[R] Accessing Results from cenmle function in NADA package

[David Winsemius]

On Nov 12, 2008, at 8:48 AM, Tom La Bone wrote:

>
> I figured it out. In case anyone else ever has this question --  
> given the
> following output from cenmle:
>
>> fit.cen <- cenmle(obs, censored, groups)
>> fit.cen
>               Value Std. Error        z         p
> (Intercept)  1.19473     0.0772  15.4695  5.58e-54
> groups1      0.00208     0.0789   0.0263  9.79e-01
> Log(scale)  -0.40221     0.0168 -23.9034 2.82e-126
>
> Scale= 0.669
>
> Log Normal distribution
> Loglik(model)= -3908.9   Loglik(intercept only)= -3908.9
> Loglik-r:  0.0006265534
>
> Chisq= 0 on 1 degrees of freedom, p= 0.98
> Number of Newton-Raphson Iterations: 1
> n = 1766
>
> The p-value is (for example):
>
> p.value <- summary(fit.cen)[[9]][[11]]

An approach that may yield somewhat more self-documenting code would  
be to examine either the fit object or the summary object with str and  
then to access results by extracting named elements. Since I don't  
have the package in question, let me use the lm object on its help  
page as an example:

  ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
  trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
  group <- gl(2,10,20, labels=c("Ctl","Trt"))
  weight <- c(ctl, trt)
  lm.D9 <- lm(weight ~ group)

  str(lm.D9)
  str(summary(lm.D9))
  summary(lm.D9)$coefficients
  summary(lm.D9)$coefficients["groupTrt", "Pr(>|t|)"]

# to get the p-value
 > summary(lm.D9)$coefficients["groupTrt","Pr(>|t|)"]
[1] 0.2490232

You had originally asked for a method to extract coefficients and for  
that purpose you may want to look at:

?coefficients

 > slope <- coefficients(lm.D9)["groupTrt"]
 > slope
groupTrt
   -0.371

-- 
David Winsemius
Heritage Labs

>
> Tom
>
>
>
>
> Tom La Bone wrote:
>>
>> The cenmle function is used to fit two sets of censored data and  
>> test if
>> they are significantly different. I can print out the results of the
>> analysis on the screen but can't seem to figure out how to access  
>> these
>> results in R and assign them to new variables, e.g., assign the slope
>> calculated with cenmle to the variable m. Any suggestions?
>>
>> Tom
>>
>
> -- 
> View this message in context: http://www.nabble.com/Accessing-Results-from-cenmle-function-in-NADA-package-tp20437420p20460676.html
> Sent from the R help mailing list archive at Nabble.com.
>
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