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wiki:exercise_rp_ratio [2018/05/11 13:15]
wiki:exercise_rp_ratio [2018/05/11 13:15] (current)
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 +====== Limited filling of the potential Pinus cembra range ====== ​
  
 +==== Introduction ====                                                                        ​
 +//Pinus Cembra// (Pinaceae L.) or Swiss Stone Pine is a localised and endemic tree species that occurs in the alpine timberline. ​
 +We are going to calculate the realized / potential range size ratio (range filling R/P) for the alpine Pine //Pinus cembra// as a measure of how well this species fulfills its potential range [[#​bibliography|Gaston 2003]]. We use the //Pinus cembra// habitat suitability modeling [[#​bibliography|Casalegno et al., 2010]] and the //Pinus cembra// distribution map [[http://​www.euforgen.org|euforgen database]] to estimate R/P ratio.
 +  * P is the total number of //Pinus cembra// suitable pixels within the study area.
 +  * R is the number of //Pinus cembra// suitable pixels within the //Pinus cembra// distribution maps pixels.
 +
 +This will quantify the extent to which //Pinus cembra// fulfills its modelled suitability range in the Alps.
 +We computed the realized / potential range size ratio (R/P) across the Alpine and Carpathian mountains area.
 +
 +==== Start a new GRASS project and define a region of analysis ====
 +We open a terminal and go to the directory corresponding to our GRASS LOCATION.
 +
 +  cd ~/​ost4sem/​grassdb/​europe
 +
 +We copy the PERMANENT MAPSET and rename it PCEM. PCEM will be our new MAPSET and grass project where we store maps for calculating the R/P ratio.
 +
 +  rm -r PCEM
 +  cp -r PERMANENT PCEM
 +
 +We start grass in the newest PCEM mapset
 +  grass -text  ~/​ost4sem/​grassdb/​europe/​PCEM
 +
 +Look at the default g.region and redefine a study area including the Carpathian and Alpine mountain ranges.
 +Set the new working region at 1km resolution and call it alpine:
 +
 +  g.region -d
 +  g.region -p
 +  g.region --o n=3070000 s=2270000 w=3900000 e=5660000 res=1000 save=alp_car
 +  g.region -p
 +
 +==== Pinus Cembra distribution map: data preparation ​ ====
 +== Import and reclass distribution map ==
 +Import the Euforgen //Pinus cembra// distribution map from [[http://​www.euforgen.org|the euforgen web page]] and convert it from a shape file to a raster file :
 +  v.in.ogr dsn=~/​ost4sem/​exercise/​rp_ratio/​pcem_euforgen/​Pinuscembra_LAEA.shp output=pcem_euforgen --overwrite
 +
 +
 +Convert the vector file to a raster file, look at the pixels values and reclass this map into a binary presence and absence of //Pinus cembra// distribution.
 +
 +<note tip>
 +You can open Qgis within the grass section and continue to work with grass using the following command
 +  qgis &
 +Once you have opened Qgis, load the pcem_euforgen@PCEM vector map and check which source of raster values you have to use for the conversion from vector to raster. You have the choice between: attr,​cat,​val,​z,​dir.
 +</​note>​
 +
 +  v.to.rast --o input=pcem_euforgen@PCEM output=pcem_euforgen use=cat
 +  v.info pcem_euforgen
 +  r.info pcem_euforgen
 +
 +The raster we generate has values running from 1 to 14 but we need a presence-absence map so we have to reclassify the pcem_euforgen raster into 0 - 1 map values.
 +
 +  r.mapcalc pcem_euforgen = "​if(pcem_euforgen > 0 , 1 ,0 )"
 +
 +==== Pinus Cembra suitability map: data preparation ​ ====
 +
 +== Import and resize suitability map ==
 +Import the random forest model of suitability for //Pinus cembra//
 +  r.in.gdal -o -e input=~/​ost4sem/​exercise/​rp_ratio/​pcem_randomforest/​gdwarp_PRESENT.tif output=pcem_potential --o
 +
 +
 +Visualise the actual suitability of //Pinus cembra// acccording to the Random Forest Model
 +  ​
 +  d.mon start=x3
 +  d.rast pcem_potential
 +
 +
 +==== Calculate the realised range of Pinus Cembra suitability ====
 +The Potential distribution map or suitability map //​pcem_potential//​ has values equal to:
 +  * 1 : No suitable or no potential
 +  * 2 : Suitable or Potential
 +  * 20: Sea 
 +
 +The distribution map //​pcem_euforgen//​ has values equal to:
 +  * NoData: absence
 +  * 1: presence
 +
 +If we sum the two maps we will be able to generate a realized range map. This is done by selecting class 3 from the sum of the two maps. Class 3 represents suitable pixels within the presence of distribution. ​
 + 
 +  r.mapcalculator amap=pcem_euforgen bmap=pcem_potential formula=A+B outfile=pcem_realized --overwrite
 +  r.mapcalc pcem_realized = "​if(pcem_realized == 3 , 1 ,0 )"
 +
 +You visualize and save results for the Realized area in a text file with the following commands:
 +  r.report -n map=pcem_realized units=k
 +  r.report -n map=pcem_realized units=k > ~/​ost4sem/​exercise/​rp_ratio/​results/​R_value.txt
 +
 +The **R** (realised distribution range) is equal to 24,606 square Kilometres. ​
 +
 +You visualize and save results for the Potential area in a text file with the following commands:
 +   ​r.report -n map=pcem_potential units=k ​
 +   ​r.report -n map=pcem_potential units=k > ~/​ost4sem/​exercise/​rp_ratio/​results/​P_value.txt
 +The P (potential distribution range) is equal to 32,538 square Kilometres. ​
 +
 +The RP ratio ⇒ 24,606 / 32,538 % 100 = 75 %
 +
 +
 +==== Bibliography ====
 +  * Casalegno S., G. Amatulli, A. Camia, A. Nelson, A. Pekkarinen. 2010. [[http://​dx.doi.org/​10.1016/​j.foreco.2009.10.001|Vulnerability of Pinus cembra L. in the Alps and the Carpathian mountains under present and future climates]]. Forest Ecology and Management 259: 70-761. ​
 +  * Gaston 2003. The Structure and Dynamics of Geographic Ranges. Series: OXFORD SERIES IN ECOLOGY AND EVOLUTION. Kevin J Gaston 266 pages, Oxford University Press. ISBN-10: 0198526407.
 +  ​
wiki/exercise_rp_ratio.txt · Last modified: 2018/05/11 13:15 (external edit)