check on:
class(temp.dat$WTD)
before and after the na.approx statement, you have changed it from
numeric to character
Best,
Tom
On Thu, Dec 30, 2010 at 3:16 PM, emorway <emorway at engr.colostate.edu>
wrote:>
> Hello,
>
> I was unable to find clues to my problem in ?optim. ?Using the data and
code
> below, I get an error ("system is exactly singular") when a
particular line
> of code is left in, but have found that 'optim' works when I
comment it out.
> The line of code in question is after the closeAllConnections() line of
code
> and contains a call to "na.approx" from the zoo package.
?What's confusing
> to me is why optim works without it versus with it? ?Any clues would be
very
> helpful in moving forward. ?The overall goal of the code below is to
> minimize the residuals between the blue circles and green squares by
> adjusting the limits of the secondary y-axis.
>
> Thanks, Eric
>
> library(zoo)
> temp.dat<-read.table(textConnection("Well Meas_Date WTD ECgw
GW_Project_Area
> Region Avg.EM.Survey.Value Avg.Soil.Paste.EC SD_EM_Survey
> 1 4/12/1999 1.75 2.27 LOWER-UPSTREAM US NA NA NA
> 1 5/11/1999 1.24 5.04 LOWER-UPSTREAM US NA NA NA
> 1 5/27/1999 1.27 4.45 LOWER-UPSTREAM US NA NA NA
> 1 6/3/1999 1.27 4.09 LOWER-UPSTREAM US 3.347069 3.126667 0.6347013
> 1 6/11/1999 1.52 2.84 LOWER-UPSTREAM US NA NA NA
> 1 6/18/1999 1.19 2.34 LOWER-UPSTREAM US NA NA NA
> 1 6/24/1999 1.21 2.48 LOWER-UPSTREAM US NA NA NA
> 1 6/30/1999 1.19 2.45 LOWER-UPSTREAM US NA NA NA
> 1 7/7/1999 1.59 2.47 LOWER-UPSTREAM US NA NA NA
> 1 7/14/1999 1.75 2.73 LOWER-UPSTREAM US NA NA NA
> 1 7/21/1999 1.75 2.33 LOWER-UPSTREAM US NA NA NA
> 1 7/28/1999 1.78 2.63 LOWER-UPSTREAM US NA NA NA
> 1 8/4/1999 1.37 2.25 LOWER-UPSTREAM US NA NA NA
> 1 8/12/1999 0.08 2.37 LOWER-UPSTREAM US 2.858553 NA 0.3560363
> 1 8/18/1999 2.29 2.48 LOWER-UPSTREAM US NA NA NA
> 1 9/4/1999 0.02 2.48 LOWER-UPSTREAM US NA NA NA
> 1 9/16/1999 1.93 2.45 LOWER-UPSTREAM US NA NA NA
> 1 10/1/1999 2.01 2.49 LOWER-UPSTREAM US NA NA NA
> 1 11/13/1999 1.91 2.32 LOWER-UPSTREAM US NA NA NA
> 1 1/4/2000 1.83 2.59 LOWER-UPSTREAM US NA NA NA
> 1 2/24/2000 1.93 2.83 LOWER-UPSTREAM US NA NA NA
> 1 3/25/2000 1.73 2.71 LOWER-UPSTREAM US NA NA NA
> 1 4/15/2000 1.47 3.12 LOWER-UPSTREAM US NA NA NA
> 1 4/28/2000 1.98 2.76 LOWER-UPSTREAM US NA NA NA
> 1 5/17/2000 1.80 2.92 LOWER-UPSTREAM US NA NA NA
> 1 5/30/2000 NA NA <NA> US 3.064330 NA 0.3970829
> 1 6/1/2000 1.58 2.83 LOWER-UPSTREAM US NA NA NA
