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1 <tool id="raster_getdata" name="Get climatic data from Worldclim" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="1.20.2">r-getopt</requirement>
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4 <requirement type="package" version="1.1.6">r-ncdf4</requirement>
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5 <requirement type="package" version="2.6_7">r-raster</requirement>
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2
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6 <requirement type="package" version="1.3.1">r-stringr</requirement>
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0
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript
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10 '$__tool_directory__/clim_data.R'
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11 'worldclim'
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12 '$usr_var'
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13 $usr_res
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14 '$usr_of'
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15
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16 #if $condi_plot.plot=='yes_plot'
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17 '$usr_var$condi_plot.var_to_plot'
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18 '$condi_plot.usr_country'
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19 #end if
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20
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21 ]]></command>
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22 <inputs>
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23 <param name="usr_var" type="select" label="Variable" help="Temperature minimum, maximum, precipitations and bioclimatic variables.">
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24 <option value="tmin">tmin</option>
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25 <option value="tmax">tmax</option>
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26 <option value="prec">prec</option>
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27 <option value="bio">bio</option>
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28 </param>
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29 <param name="usr_res" type="select" label="Resolution" help="In minutes of a degree.">
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30 <option value="2.5">2.5</option>
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31 <option value="5">5</option>
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32 <option value="10">10</option>
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33 </param>
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34 <param name="usr_of" type="select" label="Output raster format" >
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35 <option value="raster">Native raster package format .grd</option>
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36 <option value="CDF">netCDF .nc</option>
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37 </param>
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38 <conditional name="condi_plot">
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39 <param name="plot" type="select" label="Return a layers visualisation">
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40 <option value="yes_plot">Yes</option>
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41 <option value="no_plot">No</option>
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42 </param>
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43 <when value="yes_plot">
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44 <param name="var_to_plot" type="select" label="Select what you want to visualize" help="Be careful to select a layer that is present in the dowloaded raster. eg : bioclimatic variable (bio) and layer bio:Isothermality.">
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45 <option value="1">[tmin|tmax|prec]:January</option>
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46 <option value="2">[tmin|tmax|prec]:February</option>
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47 <option value="3">[tmin|tmax|prec]:March</option>
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48 <option value="4">[tmin|tmax|prec]:April</option>
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49 <option value="5">[tmin|tmax|prec]:May</option>
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50 <option value="6">[tmin|tmax|prec]:June</option>
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51 <option value="7">[tmin|tmax|prec]:July</option>
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52 <option value="8">[tmin|tmax|prec]:August</option>
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53 <option value="9">[tmin|tmax|prec]:September</option>
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54 <option value="10">[tmin|tmax|prec]:October</option>
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55 <option value="11">[tmin|tmax|prec]:November</option>
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56 <option value="12">[tmin|tmax|prec]:December</option>
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57 <option value="1">bio:Annual Mean Temperature</option>
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58 <option value="2">bio:Mean Diurnal Range (Mean of monthly (max temp - min temp))</option>
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59 <option value="3">bio:Isothermality (BIO2/BIO7) (* 100)</option>
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60 <option value="4">bio:Temperature Seasonality (standard deviation *100)</option>
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61 <option value="5">bio:Max Temperature of Warmest Month</option>
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62 <option value="6">bio:Min Temperature of Coldest Month</option>
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63 <option value="7">bio:Temperature Annual Range (BIO5-BIO6)</option>
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64 <option value="8">bio:Mean Temperature of Wettest Quarter</option>
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65 <option value="9">bio:Mean Temperature of Driest Quarter</option>
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66 <option value="10">bio:Mean Temperature of Warmest Quarter</option>
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67 <option value="11">bio:Mean Temperature of Coldest Quarter</option>
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68 <option value="12">bio:Annual Precipitation</option>
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69 <option value="13">bio:Precipitation of Wettest Month</option>
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70 <option value="14">bio:Precipitation of Driest Month</option>
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71 <option value="15">bio:Precipitation Seasonality (Coefficient of Variation)</option>
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72 <option value="16">bio:Precipitation of Wettest Quarter</option>
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73 <option value="17">bio:Precipitation of Driest Quarter</option>
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74 <option value="18">bio:Precipitation of Warmest Quarter</option>
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75 <option value="19">bio:Precipitation of Coldest Quarter</option>
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76 </param>
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77
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78 <param name="usr_country" type="select" label="Select a worldmap vision or a more precise region" >
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79 <option value="WM">Worldmap</option>
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80 <option value="NA">North America</option>
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81 <option value="EU">Europe</option>
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82 <option value="AUS">Australia</option>
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83 <option value="FRA">France</option>
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84 <option value="DEU">Germany</option>
