R help - Jan 2012 - Create subset using variable

I am trying to create a loop that will perform a series of analyses.  I am
using geeglm from geepack, which fails if there are any null values. 
Creating a subset solves this, but do not seem to be able to set the subset
dynamically based on a changing variable.  

while (j <= y.num) {

     strSubset = as.character(df.IV$IV[j])  #Gives column name in quotes
     df.data.sub = subset(df.data, strSubset>=0)

#subset dataset is not created

 # analyses on subset take place

    j = j + 1
 }

If I type the variable name in the formula it works, so I assume that I am
not creating the variable in a manner that allows it to be evaluated in the
subset function.  Any help would be greatly appreciated!

Michael 

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On Jan 21, 2012, at 3:18 PM, pansophy wrote:
> I am trying to create a loop that will perform a series of  
> analyses.  I am
> using geeglm from geepack, which fails if there are any null values.
> Creating a subset solves this, but do not seem to be able to set the  
> subset
> dynamically based on a changing variable.
This is an exercise in guesswork since you have not provided the data  
structures that you are accessing.
>
> while (j <= y.num) {
If you want to avoid NULL values in sequences you can use
seq_along()
>
>     strSubset = as.character(df.IV$IV[j])  #Gives column name in  
> quotes
Is there really a dataframe named 'df.IV' or are you perhaps an  
expatriate from another programming locale where the "." is an  
accessor operator?
>     df.data.sub = subset(df.data, strSubset>=0)
>
> #subset dataset is not created
`subset` uses nonstandard evaluation. It's very handy for interactive  
work but for programming you cannot use it in the manner you imagine.  
Try instead:

df.data.sub =df.data[ df[["IV"]] >= 0 )

Or perhaps:

df.data.sub =df.data[ df[[strSubset]] >= 0 )

Although I'm not sure what `strSubset` will evaluate to in your  
situation.

>
> # analyses on subset take place
>
>    j = j + 1
> }
>
> If I type the variable name in the formula it works, so I assume  
> that I am
> not creating the variable in a manner that allows it to be evaluated  
> in the
> subset function.
That much is certain.

-- 

David Winsemius, MD
West Hartford, CT

pansophy <mjs2134 <at> columbia.edu> writes:
> 
> I am trying to create a loop that will perform a series of analyses.  I am
> using geeglm from geepack, which fails if there are any null values. 
> Creating a subset solves this, but do not seem to be able to set the subset
> dynamically based on a changing variable.  
> 
> while (j <= y.num) {
> 
>      strSubset = as.character(df.IV$IV[j])  #Gives column name in quotes
>      df.data.sub = subset(df.data, strSubset>=0)
> 
> #subset dataset is not created
> 
>  # analyses on subset take place
> 
>     j = j + 1
>  }
> 
> If I type the variable name in the formula it works, so I assume that I am
> not creating the variable in a manner that allows it to be evaluated in the
> subset function.  Any help would be greatly appreciated!
> 
> Michael 
> 
> --
> View this message in context:
http://r.789695.n4.nabble.com/Create-subset-using-variable-tp4316812p4316812.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> 
I think you want to try and use the double bracket with your df to access the
column of interest in your data frame.  To remove null values, you could use the
na.omit() function, assuming when you say null values are represented as NAs:

while (j <= y.num) {
 
      strSubset = as.character(df.IV$IV[j])  #Gives column name in quotes
      df.data.sub = df.data[[strSubset]]
      df.data.sub = na.omit(df.data.sub) # if null values are given as NA
      df.data.sub = df.data.sub[df.data.sub >= 0] # if null values are < 0

 #subset dataset is not created
 
  # analyses on subset take place
 
     j = j + 1
  }

Hope that helps,
Ken

For example:

# dataset
age<-18:29
height<-58:69
df.ex=data.frame(age=age,height=height)
df.ex[4,1]<-NA

# dataset of columns that will be used for analysis
values<-c("age", "height")
df.variables=data.frame(values)

 # Age column has a null (NA) value.  The row must be removed for the
analysis to run
 # explicit creation  
df.ex.sub.explicit<-subset(df.ex, age >= 0)
dim(df.ex.sub.explicit) #11 obs of 2 variables

i=1
strFilter=as.character(df.variables$values[i])
df.ex.sub.passvar<-subset(df.ex,strFilter>=0)
dim(df.ex.sub.explicit) #12 obs of 2 variables


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pansophy <mjs2134 <at> columbia.edu> writes:
> 
> I am trying to create a loop that will perform a series of analyses.  I am
> using geeglm from geepack, which fails if there are any null values. 
> Creating a subset solves this, but do not seem to be able to set the subset
> dynamically based on a changing variable.  
> 
> while (j <= y.num) {
> 
>      strSubset = as.character(df.IV$IV[j])  #Gives column name in quotes
>      df.data.sub = subset(df.data, strSubset>=0)
> 
> #subset dataset is not created
> 
>  # analyses on subset take place
> 
>     j = j + 1
>  }
> 
  
  I've answered this on Stack Overflow. While I don't think there
is any formal policy against cross-posting, I (and at least a few
other participants in both lists) deprecate cross-posting because
it leads to redundant effort.

  Ben Bolker