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--- spatialspecial [2017/04/19 20:39]
qcbs [Exercice 6]
+++ spatialspecial [2019/04/15 20:58] (current)
qcbs [Exercice 7]
@@ Line 1: / Line 1: @@
 ====== QCBS workshop on the use of open source tools for advanced spatial analysis ======
-April 20 2017, McGill University.
+April 16 2019, McGill University.
   * [[https://prezi.com/z8ybqj4wxixp/qcbs-workshop-on-the-use-of-open-source-tools-for-advanced-spatial-analyses/|Link to the Prezi presentation]]
@@ Line 10: / Line 10: @@
 For Windows and Mac users
-  * Installez PostgreSQL depuis le site web [[http://www.enterprisedb.com/products-services-training/pgdownload|EntrepriseDB]]
+  * Install PostgreSQL from the EntrepriseDB website [[http://www.enterprisedb.com/products-services-training/pgdownload|EntrepriseDB]]
-  * Quand on vous demande si vous voulez utiliser stackbuilder, acceptez et choisissez d'installer  PostGIS sous "spatial extensions". Quand on vous le demande, choisissez de créer une base de données spatiale et nommez-là spatialdb. Répondez oui aux questions à propos de  GDAL_DATA, POSTGIS_GDAL_ENABLED_DRIVERS, POSTGIS_ENABLED_OUTDB_RASTERS.
+  * When asked if you want to install Stackbuilder, choose yes and select to install PostGIS under "spatial extensions". When you are asked, choose to create a new spatial database and name it spatiadb. Answer yes to questions about GDAL_DATA, POSTGIS_GDAL_ENABLED_DRIVERS, POSTGIS_ENABLED_OUTDB_RASTERS.
@@ Line 21: / Line 21: @@
 Then type
 <file>
-sudo gedit /etc/postgresql/9.6/main/postgresql.conf
+sudo gedit /etc/postgresql/11.2/main/postgresql.conf
 </file>
 remove the # in front of #listen_addresses = 'localhost'
@@ Line 29: / Line 29: @@
 sudo service postgresql restart
 </file>
+For Mac users. In the psql terminal, type:
+<file>
+SHOW hba_file;
+</file>
+You then need to edit the postgresql.conf file to remove the # in front of #listen_addresses = 'localhost'. You can also Put Trust at the end of the lines with localhost.
 To create a spatial database
@@ Line 76: / Line 83: @@
 **ST_Perimeter**(geometry) returns the length of all the rings\\
 **ST_AsSVG**(geometry) returns SVG text\\
+**ST_Transform**(geometry, SRID) change the reference system from the current one (of geom) to the one defined by SRID.\\
+Select all observations North of the 70th parallel
+<file postgresql>
+SELECT * FROM obis_whales WHERE latitude > 70
+</file>
+Select all observations South of the 60th parallel
+<file postgresql>
+SELECT tname, latitude FROM obis_whales WHERE latitude < -60
+</file>
+List the species that can be found South of the 60th parallel
+<file postgresql>
+SELECT DISTINCT tname FROM obis_whales WHERE latitude < -60
+</file>
 Create a new layer, with belugas only
@@ Line 152: / Line 175: @@
 ++++ To use a distance in meters |
+Add new empty column of type geography
 <file postgresql>
 ALTER TABLE obis_whales ADD column geog GEOGRAPHY(POINT,4326)
 </file>
+Update the geometry values as geography and store them in the new column
 <file postgresql>
 UPDATE obis_whales SET geog=geography(geom)
 </file>
+Repeat for the tm_world file
 <file postgresql>
 ALTER TABLE tm_world ADD column geog GEOGRAPHY(MULTIPOLYGON,4326)
@@ Line 212: / Line 237: @@
 \\
 \\
-===== Using PostgreSQL/PostGIS and GRASS in R =====
+===== Using PostgreSQL/PostGIS, GDAL, sf and GRASS in R =====
 {{::spatial_special_r_code.r|Download the R file containing the code for this part of the workshop}}
   * Package [[http://cran.r-project.org/web/packages/rpostgis/index.html|rpostgis]]
-  * Package [[http://cran.r-project.org/web/packages/rqgis/index.html|rQGIS]]
+  * Package [[https://github.com/jannes-m/RQGIS3|RQGIS3]]
-  * Package [[http://cran.r-project.org/web/packages/spgrass6/index.html|spgrass6]]
+  * Package [[http://cran.r-project.org/web/packages/rgrass7/index.html|rgrass7]]
   * Package [[http://cran.r-project.org/web/packages/RPostgreSQL/index.html|RPostgreSQL]]
   * Package [[http://cran.r-project.org/web/packages/rgdal/index.html|rgdal]]
@@ Line 224: / Line 250: @@
 ===== Using the Processing Framework in QGIS =====
-  * [[http://docs.qgis.org/2.8/en/docs/training_manual/processing/index.html|QGIS Training manual. Processing Guide. ]]
+You first need to install the **Processing R Provider plugin** in QGIS. Then, restart QGIS!
-  * [[http://docs.qgis.org/2.8/en/docs/user_manual/processing/index.html|QGIS User manual - Processing framework.]]
