Different NA actions for coefficients and summary of linear model in R

Question

In R, when using `lm()`, if I set `na.action = na.pass` inside the call to `lm()`, then in the summary table there is an NA for any coefficient that cannot be estimated (because of missing cells in this case). If, however, I extract just the coefficients from the summary object, using either `summary(myModel)$coefficients` or `coef(summary(myModel))`, then the NA's are omitted. I want the NA's to be included when I extract the coefficients the same way that they are included when I print the summary. Is there a way to do this? Setting `options(na.action = na.pass)` does not seem to help. Here is an example: ``` > set.seed(534) > myGroup1 <- factor(c("a","a","a","a","b","b")) > myGroup2 <- factor(c("first","second","first","second","first","first")) > myDepVar <- rnorm(6, 0, 1) > myModel <- lm(myDepVar ~ myGroup1 + myGroup2 + myGroup1:myGroup2) > summary(myModel) Call: lm(formula = myDepVar ~ myGroup1 + myGroup2 + myGroup1:myGroup2) Residuals: 1 2 3 4 5 6 -0.05813 0.55323 0.05813 -0.55…

Accepted Answer

Why don't you just extract the coefficients from the fitted model:

```
> coef(myModel)
             (Intercept)                myGroup1b 
             -0.48496169              -0.07853547 
          myGroup2second myGroup1b:myGroup2second 
              0.74546233                       NA
```

That seems the easiest option.

`na.action` has nothing to do with this. Note that you didn't pass `na.action = na.pass` in your example.

`na.action` is a global option for handling `NA` in the data passed to a model fit, usually in conjunction with a formula; it is also the name of a function `na.action()`. R builds up the so called model frame from the `data` argument and the symbolic representation of the model expressed in the formula. At this point, any `NA` would be detected and the default option for `na.action` is to use `na.omit()` to remove the `NA` from the data by dropping samples with `NA` for any variable. There are alternatives, most usefully `na.exclude()`, which would remove `NA` during fitting but add back `NA` in the correct places in the fitted values, residuals etc. Read `?na.omit` and `?na.action` for more, plus `?options` for more on this.

Different NA actions for coefficients and summary of linear model in R

Solution

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