[R] Summary.Formula: prmsd and test statistic

[Eli Kamara]

I tried the modification but no luck. Here is exactly what I'm seeing.
The command works fine, but when I add prmsd=TRUE the numbers
disappear.

> print(summary.formula(S~Kyph+Vert, data=radio, method="reverse", overall=T, continuous=5, add=TRUE, test=T))


Descriptive Statistics by S

+----+---+--------------------------+------------------------+------------------------+------------------------+-------------------------+
|    |N  |Guru Teg Bahadur Hospital |St. Stephens Hospital   |VIMHANS
Hospital        |Combined                |  Test                   |
|    |   |(N=37)                    |(N=1)                   |(N=75)
               |(N=113)                 |Statistic                |
+----+---+--------------------------+------------------------+------------------------+------------------------+-------------------------+
|Kyph|109| 13.6625/20.7100/29.1325  | 11.6400/11.6400/11.6400|
0.0000/ 9.6200/17.1650|  2.1600/12.0100/21.1900|F=9.23 d.f.=2,106
P<0.001|
+----+---+--------------------------+------------------------+------------------------+------------------------+-------------------------+
|Vert|113|          2/3/3           |          2/2/2         |
 2/2/3         |          2/2/3         |F=2.65 d.f.=2,110 P=0.075|
+----+---+--------------------------+------------------------+------------------------+------------------------+-------------------------+
> print(summary.formula(S~Kyph+Vert, data=radio, method="reverse", overall=T, continuous=5, add=TRUE, test=T), prmsd=TRUE)


Descriptive Statistics by S

+----+---+--------------------------+----------------------+-----------------+-------------+-------------------------+
|    |N  |Guru Teg Bahadur Hospital |St. Stephens Hospital |VIMHANS
Hospital |Combined     |  Test                   |
|    |   |(N=37)                    |(N=1)                 |(N=75)
      |(N=113)      |Statistic                |
+----+---+--------------------------+----------------------+-----------------+-------------+-------------------------+
|Kyph|109|                          |                      |
      |             |F=9.23 d.f.=2,106 P<0.001|
+----+---+--------------------------+----------------------+-----------------+-------------+-------------------------+
|Vert|113|                          |                      |
      |             |F=2.65 d.f.=2,110 P=0.075|
+----+---+--------------------------+----------------------+-----------------+-------------+-------------------------+
>

On Sun, May 15, 2011 at 10:03 AM, David Winsemius
<dwinsemius at comcast.net> wrote:
>
> On May 14, 2011, at 11:23 AM, Eli Kamara wrote:
>
>> Hello,
>>
>> I'm a new user to R so apologies if this is a basic question, but after
>> scouring the web on information for summary.formula, I still am searching
>> for an answer.
>>
>> I made a function to analyze my data - I have a categorical variable and
>> three continuous variables. I am analyzing my continuous variables on the
>> basis of my categorical variables.
>>
>> radioanal <- function(a)
>> {
>>
>> #Educational status first - pulling variables from my database.
>> categorical is 13 = Edu. numerical is  48=Kyph, 50=Vert, 53=HL.
>> a1= a[,c(13,48,50,53)]
>>
>> #make sure they are in numeric form
>> a2= transform(a1, Kyph=as.numeric(as.character(Kyph)),
>> Vert=as.numeric(as.character(Vert)), HL=as.numeric(as.character(HL)))
>>
>> #see boxplots of the individual variables
>> boxplot(a2$Kyph~a2$Edu, main="Education vs Kyphosis angle",
>>  xlab="Education", ylab="Kyphosis angle")
>> boxplot(a2$Vert~a2$Edu, main="Education vs # of vertebrae affected",
>>  xlab="Education", ylab="#of vertebrae affected")
>> boxplot(a2$HL~a2$Edu, main="Education vs %HL",
>>  xlab="Education", ylab="%HL")
>>
>> #see distribution of data
>> d=summary.formula(a2$Edu~a2$Kyph+a2$HL+a2$Vert, method="reverse",
>> overall=T, continuous=5, add=TRUE, test=T)
>>
> I noticed that you were addressing the columns individually. That rather
> defeats the strategy of passing a data argument to a function and using only
> the column names in the formula. It often causes strange errors in model
> calls and I wouldn be surprised if you got better results with something
> like:
>
> d=summary.formula( Edu~ Kyph+ HL+ Vert, data=a2, method="reverse",
> overall=T, continuous=5, add=TRUE, test=T)
>
> --
> David
>>
>> #perform MANOVA
>> a3=manova(cbind(Kyph, Vert, HL)~as.factor(Edu), data=a2)
>>
>> #return results
>> a4=list("Results of Educational Status MANOVA",
>> print(d),
>> summary(a3, test="Hotelling-Lawley"),
>> summary(a3, test="Roy") ,
>> summary(a3, test="Pillai"),
>> summary(a3, test="Wilks"),
>> summary.aov(a3)
>> )
>>
>> print(a4)
>>
>> }
>>
>> This function works as is, but I want to add the mean and standard
>> deviation to my table. When I add the following code to line 36 where I
>> print "d"
>> print(d, prmsd=TRUE)
>>
>> The numbers in my table disappear. When I use the same commands from the
>> command line, the same thing happens. After reading the manual, I think the
>> error might be due to the missing numbers in my database, so I tried adding
>> na.action to my set of commands:
>>
>> print(summary.formula(a2$Edu~a2$Kyph+a2$HL+a2$Vert, na.action,
>> method="reverse", overall=T, continuous=5, add=TRUE, test=T), prmsd=TRUE)
>>
>> but then I get the following error:
>> Error in as.data.frame.default(data, optional = TRUE) :
>>  cannot coerce class '"function"' into a data.frame
>
> It may be trying to do something with 'data' and doesn't find a 'data'
> object until it get to the 'data' function.
>
>>
>> Any ideas?
>>
>>
>> Also, does anyone know what kind of test statistic this function
>> calculates?
>
> Huh. You do realize this function in the rms package has a help page, right?
>
>
>> I compared the F and p values to a manual ANOVA but they were different.
>>
>
> I think you break further questions down into components and post something
> that is reproducible.
> ####------------------------------------------------------------####
>>
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> ####------------------------------------------------------------####
>>
>
> --
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
>
>