+  * [[https://docs.qgis.org/3.4/en/docs/training_manual/processing/r_syntax.html|R Syntax in Processing scripts. ]]
 **Commands to specify the input and output files and script options in Processing**
@@ Line 241: / Line 267: @@
 **folder**. A folder.\\
 **file**. A filename.\\
+To create a new R Processing script, click on the R logo on the top of the processing toolbox pane, and select Create New R Script. When you are done typing the script, give it an appropriate name and save it in the default folder that opens.
 ===== Exercice 5 =====
-Open the Processing Toolbox. Make sure that R is activated as a provider in the Toolbox options. Find "R Scripts > Create a new R script" in the toolbox. Copy and past this Processing/R script that creates 100 points distributed randomly on the earth in the latitude/longitude reference system (EPSG 4326) and that are imported as a QGIS layer.
+Create a new R script in the toolbox by copying and pasting this Processing/R script that creates 100 points distributed randomly on the earth in the latitude/longitude reference system (EPSG 4326) and that are imported as a QGIS layer.
 Overlay the result on top of the TM_World_Borders shapefile.
@@ Line 269: / Line 297: @@
 c2<-st_as_sf(countries)
 areas<-st_area(c2)
-plot(log(areas),log(c2$POP2005),xlab='Log Area',ylab='Log Population')
+plot(log(areas),log(as.numeric(c2$POP2005)),xlab='Log Area',ylab='Log Population')
-text(log(areas),log(c2$POP2005),c2$NAME,cex=0.7)
+text(log(areas),log(as.numeric(c2$POP2005)),c2$NAME,cex=0.7)
 </file>
 ++++
@@ Line 284: / Line 312: @@
 ##Layer=vector
 ##showplots
-data2=tapply(Layer$new_area,Layer$IHO_Sea,mean)
+#data2=tapply(Layer$new_area,Layer$IHO_Sea,mean)
+library('dplyr')
+Layer=data.frame(Layer)
+data2=Layer%>%group_by(IHO_Sea)%>%summarize(mean=mean(new_area))
 par(mar=c(10,4,4,2))
-barplot(data2, las=2)
+barplot(data2$mean, names.arg=data2$IHO_Sea, las=2)
 </file>
@@ Line 293: / Line 324: @@
 - Specify "Country seas" as the name of the model and "QCBS Workshop" as the group.
-- Add a vector layer to the model, name it "Countries" and specify polygon as the "shape type".
+- Add a vector layer to the model, name it "Countries" and specify polygon as the "geometry type".
 - Add a "String" to the model and name it, "Country Name".
-- Add "Extract by attributes" to the model (under QGIS geoalgorithms). Specify "Country" as the "Input Layer", = as the operator, NAME as the "Selection Attribute" and "Country Name" as the "Value".
+- Add "Extract by attributes" to the model (under Algorithms>Vector selection). Specify "Countries" as the "Input Layer", = as the operator, NAME as the "Selection Attribute", click on the Gear icon under Value, choose Model input and select "Country Name" as the "Value".
-- Add a "Fixed Distance Buffer" to the model. Specify "Output from Extract by Attributes" as the "Input", and specify the distance as 0.5 (it's in degrees since the map is in latitude/longitude). Choose to "dissolve the output".
+- Add a "Buffer" to the model. Specify "Output from Extract by Attributes" as the "Input", and specify the distance as 0.5 (it's in degrees since the map is in latitude/longitude). Choose to "dissolve the output" and leave other field blank.
-- Add another vector to the model. Name it "Zones". Specify "Polygon" as the "shape type". This will be our polygons layer containing the different seas.
+- Add another Vector Layer to the model. Name it "Sea Zones". Specify "Polygon" as the "shape type". This will be our polygons layer containing the different seas.
-- Add "Intersection" to the model. Specify an intersection between "output of the Buffer" and the layer "Zones".
+- Add "Intersection" to the model. Specify an intersection between "Buffered from Buffer" and the layer "Sea Zones". Leave other field blank.
-- Add "Field Calculator" to the model. Specify new_area as "Result Field Name" and $area as the fomula. This will calculate the area of each polygon of each section of sea in the buffer zone around the country in degrees squared.
+- Add "Field Calculator" to the model. Choose the intersection layer from the previous step as the input. Specify new_area as "Result Field Name" and $area as the fomula. This will calculate the area of each polygon of each section of sea in the buffer zone around the country in degrees squared.
 - Now, add the R script created at Step 2 to the model. "Input" is the output from Step 11 (Field Calculator). Call the output file "Country_seas"
@@ Line 311: / Line 342: @@
 Your model should look like this one:
-{{::screenshot_from_2017-04-19_11-54-37.png?direct&200|}}
+{{::screenshot_from_2019-04-15_16-51-00.png?direct&200|}}
 - You are now ready to run the model! First, save the model and name it Country_seas. Then, close the "Graphical Modeler" and double-click on your model in the Toolbox under Models. Specify TM_World_Borders as the Country layer and EEZ_IHO_union_v2 for the zones. Specify the name of a country of your choice (ex. Canada).