Re: [R] Add column to the output of summary(glht).

[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"  wrote:

>
> 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:
>
> > SumTukey
>
>  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   1.0480.717
> 3 - 1 == 0   0.6554 0.5000   1.3110.551
> 4 - 1 == 0   0.9357 0.4655   2.0100.181
> 3 - 2 == 0   0.1234 0.4174   0.2960.991
> 4 - 2 == 0   0.4037 0.3754   1.0750.700
> 4 - 3 == 0   0.2803 0.3651   0.7680.867
> (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.
> > class(SumTukey)
> [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)
>
> Confidentiality Statement:
> This email message, including any attachments, is for ...{{dropped:16}}

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[R] Add column to the output of summary(glht).

[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:
 
> SumTukey Simultaneous Tests for General Linear HypothesesMultiple Comparisons 
> of Means: Tukey ContrastsFit: 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   1.0480.7173 - 1 == 0   0.6554 0.5000   1.3110.5514 - 
> 1 == 0   0.9357 0.4655   2.0100.1813 - 2 == 0   0.1234 0.4174   
> 0.2960.9914 - 2 == 0   0.4037 0.3754   1.0750.7004 - 3 == 0   
> 0.2803 0.3651   0.7680.867(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. 
> class(SumTukey)[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) 410-605-7119410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing) 





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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) 

Confidentiality Statement:
This email message, including any attachments, is for the sole use of the 
intended recipient(s) and may contain confidential and privileged information. 
Any unauthorized use, disclosure or distribution is prohibited. If you are not 
the intended recipient, please contact the sender by reply email and destroy 
all copies of the original message. 
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Add column to the output of summary(glht).

[Marc Schwartz]

> On Jun 24, 2016, at 8:45 AM, John Sorkin  wrote:
> 
> 
> 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:
> 
>> SumTukey
> 
>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   1.0480.717
> 3 - 1 == 0   0.6554 0.5000   1.3110.551
> 4 - 1 == 0   0.9357 0.4655   2.0100.181
> 3 - 2 == 0   0.1234 0.4174   0.2960.991
> 4 - 2 == 0   0.4037 0.3754   1.0750.700
> 4 - 3 == 0   0.2803 0.3651   0.7680.867
> (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. 
>> class(SumTukey)
> [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


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

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Add column to the output of summary(glht).

[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


> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of John
> Sorkin
> Sent: Friday, June 24, 2016 3:46 PM
> To: r-help@r-project.org
> Subject: [R] Add column to the output of summary(glht).
>
>
> 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:
>
> > SumTukey
>
>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   1.0480.717
> 3 - 1 == 0   0.6554 0.5000   1.3110.551
> 4 - 1 == 0   0.9357 0.4655   2.0100.181
> 3 - 2 == 0   0.1234 0.4174   0.2960.991
> 4 - 2 == 0   0.4037 0.3754   1.0750.700
> 4 - 3 == 0   0.2803 0.3651   0.7680.867
> (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.
> > class(SumTukey)
> [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)
>
> Confidentiality Statement:
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain confidential and privileged
> information. Any unauthorized use, disclosure or distribution is prohibited. 
> If
> you are not the intended recipient, please contact the sender by reply email
> and destroy all copies of the original message.
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.


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[R] Add column to the output of summary(glht).

[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:
 
> SumTukey

 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   1.0480.717
3 - 1 == 0   0.6554 0.5000   1.3110.551
4 - 1 == 0   0.9357 0.4655   2.0100.181
3 - 2 == 0   0.1234 0.4174   0.2960.991
4 - 2 == 0   0.4037 0.3754   1.0750.700
4 - 3 == 0   0.2803 0.3651   0.7680.867
(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. 
> class(SumTukey)
[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) 

Confidentiality Statement:
This email message, including any attachments, is for the sole use of the 
intended recipient(s) and may contain confidential and privileged information. 
Any unauthorized use, disclosure or distribution is prohibited. If you are not 
the intended recipient, please contact the sender by reply email and destroy 
all copies of the original message. 
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.