Re: [R] error in for loop in function (object not found)

Irucka Embry Mon, 14 Jan 2013 18:56:39 -0800

Hi David, thanks for letting me know about the missing attachments.

This is the code for the function:


xygetN <- function(file, hasHeader = TRUE, separator = ",") 
{
totalPath <- paste(file, sep = "")
tmp <- read.csv(totalPath, header = hasHeader, sep = separator, 
fill = TRUE, comment.char = "#", as.is = TRUE, stringsAsFactors = FALSE)
retval <- as.data.frame(tmp, stringsAsFactors = FALSE)
if (ncol(retval) == 2) {
names(retval) <- c("x", "y")
}
else if (ncol(retval) == 3) {
names(retval) <- c("x", "y", "lat_00600")
}
else if (ncol(retval) == 4) {
names(retval) <- c("x", "y", "lat_00600", "lon_00600")
}
retval$y <- as.numeric(retval$y)
write.csv(Sample, file =
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/example_setofstationsassociatedtosamegages.csv")
x <- retval[,1]
y <- retval[,2]

filenwissample <-
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/da
ta/Sample/nwis_wqdata_sc_n.csv"

for(i in seq(along=x[1:6])) {
Sample <- getSampleDataFromFilecustom(filenwissample, hasHeader = TRUE,
separator =",")
Sample <- subset(Sample,station_id==i)
Sample <- subset(Sample, select=c(date, remark, value))
write.csv(Sample, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/da
ta/SampleOutputFromNWIS/.nitrogen"))

filesnwis <-
list.files(pattern="/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer
-2012-Work/EGRET/data/SampleOutputFromNWIS/.nitrogen$")

for(l in seq(along=filesnwis)) { 
Sample <- getCustomSampleDataFromFile(filesnwis[l], hasHeader = TRUE,
separator =",")
#getJulian("2000-10-01")
Sample <- subset(Sample,Julian>=55060)
#getJulian("2004-09-30")
Sample <- subset(Sample,Julian<=56520)
Sample<-removeDuplicates(Sample)
summary(Sample)
length(Sample$Date)
}

fileinfoN
<-"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/
data/Info/info_n.csv"
INFO<- getMetaDataFromFile(fileinfoN)

for(g in seq(along=filesnwis)) { 
INFO<- subset(INFO,site.no=="g")
}

filesDV <-
list.files(pattern="/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer
-2012-Work/EGRET/data/DVfromNWIS/DVfromNWIS_pooledforallMRB2sites/.rdb.g
z$")

for(m in seq(along=y)) {
for(k in seq(along=filesDV)) { 
Daily <- getDailyDataFromFileCustom(filesDV[k])
#getJulian("2000-10-01")
Daily <- subset(Daily,Julian>=55060)
#getJulian("2004-09-30")
Daily <- subset(Daily,Julian<=56520)
summary(Daily)
Sample<-mergeReport()
}
}

modelEstimation(localDaily = Daily,localSample = Sample, localINFO =
INFO, windowY=10, windowQ=2, windowS=0.5,minNumObs=10,minNumUncen=10,
env=parent.frame())
INFO<-setPA(window = 4)

annualSeries<-makeAnnualSeries()

AnnualResults<-setupYears()
AnnualResults

tableResults(localAnnualResults = AnnualResults, localINFO = INFO, qUnit
= 1, fluxUnit = 13)
yearPoints<-c(2001,2002,2003,2004)

tableChange(localAnnualResults = AnnualResults, localINFO = INFO,
fluxUnit = 13, yearPoints)
AnnualResults<- setupYears(paLong = 3, paStart = 10, localDaily = Daily)
yield <- AnnualResults$Flux/INFO$drainSqKm
write.table(INFO, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")
write.table(AnnualResults, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")
write.table(yield, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")

AnnualResults<- setupYears(paLong = 3, paStart = 1, localDaily = Daily)
yield <- AnnualResults$Flux/INFO$drainSqKm
write.table(AnnualResults, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")
write.table(yield, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")

AnnualResults<- setupYears(paLong = 3, paStart = 4, localDaily = Daily)
yield <- AnnualResults$Flux/INFO$drainSqKm
write.table(AnnualResults, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")
write.table(yield, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")

