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

From: David Hajage <dhajage.r_at_gmail.com>
Date: Sat, 26 Jul 2008 10:20:45 +0200

Oh...
No, I don't need to read the documentation again. I just need to wake up...

2008/7/25 Frank E Harrell Jr <f.harrell_at_vanderbilt.edu>

> 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
>

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