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Add column to the output of summary(glht).

4 messages · John Sorkin, PIKAL Petr, Marc Schwartz +1 more

John Sorkin
# 
I am trying to make the leap from an R users to an R aficionado . . .
 
I am trying to understand how add a column to the output of summary (and to understand how summary() works).
 
I have run a glmer
fit0 <- glmer(Fall ~ Group+(1|PID),family=poisson(link="log"),data=data[data[,"Group"]!=0,])
 
and I want to perform adjusted multiple comparisons:
 
SumTukey <- summary(glht(fit0, linfct= mcp(Group="Tukey")))
 
which gives beautiful output:
Simultaneous Tests for General Linear Hypotheses

Multiple Comparisons of Means: Tukey Contrasts


Fit: glmer(formula = Fall ~ Group + (1 | PID), data = data[data[, 
    "Group"] != 0, ], family = poisson(link = "log"))

Linear Hypotheses:
           Estimate Std. Error z value Pr(>|z|)
2 - 1 == 0   0.5320     0.5075   1.048    0.717
3 - 1 == 0   0.6554     0.5000   1.311    0.551
4 - 1 == 0   0.9357     0.4655   2.010    0.181
3 - 2 == 0   0.1234     0.4174   0.296    0.991
4 - 2 == 0   0.4037     0.3754   1.075    0.700
4 - 3 == 0   0.2803     0.3651   0.768    0.867
(Adjusted p values reported -- single-step method)
 
I want to add a column to the output (unadjusted p-values), but I don't see how this might be done. The output
is not a dataframe, nor is it a matix.
[1] "summary.glht" "glht"  

It is some class of objects that I don't understand and know nothing
about. How can I add a column to the output of SumTukey [a.k.a. summary(glht(fit0, linfct= mcp(Group="Tukey")))] ?
 
Thank you
John
 
 
John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and Geriatric Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing) 

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PIKAL Petr
# 
Hi

you can check structure of any object by str so

str(fit0)

should give you an insight how fit0 is structured and

str(SumTukey)

gives you structure of SumTukey object (which is probably list). You can manipulate with the output as you wish according to the rules of R.

Cheers
Petr
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Marc Schwartz
# 
Hi John,

Two things that can be helpful are to review the structure of the object returned by summary.glht(), which in your code above would be (see ?str):

 str(SumTukey)

and also review the print method for the object that actually generates the console output. In this case, using:

  multcomp:::print.summary.glht

or 

 getAnywhere(print.summary.glht)

will reveal the code that is used to generate the output that you see above. The print method is not exported from the package's namespace. 

You can review the print method code to see which components of 'SumTukey' are then used to create the output and what internal functions are used to do that.

Once you understand the structure of the object and how that object's content is formatted and output for display by the associated print method for the object class, you can modify things to fit your need by creating, if need be, your own functions to modify the required part or parts of the object itself and then output them.

If you want to understand what summary.glht() is doing, take the same approach as above for the print method, since it is not exported either:

  multcomp:::summary.glht

or 

  getAnywhere(summary.glht)


Regards,

Marc Schwartz
Ista Zahn
# 
This won't make you an R aficionado, but depending on your needs

library(broom)
tidy(SumTukey)

might be useful. This converts the output to a familiar data.frame, making
it much easier to work with.

Best,
Ista
On Jun 24, 2016 9:48 AM, "John Sorkin" <JSorkin at grecc.umaryland.edu> wrote: