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

From: David Hajage <dhajage.r_at_gmail.com>
Date: Fri, 25 Jul 2008 10:54:47 +0200

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|
+----------------------------+-------------------------+-------------------------+-----------------------------+
+----------------------------+------------------------------------------+------------------------------------------+------------------------------------+
|                            |Drug
|Placebo                                   |
Test                              |
|                            |(N=31)
|(N=19)
|Statistic                           |
+----------------------------+------------------------------------------+------------------------------------------+------------------------------------+
|age                         |45.9263/48.7501/54.0194  49.1817+/-
5.2751|47.3436/50.7276/53.6963  51.1313+/- 5.5868|           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 |
+----------------------------+------------------------------------------+------------------------------------------+------------------------------------+


rowlabel,      col.just = col.just, numeric.dollar = FALSE, insert.bottom =
legend,      rowname = lab, dcolumn = dcolumn, extracolheads =
extracolheads,      extracolsize = Nsize, ...)

%
\begin{table}[!tbp]
 \caption{Descriptive Statistics by treatment\label{f}}
\begin{center}
\begin{tabular}{lccc}\hline\hline
\multicolumn{1}{l}{}&
\multicolumn{1}{c}{Drug}&
\multicolumn{1}{c}{Placebo}&


\multicolumn{1}{c}{Test Statistic}
\\ &\multicolumn{1}{c}{{\scriptsize
$N=31$}}&\multicolumn{1}{c}{{\scriptsize $N=19$}}&\\ \hline age&{\scriptsize 45.92627049~}{48.75014585 }{\scriptsize 54.01942542} &{\scriptsize 47.34358486~}{50.72757132 }{\scriptsize 53.69634575} &$F_{1,48}=0.9 ,~ P<0.5 ^{1}$\\
sex&&&$\chi^{2}_{2}=0.3 ,~ P=0.859 ^{2}$\\
~~~~?&25.806\%~{\scriptsize~(~8)}&26.316\%~{\scriptsize~(~5)}&\\
~~~~f&38.710\%~{\scriptsize~(12)}&31.579\%~{\scriptsize~(~6)}&\\
~~~~m&35.484\%~{\scriptsize~(11)}&42.105\%~{\scriptsize~(~8)}&\\

Primary~Symptoms&&&\\
~~~~Depressed&41.935\%~{\scriptsize~(13)}&63.158\%~{\scriptsize~(12)}&$\chi^{2}_{1}=2.12 ,~ P=0.145 ^{2}$\\
~~~~Hangnail&48.387\%~{\scriptsize~(15)}&42.105\%~{\scriptsize~(~8)}&$\chi^{2}_{1}=0.19 ,~ P=0.665 ^{2}$\\
~~~~Stomach~Ache&45.161\%~{\scriptsize~(14)}&68.421\%~{\scriptsize~(13)}&$\chi^{2}_{1}=2.57 ,~ P=0.109 ^{2}$\\
~~~~Muscle~Ache&54.839\%~{\scriptsize~(17)}&26.316\%~{\scriptsize~(~5)}&$\chi^{2}_{1}=3.89 ,~ P=0.049 ^{2}$\\
~~~~Headache&51.613\%~{\scriptsize~(16)}&36.842\%~{\scriptsize~(~7)}&$\chi^{2}_{1}=1.03 ,~ P=0.309 ^{2}$\\
\hline
\end{tabular}



\end{center}

\noindent {\scriptsize $a$\ }{$b$\ }{\scriptsize $c$\ } represent the lower quartile $a$, the median $b$, and the upper quartile $c$\ for continuous variables.\\
Numbers after percents are frequencies.\\
\indent Tests used: $^{1}$Wilcoxon test; $^{2}$Pearson test \end{table}

I would like to understand :

• why does option 'pctdig' affect both percentages and quantiles in the 'print' command (pctdig : 'number of digits to the right of the decimal place for *printing percentages*. The default is zero, so percents will be rounded to the nearest percent');
• how can I change the number of decimal for continuous variables in the 'latex' command ?
• why doesn't option 'eps' affect all p-value ?

I've just discover these wonderfull functions. Thank you to Frank Harrell for this package.

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