R help - Apr 2003 - summary.formula: method reverse does not use fun argument

hi,

recently i discovered the functionability summary.formula, awesome!
from the help page i understand that method=reverse allows to
summarize all variables on the right hand side of formula 
(the help page on line 229 wrongly refers to the left? hand side variables)
in categories which are determined by a single left hand side
variable.

my problem is that the argument fun seems not to be compatible with
method=reverse!? every continuous variable is summarized in three
quantiles.

here is an example:

hist is a factor, PET and CT are "numeric" 

summary(PET~hist,data=her,fun=sum)
PET    N=47

+-------+------------------+--+---+
|       |                  |N |PET|
+-------+------------------+--+---+
|hist   |Morbus Hodgkin    |18| 81|
|       |Niedrigmaligne NHL|11| 39|
|       |Hochmaligne NHL   |18| 49|
+-------+------------------+--+---+
|Overall|                  |47|169|
+-------+------------------+--+---+
> summary(CT~hist,data=her,fun=sum)
CT    N=47

+-------+------------------+--+---+
|       |                  |N |CT |
+-------+------------------+--+---+
|hist   |Morbus Hodgkin    |18| 70|
|       |Niedrigmaligne NHL|11| 16|
|       |Hochmaligne NHL   |18| 32|
+-------+------------------+--+---+
|Overall|                  |47|118|
+-------+------------------+--+---+

it would be desirable to combine both tables such that there is one
column for PET and one for CT ... is this possible?

trying method=reverse gives:

summary(hist~PET+CT,data=her,fun=sum,method="reverse") 

Descriptive Statistics by hist

+------+---------------+-------------------+----------------+
|      |Morbus Hodgkin |Niedrigmaligne NHL |Hochmaligne NHL |
|      |(N=18)         |(N=11)             |(N=18)          |
+------+---------------+-------------------+----------------+
|PET   |3.00/3.50/6.75 |1.50/3.00/6.00     |1.00/2.00/3.75  |
+------+---------------+-------------------+----------------+
|CT : 0|     0% (0)    |    36% (4)        |    28% (5)     |
+------+---------------+-------------------+----------------+
|    1 |    11% (2)    |     9% (1)        |    28% (5)     |
+------+---------------+-------------------+----------------+
|    2 |    28% (5)    |    36% (4)        |    11% (2)     |
+------+---------------+-------------------+----------------+
|    3 |    17% (3)    |     9% (1)        |    11% (2)     |
+------+---------------+-------------------+----------------+
|    4 |    11% (2)    |     9% (1)        |    17% (3)     |
+------+---------------+-------------------+----------------+
|    5 |     6% (1)    |     0% (0)        |     6% (1)     |
+------+---------------+-------------------+----------------+
|    6 |     6% (1)    |     0% (0)        |     0% (0)     |
+------+---------------+-------------------+----------------+
|    7 |    11% (2)    |     0% (0)        |     0% (0)     |
+------+---------------+-------------------+----------------+
|    8 |    11% (2)    |     0% (0)        |     0% (0)     |
+------+---------------+-------------------+----------------+

