first version of output analysis included

dream/simulation/outputanalysis/ConfidenceIntervals.py

+# ===========================================================================
+# Copyright 2013 University of Limerick
+#
+# This file is part of DREAM.
+#
+# DREAM is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# DREAM is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with DREAM.  If not, see <http://www.gnu.org/licenses/>.
+# ===========================================================================
+
+'''
+Created on 16 Nov 2013
+
+@author: Panos
+'''
+from rpy2.robjects.packages import importr
+from rpy2 import robjects
+
+MASS= importr('MASS')
+
+
+class Intervals:
+    
+    
+    def ConfidIntervals(self,data,p): 
+  
+        data=robjects.FloatVector(data)  
+        alpha=1-p
+        rsqrt=robjects.r['sqrt']
+        rsd=robjects.r['sd']
+        rmean=robjects.r['mean']
+        t=len(data)
+        n=rsqrt(t)
+        b=rsd(data)
+
+        rqt=robjects.r['qt']
+        q=rqt((1-(alpha/2)),t-1)
+        m=rmean(data)
+
+        me=q[0]*(b[0]/n[0])
+
+        lo=m[0]-me
+        up=m[0]+me
+        l=[lo,up]
+        return l
+
+
+
+

dream/simulation/outputanalysis/Plots.py

+# ===========================================================================
+# Copyright 2013 University of Limerick
+#
+# This file is part of DREAM.
+#
+# DREAM is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# DREAM is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with DREAM.  If not, see <http://www.gnu.org/licenses/>.
+# ===========================================================================
+
+'''
+Created on 16 Dec 2013
+
+@author: Panos
+'''
+from rpy2 import robjects
+
+class Graphs:
+    
+    def Plots(self,data, fileName="plotChart.jpg"):
+        data=robjects.FloatVector(data)
+        rplot=robjects.r['plot']
+        rdev=robjects.r['dev.off']
+        rjpeg=robjects.r['jpeg']
+    
+        output=rjpeg(fileName)
+        rplot(data, type="o", col="blue")
+        rdev
+        return output
+    
+    def ScatterPlot(self,data1,data2, fileName="scatterplot.jpg"):
+        data1=robjects.FloatVector(data1)
+        data2=robjects.FloatVector(data2)
+        
+        rplot=robjects.r['plot']
+        rdev=robjects.r['dev.off']
+        rjpeg=robjects.r['jpeg']
+    
+        output=rjpeg(fileName)
+        rplot(data1,data2, type="o", col="red")
+        rdev
+        return output
+
+    def Pie(self, data1, fileName="pieChart.jpg"):
+        data1=robjects.FloatVector(data1)
+        rpaste=robjects.r['paste']
+        rround=robjects.r['round']
+        rsum=robjects.r['sum']
+        rpie=robjects.r['pie']
+   
+        rdev=robjects.r['dev.off']
+
+        colors=robjects.StrVector(["white","grey70","grey90","grey50","grey60","black"])
+        s=rsum(data1)
+        d_labels=[0]*(len(data1))
+   
+        i=0
+        while i<len(data1):
+            d_labels[i]=((rround((data1[i]/s[0])*100,1)))
+            i+=1
+    
+        d_labels=rpaste(d_labels,"%",sep="")
+        rjpeg=robjects.r['jpeg']
+    
+        export=rjpeg(fileName)
+        rpie(data1,main="Data",col=colors,labels=d_labels,cex=0.8)
+        rdev
+        return export
+
+

dream/simulation/outputanalysis/StatisticalMeasures.py

+# ===========================================================================
+# Copyright 2013 University of Limerick
+#
+# This file is part of DREAM.
+#
+# DREAM is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# DREAM is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with DREAM.  If not, see <http://www.gnu.org/licenses/>.
+# ===========================================================================
+
+'''
+Created on 14 Nov 2013
+
+@author: Panos
+'''
+import rpy2.robjects as robjects
+from rpy2.robjects.packages import importr
+
+MASS= importr('MASS')
+
+class BasicStatisticalMeasures:
+
+    def length(self, data):
+        data=robjects.FloatVector(data)
+        rlength = robjects.r['length']
+        return rlength(data)
+     
+    def summary(self, data):
+        data=robjects.FloatVector(data)
+        rsummary = robjects.r['summary']
+        return rsummary(data)
+        
+    def quantile(self,data):
+        data=robjects.FloatVector(data)
+        rquantile = robjects.r['quantile']
+        return rquantile(data)
+    
+    def frequency(self,data):
+        data=robjects.FloatVector(data)
+        rtable= robjects.r['table']
+        return rtable(data)
+        
+    def mean (self, data):
+        data=robjects.FloatVector(data)
+        rmean = robjects.r['mean']
+        return rmean(data)
+    
+    def var (self, data):
+        data=robjects.FloatVector(data)
+        rvar = robjects.r['var']
+        return rvar(data)
+    
+    def sd (self, data):
+        data=robjects.FloatVector(data)
+        rsd = robjects.r['sd']
+        return rsd(data)
+
+    def range (self, data):
+        data=robjects.FloatVector(data)
+        rrange = robjects.r['range']
+        return rrange(data)
+        
+    def IQR (self, data):
+        data=robjects.FloatVector(data)
+        rIQR = robjects.r['IQR']
+        return rIQR(data)
+    
+    def all(self, data):
+        data=robjects.FloatVector(data)
+        print 'The length of the data set is:', self.length(data)[0]
+        print 'The summary is:', self.summary(data)
+        print 'The quartiles and percentiles of the data set are:', self.quantile(data)
+        print 'The frequency of the datapoints are:', self.frequency(data)
+        print 'The mean value is:', self.mean(data)[0]
+        print 'The standard deviation is:', self.sd(data)[0]
+        print 'The variance is:', self.var(data)[0]
+        print 'The range is:', self.range(data)[0]
+        print 'The Interquartile Range is:', self.IQR(data)[0]
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dream/simulation/outputanalysis/__init__.py

+# ===========================================================================
+# Copyright 2013 University of Limerick
+#
+# This file is part of DREAM.
+#
+# DREAM is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# DREAM is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with DREAM.  If not, see <http://www.gnu.org/licenses/>.
+# ===========================================================================
+# See http://peak.telecommunity.com/DevCenter/setuptools#namespace-packages
+try:
+    __import__('pkg_resources').declare_namespace(__name__)
+except ImportError:
+    from pkgutil import extend_path
+    __path__ = extend_path(__path__, __name__)
\ No newline at end of file