      "knowledge\n",
+      ".484 .000 .189 .144 .235 .037 .182 .117\n",
+      "Participation in\n",
+      "Bear Project∗∗\n",
+      ".145 .087 .149 .132 .063 .447 .387 .000\n",
+      "Adjusted R2 .266 .081 .159 .232\n",
+      "SE of the estimate .773 1 .108 .916 .850\n",
+      "N 121 121 145 114\n",
+      "∗Male = 1, Female = 0; ∗∗ Yes = 1, No = 0.\n",
+      "each lasting approximately 1.5 hrs, were conducted with teachers (\n",
+      "\n",
+      "[Metadata]: {'producer': 'Acrobat Distiller 6.0.1 (Windows)', 'creator': 'dvips(k) 5.95a Copyright 2005 Radical Eye Software', 'creationdate': '2011-11-09T13:01:02+05:30', 'moddate': '2011-11-09T13:01:23+05:30', 'title': 'Human-Wildlife Conflict and Environmental Education: Evaluating a Community Program to Protect the A', 'source': 'hwc\\\\Espinosa et al. 2011.pdf', 'total_pages': 12, 'page': 5, 'page_label': '59'}\n",
+      "\n",
+      "--- Document #3 ---\n",
+      "Americas. In recent decades, extensive fragmentation of\n",
+      "jaguar habitat and expansion of human activities into such\n",
+      "areas has increased both jaguar depredation on livestock as\n",
+      "well as conflict with humans (Rabinowitz and Nottingham\n",
+      "1986, Weber and Rabinowitz 1996). However, there has\n",
+      "been limited assessment of the magnitude of jaguar use of\n",
+      "livestock as prey or of factors predisposing livestock to\n",
+      "depredation by jaguars. For instance, the demonstrated\n",
+      "preference by jaguars for forested habitats in close\n",
+      "association with standing water is attributed to increased\n",
+      "wild prey vulnerability to predation in such habitats\n",
+      "(Crawshaw and Quigley 1991, Quigley and Crawshaw\n",
+      "1992). Similar patterns may apply to jaguar selection of\n",
+      "domestic prey. Inappropriate husbandry practices and wild\n",
+      "prey availability and vulnerability are factors reported to\n",
+      "influence vulnerability of livestock to depredation by jaguars,\n",
+      "particularly among calves (Quigley and Crawshaw 1992,\n",
+      "Hoogesteijn et al. 1993, Polisar et al.\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDFlib PLOP 2.0.0p6 (SunOS)/Acrobat Distiller 7.0.5 (Windows); modified using iText 4.2.0 by 1T3XT', 'creator': '3B2 Total Publishing System 8.07c/W', 'creationdate': '2007-08-21T03:47:13-05:00', 'moddate': '2025-05-27T11:54:37-07:00', 'subject': 'J Wildl Manag 2007.71:2379-2386', 'wps-proclevel': '2', 'wps-journaldoi': '10.1111/jwmg.2007.71.issue-7', 'title': 'Evaluation of Potential Factors Predisposing Livestock to Predation by Jaguars', 'wps-articledoi': '10.2193/2006-520', 'source': 'hwc\\\\Azevedo and Murray 2007.pdf', 'total_pages': 8, 'page': 0, 'page_label': '1'}\n",
+      "\n",
+      "--- Document #4 ---\n",
+      "Convention on the Conservation of European Wildlife and Natural HabitatsNature\n",
+      "and Environment Series 113. Council of Europe, Strasbourg.\n",
+      "Boitani, L., Ciucci, P., Raganella-Pelliccioni, E., 2010.Ex-post compensation payments for\n",
+      "wolf predation on livestock in Italy: a tool for conservation? Wildl. Res. 37, 722–730.\n",
+      "Bradley, E.H., Pletscher, D.H., 2005.Assessing factors related to wolf depredation of cattle\n",
+      "in fenced pastures in Montana and Idaho. Wildl. Soc. Bull. 33, 1256–1265.\n",
+      "Breck, S.W., Meier, T., 2004.Managing wolf depredation in the United States: past, pres-\n",
+      "ent, and future. Sheep Goat Res. J. 19 (Special Issue: Predation), 41–46.\n",
+      "Burnham, K.P., Anderson, D.R., 2002.Model Selection and Multimodel Inference. A Practi-\n",
+      "cal Information-Theoretic Approach. Springer-Verlag.\n",
+      "Cade, B.S., 2015.Model averaging and muddled multimodel inferences. Ecology 96,\n",
+      "2370–2382.\n",
+      "Chapron, G., Kaczensky, P., Linnell, J.D., von Arx, M., Huber, D., Andrén, H., ... Boitani, L.,\n",
+      "2014. Recovery of large c\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDF Architect 3', 'creator': 'PDF Architect 3', 'creationdate': '2017-01-25T14:50:41+00:00', 'author': 'V. Pimenta', 'moddate': '2017-01-25T14:52:31+00:00', 'source': 'hwc\\\\Pimenta et al. 2017.pdf', 'total_pages': 20, 'page': 8, 'page_label': '9'}\n",
+      "\n",
+      "--- Document #5 ---\n",
+      "attacked bomas ranged from 54% (at 0–1 km); 31% (at 1–2 km); 11% (at 2–3 km) to 4% (at >3\n",
+      "km from the park boundary). We also found a significant yearly increase in mean distance of\n",
+      "attacks from the park boundary, from the application of flashlights in 2012 (Mann-Whitney U\n",
+      "test t = 11.291, df = 79.002, p-value = 0.0001) (Fig 7). The yearly regression with intercept of\n",
+      "2.001+03 and slope of 0.008, shows that every 3 years, there is 2km increase in distance of\n",
+      "attack.\n",
+      "The fence height in relation to percentages of attack (high = 12%, medium 23%, short =\n",
+      "71% and χ\n",
+      "2\n",
+      "= 8.088, df = 2, p-value = 0.017.This shows that bomas without flashlights and\n",
+      "those with short-medium fences are more likely to be attacked by lion than those with flash-\n",
+      "lights and higher fences. The data normality distribution test was W = 0.87567, p-value <\n",
+      "0.00001.\n",
+      "Fig 5. Cumulative flashlights installed and Mean nocturnal and diurnal livestock predation at bomas with and without\n",
+      "flashlights .\n",
+      "https://do i.org/10.1371/j o\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDFlib+PDI 8.0.2p1 (C++/Win64); modified using iTextSharp™ 5.5.3 ©2000-2014 iText Group NV (AGPL-version)', 'creator': 'Arbortext Advanced Print Publisher 11.0.2857/W Unicode-x64', 'creationdate': '2018-01-10T21:11:13+05:30', 'title': 'Effectiveness of a LED flashlight technique in reducing livestock depredation by lions (Panthera leo) around Nairobi National Park, Kenya', 'eps_processor': 'PStill version 1.76.22', 'moddate': '2018-01-10T21:12:24+05:30', 'author': \"Francis Lesilau, Myrthe Fonck, Maria Gatta, Charles Musyoki, Maarten van 't Zelfde, Gerard A. Persoon, Kees C. J. M. Musters, Geert R. de Snoo, Hans H. de Iongh\", 'source': 'hwc\\\\Lesilau et al. 2018.pdf', 'total_pages': 18, 'page': 9, 'page_label': '10'}\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<function __main__.test_retriever_only(query: str, k: int = 5)>"
+      ]
+     },
+     "execution_count": 30,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "test_query = \"What should I do if elephants are destroying my crops? And what are the most cost-effective prevention methods, if there are any you know of? Can you check these pdfs to see which ones might help?\"\n",
+    "test_retriever_only(test_query, k=5)\n",
+    "test_retriever_only"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 31,
+   "id": "327f96c5-2656-4ed6-8bba-2bd4bd652f83",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      " Query: I know jaguars can prey on goats and cattle, which I have; what measures can I take to save them from getting harmed? Can you check these pdfs to see which ones might help? \n",
+      "\n",
+      " Top 5 Retrieved Documents:\n",
+      "------------------------------------------------------------\n",
+      "\n",
+      "--- Document #1 ---\n",
+      "458 SELECTIVE REMOVAL OF COYOTES * Blejwas et al. J. Wildl. Manage. 66(2):2002 \n",
+      " was monitored, predation resumed only after the \n",
+      " new pair had formed (K. M. Blejwas, unpublished \n",
+      " data). These data suggest that loss of a mate and \n",
+      " the associated process of forming a new pair \n",
+      " bond alters the behavior of the surviving breeder, \n",
+      " temporarily interrupting predation on sheep. \n",
+      " Why Breeding Coyotes Kill Sheep \n",
+      " It is not surprising that breeding pairs are \n",
+      " responsible for most depredations of ewes and \n",
+      " large lambs. Most observations of coyotes attack- \n",
+      " ing large ungulate prey indicate that these are \n",
+      " cooperative endeavors involving more than 1 coy- \n",
+      " ote (Cahalane 1947, Robinson 1952, Bowyer \n",
+      " 1987, Gese and Grothe 1995, Lingle 2000). Most \n",
+      " observations of coyotes attacking ungulate fawns \n",
+      " also involve pairs or groups of coyotes (Mac- \n",
+      " Connell-Yount and Smith 1978, Hamlin and \n",
+      " Schweitzer 1979, Truett 1979, Bowyer 1987), and \n",
+      " a pair may be present even when only 1 coyote is \n",
+      " in\n",
+      "\n",
+      "[Metadata]: {'producer': 'iText® 5.5.8 ©2000-2015 iText Group NV (AGPL-version); modified using iText® 7.1.3 ©2000-2018 iText Group NV (JSTOR Michigan; licensed version)', 'creator': 'page2pdf-2.1', 'creationdate': '2016-08-07T19:47:10+00:00', 'moddate': '2020-09-14T14:51:37+00:00', 'title': 'The Effectiveness of Selective Removal of Breeding Coyotes in Reducing Sheep Predation', 'source': 'hwc\\\\Blejwas et al. 2002.pdf', 'total_pages': 13, 'page': 8, 'page_label': '459'}\n",
+      "\n",
+      "--- Document #2 ---\n",
+      "Gittleman, J.L., Funk, S.M., Macdonald, D.W. & Wayne,\n",
+      "R.K. (2001). Why ‘carnivore conservation’? InCarnivore\n",
+      "conservation: 1–8. Gittleman, J.L., Funk, S.M., Macdo-\n",
+      "nald, D. & Wayne, R.K. (Eds). Cambridge: Cambridge\n",
+      "University Press.\n",
+      "Gonz ´alez, F. (1995). Livestock predation in the Venezuelan\n",
+      "Llanos. Cat News 22, 14–15.\n",
+      "Hoogesteijn, R., Hoogesteijn, A. & Mondolfi, E. (1993).\n",
+      "Jaguar predation and conservation: cattle mortality caused\n",
+      "by felines on three ranches in the Venezuelan Llanos. In\n",
+      "Mammals as predators : 391–407. Dunstone, N. & Gorman,\n",
+      "M.L. (Eds). London: Oxford University Press.\n",
+      "Hoogesteijn, R. & Mondolfi, E. (1992).The jaguar. Caracas:\n",
+      "Armitano Publishers.\n",
+      "Instituto Brasileiro de Geografia e Estat´ıstica (IBGE). (2004)\n",
+      "Pesquisa Pecu´aria Municipal 1990–2003. Available at\n",
+      "http://www.ibge.gov.br/bda/pecua.\n",
+      "Iriarte, J.A., Johnson, W.E. & Franklin, W.L. (1991). Feeding\n",
+      "ecology of the Patagonia puma in southernmost Chile.Rev.\n",
+      "Chil. Hist. Nat. 64, 145–156.\n",
+      "Jackson, R., Wang, Z.Y., Lu, \n",
+      "\n",
+      "[Metadata]: {'producer': 'PDFlib PLOP 3.0 (.NET/Win32)/Acrobat Distiller 6.0.1 (Windows); modified using iText 4.2.0 by 1T3XT', 'creator': '3B2 Total Publishing System 8.07f/W', 'creationdate': '2006-03-25T19:46:31+05:30', 'moddate': '2025-05-27T11:47:43-07:00', 'subject': 'Animal Conservation 2006.9:179-188', 'wps-proclevel': '2', 'title': 'Human��wildlife conflicts in a fragmented Amazonian forest landscape: determinants of large felid depredation on livestock', 'wps-articledoi': '10.1111/j.1469-1795.2006.00025.x', 'source': 'hwc\\\\Michalski et al. 2006.pdf', 'total_pages': 10, 'page': 8, 'page_label': '9'}\n",
+      "\n",
+      "--- Document #3 ---\n",
+      "See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/305358233\n",
+      "Fencing: A Valuable Tool for Reducing Wildlife-Vehicle Collisions and\n",
+      "Funnelling Fauna to Crossing Structures\n",
+      "Chapter · January 2015\n",
+      "DOI: 10.1002/9781118568170.ch20\n",
+      "CITATIONS\n",
+      "54\n",
+      "READS\n",
+      "3,350\n",
+      "3 authors, including:\n",
+      "Rodney van der Ree\n",
+      "University of Melbourne\n",
+      "148 PUBLICATIONS   5,823 CITATIONS   \n",
+      "SEE PROFILE\n",
+      "All content following this page was uploaded by Rodney van der Ree on 23 July 2018.\n",
+      "The user has requested enhancement of the downloaded file.\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDFlib PLOP 2.0.0p6 (SunOS)/iTextSharp™ 5.5.0 ©2000-2013 iText Group NV (AGPL-version)', 'creator': 'PyPDF', 'creationdate': '2015-03-24T09:28:20+05:30', 'title': 'Fencing', 'wps-articledoi': '10.1002/9781118568170.ch20', 'wps-proclevel': '3', 'moddate': '2015-04-24T21:50:27-04:00', 'author': 'Rodney van der Ree', 'rgid': 'PB:305358233_AS:651478247145472@1532335926046', 'source': 'hwc\\\\van der Ree et al. 2015.pdf', 'total_pages': 14, 'page': 0, 'page_label': '159'}\n",
+      "\n",
+      "--- Document #4 ---\n",
+      "timating the percent loss of kernels (Woronecki et al.\n",
+      "1980) and converting to yield loss per hectare. Fruit loss\n",
+      "can be estimated by counting the numbers of undamaged,\n",
+      "pecked, and removed fruits per sampled branch (Tobin\n",
+      "and Dolbeer 1987). Sprouting rice removed by birds can\n",
+      "be estimated by companng plant density in exposed plots\n",
+      "with that in adjacent plots with wire bird exclosures (Otis\n",
+      "et al. 1983). The seeded surface area of sunflower heads\n",
+      "destroyed by birds can be estimated with the aid of a clear\n",
+      "plastic template (Dolbeer 1975).\n",
+      "Losses of agricultural crops to birds can be estimated\n",
