Add OBIS EOV notebook & update env

.binder/environment-python_and_r.yml

@@ -74,10 +74,12 @@ dependencies:
   # R packages.
   - rpy2
   - r-base=4
+  - r-dplyr
   - r-dt
   - r-finch
   - r-ggfortify
   - r-ggplot2
+  - r-gh
   - r-gsw
   - r-httr
   - r-irkernel

jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2024-09-13-OBIS_EOVs.ipynb

@@ -0,0 +1,179 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "ad98f7a1-d7a1-4a51-a9a2-0da9da7fe042",
+   "metadata": {},
+   "source": [
+    "# Using aphiaIDs to download OBIS occurrences for Bio/Eco EOVs\n",
+    "\n",
+    "Created: 2024-09-13\n",
+    "\n",
+    "The [IOOS Marine Life Data Network](https://ioos.github.io/marine_life_data_network/) has developed a list of aphiaIDs for taxa mentioned in the [GOOS Biology and Ecosystems Variables](https://goosocean.org/what-we-do/framework/essential-ocean-variables/). These lists are meant to assist in querying OBIS to evaluate the abundance and distribution of these taxa. Here is an R notebook of how this might work using mangroves as an example."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "390bf2be-3828-4705-b64b-ed68005ff98b",
+   "metadata": {
+    "scrolled": true,
+    "vscode": {
+     "languageId": "r"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "library(gh)\n",
+    "library(readr)\n",
+    "library(robis)\n",
+    "library(dplyr)\n",
+    "library(htmlwidgets)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3089302a",
+   "metadata": {},
+   "source": [
+    "First, we will pull the file with the mangrove aphiaIDs from the Marine Life Data Network GitHub repo. **Note**: the acceptedTaxonIds in these files are based on what was up-to-date in the [WoRMS](https://marinespecies.org/) database as of the date this script was written."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "43964864-7fe8-4139-a9d0-2a844161ccd1",
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "mangroves <- read.csv(\"https://raw.githubusercontent.com/ioos/marine_life_data_network/main/eov_taxonomy/mangroves.csv\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "45fa26db",
+   "metadata": {},
+   "source": [
+    "Now we will do a bit of cleanup to get a list of aphiaIDs for mangroves so we can run our `robis` query using these as taxon identifiers."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "0bb6ab17-d239-410c-90d0-dcb50359b095",
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "mangroves$ID <- gsub(\"urn:lsid:marinespecies.org:taxname.\", \"\", mangroves$acceptedTaxonId)\n",
+    "mangroves$ID <- as.numeric(mangroves$ID)\n",
+    "mangroveIdentifiers <- paste(mangroves$ID, collapse = \", \")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8a6cefa9",
+   "metadata": {},
+   "source": [
+    "Using the taxonIDs from the last step, let's query OBIS for occurrence data for mangroves. This step may take a bit of time to run. When this script was written, there were over 130,000 records for mangroves in OBIS."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d9aa2697-4ca0-4631-8d77-b0407e7a73b5",
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "mangrove_occ <- robis::occurrence(taxonid = mangroveIdentifiers)\n",
+    "# let's check how many occurrences we got from OBIS\n",
+    "nrow(mangrove_occ)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c837a3ac",
+   "metadata": {},
+   "source": [
+    "Now that we have all of our mangrove records from OBIS, we will map the global distribution of records using the `map_leaflet` function found in the `robis` package. With the leaflet functionality, you can zoom into records, click them, and it list the scientific name for that occurrence record."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1ccc9837-4585-4020-852b-cdc6b33ae62d",
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "m <- map_leaflet(mangrove_occ,\n",
+    "            provider_tiles = \"Esri.WorldGrayCanvas\",\n",
+    "            popup = function(x) { x[\"scientificName\"] },\n",
+    "            )\n",
+    "m"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "202e2512",
+   "metadata": {},
+   "source": [
+    "This next step is not required, but if you'd like to save this map to view it outside of R, here's how."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "13a8bc6c-5963-4e4e-acab-f0f6de776045",
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "\n",
+    "saveWidget(m, \"mangroveMap.html\", selfcontained = TRUE)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "31bf8a8b",
+   "metadata": {},
+   "source": [
+    "For more information and code about how to get EOV data from OBIS, see the [NOAA GIS For The Ocean GitHub project](https://github.com/NOAA-GIS4Ocean/BioEco_EOV)."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "R",
+   "language": "R",
+   "name": "ir"
+  },
+  "language_info": {
+   "codemirror_mode": "r",
+   "file_extension": ".r",
+   "mimetype": "text/x-r-source",
+   "name": "R",
+   "pygments_lexer": "r",
+   "version": "4.1.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}