AnnualResults<- setupYears(paLong = 3, paStart = 7, localDaily = Daily)
yield <- AnnualResults$Flux/INFO$drainSqKm
write.table(AnnualResults, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")
write.table(yield, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")
}





filesstoretsample <-
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/da
ta/STORET/storetdata_SC/joinedstoretother_wqdata_sc.csv"
Sample <- getSampleDataFromFilecustom(filesstoretsample, hasHeader =
TRUE, separator =",")

for(h in seq(along=x[7:74])) {
for(p in seq(along=y)){
Sample <- subset(Sample,station_id=="h")
Sample <- subset(Sample, select=c(date, remark, value))
write.csv(Sample, file=paste(h,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/da
ta/SampleOutputFromNWIS/.nitrogen"))

filesstoret <-
list.files(pattern="/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer
-2012-Work/EGRET/data/SampleOutputFromNWIS/.nitrogen$")

for(v in seq(along=filesstoret)) { 
Sample <- getCustomSampleDataFromFile(filesstoret[v], hasHeader = TRUE,
separator =",")
#getJulian("2000-10-01")
Sample <- subset(Sample,Julian>=55060)
#getJulian("2004-09-30")
Sample <- subset(Sample,Julian<=56520)
Sample<-removeDuplicates(Sample)
summary(Sample)
length(Sample$Date)
}

fileinfoN
<-"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/
data/Info/info_n.csv"
INFO<- getMetaDataFromFile(fileinfoN)

for(d in seq(along=filesstoret)) { 
INFO<- subset(INFO,site.no=="d")
}

const = INFO$drainSqKm/INFO$drainSqKmFlow

filesDV <-
list.files(pattern="/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer
-2012-Work/EGRET/data/DVfromNWIS/DVfromNWIS_pooledforallMRB2sites/.rdb.g
z$")

for(a in seq(along=y)) {
for(c in seq(along=filesDV)) { 
Daily <- getDailyDataFromFileCustom(filesDV[c])
#getJulian("2000-10-01")
Daily <- subset(Daily,Julian>=55060)
#getJulian("2004-09-30")
Daily <- subset(Daily,Julian<=56520)
DailyModeled <- data.frame(Date=Daily$Date)
DailyModeled$Q <- Daily$Q*INFO$drainSqKmFlow
DailyModeled <- getPreLoadedDailyData(DailyModeled, qUnit =
1,interactive = TRUE)
Daily <- DailyModeled
summary(Daily)
Sample<-mergeReport()
}
}

modelEstimation(localDaily = Daily,localSample = Sample, localINFO =
INFO, windowY=10, windowQ=2, windowS=0.5,minNumObs=10,minNumUncen=10,
env=parent.frame())
INFO<-setPA(window = 4)

annualSeries<-makeAnnualSeries()

AnnualResults<-setupYears()
AnnualResults

tableResults(localAnnualResults = AnnualResults, localINFO = INFO, qUnit
= 1, fluxUnit = 13)
yearPoints<-c(2001,2002,2003,2004)

tableChange(localAnnualResults = AnnualResults, localINFO = INFO,
fluxUnit = 13, yearPoints)
AnnualResults<- setupYears(paLong = 3, paStart = 10, localDaily = Daily)
yield <- AnnualResults$Flux/INFO$drainSqKm
write.table(INFO, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")
write.table(AnnualResults, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")
write.table(yield, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")

AnnualResults<- setupYears(paLong = 3, paStart = 1, localDaily = Daily)
yield <- AnnualResults$Flux/INFO$drainSqKm
write.table(AnnualResults, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")
write.table(yield, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")

AnnualResults<- setupYears(paLong = 3, paStart = 4, localDaily = Daily)
yield <- AnnualResults$Flux/INFO$drainSqKm
write.table(AnnualResults, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")
write.table(yield, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")

AnnualResults<- setupYears(paLong = 3, paStart = 7, localDaily = Daily)
yield <- AnnualResults$Flux/INFO$drainSqKm
write.table(AnnualResults, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")
write.table(yield, file=paste(i ,
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
libration/Calibration_Results/.AnnualResults"), append=T,col.names= NA,
sep = ",")}
}
}


Thank-you.

Irucka Embry

<-----Original Message-----> 
>From: David Winsemius [dwinsem...@comcast.net]
>Sent: 1/14/2013 7:46:52 PM
>To: iruc...@mail2world.com
>Cc: r-help@r-project.org
>Subject: Re: [R] error in for loop in function (object not found)
>
>Nothing attached. Please read the Webpage link and the Posting Guide
more
>thoroughly.
>
>-- 
>David.
>On Jan 14, 2013, at 5:31 PM, Irucka Embry wrote:
>
>> Hi all, I have attached the function file (revisedfunction) and the
list
>> of station IDs (StationIDs) in .pdf format.
>> 
>> I have written a function to perform various operations on the
station
>> IDs in two groups. The first 6 station IDs require one less step than
>> the remaining 68 station IDs. The file referenced at the beginning of
>> the function is the file containing the StationIDs.
>> 
>>> file =
>>
"/home/ie/IE2/Documents/USGS-2012-Work/SPARROW-Summer-2012-Work/EGRET/ca
>> libration/example_setofstationsassociatedtosamegage.csv"
>>> xynowget <- xygetN(file, hasHeader = TRUE, separator =",")
>> Error in is.data.frame(x) : object 'Sample' not found
>> 
>> Can you assist me in fixing the attached function file?
>> 
>> Thank-you.
>> 
>> Irucka Embry
>> 
>snip
>> 
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>David Winsemius
>Alameda, CA, USA
>
>.
> 


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Re: [R] error in for loop in function (object not found)

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