+      "indirectly through avian bioenergetics. By estimating the\n",
+      "number of birds of the depredating species feeding in an\n",
+      "area, thc percentage of thc agncultural crop in the birds'\n",
+      "diet, the caloric value of the crop, and the daily caloric\n",
+      "requirements of the birds, one can project thc total bio-\n",
+      "mass of crop removed by birds on a daily or seasonal\n",
+      "basis (Weathcrhead et al. 1982, White et al. 1985).\n",
+      "Specie\n",
+      "\n",
+      "[Metadata]: {'producer': 'Canon iR C5800', 'creator': 'Canon iR C5800', 'creationdate': '2009-03-09T08:39:40-05:00', 'subject': 'Image', 'source': 'hwc\\\\Dolbeer et al. 1994.pdf', 'total_pages': 34, 'page': 2, 'page_label': '3'}\n",
+      "\n",
+      "--- Document #5 ---\n",
+      "7,3 1 7e325\n",
+      ".\n",
+      "Hovick, T. J., Elmore, R. D., Dahlgren, D. K., Fuhlendorf, S. D., & Engle, D. M. (2014).\n",
+      "Evidence of negative effects of anthropogenic structures on wildlife: A review of\n",
+      "grouse survival and behaviour.Journal of Applied Ecology, 51, 1680e1689.\n",
+      "Huijser, M., McGowen, P., Fuller, J., Hardy, A., Kociolek, A., Clevenger, A. P., et al.\n",
+      "(2008). Wildlifeevehicle collision reduction study: Report to congress [No.\n",
+      "FHWAeHRTe08e034]. Washington, D.C.: U.S. Department of Transportation.\n",
+      "Hunt, W. G., McClure, C. J. W., & Allison, T. D. (2015). Do raptors react to ultraviolet\n",
+      "light? Journal of Raptor Research, 49, 342e343.\n",
+      "Jaeger, M. M., Blejwas, K. M., Sacks, B. N., Neale, J. C. C., Conner, M. M., &\n",
+      "McCullough, D. R. (2001). Targeting alphas can make coyote control more\n",
+      "effective and socially acceptable.California Agriculture, 55,3 2e36.\n",
+      "Johnson, H. E., Breck, S. W., Baruch-Mordo, S., Lewis, D. L., Lackey, C. W.,\n",
+      "Wilson, K. R., et al. (2015). Shifting perceptions of risk and reward: Te\n",
+      "\n",
+      "[Metadata]: {'producer': 'Acrobat Distiller 8.1.0 (Windows)', 'creator': 'Elsevier', 'creationdate': '2016-09-26T20:02:29+05:30', 'crossmarkdomains[2]': 'elsevier.com', 'crossmarkmajorversiondate': '2010-04-23', 'subject': 'Animal Behaviour, 120 (2016) 245-254. doi:10.1016/j.anbehav.2016.07.013', 'author': 'Bradley F. Blackwell', 'elsevierwebpdfspecifications': '6.5', 'crossmarkdomainexclusive': 'true', 'robots': 'noindex', 'moddate': '2016-09-26T20:03:01+05:30', 'doi': '10.1016/j.anbehav.2016.07.013', 'crossmarkdomains[1]': 'sciencedirect.com', 'title': 'No single solution: application of behavioural principles in mitigating human-wildlife conflict', 'source': 'hwc\\\\Blackwell et al. 2016.pdf', 'total_pages': 10, 'page': 8, 'page_label': '253'}\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<function __main__.test_retriever_only(query: str, k: int = 5)>"
+      ]
+     },
+     "execution_count": 31,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "test_query = \"I know jaguars can prey on goats and cattle, which I have; what measures can I take to save them from getting harmed? Can you check these pdfs to see which ones might help? \"\n",
+    "test_retriever_only(test_query, k=5)\n",
+    "test_retriever_only"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 32,
+   "id": "5afb060d-0444-4167-bdd5-b63501475773",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      " Query: I am trying to prevent coyotes from eating the calves of my free-range cattle. What may work best and incentivize them to stay away? Can you check these pdfs to see which ones might help? https://minio.carlboettiger.info/public-data/hwc.zip\n",
+      "\n",
+      " Top 5 Retrieved Documents:\n",
+      "------------------------------------------------------------\n",
+      "\n",
+      "--- Document #1 ---\n",
+      "242 Conflict Intervention Priorities\n",
+      "helps foster more effective collaboration (Game et al.\n",
+      "2013; Lute et al. 2018). Third, both the survey results\n",
+      "and feedback were consistent with recent scholarship\n",
+      "(Redpath et al. 2017) that highlights participatory and\n",
+      "stakeholder-first conflict interventions as best practice\n",
+      "and advocates multipronged (Hazzah et al. 2014) and\n",
+      "adaptive management strategies (Bunnefeld et al. 2017).\n",
+      "Education and awareness programs were often cited in\n",
+      "feedback as being necessary additions to any interven-\n",
+      "tions. However, given the failures of many awareness-\n",
+      "based conservation programs (Schultz 2011), a further\n",
+      "exploration into why and where conservation decision\n",
+      "makers deem them most appropriate is important. Ap-\n",
+      "proaches that are specifically aimed at a particular au-\n",
+      "dience, such as social marketing (Salazar et al. 2018),\n",
+      "may be more effective than simple information provision\n",
+      "or—often-problematic—enforcement (Duffy et al. 2019).\n",
+      "However, how different interventio\n",
+      "\n",
+      "[Metadata]: {'producer': 'Acrobat Distiller 10.1.10 (Windows); modified using iText 4.2.0 by 1T3XT', 'creator': 'LaTeX with hyperref package', 'creationdate': '2020-01-16T12:33:42+05:30', 'keywords': '', 'moddate': '2025-05-27T12:12:25-07:00', 'subject': 'Conservation Biology 2020.34:232-243', 'wps-proclevel': '3', 'wps-journaldoi': '10.1111/(ISSN)1523-1739', 'author': '', 'title': 'Predicting intervention priorities for wildlife conflicts', 'wps-articledoi': '10.1111/cobi.13372', 'source': 'hwc\\\\Baynham-Herd et al. 2019.pdf', 'total_pages': 12, 'page': 10, 'page_label': '242'}\n",
+      "\n",
+      "--- Document #2 ---\n",
+      "Fig 1. The effects of AC programs on three metrics of black bear wariness, Whistler BC, 2007–2008. A and B show\n",
+      "the average observed percent change in overt reaction distance and displace ment distance among bears in the AC\n",
+      "Group and the Control Group. Error bars represent standard error. C shows the predicted effect of the number of AC\n",
+      "events conduc ted during the previous 30 days on the likeliho od that a bear will flee from research ers prior to their\n",
+      "beginning AC treatm ent.\n",
+      "https://d oi.org/10.1371/j ournal.pon e.0295989.g0 01\n",
+      "PLOS ONE\n",
+      "Aversive condition ing of conflict black bears\n",
