[R] Package Hmisc, functions summary.formula() and latex(), options pdig, pctdig, eps and prmsd

[Frank E Harrell Jr]

David Hajage wrote:
> 
> 
> 2008/7/25 Frank E Harrell Jr <f.harrell at vanderbilt.edu 
> <mailto:f.harrell at vanderbilt.edu>>
> 
>     David Hajage wrote:
> 
>         Hello R users,
> 
>         I have several problems with the functions summary.formula and
>         latex in
>         package Hmisc. Here an example :
> 
>         ####
>         library(Hmisc)
>         sex <- factor(sample(c("m","f", "?"), 50, rep=TRUE))
>         age <- rnorm(50, 50, 5)
>         treatment <- factor(sample(c("Drug","Placebo"), 50, rep=TRUE))
>         symp <- c('Headache','Stomach Ache','Hangnail',
>                  'Muscle Ache','Depressed')
>         symptom1 <- sample(symp, 50,TRUE)
>         symptom2 <- sample(symp, 50,TRUE)
>         symptom3 <- sample(symp, 50,TRUE)
>         Symptoms <- mChoice(symptom1, symptom2, symptom3, label='Primary
>         Symptoms')
> 
>         f <- summary(treatment ~ age + sex + Symptoms, method="reverse",
>         test=TRUE)
>         print(f, digits = 5, pdig = 2, pctdig = 3, eps = 0.5, prmsd = F)
>         print(f, digits = 5, pdig = 2, pctdig = 3, eps = 0.5, prmsd = T)
>         latex(f, long = T, pdig = 2, pctdig = 3, eps = 0.5, prmsd = F,
>         file = "")
>         ###
> 
>         Here the problems :
>          - The first print(f, ...) doesn't replace all p-value <0.5 by
>         "P<0.5" :
> 
>         +----------------------------+-------------------------+-------------------------+-----------------------------+
>         |                            |Drug
>         |Placebo                  |  Test                       |
>         |                            |(N=31)
>         |(N=19)                   |Statistic                    |
>         +----------------------------+-------------------------+-------------------------+-----------------------------+
>         |age                         |     45.926/48.750/54.019|
>         47.344/50.728/53.696|    F=0.9 d.f.=1,48 P<0.5    |
>         +----------------------------+-------------------------+-------------------------+-----------------------------+
>         |sex : ?                     |         25.806% ( 8)    |        
>         26.316% (
>         5)    | Chi-square=0.3 d.f.=2 P=0.86|
>         +----------------------------+-------------------------+-------------------------+-----------------------------+
>         |    f                       |         38.710% (12)    |        
>         31.579% (
>         6)    |                             |
>         +----------------------------+-------------------------+-------------------------+-----------------------------+
>         |    m                       |         35.484% (11)    |        
>         42.105% (
>         8)    |                             |
>         +----------------------------+-------------------------+-------------------------+-----------------------------+
>         |Primary Symptoms : Depressed|         41.935% (13)    |        
>         63.158%
>         (12)    | Chi-square=2.12 d.f.=1 P<0.5|
>         +----------------------------+-------------------------+-------------------------+-----------------------------+
>         |    Hangnail                |         48.387% (15)    |        
>         42.105% (
>         8)    |Chi-square=0.19 d.f.=1 P=0.67|
>         +----------------------------+-------------------------+-------------------------+-----------------------------+
>         |    Stomach Ache            |         45.161% (14)    |        
>         68.421%
>         (13)    | Chi-square=2.57 d.f.=1 P<0.5|
>         +----------------------------+-------------------------+-------------------------+-----------------------------+
>         |    Muscle Ache             |         54.839% (17)    |        
>         26.316% (
>         5)    | Chi-square=3.89 d.f.=1 P<0.5|
>         +----------------------------+-------------------------+-------------------------+-----------------------------+
>         |    Headache                |         51.613% (16)    |        
>         36.842% (
>         7)    | Chi-square=1.03 d.f.=1 P<0.5|
>         +----------------------------+-------------------------+-------------------------+-----------------------------+
> 
> 
>     I did not see an instance of P < 0.5 that was not replaced by
>     "P<0.5". This is an unusual cutoff, and you are printing many more
>     digits of precision than offered by the data.
> 
>  
> For example 'Hangnail', p-value is printed as 'P=0.67' instead of 
> 'P<0.5'. I know this is an unusual cutoff, I don't remember why I chose 
> that for this example...

But 0.67 is not less than 0.5.  Please read the documentation again.

Frank