Merge pull request #27 from jread-usgs/master

updated examples to current version of rGLM

Examples/GLMncExample.R

@@ -1,18 +1,16 @@
 # example usage of GLMnetCDF
+require('rGLM')
+
+
 
-source('../Source/GLMnetCDF.R')
 # 1) create data frame for GLM water temperature on a uniform grid:
-lyrDz <-  0.25  # grid vertical thickness for resampling
-GLMfolder <-  '../Data/'
-GLMfile <-  'output.nc4'
+#lyrDz <-  0.25  # grid vertical thickness for resampling
+out.depths <- c(0,.5,1.5,5,10)
+GLMfolder <-  '../resources/'
+GLMfile <-  'output.nc'
 GLMnc  <- getGLMnc(fileName=GLMfile,folder=GLMfolder)
-GLMwtr <-  resampleGLM(GLMnc,lyrDz=lyrDz)
+GLMwtr <-  getTempGLMnc(GLMnc=GLMnc,ref='surface',z.out=out.depths)
 
 # 2) write data to a text file
-outFile <- 'GLMout.txt'
 outFolder <-  '../Examples/'
-writeGLM(GLMwtr,fileName=outFile,folder=outFolder)
-
-# 3) plot a heatmap and save
-figureName <- 'exampleFig'
-plotGLM(GLMwtr,figName=figureName,folder=outFolder)
+write.wtr(wtr=GLMwtr,lakeName='testLake',folder=outFolder)

Examples/nml_readwrite.R

@@ -0,0 +1,31 @@
+# example for writing all Lake Analyzer files from GLM output
+require('rGLM')
+
+# 1) open existing gml.nml file
+GLMfolder	<-	'../resources/'
+NMLfile	<-	'glm.nml'
+nml	<-	read.nml(folder=GLMfolder,fileName=NMLfile)
+
+# 2) pretty print the nml list 
+pretty.nml(nml) 
+
+# 3) get existing value from nml for Kw parameter
+get.nml(nml,argName='Kw')
+
+# 4) change Kw value to a new one
+nml	<-	set.nml(nml,argName='Kw',argVal=0.4)
+
+# 5) view the change in the nml
+get.nml(nml,argName='Kw')
+
+# 6) change a list of params
+nml	<-	set.nml(nml,argList=list('Kw'=0.4,'outflow_factor'=0.9))
+
+# 7) try to set a param that doesn't exist (will error). Un-comment this to try:
+#nml	<-	set.nml(nml,argName='donkey',argVal=23)
+
+# 8) pretty print the nml list 
+pretty.nml(nml)
+
+# 9) write it back to glm.nml so it can be used in GLM
+write.nml(nml,folder=GLMfolder,fileName='glm2.nml')

Examples/writeAll_LA.R

@@ -0,0 +1,33 @@
+# example for writing all Lake Analyzer files from GLM output
+require('rGLM')
+
+# 1) create data frame for GLM water temperature on a uniform grid:
+lyrDz	<-  0.5  # grid vertical thickness for resampling
+lkName	<-	"testLake"
+GLMfolder	<-	'../resources/'
+out.folder	<-	'.'
+GLMfile	<-	'output.nc'
+NMLfile	<-	'glm.nml'
+GLMnc	<-	getGLMnc(fileName=GLMfile,folder=GLMfolder)
+nml	<-	read.nml(folder=GLMfolder,fileName=NMLfile)
+lke	<-	init.lke()	# gets a default list of lke parameters
+pretty.nml(nml) # print the nml list 
+
+bth	<-	get.bth(nml)
+mxDep	<-	max(bth[,1])
+
+write.bth(bth,lkName,folder=out.folder)		# write the .bth file
+
+lke	<-	set.lke(lke,'totalDep',mxDep)
+write.lke(lke,lkName,folder=out.folder)		# write the .lke file
+
+lvl	<-	get.lvl(GLMnc,nml)
+write.lvl(lvl,lkName,folder=out.folder)		# write the .lvl file
+
+depths	<-	seq(0,mxDep,by=lyrDz)
+wtr	<-	get.wtr(GLMnc,ref='surface',z.out=depths)
+write.wtr(wtr,lkName,folder=out.folder)		# write the .wtr file
+
+wnd	<-	get.wnd(GLMnc)
+write.wnd(wnd,lkName,folder=out.folder)		# write the .wtr file
+

R/GLM.LA.R

@@ -44,7 +44,7 @@ get.lvl	<-	function(GLMnc,nml){
 	DateTime	<-	getTimeGLMnc(GLMnc)
 	GLM	<-	getTempGLMnc(GLMnc,lyrDz=0.25)
 	surfaceElv	<-	getSurfaceElevGLM(GLM)
-	mxDep	<-	getMaxDepth(nml)
+	mxDep	<-	max(get.nml(nml,argName="H"))-min(get.nml(nml,argName="H"))
 	dif	<-	mxDep-surfaceElv
 	dif[dif<0]	<-	0
 	lvl	<-	data.frame(DateTime)
@@ -69,16 +69,15 @@ get.bth	<-	function(nml){
 	return(bth)
 }
 
-get.wtr	<-	function(GLMnc,depths,lyrDz=0.25){
-	GLMwtr	<-	getTempGLMnc(GLMnc,lyrDz)
-	wtr	<-	depthsampleGLM(GLMwtr, depths)
+get.wtr	<-	function(GLMnc,ref='surface',z.out){
+	wtr	<-getTempGLMnc(GLMnc,ref=ref,z.out=z.out)
 	return(wtr)
 }
 
 get.wnd	<-	function(GLMnc){
 	wnd	<-	data.frame(getTimeGLMnc(GLMnc))
 	wnd	<-	cbind(wnd,getWndGLMnc(GLMnc))
-	names(wnd)	<-	c(timeID,"wnd")
+	names(wnd)	<-	c("DateTime","wnd")
 	return(wnd)
 }
 
@@ -88,7 +87,7 @@ set.lke	<-	function(lke,argName,argVal){
 }
 
 write.lke	<-	function(lke,lakeName = 'lake',folder='../Supporting Files/'){	
-	lkeMeta	<-	getLkeMeta()
+	lkeMeta	<-	init.lkeMeta()
 
 	if (any(is.na(lke))){stop("no lke parameters can be NA")}
 	fileName	<-	gsub(" ","",paste(c(lakeName,'.lke'),collapse=""))

man/set.nml.Rd

@@ -4,7 +4,7 @@
 \title{sets value in R nml list}
 \description{This function sets the specified value in the nml list for GLM. All data types are converted tested against initial data type formats of logical, numerical, or character arrays}
 \usage{
-set.nml(nml,argName))
+set.nml(nml,argName,argVal,argList)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{