+      "PLOS ONE | https://doi.or g/10.137 1/journal.po ne.02959 89 January 2, 2024 8 / 19\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDFlib+PDI 9.3.1p2 (C++/Win64)', 'creator': 'PTC Arbortext Layout Developer 12.1.6180/W-x64', 'creationdate': '2023-12-25T16:46:13+05:30', 'title': 'Aversive conditioning increases short-term wariness but does not change habitat use in black bears associated with conflict', 'epsprocessor': 'PStill version 1.84.42', 'author': 'Lori Homstol, Sage Raymond, Claire Edwards, Anthony N. Hamilton, Colleen Cassady St. Clair', 'moddate': '2023-12-25T16:46:13+05:30', 'source': 'hwc\\\\Homstol et al. 2024.pdf', 'total_pages': 19, 'page': 7, 'page_label': '8'}\n",
+      "\n",
+      "--- Document #3 ---\n",
+      "51] and other carnivores, such as coyotes (Canis latrans) [69, 70], African lions (Panthera leo)\n",
+      "[71], and wolves (Canis lupus) [72]. The relative effectiveness of these AC programs for\n",
+      "increasing wariness could relate to several aspects of program implementation. Because we\n",
+      "subjected bears to aversive stimuli as they engaged in problematic behaviour [48, 50], we\n",
+      "increased the likelihood that bears associated the conditioning stimulus (conflict behaviour)\n",
+      "with the unconditioned stimulus (pain/ stress) [38, 52]. This principle of immediacy in aver-\n",
+      "sive conditioning [54] is not achieved when aversive conditioning occurs upon release of a\n",
+      "captured bear, sometimes hours later and kilometres distant from the capture location where\n",
+      "conflict occurred [32]. Repetition of treatments allowed bears to generalize among experiences\n",
+      "instead of associating the painful stimulus with a single location or human individual, which\n",
+      "has been identified as important to AC programs targeting bold coyotes [69\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDFlib+PDI 9.3.1p2 (C++/Win64)', 'creator': 'PTC Arbortext Layout Developer 12.1.6180/W-x64', 'creationdate': '2023-12-25T16:46:13+05:30', 'title': 'Aversive conditioning increases short-term wariness but does not change habitat use in black bears associated with conflict', 'epsprocessor': 'PStill version 1.84.42', 'author': 'Lori Homstol, Sage Raymond, Claire Edwards, Anthony N. Hamilton, Colleen Cassady St. Clair', 'moddate': '2023-12-25T16:46:13+05:30', 'source': 'hwc\\\\Homstol et al. 2024.pdf', 'total_pages': 19, 'page': 12, 'page_label': '13'}\n",
+      "\n",
+      "--- Document #4 ---\n",
+      "8 \n",
+      " \n",
+      " \n",
+      " \n",
+      " \n",
+      " \n",
+      "Figure A5. Silhouette width plot of the k-medoid partitions with k = 2 to 10 used to estimate the best \n",
+      "number of clusters to describe livestock husbandry systems within the wolf range in northern Portugal \n",
+      "(see the main text for details). \n",
+      "  \n",
+      "2 4 6 8 10 \n",
+      "0.20 0.22 0.24 0.26 0.28 0.30 0.32 \n",
+      "Number of clusters \n",
+      "Silhouette Width\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDF Architect 3', 'creator': 'PDF Architect 3', 'creationdate': '2017-01-25T14:50:41+00:00', 'author': 'V. Pimenta', 'moddate': '2017-01-25T14:52:31+00:00', 'source': 'hwc\\\\Pimenta et al. 2017.pdf', 'total_pages': 20, 'page': 17, 'page_label': '18'}\n",
+      "\n",
+      "--- Document #5 ---\n",
+      "3\n",
+      "Vol.:(0123456789)Scientific RepoRtS  |        (2020) 10:15341  | https://doi.org/10.1038/s41598-020-72343-6\n",
+      "www.nature.com/scientificreports/\n",
+      "numbers increase and more bears need more  food26,43,44. Hence, the effectiveness of anti-bear interventions can \n",
+      "be lower than expected when hungry bears become persistent and more aggressive in damaging behaviour. As \n",
+      "high density may lead to more bears involved in conflicts, it also could increase the demand for bear  removal45 \n",
+      "and affect the effectiveness of removal techniques such as translocation and lethal control.\n",
+      "In this paper, we compiled a global database of intervention effectiveness against bears and studied how it \n",
+      "is related to bear species and densities, duration of intervention application, and intervention techniques. We \n",
+      "attempted to find and describe the most effective and the least effective interventions against bears. Further, we \n",
+      "tested several hypotheses: (1) lethal control and invasive management are less effective th\n",
+      "\n",
+      "[Metadata]: {'producer': 'Adobe PDF Library 15.0; modified using iText® 5.3.5 ©2000-2012 1T3XT BVBA (SPRINGER SBM; licensed version)', 'creator': 'Springer', 'creationdate': '2020-09-14T15:09:33+05:30', 'crossmarkdomains[1]': 'springer.com', 'moddate': '2020-09-14T15:58:07+02:00', 'crossmarkmajorversiondate': '2010-04-23', 'subject': 'Scientific Reports, https://doi.org/10.1038/s41598-020-72343-6', 'author': 'Igor Khorozyan', 'title': 'Variation and conservation implications of the effectiveness of anti-bear interventions', 'crossmarkdomainexclusive': 'true', 'robots': 'noindex', 'doi': '10.1038/s41598-020-72343-6', 'crossmarkdomains[2]': 'springerlink.com', 'source': 'hwc\\\\Khorozyan and Waltert 2020.pdf', 'total_pages': 9, 'page': 2, 'page_label': '3'}\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<function __main__.test_retriever_only(query: str, k: int = 5)>"
+      ]
+     },
+     "execution_count": 32,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "test_query = \"I am trying to prevent coyotes from eating the calves of my free-range cattle. What may work best and incentivize them to stay away? Can you check these pdfs to see which ones might help? https://minio.carlboettiger.info/public-data/hwc.zip\"\n",
+    "test_retriever_only(test_query, k=5)\n",
+    "test_retriever_only\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 33,
+   "id": "64e672ff-8341-4144-a0cf-b9756661475e",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      " Query: Deers keep destroying and takiing over our large agricultural fields. Is there anything I can try to prevent this that won’t break the bank? Can you check these pdfs to see which ones might help? https://minio.carlboettiger.info/public-data/hwc.zip\n",
+      "\n",
+      " Top 5 Retrieved Documents:\n",
+      "------------------------------------------------------------\n",
+      "\n",
+      "--- Document #1 ---\n",
+      "242 Conflict Intervention Priorities\n",
+      "helps foster more effective collaboration (Game et al.\n",
+      "2013; Lute et al. 2018). Third, both the survey results\n",