> 1 6/6/2000 1.65 2.97 LOWER-UPSTREAM US NA NA NA
> 1 6/15/2000 1.85 2.65 LOWER-UPSTREAM US NA NA NA
> 1 6/23/2000 1.90 2.78 LOWER-UPSTREAM US NA NA NA
> 1 6/29/2000 1.80 2.67 LOWER-UPSTREAM US NA NA NA
> 1 7/6/2000 2.00 2.69 LOWER-UPSTREAM US NA NA NA
> 1 7/14/2000 1.97 3.46 LOWER-UPSTREAM US NA NA NA
> 1 7/20/2000 1.69 2.57 LOWER-UPSTREAM US NA NA NA
> 1 7/27/2000 1.95 3.16 LOWER-UPSTREAM US NA NA NA
> 1 8/2/2000 2.03 3.12 LOWER-UPSTREAM US NA NA NA
> 1 8/8/2000 NA NA <NA> US 3.185567 2.522467 0.3765025
> 1 8/11/2000 2.00 2.65 LOWER-UPSTREAM US NA NA NA
> 1 8/19/2000 1.95 2.50 LOWER-UPSTREAM US NA NA NA
> 1 9/29/2000 2.11 2.11 LOWER-UPSTREAM US NA NA NA
> 1 10/20/2000 2.16 2.75 LOWER-UPSTREAM US NA NA NA
> 1 12/1/2000 1.83 2.81 LOWER-UPSTREAM US NA NA NA
> 1 1/19/2001 2.01 3.01 LOWER-UPSTREAM US NA NA NA
> 1 3/5/2001 2.01 2.35 LOWER-UPSTREAM US NA NA NA
> 1 3/30/2001 2.13 2.10 LOWER-UPSTREAM US NA NA NA
> 1 4/21/2001 1.87 2.36 LOWER-UPSTREAM US NA NA NA
> 1 5/15/2001 2.00 2.37 LOWER-UPSTREAM US NA NA NA
> 1 5/29/2001 1.60 2.59 LOWER-UPSTREAM US NA NA NA
> 1 6/4/2001 NA NA <NA> US 4.233636 NA 1.3738540
> 1 6/7/2001 1.71 2.55 LOWER-UPSTREAM US NA NA NA
> 1 6/14/2001 1.83 2.75 LOWER-UPSTREAM US NA NA NA
> 1 6/20/2001 1.93 3.02 LOWER-UPSTREAM US NA NA NA
> 1 6/29/2001 1.80 2.74 LOWER-UPSTREAM US NA NA NA
> 1 7/6/2001 1.91 2.70 LOWER-UPSTREAM US NA NA NA
> 1 7/12/2001 2.04 2.46 LOWER-UPSTREAM US NA NA NA
> 1 7/18/2001 1.87 2.55 LOWER-UPSTREAM US NA NA NA
> 1 7/25/2001 1.96 2.67 LOWER-UPSTREAM US NA NA NA
> 1 8/2/2001 2.02 2.42 LOWER-UPSTREAM US NA NA NA
> 1 8/8/2001 NA NA <NA> US 2.946731 NA 0.3748240
> 1 8/10/2001 1.94 2.36 LOWER-UPSTREAM US NA NA NA
> 1 8/17/2001 1.94 0.75 LOWER-UPSTREAM US NA NA NA
> 1 9/1/2001 2.12 2.22 LOWER-UPSTREAM US NA NA NA
> 1 9/15/2001 2.15 2.35 LOWER-UPSTREAM US NA NA NA
> 1 9/29/2001 1.95 2.20 LOWER-UPSTREAM US NA NA NA
> 1 10/27/2001 1.08 1.72 LOWER-UPSTREAM US NA NA NA
> 1 11/17/2001 1.99 2.21 LOWER-UPSTREAM US NA NA NA
> 1 1/10/2002 2.01 2.31 LOWER-UPSTREAM US NA NA NA
> 1 2/16/2002 1.94 1.74 LOWER-UPSTREAM US NA NA NA
> 1 3/23/2002 2.03 2.46 LOWER-UPSTREAM US NA NA NA
> 1 4/13/2002 2.11 2.50 LOWER-UPSTREAM US NA NA NA
> 1 5/11/2002 2.11 2.54 LOWER-UPSTREAM US NA NA NA
> 1 5/21/2002 NA NA <NA> US 2.368000 NA 0.3235852
> 1 5/30/2002 2.07 2.56 LOWER-UPSTREAM US NA NA NA
> 1 6/6/2002 2.11 2.55 LOWER-UPSTREAM US NA NA NA
> 1 6/13/2002 2.03 2.66 LOWER-UPSTREAM US NA NA NA
