added R packages

Dockerfile

@@ -33,6 +33,7 @@ RUN apt-get -qq update && apt-get install --fix-missing -y --force-yes --allow-u
 	postgresql-8.4 \
 	sshpass \
 	git-core \
+	bzip2 \
 	apt-transport-https \
 	net-tools \
 	imagemagick

README.md

@@ -43,7 +43,7 @@ Reproduction of the computations on the article "Spatio-Temporal Change Detectio
         </ul>
       </li>
 
-      <li>Scrpts for running the expriement:
+      <li>Scripts for running the expriement:
         <ul>
           <li><code>reprosarefp.R</code> - .</li>
           <li><code>rexec_sar_efp_f.R</code> - .</li>

containerSetup.sh

@@ -9,6 +9,7 @@
 		build-essential \
 		cmake \
 		libgdal-dev \
+		libproj-dev \
 		gdal-bin \
 		g++ \
 		python-dev \
@@ -80,12 +81,23 @@ echo "***** Installing additional stuff..."
 #********************************************************
 cd ~
 yes | /root/./installR.sh
-Rscript /home/scidb/installPackages.R packages=scidb,Rserve verbose=0 quiet=0
+
+
+Rscript /home/scidb/installPackages.R packages=spdep,bfast,forecast,sandwich,scidb,Rserve verbose=0 quiet=0
+git clone https://github.com/mengluchu/strucchange.git
+git clone https://github.com/mengluchu/bfast2.git
+R CMD INSTALL strucchange/
+R CMD INSTALL bfast2/
+
+
 yes | /root/./installParallel.sh
 yes | /root/./installBoost_1570.sh
 yes | /root/./installGribModis2SciDB.sh
 ldconfig
 cp /root/libr_exec.so /opt/scidb/14.12/lib/scidb/plugins
+#********************************************************
+echo "***** Starting RSERVE..."
+#********************************************************
 R CMD Rserve
 #********************************************************
 echo "***** Installing SHIM..."
@@ -157,6 +169,12 @@ echo "***** ***** Executing BFAST..."
 #********************************************************
 
 
+# Subset just Juara
+iquery -naq "store(between(MOD09Q1, 58828, 48103, 0, 59679, 49050, 9200), MOD09Q1_JUARA);"
+# Redimension
+iquery -naq "store(repart(MOD09Q1_JUARA, <red:int16,nir:int16,quality:uint16> [col_id=57600:62399,502,5,row_id=48000:52799,502,5,time_id=0:9200,1,0]),  MOD09Q1_repart);"
+
+
 
 
 

rexec_sar_efp_f.R

@@ -3,6 +3,10 @@ scidbconnect("localhost", 8083, "scidb", "xxxx.xxxx.xxxx")
 #########################################
 ######  subset and prepare scidb array ##
 #########################################
+
+
+# NOTE: Adjust the schema accordingly. Meng uses this query to remove overlap
+# => remove overlap since data load
 iquery("
        store(
        project(
@@ -11,9 +15,8 @@ iquery("
        apply(
        subarray(
        repart(
-       MOD09Q1,
-       <red:int16,nir:int16,quality:uint16> [col_id=58828:59679,502,0,row_id=48103:49050,502,0,time_id=0:9200,1,0]),
-
+       MOD09Q1_JUARA,
+       <red:int16,nir:int16,quality:uint16> [col_id=57600:62399,502,5,row_id=48000:52799,502,5,time_id=0:9200,1,0]),
        58930,48210,6,59079,48359,643),
        evi2,2.5*((nir*0.0001-red*0.0001)/(nir*0.0001+2.4*red*0.0001+1.0))),
        <red:int16,nir:int16,quality:uint16,evi2:double>[col_id=0:149,1,1,row_id=0:149,1,1,time_id=0:637,638,0]),