+      "and feedback were consistent with recent scholarship\n",
+      "(Redpath et al. 2017) that highlights participatory and\n",
+      "stakeholder-first conflict interventions as best practice\n",
+      "and advocates multipronged (Hazzah et al. 2014) and\n",
+      "adaptive management strategies (Bunnefeld et al. 2017).\n",
+      "Education and awareness programs were often cited in\n",
+      "feedback as being necessary additions to any interven-\n",
+      "tions. However, given the failures of many awareness-\n",
+      "based conservation programs (Schultz 2011), a further\n",
+      "exploration into why and where conservation decision\n",
+      "makers deem them most appropriate is important. Ap-\n",
+      "proaches that are specifically aimed at a particular au-\n",
+      "dience, such as social marketing (Salazar et al. 2018),\n",
+      "may be more effective than simple information provision\n",
+      "or—often-problematic—enforcement (Duffy et al. 2019).\n",
+      "However, how different interventio\n",
+      "\n",
+      "[Metadata]: {'producer': 'Acrobat Distiller 10.1.10 (Windows); modified using iText 4.2.0 by 1T3XT', 'creator': 'LaTeX with hyperref package', 'creationdate': '2020-01-16T12:33:42+05:30', 'keywords': '', 'moddate': '2025-05-27T12:12:25-07:00', 'subject': 'Conservation Biology 2020.34:232-243', 'wps-proclevel': '3', 'wps-journaldoi': '10.1111/(ISSN)1523-1739', 'author': '', 'title': 'Predicting intervention priorities for wildlife conflicts', 'wps-articledoi': '10.1111/cobi.13372', 'source': 'hwc\\\\Baynham-Herd et al. 2019.pdf', 'total_pages': 12, 'page': 10, 'page_label': '242'}\n",
+      "\n",
+      "--- Document #2 ---\n",
+      "8 \n",
+      " \n",
+      " \n",
+      " \n",
+      " \n",
+      " \n",
+      "Figure A5. Silhouette width plot of the k-medoid partitions with k = 2 to 10 used to estimate the best \n",
+      "number of clusters to describe livestock husbandry systems within the wolf range in northern Portugal \n",
+      "(see the main text for details). \n",
+      "  \n",
+      "2 4 6 8 10 \n",
+      "0.20 0.22 0.24 0.26 0.28 0.30 0.32 \n",
+      "Number of clusters \n",
+      "Silhouette Width\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDF Architect 3', 'creator': 'PDF Architect 3', 'creationdate': '2017-01-25T14:50:41+00:00', 'author': 'V. Pimenta', 'moddate': '2017-01-25T14:52:31+00:00', 'source': 'hwc\\\\Pimenta et al. 2017.pdf', 'total_pages': 20, 'page': 17, 'page_label': '18'}\n",
+      "\n",
+      "--- Document #3 ---\n",
+      "Fig 1. The effects of AC programs on three metrics of black bear wariness, Whistler BC, 2007–2008. A and B show\n",
+      "the average observed percent change in overt reaction distance and displace ment distance among bears in the AC\n",
+      "Group and the Control Group. Error bars represent standard error. C shows the predicted effect of the number of AC\n",
+      "events conduc ted during the previous 30 days on the likeliho od that a bear will flee from research ers prior to their\n",
+      "beginning AC treatm ent.\n",
+      "https://d oi.org/10.1371/j ournal.pon e.0295989.g0 01\n",
+      "PLOS ONE\n",
+      "Aversive condition ing of conflict black bears\n",
+      "PLOS ONE | https://doi.or g/10.137 1/journal.po ne.02959 89 January 2, 2024 8 / 19\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDFlib+PDI 9.3.1p2 (C++/Win64)', 'creator': 'PTC Arbortext Layout Developer 12.1.6180/W-x64', 'creationdate': '2023-12-25T16:46:13+05:30', 'title': 'Aversive conditioning increases short-term wariness but does not change habitat use in black bears associated with conflict', 'epsprocessor': 'PStill version 1.84.42', 'author': 'Lori Homstol, Sage Raymond, Claire Edwards, Anthony N. Hamilton, Colleen Cassady St. Clair', 'moddate': '2023-12-25T16:46:13+05:30', 'source': 'hwc\\\\Homstol et al. 2024.pdf', 'total_pages': 19, 'page': 7, 'page_label': '8'}\n",
+      "\n",
+      "--- Document #4 ---\n",
+      "3\n",
+      "Vol.:(0123456789)Scientific RepoRtS  |        (2020) 10:15341  | https://doi.org/10.1038/s41598-020-72343-6\n",
+      "www.nature.com/scientificreports/\n",
+      "numbers increase and more bears need more  food26,43,44. Hence, the effectiveness of anti-bear interventions can \n",
+      "be lower than expected when hungry bears become persistent and more aggressive in damaging behaviour. As \n",
+      "high density may lead to more bears involved in conflicts, it also could increase the demand for bear  removal45 \n",
+      "and affect the effectiveness of removal techniques such as translocation and lethal control.\n",
+      "In this paper, we compiled a global database of intervention effectiveness against bears and studied how it \n",
+      "is related to bear species and densities, duration of intervention application, and intervention techniques. We \n",
+      "attempted to find and describe the most effective and the least effective interventions against bears. Further, we \n",
+      "tested several hypotheses: (1) lethal control and invasive management are less effective th\n",
+      "\n",
+      "[Metadata]: {'producer': 'Adobe PDF Library 15.0; modified using iText® 5.3.5 ©2000-2012 1T3XT BVBA (SPRINGER SBM; licensed version)', 'creator': 'Springer', 'creationdate': '2020-09-14T15:09:33+05:30', 'crossmarkdomains[1]': 'springer.com', 'moddate': '2020-09-14T15:58:07+02:00', 'crossmarkmajorversiondate': '2010-04-23', 'subject': 'Scientific Reports, https://doi.org/10.1038/s41598-020-72343-6', 'author': 'Igor Khorozyan', 'title': 'Variation and conservation implications of the effectiveness of anti-bear interventions', 'crossmarkdomainexclusive': 'true', 'robots': 'noindex', 'doi': '10.1038/s41598-020-72343-6', 'crossmarkdomains[2]': 'springerlink.com', 'source': 'hwc\\\\Khorozyan and Waltert 2020.pdf', 'total_pages': 9, 'page': 2, 'page_label': '3'}\n",
+      "\n",
+      "--- Document #5 ---\n",
+      "51] and other carnivores, such as coyotes (Canis latrans) [69, 70], African lions (Panthera leo)\n",
+      "[71], and wolves (Canis lupus) [72]. The relative effectiveness of these AC programs for\n",
+      "increasing wariness could relate to several aspects of program implementation. Because we\n",
+      "subjected bears to aversive stimuli as they engaged in problematic behaviour [48, 50], we\n",
+      "increased the likelihood that bears associated the conditioning stimulus (conflict behaviour)\n",