> 1 6/27/2002 2.19 2.55 LOWER-UPSTREAM US NA NA NA
> 1 7/3/2002 2.22 2.68 LOWER-UPSTREAM US NA NA NA
> 1 7/11/2002 2.06 2.61 LOWER-UPSTREAM US NA NA NA
> 1 7/18/2002 2.23 2.58 LOWER-UPSTREAM US NA NA NA
> 1 7/25/2002 2.23 2.62 LOWER-UPSTREAM US NA NA NA
> 1 8/1/2002 2.21 2.60 LOWER-UPSTREAM US NA NA NA
> 1 8/8/2002 2.29 2.60 LOWER-UPSTREAM US NA NA NA
> 1 8/14/2002 NA NA <NA> US 1.863548 NA 0.2400621
> 1 8/15/2002 2.26 2.61 LOWER-UPSTREAM US NA NA NA
> 1 8/21/2002 2.34 2.51 LOWER-UPSTREAM US NA NA NA
> 1 9/6/2002 2.31 2.51 LOWER-UPSTREAM US NA NA NA
> 1 9/21/2002 2.25 2.55 LOWER-UPSTREAM US NA NA NA
> 1 10/5/2002 2.21 2.57 LOWER-UPSTREAM US NA NA NA
> 1 11/8/2002 2.09 2.50 LOWER-UPSTREAM US NA NA NA
> 1 12/23/2002 2.19 2.16 LOWER-UPSTREAM US NA NA NA
> 1 1/16/2003 2.23 2.15 LOWER-UPSTREAM US NA NA NA
> 1 3/1/2003 2.12 2.11 LOWER-UPSTREAM US NA NA NA
> 1 4/5/2003 2.03 1.99 LOWER-UPSTREAM US NA NA NA
> 1 5/2/2003 2.00 2.42 LOWER-UPSTREAM US NA NA NA
> 1 5/30/2003 1.66 2.09 LOWER-UPSTREAM US NA NA NA
> 1 6/3/2003 NA NA <NA> US 3.066333 NA 0.2926846
> 1 6/6/2003 1.43 2.24 LOWER-UPSTREAM US NA NA NA
> 1 6/12/2003 1.73 2.81 LOWER-UPSTREAM US NA NA NA
> 1 6/19/2003 1.51 2.97 LOWER-UPSTREAM US NA NA NA
> 1 7/3/2003 1.84 3.35 LOWER-UPSTREAM US NA NA NA
> 1 7/11/2003 2.00 2.52 LOWER-UPSTREAM US NA NA NA
> 1 7/17/2003 2.04 2.76 LOWER-UPSTREAM US NA NA NA
> 1 7/24/2003 2.02 2.40 LOWER-UPSTREAM US NA NA NA
> 1 7/31/2003 1.96 2.14 LOWER-UPSTREAM US NA NA NA
> 1 8/16/2003 2.29 1.85 LOWER-UPSTREAM US NA NA NA
> 1 8/20/2003 2.14 2.11 LOWER-UPSTREAM US NA NA NA
> 1 9/5/2003 2.03 1.45 LOWER-UPSTREAM US NA NA NA
> 1 10/10/2003 2.10 2.21 LOWER-UPSTREAM US NA NA NA
> 1 11/15/2003 1.95 1.83 LOWER-UPSTREAM US NA NA NA
> 1 12/22/2003 2.13 NA LOWER-UPSTREAM US NA NA NA
> 1 1/16/2004 2.16 2.30 LOWER-UPSTREAM US NA NA NA
> 1 2/13/2004 2.12 2.13 LOWER-UPSTREAM US NA NA NA
> 1 3/19/2004 2.02 2.11 LOWER-UPSTREAM US NA NA NA
> 1 4/23/2004 2.09 2.10 LOWER-UPSTREAM US NA NA NA
> 1 5/3/2004 1.89 2.42 LOWER-UPSTREAM US NA NA NA
> 1 5/17/2004 2.02 2.31 LOWER-UPSTREAM US NA NA NA
> 1 5/24/2004 1.97 2.58 LOWER-UPSTREAM US NA NA NA
> 1 5/26/2004 NA NA <NA> US 3.532614 NA 0.6329923
> 1 6/7/2004 1.81 2.70 LOWER-UPSTREAM US NA NA NA
> 1 6/14/2004 1.66 2.35 LOWER-UPSTREAM US NA NA NA
> 1 6/28/2004 2.10 2.70 LOWER-UPSTREAM US NA NA NA
> 1 7/5/2004 1.86 3.25 LOWER-UPSTREAM US NA NA NA
> 1 7/12/2004 2.00 2.93 LOWER-UPSTREAM US NA NA NA
