[R] extracting information from an object

[Erik Iverson]

David,

> I was working on a project involving a linear model, and wanted to 
> extract the standard error of a predictor. I am able to do so, but not 
> in the way I would expect.
> 
> I would have expected that if a created a model such as Model1 <- 
> lm(y~x,z,d), the object Model1 would contain that information even 
> though it does not print it out when I simply type Model1. 

You can always see what information objects contain by using the ?str
function on them.

In this instance, str(Model1) will show the components of the Model1
object.


> I would also 
> have (wrongly) suspected that if I type summary(Model1) R would simply 
> look at the object Model1 and find whatever it needs. But it doesn't 
> work that way. 

Correct.  You can always see what a function does by printing its
definition at the R prompt.  In this case, typing summary.lm will
show you what the summary function does when passed an 'lm' object.


> If I want that standard error I have to first create a 
> summary of Model1 and then extract the standard error from the summary 
> with something like summary(Model1)$coefficients or, more specifically, 
> summary(Model)$coefficients[2,2]. 

Use the ?coef function for this purpose, which works with most modelling
functions, including 'lm'.

> [I know that I can cram all of that 
> into one line if I want to.] But doesn't that mean that when I ask for a 
> summary R has to recreate the linear model all over again before pulling 
> out the standard error. (Venables and Ripley, p. 77) 

Which book? I don't think MASS 4th edition.


suggest that this
> could happen if the method is not written correctly, but how is it not 
> happening anyway?) 

The Model1 object contains the necessary components to calculate the
quantity.  Look at how it's done in summary.lm.

> And if so, if Model1 doesn't contain the raw data, 
> how does summary produce an answer even if I delete one of the variables 
> before calling it?
> 

By default, an 'lm' object will contain the model.matrix.  See the ?lm 
value section for other components.

In general, it would be bad practice to have a function like summary.lm
depend not only on a supplied argument, but on some other object that it
is not a function of being present in the workspace.

> As you can see, I have figured out how to get what I want, but I don't 
> understand the process of building objects, which is the important thing 
> to understand. Perhaps I don't understand "methods" well enough.

I think a combination of the ?str function, looking at the actual lm and 
summary.lm functions, and a careful reading of the help pages will help.

> 
> Below is sample code:
> 
> #Sample for linear model
> 
> x <- c(3,7,9,15,18)
> y <- c(5,4,8,6,9)
> reg <- lm(y~x)
> reg
> #Produces only the regression coefficients and using str(reg) indicates 
> that
> # that is all that it has.
> regsummary <- summary(reg)
> #Produces what I need and str(regsummary) shows that st. errors are part 
> of the object.
> regsummary$coefficients[1:2, 1:4]
> 
> rm(y)
> out <- summary(reg)
> # works just fine although y is no longer available and reg doesn't look 
> like it
> # could supply it.

reg$model
reg$qr