R help - Jan 2014 - unable to carry through object in a nested function

Hi There,
I am having trouble carrying through an object listed in the outer function into
the inner function of a nested pair.
This is my code:

FindGreaterThanProportion<- function (y, SSThreshold) {
    DenomCells<-length(y)
    NumerCells<-subset(y,y>SSThreshold)
    PropCells<-length(NumerCells)/DenomCells
    return (PropCells)
    }


GetPropPlot<- function (PrePropData, direction, SSThreshold, cell, stim) {
    # Split up the dataframe with ddply and apply the function
    print(direction)
    print (SSThreshold)

    if (direction==">") {
        PropData<-ddply(PrePropData,.(SUBJECT, STIM, CELL, SIGNAL, DAY),
summarise,
            PROP=FindGreaterThanProportion(SIMSCORE, SSThreshold))
        }

    PlotSubset <- subset(PropData, PropData$STIM==stim & PropData$CELL ==
cell)
    PropPlot<-ggplot(data=PlotSubset, aes(x=DAY, y=PROP)) +
        geom_line() +
        geom_point() +
        facet_grid(SIGNAL~SUBJECT)
    return(FinalPropPlot)
    }

When I run the code, I get this error:
[1] ">"
[1] 2
Error in subset.default(y, y > SSThreshold) :
  object 'SSThreshold' not found

It seems as if SSThreshold is not being passed into FindGreaterThanProportion.

Any help would be appreciated to determine what I am doing incorrectly.
Thanks in advance.

George Chen



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Hi,
This is a resend of a previous message reproduced below but with sample data to
run.
Thanks.
George Chen



Hi There,
I am having trouble carrying through an object listed in the outer function into
the inner function of a nested pair.

--------sample data below ---------
library(plyr)

SUBJECT<-c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1)
STIM<-c("No","No","No","No","No","No","No","No","No","No","No","No","No","No","No","No","No","No","No","No")
CELL<-c("CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4")
SIGNAL<-c("ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC")
DAY<-c(7,7,7,7,7,7,7,7,7,7,1,1,1,1,1,1,1,1,1,1)
SIMSCORE<-c(2,3,4,5,2,3,4,5,2,3,4,5,2,3,4,5,2,3,4,5)
PrePropData<-data.frame(SUBJECT, STIM, CELL, SIGNAL, DAY, SIMSCORE)
________________________________


This is my code:

FindGreaterThanProportion<- function (y, SSThreshold) {
    DenomCells<-length(y)
    NumerCells<-subset(y,y>SSThreshold)
    PropCells<-length(NumerCells)/DenomCells
    return (PropCells)
    }


GetPropPlot<- function (PrePropData, direction, SSThreshold, cell, stim) {
    # Split up the dataframe with ddply and apply the function
    print(direction)
    print (SSThreshold)

    if (direction==">") {
        PropData<-ddply(PrePropData,.(SUBJECT, STIM, CELL, SIGNAL, DAY),
summarise,
            PROP=FindGreaterThanProportion(SIMSCORE, SSThreshold))
        }

    PlotSubset <- subset(PropData, PropData$STIM==stim & PropData$CELL ==
cell)
    PropPlot<-ggplot(data=PlotSubset, aes(x=DAY, y=PROP)) +
        geom_line() +
        geom_point() +
        facet_grid(SIGNAL~SUBJECT)
    return(FinalPropPlot)
    }

GetPropPlot(PrePropData, direction=">", SSThreshold=3,
"CD4", "No")

When I run the code, I get this error:
[1] ">"
[1] 3
Error in subset.default(y, y > SSThreshold) :
  object 'SSThreshold' not found

It seems as if SSThreshold is not being passed into FindGreaterThanProportion.

Any help would be appreciated to determine what I am doing incorrectly.
Thanks in advance.

George Chen



This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee or agent
responsible for the delivery of this message to the intended recipient(s), you
are hereby notified that any disclosure, copying, distribution, or use of this
email message is prohibited.  If you have received this message in error, please
notify the sender immediately by e-mail and delete this email message from your
computer. Thank you.