+      "with the unconditioned stimulus (pain/ stress) [38, 52]. This principle of immediacy in aver-\n",
+      "sive conditioning [54] is not achieved when aversive conditioning occurs upon release of a\n",
+      "captured bear, sometimes hours later and kilometres distant from the capture location where\n",
+      "conflict occurred [32]. Repetition of treatments allowed bears to generalize among experiences\n",
+      "instead of associating the painful stimulus with a single location or human individual, which\n",
+      "has been identified as important to AC programs targeting bold coyotes [69\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDFlib+PDI 9.3.1p2 (C++/Win64)', 'creator': 'PTC Arbortext Layout Developer 12.1.6180/W-x64', 'creationdate': '2023-12-25T16:46:13+05:30', 'title': 'Aversive conditioning increases short-term wariness but does not change habitat use in black bears associated with conflict', 'epsprocessor': 'PStill version 1.84.42', 'author': 'Lori Homstol, Sage Raymond, Claire Edwards, Anthony N. Hamilton, Colleen Cassady St. Clair', 'moddate': '2023-12-25T16:46:13+05:30', 'source': 'hwc\\\\Homstol et al. 2024.pdf', 'total_pages': 19, 'page': 12, 'page_label': '13'}\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<function __main__.test_retriever_only(query: str, k: int = 5)>"
+      ]
+     },
+     "execution_count": 33,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "test_query = \"Deers keep destroying and takiing over our large agricultural fields. Is there anything I can try to prevent this that won’t break the bank? Can you check these pdfs to see which ones might help? https://minio.carlboettiger.info/public-data/hwc.zip\"\n",
+    "test_retriever_only(test_query, k=5)\n",
+    "test_retriever_only"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 34,
+   "id": "02565fb4-321b-4cfc-be06-7ffaf1f7f37e",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      " Query: We live in a suburb and bears sometimes come into our town to eat from our fruit trees and trash. What are the best ways for us to prevent this as a community without removing our fruit trees? Can you check these pdfs to see which ones might help? https://minio.carlboettiger.info/public-data/hwc.zip\n",
+      "\n",
+      " Top 5 Retrieved Documents:\n",
+      "------------------------------------------------------------\n",
+      "\n",
+      "--- Document #1 ---\n",
+      "242 Conflict Intervention Priorities\n",
+      "helps foster more effective collaboration (Game et al.\n",
+      "2013; Lute et al. 2018). Third, both the survey results\n",
+      "and feedback were consistent with recent scholarship\n",
+      "(Redpath et al. 2017) that highlights participatory and\n",
+      "stakeholder-first conflict interventions as best practice\n",
+      "and advocates multipronged (Hazzah et al. 2014) and\n",
+      "adaptive management strategies (Bunnefeld et al. 2017).\n",
+      "Education and awareness programs were often cited in\n",
+      "feedback as being necessary additions to any interven-\n",
+      "tions. However, given the failures of many awareness-\n",
+      "based conservation programs (Schultz 2011), a further\n",
+      "exploration into why and where conservation decision\n",
+      "makers deem them most appropriate is important. Ap-\n",
+      "proaches that are specifically aimed at a particular au-\n",
+      "dience, such as social marketing (Salazar et al. 2018),\n",
+      "may be more effective than simple information provision\n",
+      "or—often-problematic—enforcement (Duffy et al. 2019).\n",
+      "However, how different interventio\n",
+      "\n",
+      "[Metadata]: {'producer': 'Acrobat Distiller 10.1.10 (Windows); modified using iText 4.2.0 by 1T3XT', 'creator': 'LaTeX with hyperref package', 'creationdate': '2020-01-16T12:33:42+05:30', 'keywords': '', 'moddate': '2025-05-27T12:12:25-07:00', 'subject': 'Conservation Biology 2020.34:232-243', 'wps-proclevel': '3', 'wps-journaldoi': '10.1111/(ISSN)1523-1739', 'author': '', 'title': 'Predicting intervention priorities for wildlife conflicts', 'wps-articledoi': '10.1111/cobi.13372', 'source': 'hwc\\\\Baynham-Herd et al. 2019.pdf', 'total_pages': 12, 'page': 10, 'page_label': '242'}\n",
+      "\n",
+      "--- Document #2 ---\n",
+      "8 \n",
+      " \n",
+      " \n",
+      " \n",
+      " \n",
+      " \n",
+      "Figure A5. Silhouette width plot of the k-medoid partitions with k = 2 to 10 used to estimate the best \n",
+      "number of clusters to describe livestock husbandry systems within the wolf range in northern Portugal \n",
+      "(see the main text for details). \n",
+      "  \n",
+      "2 4 6 8 10 \n",
+      "0.20 0.22 0.24 0.26 0.28 0.30 0.32 \n",
+      "Number of clusters \n",
+      "Silhouette Width\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDF Architect 3', 'creator': 'PDF Architect 3', 'creationdate': '2017-01-25T14:50:41+00:00', 'author': 'V. Pimenta', 'moddate': '2017-01-25T14:52:31+00:00', 'source': 'hwc\\\\Pimenta et al. 2017.pdf', 'total_pages': 20, 'page': 17, 'page_label': '18'}\n",
+      "\n",
+      "--- Document #3 ---\n",
+      "51] and other carnivores, such as coyotes (Canis latrans) [69, 70], African lions (Panthera leo)\n",
+      "[71], and wolves (Canis lupus) [72]. The relative effectiveness of these AC programs for\n",
+      "increasing wariness could relate to several aspects of program implementation. Because we\n",
+      "subjected bears to aversive stimuli as they engaged in problematic behaviour [48, 50], we\n",
+      "increased the likelihood that bears associated the conditioning stimulus (conflict behaviour)\n",
+      "with the unconditioned stimulus (pain/ stress) [38, 52]. This principle of immediacy in aver-\n",
+      "sive conditioning [54] is not achieved when aversive conditioning occurs upon release of a\n",
+      "captured bear, sometimes hours later and kilometres distant from the capture location where\n",
+      "conflict occurred [32]. Repetition of treatments allowed bears to generalize among experiences\n",
+      "instead of associating the painful stimulus with a single location or human individual, which\n",