> 1 7/19/2004 1.63 2.55 LOWER-UPSTREAM US NA NA NA
> 1 7/26/2004 2.01 2.65 LOWER-UPSTREAM US NA NA NA
> 1 8/2/2004 1.91 2.89 LOWER-UPSTREAM US NA NA NA
> 1 8/9/2004 2.00 2.87 LOWER-UPSTREAM US NA NA NA
> 1 8/17/2004 2.07 2.77 LOWER-UPSTREAM US NA NA NA
> 1 9/18/2004 2.18 2.67 LOWER-UPSTREAM US NA NA NA
> 1 10/23/2004 2.14 2.43 LOWER-UPSTREAM US NA NA NA
> 1 11/22/2004 2.17 2.38 LOWER-UPSTREAM US NA NA NA
> 1 12/20/2004 0.32 2.48 LOWER-UPSTREAM US NA NA NA
> 1 1/11/2005 2.16 2.44 LOWER-UPSTREAM US NA NA NA
> 1 2/18/2005 2.22 2.27 LOWER-UPSTREAM US NA NA NA
> 1 3/16/2005 2.06 2.59 LOWER-UPSTREAM US NA NA NA
> 1 4/9/2005 2.02 2.50 LOWER-UPSTREAM US NA NA NA
> 1 5/13/2005 1.96 2.62 LOWER-UPSTREAM US NA NA NA
> 1 6/7/2005 1.96 2.99 LOWER-UPSTREAM US NA NA NA
> 1 6/13/2005 1.77 2.22 LOWER-UPSTREAM US NA NA NA
> 1 6/20/2005 1.87 3.05 LOWER-UPSTREAM US NA NA NA
> 1 6/28/2005 1.76 3.50 LOWER-UPSTREAM US NA NA NA
> 1 7/5/2005 1.58 3.56 LOWER-UPSTREAM US NA NA NA
> 1 7/11/2005 1.72 3.22 LOWER-UPSTREAM US NA NA NA
> 1 7/19/2005 1.98 3.11 LOWER-UPSTREAM US NA NA NA
> 1 8/1/2005 2.14 3.02 LOWER-UPSTREAM US NA NA NA
> 1 8/10/2005 NA NA <NA> US 3.465650 4.032000 0.3743813
> 1 8/16/2005 1.79 3.00 LOWER-UPSTREAM US NA NA NA
> 1 10/21/2005 4.34 1.07 LOWER-UPSTREAM US NA NA NA
> 1 11/23/2005 2.08 1.08 LOWER-UPSTREAM US NA NA NA
> 1 12/21/2005 1.64 2.54 LOWER-UPSTREAM US NA NA NA
> 1 1/13/2006 2.05 2.01 LOWER-UPSTREAM US NA NA NA
> 1 2/9/2006 2.10 1.73 LOWER-UPSTREAM US NA NA NA
> 1 3/13/2006 2.03 2.22 LOWER-UPSTREAM US NA NA NA
> 1 5/22/2006 1.62 2.38 LOWER-UPSTREAM US NA NA NA
> 1 5/29/2006 1.61 2.29 LOWER-UPSTREAM US NA NA NA
> 1 6/13/2006 1.53 2.39 LOWER-UPSTREAM US NA NA NA
> 1 6/19/2006 1.77 2.49 LOWER-UPSTREAM US NA NA NA
> 1 6/20/2006 1.86 NA LOWER-UPSTREAM US NA NA NA
> 1 6/26/2006 1.89 3.12 LOWER-UPSTREAM US NA NA NA
> 1 7/3/2006 1.90 2.95 LOWER-UPSTREAM US NA NA NA
> 1 7/11/2006 1.26 2.49 LOWER-UPSTREAM US NA NA NA
> 1 7/18/2006 1.83 2.86 LOWER-UPSTREAM US NA NA NA
> 1 7/31/2006 1.92 2.89 LOWER-UPSTREAM US NA NA NA
> 1 8/15/2006 2.00 1.87 LOWER-UPSTREAM US NA NA NA
> 1 9/22/2006 2.07 1.62 LOWER-UPSTREAM US NA NA NA
> 1 11/5/2006 1.92 1.67 LOWER-UPSTREAM US NA NA NA
> 1 12/18/2006 2.03 1.66 LOWER-UPSTREAM US NA NA NA
> 1 5/24/2007 1.49 NA LOWER-UPSTREAM US NA NA NA
> 1 10/6/2007 2.13 NA LOWER-UPSTREAM US NA NA NA
> 1 12/16/2007 2.03 1.36 LOWER-UPSTREAM US NA NA NA
> 1 1/18/2008 2.07 1.73 LOWER-UPSTREAM US NA NA NA
> 1 4/19/2008 1.92 1.91 LOWER-UPSTREAM US NA NA NA
