[R] problem with 'svyby' function from SURVEY package
Thomas Lumley
tlumley at u.washington.edu
Thu Jun 3 18:05:26 CEST 2010
On Thu, 3 Jun 2010, Roni Kobrosly wrote:
> Hello,
>
> I'm using a complex survey dataset and my goal is to simply spit out a bunch of probability-weighted outcome variable means for the different levels of covariate. So I first define the structure of the study design (I'm using the CDC's NHANES data):
>
> dhanes <- svydesign(id=~PSU, strat=~STRATA, weight=~lab_weight, data=final, nest=TRUE)
>
> No problem there.
> Now I use the "svyby" function as follows:
>
> svyby(~outcome, ~covariate, design=dhanes, svymean, na.rm=T) -> haha
> print(haha)
>
> covariate outcome se.outcome
> 1 1 0.4961189 0.08828457
> 2 2 0.4474706 0.22214557
> 3 3 0.5157026 0.12076008
> 4 4 0.6773910 0.20605025
> NA NA 0.8728167 0.15622274
>
> ...and it works just fine. I get a nice table of the mean and standard error for each level of the covariate. I started writing a custom function to automate this and I had problems. Consider this really basic custom function (that does not seem very different from the above code):
>
> this_is_a_test <-function(outcome, covariate)
> {
>
> svyby(~outcome, ~covariate, design=dhanes, svymean, na.rm=T) -> haha
>
> print(hah)
>
>
> }
>
You are asking for the mean of a variable called 'outcome', divided up according to a variable called 'covariate'. Presumably you don't have variables with either of those names, so R is getting confused.
Formulas don't work the way you want them to. As a simpler example with nothing to do with the survey package
this_is_a_simpler_example<-function(outcome){
~outcome
}
> this_is_a_simpler_example(test)
~outcome
If you want to substitute a variable into a formula, you need to do it yourself. In your case, you probably want to use make.formula(), from the survey package
> make.formula("test")
~test
> make.formula(c("fred","barney","wilma"))
~fred + barney + wilma
Presumably you want to do something like
approach_that_works <-function(outcome, covariate, design=dhanes,...) svyby(make.formula(outcome), make.formula(covariate), design,...)
some_outcomes <- colnames(dhanes)[47:63]
some_covariates <- colnames(dhanes)[83:95]
lapply( some_outcomes,
function(an_outcome) lapply(some_covariates, approach_that_works, outcome=an_outcome)
)
For another recent thread using another approach to a related question, see http://tolstoy.newcastle.edu.au/R/e10/help/10/05/5676.html
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlumley at u.washington.edu University of Washington, Seattle
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