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85 <option value="GBR">United Kingdom</option>
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86 <option value="ESP">Spain</option>
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87 <option value="ITA">Italy</option>
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88 </param>
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89 </when>
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90 <when value="no_plot">
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91 </when>
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92 </conditional>
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93 </inputs>
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94 <outputs>
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95 <data name="output_df" from_work_dir="output_writeRaster.nc" label="WorldClim data - NetCDF format">
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96 <filter> usr_of=='CDF'</filter>
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97 </data>
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98 <data name="output_grd" from_work_dir="output_writeRaster.grd" label="WorldClim data - Native raster pkg format .grd">
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99 <filter> usr_of=='raster'</filter>
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100 </data>
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101 <data name="output_gri" from_work_dir="output_writeRaster.gri" label="WorldClim data - Native raster pkg format .gri">
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102 <filter> usr_of=='raster'</filter>
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103 </data>
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104 <data name="plot_jpeg" from_work_dir="worldclim_plot_usr_region.jpeg" format="jpg" label="WorldClim data - Visualisation">
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105 <filter> plot=='yes_plot'</filter>
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106 </data>
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107 </outputs>
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108 <help><![CDATA[
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109
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110 .. class:: infomark
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111
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112 =======================================
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113 Get global climate data from Worldclim
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114 =======================================
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115
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116 |
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117
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118 **What it does**
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119
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120 This tool retrieve global climate data from Wordclim using the R raster package.
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121
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122 The climatic data available are :
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123
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124 * Minimum temperature (°C x10)
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125
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4
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126 * Maximum temperature (°C x10)
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0
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127
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128 * Precipitation (mm)
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129
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130 * Bioclimatic variables :
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131
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132 * BIO1 = Annual Mean Temperature
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133
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134 * BIO2 = Mean Diurnal Range (Mean of monthly (max temp - min temp))
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135
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136 * BIO3 = Isothermality (BIO2/BIO7) (x 100)
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137
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138 * BIO4 = Temperature Seasonality (standard deviation x100)
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139
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140 * BIO5 = Max Temperature of Warmest Month
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141
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142 * BIO6 = Min Temperature of Coldest Month
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143
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144 * BIO7 = Temperature Annual Range (BIO5-BIO6)
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145
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146 * BIO8 = Mean Temperature of Wettest Quarter
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147
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148 * BIO9 = Mean Temperature of Driest Quarter
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149
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150 * BIO10 = Mean Temperature of Warmest Quarter
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151
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152 * BIO11 = Mean Temperature of Coldest Quarter
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153
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154 * BIO12 = Annual Precipitation
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155
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156 * BIO13 = Precipitation of Wettest Month
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157
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158 * BIO14 = Precipitation of Driest Month
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159
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160 * BIO15 = Precipitation Seasonality (Coefficient of Variation)
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161
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162 * BIO16 = Precipitation of Wettest Quarter
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163
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164 * BIO17 = Precipitation of Driest Quarter
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165
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166 * BIO18 = Precipitation of Warmest Quarter
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167
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168 * BIO19 = Precipitation of Coldest Quarter
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169
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170 |
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171
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172 **How to use it**
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173
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174 Simply select the variable to return and the resolution : 2.5, 5 or 10 minutes of a degree.
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175
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176 Available output format are : netcdf and grd (Native raster package format).
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177
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178 |
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179
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180 **Sources**
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181
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182 Worldclim : http://www.worldclim.org/
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183
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184 Raster package : https://cran.r-project.org/web/packages/raster/index.html
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185
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186 ]]></help>
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187 </tool>
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