Changeset 825

Timestamp:

08/03/11 17:48:38 (22 months ago)

Author:

jjr8

Message:

Continued development of Linear Mixed Modeling tools.

Location:

MGET/Branches/Jason/PythonPackage/src/GeoEco/Statistics

Files:

• FitLMEForDataframe.r (modified) (3 diffs)
• Modeling.py (modified) (3 diffs)

MGET/Branches/Jason/PythonPackage/src/GeoEco/Statistics/FitLMEForDataframe.r

@@ -18 +18 @@
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 
-FitLMEForDataframe <- function(fixed, data, outputModelFile, random=NULL, correlation=NULL, method=NULL, xVar=NULL, yVar=NULL, zVar=NULL, mVar=NULL, coordinateSystem=NULL, writeSummaryFile=TRUE, plotFileFormat="png", res=1000.0, width=3000.0, height=3000.0, pointSize=10.0, bg="white")
+FitLMEForDataframe <- function(fixed, data, outputModelFile, random=NULL, correlation="NULL", method=NULL, xVar=NULL, yVar=NULL, zVar=NULL, mVar=NULL, coordinateSystem=NULL, writeSummaryFile=TRUE, plotFileFormat="png", res=1000.0, width=3000.0, height=3000.0, pointSize=10.0, bg="white")
 {
     # Fit the model.
@@ -32 +32 @@
                           "==============\n",
                           "\n",
-                          paste(capture.output(summary(model)), sep="", collapse="\n"), "\n",
+                          sub("Fixed effects: list\\(fixed\\)", paste("Fixed effects: ", as.character(fixed)[2], as.character(fixed)[1], as.character(fixed)[3]), paste(capture.output(summary(model)), sep="", collapse="\n")), "\n",
                           "\n",
                           "ANOVA:\n",
@@ -43 +43 @@
     # Write the output file.
     
-    save(model, xVar, yVar, zVar, mVar, coordinateSystem, file=outputModelFile, compress=FALSE)
+    save(model, fixed, random, xVar, yVar, zVar, mVar, coordinateSystem, file=outputModelFile, compress=FALSE)
 
     # Strip the extension, if one exists, off the output file path.

MGET/Branches/Jason/PythonPackage/src/GeoEco/Statistics/Modeling.py

@@ -417 +417 @@
                          where=None, method=u'REML', correlationStructure=None, correlationFormula=None, range_=None, nugget=None, metric=None, fixed=False,
                          xColumnName=None, yColumnName=None, zColumnName=None, mColumnName=None,
-                         writeSummaryFile=True, plotFileFormat=u'png', res=1000., width=3000., height=3000., pointSize=10.0, bg=u'white',
+                         writeSummaryFile=True, writeDiagnosticPlots=True, plotFileFormat=u'png', res=1000., width=3000., height=3000., pointSize=10.0, bg=u'white',
                          overwriteExisting=False):
         cls.__doc__.Obj.ValidateMethodInvocation()
+
+        # Perform additional validation.
+
+        if correlationStructure is not None and correlationFormula is None or correlationStructure is None and correlationFormula is not None:
+            Logger.RaiseException(ValueError(_('To fit a model that includes for within-group correlation, you must specify both the a correlation structure and a correlation formula. If you do not wish to include within-group correlation, you must omit both of those parameters.')))
+
+        if correlationStructure is not None and range_ is None and nugget is not None:
+            Logger.RaiseException(ValueError(_('If the Nugget parameter is specified, the Range parameter must also be specified.')))
 
         # Load the table into a temporary data frame.
@@ -439 +447 @@
                 randomFormula = u'NULL'
 
-            r('FitLMEForDataframe(fixed=%s, data=%s, outputModelFile="%s", random=%s, correlation=NULL, method="%s", xVar=%s, yVar=%s, zVar=%s, mVar=%s, coordinateSystem=%s, writeSummaryFile=%s, plotFileFormat="%s", res=%f, width=%f, height=%f, pointSize=%f, bg="%s")' %
-              (fixedFormula, dataFrameName, tempOutputFile.replace('\\', '\\\\'), randomFormula, method,
+            if correlationStructure is not None:
+                if correlationStructure == u'exponential':
+                    correlation = u'corExp('
+                elif correlationStructure == u'gaussian':
+                    correlation = u'corGaus('
+                elif correlationStructure == u'linear':
+                    correlation = u'corLin('
+                elif correlationStructure == u'rational quadratic':
+                    correlation = u'corRatio('
+                elif correlationStructure == u'spherical':
+                    correlation = u'corSpher('
+                else:
+                    Logger.RaiseException(RuntimeError(_('Unknown correlationStructure value \'%(cs)s\'. Please contact the author of this tool for assistance.') % {u'cs': correlationStructure}))
+
+                if range_ is not None:
+                    if nugget is None:
+                        correlation += repr(range_) + ', '
+                    else:
+                        correlation += u'c(' + repr(range_) + u', ' + repr(nugget) + u'), '
+
+                correlation += u'form=' + correlationFormula + u', nugget=' + repr(nugget is not None).upper()
+
+                if metric is not None:
+                    correlation += u', metric="' + metric + u'"'
+
+                correlation += u', fixed=' + repr(fixed).upper() + u')'
+
+            else:
+                correlation = u'NULL'
+
+            r('library(nlme)')      # Required here so we can instantiate correlation classes
+
+            r('FitLMEForDataframe(fixed=%s, data=%s, outputModelFile="%s", random=%s, correlation=%s, method="%s", xVar=%s, yVar=%s, zVar=%s, mVar=%s, coordinateSystem=%s, writeSummaryFile=%s, plotFileFormat="%s", res=%f, width=%f, height=%f, pointSize=%f, bg="%s")' %
+              (fixedFormula, dataFrameName, tempOutputFile.replace('\\', '\\\\'), randomFormula, correlation, method,
                xColumnParam, yColumnParam, zColumnParam, mColumnParam, coordinateSystemParam,
                str(writeSummaryFile).upper(), plotFileFormat, res, width, height, pointSize, bg))
@@ -3584 +3624 @@
 
 AddArgumentMetadata(LinearMixedModel.FitToArcGISTable, u'correlationStructure',
-    typeMetadata=UnicodeStringTypeMetadata(canBeNone=True, allowedValues=[u'Exponential', u'Gaussian', u'Linear', u'Rational quadratic', u'Spherical']),
+    typeMetadata=UnicodeStringTypeMetadata(canBeNone=True, makeLowercase=True, allowedValues=[u'Exponential', u'Gaussian', u'Linear', u'Rational quadratic', u'Spherical']),
     description=_(
 u"""TODO: Write documentation for this parameter."""),