Convert all R notebooks to jupyter exclusively

Also add links to NMDC runtime API documentation, closes #3

NEON_soil_metadata/R/NEON_data_exploration.ipynb

@@ -13,35 +13,25 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Loading required package: maps\n",
-      "\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Load essential libraries\n",
-    "knitr::opts_chunk$set(echo = TRUE)\n",
     "library(jsonlite, warn.conflicts=FALSE)\n",
     "library(dplyr, warn.conflicts=FALSE)\n",
     "library(tidyr, warn.conflicts=FALSE)\n",
     "library(ggplot2, warn.conflicts=FALSE)\n",
     "library(forcats, warn.conflicts=FALSE)\n",
     "library(lubridate, warn.conflicts=FALSE)\n",
-    "if (!require('maps')) install.packages('maps', quiet = TRUE); library('maps', warn.conflicts=FALSE)"
+    "if (!require('maps', quiet = TRUE)) install.packages('maps', quiet = TRUE); library('maps', warn.conflicts=FALSE)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Get study IDs associated with NEON sites using API\n",
+    "## Get study IDs associated with NEON sites using NMDC runtime API\n",
     "\n",
-    "Using R's jsonlite package and the [NMDC studies find endpoint](https://api.microbiomedata.org/docs#/find/find_studies_studies_get), we can get the NMDC study ID to filter by. "
+    "Using R's jsonlite package and the [NMDC studies find endpoint](https://api.microbiomedata.org/docs#/find/find_studies_studies_get), we can get the NMDC study ID to filter by. More information regarding the API can be found [here](https://github.com/microbiomedata/NMDC_documentation/blob/main/docs/howto_guides/api_gui.md)"
    ]
   },
   {