+      "has been identified as important to AC programs targeting bold coyotes [69\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDFlib+PDI 9.3.1p2 (C++/Win64)', 'creator': 'PTC Arbortext Layout Developer 12.1.6180/W-x64', 'creationdate': '2023-12-25T16:46:13+05:30', 'title': 'Aversive conditioning increases short-term wariness but does not change habitat use in black bears associated with conflict', 'epsprocessor': 'PStill version 1.84.42', 'author': 'Lori Homstol, Sage Raymond, Claire Edwards, Anthony N. Hamilton, Colleen Cassady St. Clair', 'moddate': '2023-12-25T16:46:13+05:30', 'source': 'hwc\\\\Homstol et al. 2024.pdf', 'total_pages': 19, 'page': 12, 'page_label': '13'}\n",
+      "\n",
+      "--- Document #4 ---\n",
+      "Fig 1. The effects of AC programs on three metrics of black bear wariness, Whistler BC, 2007–2008. A and B show\n",
+      "the average observed percent change in overt reaction distance and displace ment distance among bears in the AC\n",
+      "Group and the Control Group. Error bars represent standard error. C shows the predicted effect of the number of AC\n",
+      "events conduc ted during the previous 30 days on the likeliho od that a bear will flee from research ers prior to their\n",
+      "beginning AC treatm ent.\n",
+      "https://d oi.org/10.1371/j ournal.pon e.0295989.g0 01\n",
+      "PLOS ONE\n",
+      "Aversive condition ing of conflict black bears\n",
+      "PLOS ONE | https://doi.or g/10.137 1/journal.po ne.02959 89 January 2, 2024 8 / 19\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDFlib+PDI 9.3.1p2 (C++/Win64)', 'creator': 'PTC Arbortext Layout Developer 12.1.6180/W-x64', 'creationdate': '2023-12-25T16:46:13+05:30', 'title': 'Aversive conditioning increases short-term wariness but does not change habitat use in black bears associated with conflict', 'epsprocessor': 'PStill version 1.84.42', 'author': 'Lori Homstol, Sage Raymond, Claire Edwards, Anthony N. Hamilton, Colleen Cassady St. Clair', 'moddate': '2023-12-25T16:46:13+05:30', 'source': 'hwc\\\\Homstol et al. 2024.pdf', 'total_pages': 19, 'page': 7, 'page_label': '8'}\n",
+      "\n",
+      "--- Document #5 ---\n",
+      "* Correspondence: B. F. Blackwell, U.S. Department of Agriculture, Animal and\n",
+      "Plant Health Inspection Service, Wildlife Services, National Wildlife Research\n",
+      "Center, Ohio Field Station, Sandusky, OH, 44870, U.S.A.\n",
+      "E-mail address: bradley.f.blackwell@aphis.usda.gov (B. F. Blackwell).\n",
+      "Contents lists available atScienceDirect\n",
+      "Animal Behaviour\n",
+      "journal homepage: www.elsevier.com/locate/anbehav\n",
+      "http://dx.doi.org/10.1016/j.anbehav.2016.07.013\n",
+      "0003-3472/Published by Elsevier Ltd on behalf of The Association for the Study of Animal Behaviour.\n",
+      "Animal Behaviour 120 (2016) 245e254\n",
+      "SPECIAL ISSUE: CONSERVATION BEHAVIOUR\n",
+      "\n",
+      "[Metadata]: {'producer': 'Acrobat Distiller 8.1.0 (Windows)', 'creator': 'Elsevier', 'creationdate': '2016-09-26T20:02:29+05:30', 'crossmarkdomains[2]': 'elsevier.com', 'crossmarkmajorversiondate': '2010-04-23', 'subject': 'Animal Behaviour, 120 (2016) 245-254. doi:10.1016/j.anbehav.2016.07.013', 'author': 'Bradley F. Blackwell', 'elsevierwebpdfspecifications': '6.5', 'crossmarkdomainexclusive': 'true', 'robots': 'noindex', 'moddate': '2016-09-26T20:03:01+05:30', 'doi': '10.1016/j.anbehav.2016.07.013', 'crossmarkdomains[1]': 'sciencedirect.com', 'title': 'No single solution: application of behavioural principles in mitigating human-wildlife conflict', 'source': 'hwc\\\\Blackwell et al. 2016.pdf', 'total_pages': 10, 'page': 0, 'page_label': '245'}\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<function __main__.test_retriever_only(query: str, k: int = 5)>"
+      ]
+     },
+     "execution_count": 34,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "test_query = \"We live in a suburb and bears sometimes come into our town to eat from our fruit trees and trash. What are the best ways for us to prevent this as a community without removing our fruit trees? Can you check these pdfs to see which ones might help? https://minio.carlboettiger.info/public-data/hwc.zip\"\n",
+    "test_retriever_only(test_query, k=5)\n",
+    "test_retriever_only"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 35,
+   "id": "ed58ac9d-edda-483b-b617-1e8bed445fe7",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      " Query: If we live in an area with a lot of wolves, what cattle husbandry strategies should I employ to prevent any sort of wildlife-human conflict? Can you check these pdfs to see which ones might help? https://minio.carlboettiger.info/public-data/hwc.zip\n",
+      "\n",
+      " Top 5 Retrieved Documents:\n",
+      "------------------------------------------------------------\n",
+      "\n",
+      "--- Document #1 ---\n",
+      "242 Conflict Intervention Priorities\n",
+      "helps foster more effective collaboration (Game et al.\n",
+      "2013; Lute et al. 2018). Third, both the survey results\n",
+      "and feedback were consistent with recent scholarship\n",
+      "(Redpath et al. 2017) that highlights participatory and\n",
+      "stakeholder-first conflict interventions as best practice\n",
+      "and advocates multipronged (Hazzah et al. 2014) and\n",
+      "adaptive management strategies (Bunnefeld et al. 2017).\n",
+      "Education and awareness programs were often cited in\n",
+      "feedback as being necessary additions to any interven-\n",
+      "tions. However, given the failures of many awareness-\n",
+      "based conservation programs (Schultz 2011), a further\n",
+      "exploration into why and where conservation decision\n",
+      "makers deem them most appropriate is important. Ap-\n",
+      "proaches that are specifically aimed at a particular au-\n",
+      "dience, such as social marketing (Salazar et al. 2018),\n",
+      "may be more effective than simple information provision\n",
+      "or—often-problematic—enforcement (Duffy et al. 2019).\n",
+      "However, how different interventio\n",
+      "\n",
+      "[Metadata]: {'producer': 'Acrobat Distiller 10.1.10 (Windows); modified using iText 4.2.0 by 1T3XT', 'creator': 'LaTeX with hyperref package', 'creationdate': '2020-01-16T12:33:42+05:30', 'keywords': '', 'moddate': '2025-05-27T12:12:25-07:00', 'subject': 'Conservation Biology 2020.34:232-243', 'wps-proclevel': '3', 'wps-journaldoi': '10.1111/(ISSN)1523-1739', 'author': '', 'title': 'Predicting intervention priorities for wildlife conflicts', 'wps-articledoi': '10.1111/cobi.13372', 'source': 'hwc\\\\Baynham-Herd et al. 2019.pdf', 'total_pages': 12, 'page': 10, 'page_label': '242'}\n",
+      "\n",
+      "--- Document #2 ---\n",
+      "Fig 1. The effects of AC programs on three metrics of black bear wariness, Whistler BC, 2007–2008. A and B show\n",
