{ "cells": [ { "cell_type": "markdown", "id": "638df9a2", "metadata": {}, "source": [ "# sPlotOpen Preprocessing" ] }, { "cell_type": "markdown", "id": "d15d079d", "metadata": {}, "source": [ "sPlotOpen (Sabatini et al, 2021) is an open-access and environmentally and spatially balanced subset of the global sPlot vegetation plots data set v2.1 (Bruelheide et al, 2019).\n", "\n", "This section covers:\n", "\n", "- Link plot coordinates with community wighted means (cwm)\n", "- Visualize plot density" ] }, { "cell_type": "markdown", "id": "e8581c38", "metadata": {}, "source": [ "## Download" ] }, { "cell_type": "markdown", "id": "72f1187e", "metadata": {}, "source": [ "sPlotOpen Data is available at the *iDiv Data Repository*. For this study we used version 52.\n", "\n", "https://idata.idiv.de/ddm/Data/ShowData/3474\n", "\n" ] }, { "cell_type": "markdown", "id": "18e4aba2", "metadata": {}, "source": [ "## Packages" ] }, { "cell_type": "code", "execution_count": null, "id": "73975506", "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "import numpy as np\n", "import os\n", "import matplotlib.pyplot as plt\n", "import seaborn as sns\n", "from matplotlib.colors import LogNorm, Normalize\n", "import cartopy.crs as ccrs\n", "import cartopy as cart\n", "from matplotlib.colors import BoundaryNorm\n", "from matplotlib.ticker import MaxNLocator\n", "from mpl_toolkits.axes_grid1 import make_axes_locatable" ] }, { "cell_type": "markdown", "id": "b4e70409", "metadata": {}, "source": [ "## Link plot coordinates to cmw data" ] }, { "cell_type": "markdown", "id": "5557c6b1", "metadata": {}, "source": [ "The data is stored in various tab-separated files:\n", "\n", "- **sPlotOpen_header(2).txt** : contains information on each plot, such as coordinates, date, biome, country, etc.\n", "\n", "\n", "- **sPlotOpen_DT(1).txt** : contains information per plot and species with abundance and relative cover\n", "\n", "\n", "- **sPlotOpen_CWM_CWV(1).txt** : contains information on trait community weighted means and variances for each plot and 18 traits (ln-transformed)\n" ] }, { "cell_type": "code", "execution_count": 5, "id": "f78f0c93", "metadata": {}, "outputs": [], "source": [ "# load the community weighted means\n", "\n", "cwm = pd.read_csv(\"./sPlotOpen/sPlotOpen_CWM_CWV(1).txt\", sep= \"\\t\")" ] }, { "cell_type": "code", "execution_count": 6, "id": "5846917d", "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/net/home/swolf/.conda/envs/cartopy/lib/python3.8/site-packages/IPython/core/interactiveshell.py:3172: DtypeWarning: Columns (16) have mixed types.Specify dtype option on import or set low_memory=False.\n", " has_raised = await self.run_ast_nodes(code_ast.body, cell_name,\n" ] } ], "source": [ "plots = pd.read_csv(\"./sPlotOpen/sPlotOpen_header(2).txt\", sep= \"\\t\")" ] }, { "cell_type": "code", "execution_count": 7, "id": "edaf606d", "metadata": {}, "outputs": [], "source": [ "sPlot = pd.merge(cwm, plots, on='PlotObservationID', how='inner')" ] }, { "cell_type": "code", "execution_count": 8, "id": "20d2145a", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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5 rows × 86 columns
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