thanks a lot in advance,
tomy

-- 
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On Fri, 11 Apr 2003 10:25:41 +0200
Thomas Gerds <gerds at fdm.uni-freiburg.de> wrote:
> hi,
> 
> recently i discovered the functionability summary.formula, awesome!
> from the help page i understand that method=reverse allows to
> summarize all variables on the right hand side of formula 
> (the help page on line 229 wrongly refers to the left? hand side variables)
> in categories which are determined by a single left hand side
> variable.
Sorry about the typo.  You are correct, that should have been "right hand
side variables".
> 
> my problem is that the argument fun seems not to be compatible with
> method=reverse!? every continuous variable is summarized in three
> quantiles.
As stated in the documentation, fun applies only to method='response'
and method='cross'.
> 
> here is an example:
> 
> hist is a factor, PET and CT are "numeric" 
> 
> summary(PET~hist,data=her,fun=sum)
> PET    N=47
> 
> +-------+------------------+--+---+
> |       |                  |N |PET|
> +-------+------------------+--+---+
> |hist   |Morbus Hodgkin    |18| 81|
> |       |Niedrigmaligne NHL|11| 39|
> |       |Hochmaligne NHL   |18| 49|
> +-------+------------------+--+---+
> |Overall|                  |47|169|
> +-------+------------------+--+---+
> 
> > summary(CT~hist,data=her,fun=sum)
> CT    N=47
> 
> +-------+------------------+--+---+
> |       |                  |N |CT |
> +-------+------------------+--+---+
> |hist   |Morbus Hodgkin    |18| 70|
> |       |Niedrigmaligne NHL|11| 16|
> |       |Hochmaligne NHL   |18| 32|
> +-------+------------------+--+---+
> |Overall|                  |47|118|
> +-------+------------------+--+---+
> 
> it would be desirable to combine both tables such that there is one
> column for PET and one for CT ... is this possible?
Yes, see the documentation.  Create a bivariate response variable with cbind and
use a bivariate summarization function as 'fun'.  And note that using
'stratify(someothervariable)' you can create multiple groups across
columns as with method='reverse'; you just can't get statistical
tests for them with method='response'.

Frank Harrell
> 
> trying method=reverse gives:
> 
> summary(hist~PET+CT,data=her,fun=sum,method="reverse") 
> 
> Descriptive Statistics by hist
> 
> +------+---------------+-------------------+----------------+
> |      |Morbus Hodgkin |Niedrigmaligne NHL |Hochmaligne NHL |
> |      |(N=18)         |(N=11)             |(N=18)          |
> +------+---------------+-------------------+----------------+
> |PET   |3.00/3.50/6.75 |1.50/3.00/6.00     |1.00/2.00/3.75  |
> +------+---------------+-------------------+----------------+
> |CT : 0|     0% (0)    |    36% (4)        |    28% (5)     |
> +------+---------------+-------------------+----------------+
> |    1 |    11% (2)    |     9% (1)        |    28% (5)     |
> +------+---------------+-------------------+----------------+
> |    2 |    28% (5)    |    36% (4)        |    11% (2)     |
> +------+---------------+-------------------+----------------+
> |    3 |    17% (3)    |     9% (1)        |    11% (2)     |
> +------+---------------+-------------------+----------------+
> |    4 |    11% (2)    |     9% (1)        |    17% (3)     |
> +------+---------------+-------------------+----------------+
> |    5 |     6% (1)    |     0% (0)        |     6% (1)     |
> +------+---------------+-------------------+----------------+
> |    6 |     6% (1)    |     0% (0)        |     0% (0)     |
> +------+---------------+-------------------+----------------+
> |    7 |    11% (2)    |     0% (0)        |     0% (0)     |
> +------+---------------+-------------------+----------------+
> |    8 |    11% (2)    |     0% (0)        |     0% (0)     |
> +------+---------------+-------------------+----------------+
> 
> thanks a lot in advance,
> tomy
-- 
Frank E Harrell Jr              Prof. of Biostatistics & Statistics
Div. of Biostatistics & Epidem. Dept. of Health Evaluation Sciences
U. Virginia School of Medicine  http://hesweb1.med.virginia.edu/biostat

On Fri, 11 Apr 2003, Thomas Gerds wrote:
> hi,
>
> recently i discovered the functionability summary.formula, awesome!
It would be useful to say *where* you discovered it -- it is in a package
that isn't yet on CRAN.

> from the help page i understand that method=reverse allows to
> summarize all variables on the right hand side of formula
> (the help page on line 229 wrongly refers to the left? hand side variables)
> in categories which are determined by a single left hand side
> variable.
>
> my problem is that the argument fun seems not to be compatible with
> method=reverse!? every continuous variable is summarized in three
> quantiles.
Yes, that's what the help page says.

It also says that for the default method="response" the response
variable
can be multivariate, which seems to be what you want.  It says many other
helpful things, too.


