Embedding+Vector.ipynb

{
 "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": {},
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    }
   ],
   "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": {},
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     "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"
     ]
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    {
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       "<function __main__.test_retriever_only(query: str, k: int = 5)>"
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     "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"
   ]
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  {
   "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"
     ]
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    {
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       "<function __main__.test_retriever_only(query: str, k: int = 5)>"
      ]
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     "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"
   ]
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  {
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   "execution_count": 33,
   "id": "64e672ff-8341-4144-a0cf-b9756661475e",
   "metadata": {},
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    {
     "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"
     ]
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    {
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       "<function __main__.test_retriever_only(query: str, k: int = 5)>"
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   ],
   "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"
     ]
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    {
     "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"
   ]
  }
 ],
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