[R] summary.formula: method reverse does not use fun argument

[Frank E Harrell Jr]

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