> 1 3/18/2010 0.61 3.20 LOWER-UPSTREAM US NA NA NA
> 1 5/24/2010 2.04 2.22 LOWER-UPSTREAM US NA NA NA"),header=T)
> closeAllConnections()
>
> #interpolate missing WTD values
>
temp.dat$WTD<-na.approx(temp.dat$WTD,as.numeric(as.Date(temp.dat$Meas_Date,"%m/%d/%Y")))
>
> #the current limits of the left and right y-axes
> ylim_1<-rev(c(0,max(na.omit(temp.dat$WTD))+1))
>
ylim_2<-c(floor(min(range(na.omit(temp.dat$Avg.EM.Survey.Value))[1],range(na.omit(temp.dat$Avg.Soil.Paste.EC))[1])),ceiling(max(range(na.omit(temp.dat$Avg.EM.Survey.Value))[2],range(na.omit(temp.dat$Avg.Soil.Paste.EC))[2])))
>
>
plot(as.Date(temp.dat$Meas_Date,"%m/%d/%Y"),temp.dat$WTD,xlim=c(as.Date("1999-01-01"),as.Date("2005-11-01")),ylim=ylim_1,pch=19,lwd=1.5,col="blue",cex=0.5,xlab="",ylab="",xaxt="n",type="p",las=1)
> par(new=T)
>
plot(as.Date(temp.dat$Meas_Date,"%m/%d/%Y"),temp.dat$Avg.EM.Survey.Value,xlim=c(as.Date("1999-01-01"),as.Date("2005-11-01")),ylim=ylim_2,xlab="",ylab="WTD
>
(m)",xaxt="n",yaxt="n",pch=15,col="darkgreen",cex=0.75)
>
axis(side=4,at=seq(floor(min(range(na.omit(temp.dat$Avg.EM.Survey.Value))[1],range(na.omit(temp.dat$Avg.Soil.Paste.EC))[1])),ceiling(max(range(na.omit(temp.dat$Avg.EM.Survey.Value))[2],range(na.omit(temp.dat$Avg.Soil.Paste.EC))[2])),by=1),labels=seq(floor(min(range(na.omit(temp.dat$Avg.EM.Survey.Value))[1],range(na.omit(temp.dat$Avg.Soil.Paste.EC))[1])),ceiling(max(range(na.omit(temp.dat$Avg.EM.Survey.Value))[2],range(na.omit(temp.dat$Avg.Soil.Paste.EC))[2])),by=1),las=1)
>
>
> f<-function(ylim_2){
> ?y2_l<-ylim_2[1]
> ?y2_u<-ylim_2[2]
> ?#solve for "x", the coeffs to map the right
> ?#referenced values to their left-axis equivalent
> ?A<-matrix(c(y2_l,y2_u,1,1),nrow=2,ncol=2,byrow=F)
> ?RHS<-matrix(ylim_1,nrow=2,ncol=1,byrow=T)
> ?x<-solve(A,RHS)
>
> ?#map the right-referenced values to their
> ?#corresponding left-axis values
> ?temp.dat.mapped<-x[1,1]*temp.dat$Avg.EM.Survey.Value+x[2,1]
>
> ?#calculate the resids between green squares and blue circles
>
>
resids<-na.omit(data.frame(Col1=temp.dat$WTD,Col2=temp.dat.mapped,SumSqrDiff=(temp.dat$WTD-temp.dat.mapped)^2))
>
> ?#quantity to be minimized
> ?min_this<-sum(resids$SumSqrDiff)
> ?min_this
> }
>
edm<-optim(ylim_2,f,lower=c(0,0),upper=c(100,100),method="L-BFGS-B")
> ylim_2<-edm$par
>
> --
> View this message in context:
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>
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