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|
+----------------------------+-------------------------+-------------------------+-----------------------------+
- The second print(f, ..., prmsd = T) has the same problem for p-value.
There is also 4 decimals in the first line instead of 3 :
+----------------------------+------------------------------------------+------------------------------------------+------------------------------------+
| |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 |
+----------------------------+------------------------------------------+------------------------------------------+------------------------------------+
- In the latex(f, ...), only the first-line p-value is replaced by "< 0.5",
and the quantiles for age have too much decimal :
% latex.default(cstats, title = title, caption = caption, rowlabel =
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.
DH
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