[R] by() function doesn't work inside another function

From: Russell Ivory <Russell.Ivory_at_merrickbank.com>
Date: Thu, 10 Jul 2008 10:21:47 -0600

I have a longitudinal data set in long format and I want to run individual regressions. I do this by using the by() function as follows:  

temp <- by(tolerance.pp, tolerance.pp$id, function(x) summary(lm(tolerance ~ time, data=x)))  

This works fine. Coefficients for the first two subjects are shown below.  


            Estimate Std. Error t value Pr(>|t|)

(Intercept) 1.9020 0.2519 7.549 0.00482 **

time 0.1190 0.1029 1.157 0.33105  


            Estimate Std. Error t value Pr(>|t|)

(Intercept) 1.14400 0.13336 8.578 0.00333 **

time 0.17400 0.05444 3.196 0.04948 *    

Each subject has five rows of data, measured at periods 0,1,2,3,4. There are 16 subjects so 80 total rows and the output is 16 regression models.  

However, if I put this inside another function, the by() function no longer generates regressions by subject id. It does generate 16 models; but each model is identical which is a regression using all 80 rows at once. The function and coefficients for the first two models are shown below.    

test <- function(X,x,y,id)


temp <- by(X, id, function(z) summary(lm(y~x,data=z)))




test(tolerance.pp, time, tolerance, id)



            Estimate Std. Error t value Pr(>|t|)

(Intercept) 1.35775 0.08952 15.167 < 2e-16 ***

x 0.13081 0.03655 3.579 0.000596 ***  


            Estimate Std. Error t value Pr(>|t|)

(Intercept) 1.35775 0.08952 15.167 < 2e-16 ***

x 0.13081 0.03655 3.579 0.000596 ***    

Without attaching the data I've even tried  

test(tolerance.pp, tolerance.pp$time, tolerance.pp$tolerance, tolerance.pp$id)  

but get the same results. Any thoughts are greatly appreciated.    

Russell Ivory

Merrick Bank

South Jordan, UT

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