+      "the average observed percent change in overt reaction distance and displace ment distance among bears in the AC\n",
+      "Group and the Control Group. Error bars represent standard error. C shows the predicted effect of the number of AC\n",
+      "events conduc ted during the previous 30 days on the likeliho od that a bear will flee from research ers prior to their\n",
+      "beginning AC treatm ent.\n",
+      "https://d oi.org/10.1371/j ournal.pon e.0295989.g0 01\n",
+      "PLOS ONE\n",
+      "Aversive condition ing of conflict black bears\n",
+      "PLOS ONE | https://doi.or g/10.137 1/journal.po ne.02959 89 January 2, 2024 8 / 19\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDFlib+PDI 9.3.1p2 (C++/Win64)', 'creator': 'PTC Arbortext Layout Developer 12.1.6180/W-x64', 'creationdate': '2023-12-25T16:46:13+05:30', 'title': 'Aversive conditioning increases short-term wariness but does not change habitat use in black bears associated with conflict', 'epsprocessor': 'PStill version 1.84.42', 'author': 'Lori Homstol, Sage Raymond, Claire Edwards, Anthony N. Hamilton, Colleen Cassady St. Clair', 'moddate': '2023-12-25T16:46:13+05:30', 'source': 'hwc\\\\Homstol et al. 2024.pdf', 'total_pages': 19, 'page': 7, 'page_label': '8'}\n",
+      "\n",
+      "--- Document #3 ---\n",
+      "51] and other carnivores, such as coyotes (Canis latrans) [69, 70], African lions (Panthera leo)\n",
+      "[71], and wolves (Canis lupus) [72]. The relative effectiveness of these AC programs for\n",
+      "increasing wariness could relate to several aspects of program implementation. Because we\n",
+      "subjected bears to aversive stimuli as they engaged in problematic behaviour [48, 50], we\n",
+      "increased the likelihood that bears associated the conditioning stimulus (conflict behaviour)\n",
+      "with the unconditioned stimulus (pain/ stress) [38, 52]. This principle of immediacy in aver-\n",
+      "sive conditioning [54] is not achieved when aversive conditioning occurs upon release of a\n",
+      "captured bear, sometimes hours later and kilometres distant from the capture location where\n",
+      "conflict occurred [32]. Repetition of treatments allowed bears to generalize among experiences\n",
+      "instead of associating the painful stimulus with a single location or human individual, which\n",
+      "has been identified as important to AC programs targeting bold coyotes [69\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDFlib+PDI 9.3.1p2 (C++/Win64)', 'creator': 'PTC Arbortext Layout Developer 12.1.6180/W-x64', 'creationdate': '2023-12-25T16:46:13+05:30', 'title': 'Aversive conditioning increases short-term wariness but does not change habitat use in black bears associated with conflict', 'epsprocessor': 'PStill version 1.84.42', 'author': 'Lori Homstol, Sage Raymond, Claire Edwards, Anthony N. Hamilton, Colleen Cassady St. Clair', 'moddate': '2023-12-25T16:46:13+05:30', 'source': 'hwc\\\\Homstol et al. 2024.pdf', 'total_pages': 19, 'page': 12, 'page_label': '13'}\n",
+      "\n",
+      "--- Document #4 ---\n",
+      "3\n",
+      "Vol.:(0123456789)Scientific RepoRtS  |        (2020) 10:15341  | https://doi.org/10.1038/s41598-020-72343-6\n",
+      "www.nature.com/scientificreports/\n",
+      "numbers increase and more bears need more  food26,43,44. Hence, the effectiveness of anti-bear interventions can \n",
+      "be lower than expected when hungry bears become persistent and more aggressive in damaging behaviour. As \n",
+      "high density may lead to more bears involved in conflicts, it also could increase the demand for bear  removal45 \n",
+      "and affect the effectiveness of removal techniques such as translocation and lethal control.\n",
+      "In this paper, we compiled a global database of intervention effectiveness against bears and studied how it \n",
+      "is related to bear species and densities, duration of intervention application, and intervention techniques. We \n",
+      "attempted to find and describe the most effective and the least effective interventions against bears. Further, we \n",
+      "tested several hypotheses: (1) lethal control and invasive management are less effective th\n",
+      "\n",
+      "[Metadata]: {'producer': 'Adobe PDF Library 15.0; modified using iText® 5.3.5 ©2000-2012 1T3XT BVBA (SPRINGER SBM; licensed version)', 'creator': 'Springer', 'creationdate': '2020-09-14T15:09:33+05:30', 'crossmarkdomains[1]': 'springer.com', 'moddate': '2020-09-14T15:58:07+02:00', 'crossmarkmajorversiondate': '2010-04-23', 'subject': 'Scientific Reports, https://doi.org/10.1038/s41598-020-72343-6', 'author': 'Igor Khorozyan', 'title': 'Variation and conservation implications of the effectiveness of anti-bear interventions', 'crossmarkdomainexclusive': 'true', 'robots': 'noindex', 'doi': '10.1038/s41598-020-72343-6', 'crossmarkdomains[2]': 'springerlink.com', 'source': 'hwc\\\\Khorozyan and Waltert 2020.pdf', 'total_pages': 9, 'page': 2, 'page_label': '3'}\n",
+      "\n",
+      "--- Document #5 ---\n",
+      "8 \n",
+      " \n",
+      " \n",
+      " \n",
+      " \n",
+      " \n",
+      "Figure A5. Silhouette width plot of the k-medoid partitions with k = 2 to 10 used to estimate the best \n",
+      "number of clusters to describe livestock husbandry systems within the wolf range in northern Portugal \n",
+      "(see the main text for details). \n",
+      "  \n",
+      "2 4 6 8 10 \n",
+      "0.20 0.22 0.24 0.26 0.28 0.30 0.32 \n",
+      "Number of clusters \n",
+      "Silhouette Width\n",
+      "\n",
+      "[Metadata]: {'producer': 'PDF Architect 3', 'creator': 'PDF Architect 3', 'creationdate': '2017-01-25T14:50:41+00:00', 'author': 'V. Pimenta', 'moddate': '2017-01-25T14:52:31+00:00', 'source': 'hwc\\\\Pimenta et al. 2017.pdf', 'total_pages': 20, 'page': 17, 'page_label': '18'}\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<function __main__.test_retriever_only(query: str, k: int = 5)>"
+      ]
+     },
+     "execution_count": 35,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "test_query = \"If we live in an area with a lot of wolves, what cattle husbandry strategies should I employ to prevent any sort of wildlife-human conflict? Can you check these pdfs to see which ones might help? https://minio.carlboettiger.info/public-data/hwc.zip\"\n",
+    "test_retriever_only(test_query, k=5)\n",
+    "test_retriever_only"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}