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

From: Frank E Harrell Jr <f.harrell_at_vanderbilt.edu>
Date: Fri, 25 Jul 2008 11:39:21 -0500

David Hajage wrote:
>
>
> 2008/7/25 Frank E Harrell Jr <f.harrell@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



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