	-thomas

Thanks also to Thomas Lumley for his reply concerning summary.formula in the
Hmisc package.  See below for some more notes.  -FH

On Fri, 11 Apr 2003 10:25:41 +0200
Thomas Gerds <gerds at fdm.uni-freiburg.de> wrote:
> hi,
> 
> recently i discovered the functionability summary.formula, awesome!
> from the help page i understand that method=reverse allows to
> summarize all variables on the right hand side of formula 
> (the help page on line 229 wrongly refers to the left? hand side variables)
> in categories which are determined by a single left hand side
> variable.
Sorry about the typo.  You are correct, that should have been "right hand
side variables".
> 
> my problem is that the argument fun seems not to be compatible with
> method=reverse!? every continuous variable is summarized in three
> quantiles.
As stated in the documentation, fun applies only to method='response'
and method='cross'.
> 
> here is an example:
> 
> hist is a factor, PET and CT are "numeric" 
> 
> summary(PET~hist,data=her,fun=sum)
> PET    N=47
> 
> +-------+------------------+--+---+
> |       |                  |N |PET|
> +-------+------------------+--+---+
> |hist   |Morbus Hodgkin    |18| 81|
> |       |Niedrigmaligne NHL|11| 39|
> |       |Hochmaligne NHL   |18| 49|
> +-------+------------------+--+---+
> |Overall|                  |47|169|
> +-------+------------------+--+---+
> 
> > summary(CT~hist,data=her,fun=sum)
> CT    N=47
> 
> +-------+------------------+--+---+
> |       |                  |N |CT |
> +-------+------------------+--+---+
> |hist   |Morbus Hodgkin    |18| 70|
> |       |Niedrigmaligne NHL|11| 16|
> |       |Hochmaligne NHL   |18| 32|
> +-------+------------------+--+---+
> |Overall|                  |47|118|
> +-------+------------------+--+---+
> 
> it would be desirable to combine both tables such that there is one
> column for PET and one for CT ... is this possible?
Yes, see the documentation.  Create a bivariate response variable with cbind and
use a bivariate summarization function as 'fun'.  And note that using
'stratify(someothervariable)' you can create multiple groups across
columns as with method='reverse'; you just can't get statistical
tests for them with method='response'.

Frank Harrell
> 
> trying method=reverse gives:
> 
> summary(hist~PET+CT,data=her,fun=sum,method="reverse") 
> 
> Descriptive Statistics by hist
> 
> +------+---------------+-------------------+----------------+
> |      |Morbus Hodgkin |Niedrigmaligne NHL |Hochmaligne NHL |
> |      |(N=18)         |(N=11)             |(N=18)          |
> +------+---------------+-------------------+----------------+
> |PET   |3.00/3.50/6.75 |1.50/3.00/6.00     |1.00/2.00/3.75  |
> +------+---------------+-------------------+----------------+
> |CT : 0|     0% (0)    |    36% (4)        |    28% (5)     |
> +------+---------------+-------------------+----------------+
> |    1 |    11% (2)    |     9% (1)        |    28% (5)     |
> +------+---------------+-------------------+----------------+
> |    2 |    28% (5)    |    36% (4)        |    11% (2)     |
> +------+---------------+-------------------+----------------+
> |    3 |    17% (3)    |     9% (1)        |    11% (2)     |
> +------+---------------+-------------------+----------------+
> |    4 |    11% (2)    |     9% (1)        |    17% (3)     |
> +------+---------------+-------------------+----------------+
> |    5 |     6% (1)    |     0% (0)        |     6% (1)     |
> +------+---------------+-------------------+----------------+
> |    6 |     6% (1)    |     0% (0)        |     0% (0)     |
> +------+---------------+-------------------+----------------+
> |    7 |    11% (2)    |     0% (0)        |     0% (0)     |
> +------+---------------+-------------------+----------------+
> |    8 |    11% (2)    |     0% (0)        |     0% (0)     |
> +------+---------------+-------------------+----------------+
> 
> thanks a lot in advance,
> tomy
---
Frank E Harrell Jr              Prof. of Biostatistics & Statistics
Div. of Biostatistics & Epidem. Dept. of Health Evaluation Sciences
U. Virginia School of Medicine  http://hesweb1.med.virginia.edu/biostat