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.
- 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 :
Try modifying the digits argument.
+----------------------------+------------------------------------------+------------------------------------------+------------------------------------+
| |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 :
This is a bug. An override source is below, to use until the next release.
% 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 ?
I hope to address these 2 questions soon.
Frank
- 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
latex.summary.formula.reverse <-
function(object, title=first.word(deparse(substitute(object))),
digits, prn = any(n!=N), pctdig=0,
npct=c('numerator','both','denominator','none'),
npct.size='scriptsize', Nsize='scriptsize',
exclude1=TRUE, vnames=c("labels","names"), prUnits=TRUE,
middle.bold=FALSE, outer.size="scriptsize",
caption, rowlabel="",
insert.bottom=TRUE, dcolumn=FALSE, formatArgs=NULL, round=NULL,
prtest=c('P','stat','df','name'), prmsd=FALSE, msdsize=NULL,
long=dotchart, pdig=3, eps=.001, auxCol=NULL,
dotchart=FALSE, ...)
{
x <- object
npct <- match.arg(npct)
vnames <- match.arg(vnames)
if(is.logical(prtest) && !prtest)
prtest <- 'none'
stats <- x$stats
nv <- length(stats)
cstats <- lab <- character(0)
nn <- integer(0)
type <- x$type
n <- x$n
N <- x$N
nams <- names(stats)
labels <- x$labels
Units <- x$units
nw <- if(lg <- length(x$group.freq)) lg
else 1 #23Nov98
gnames <- names(x$group.freq)
test <- x$testresults
if(!length(test))
prtest <- 'none'
gt1.test <-
if(all(prtest=='none'))
FALSE
else
length(unique(sapply(test,function(a)a$testname))) > 1
if(!missing(digits)) { #.Options$digits <- digits 6Aug00
oldopt <- options(digits=digits)
on.exit(options(oldopt))
}
if(missing(caption))
caption <- paste("Descriptive Statistics",
if(length(x$group.label))
paste(" by",x$group.label)
else
paste(" $(N=",x$N,")$",sep=""), sep="")
bld <- if(middle.bold) '\\bf '
else ''
cstats <- NULL
testUsed <- auxc <- character(0)
for(i in 1:nv) {
if(length(auxCol))
auxc <- c(auxc, auxCol[[1]][i])
nn <- c(nn, n[i]) ## 12aug02
nam <- if(vnames=="names") nams[i]
else labels[i]
if(prUnits && nchar(Units[i]) > 0)
nam <- paste(nam, '~\\hfill\\tiny{',translate(Units[i],'*','
'),'}',sep='')
tr <- if(length(test) && all(prtest!='none')) test[[nams[i]]]
else NULL
if(length(test) && all(prtest!='none'))
testUsed <- unique(c(testUsed, tr$testname))
if(type[i]==1 || type[i]==3) {
cs <- formatCats(stats[[i]], nam, tr, type[i],
if(length(x$group.freq)) x$group.freq else x$n[i],
npct, pctdig, exclude1, long, prtest,
latex=TRUE, testUsed=testUsed,
npct.size=npct.size,
pdig=pdig, eps=eps,
footnoteTest=gt1.test, dotchart=dotchart)
nn <- c(nn, rep(NA, nrow(cs)-1))
} else cs <- formatCons(stats[[i]], nam, tr, x$group.freq, prmsd,
prtest=prtest, formatArgs=formatArgs,
round=round,
latex=TRUE, testUsed=testUsed,
middle.bold=middle.bold,
outer.size=outer.size, msdsize=msdsize,
pdig=pdig, eps=eps, footnoteTest=gt1.test)
cstats <- rbind(cstats, cs)
if(length(auxc) && nrow(cstats) > 1)
auxc <- c(auxc, rep(NA, nrow(cs)-1))
}
lab <- dimnames(cstats)[[1]]
gl <- names(x$group.freq)
##gl <- if(length(gl)) paste(gl, " $(N=",x$group.freq,")$",sep="")
else " "
## Thanks: Eran Bellin <[EMAIL PROTECTED]> 3Aug01
if(!length(gl))
gl <- " "
lab <- sedit(lab,c(" ","&"),c("~","\\&")) #was format(lab) 21Jan99
lab <- latexTranslate(lab, greek=.R.)
gl <- latexTranslate(gl, greek=.R.)
## if(any(gl != " ")) gl <- paste(gl, "
$(N=",x$group.freq,")$",sep="") # 3Aug01
## Added any( ) 26Mar02 21jan03
extracolheads <-
if(any(gl != " "))
c(if(prn)'', paste('$N=',x$group.freq,'$',sep=''))
else NULL # 21jan03
if(length(test) && !all(prtest=='none')) {
gl <- c(gl,
if(length(prtest)==1 && prtest!='stat')
if(prtest=='P') 'P-value'
else prtest
else 'Test Statistic')
if(length(extracolheads)) extracolheads <- c(extracolheads,'') #
21jan03
}
dimnames(cstats) <- list(NULL,gl)
## was dimnames(cstats) <- list(lab, gl) 12aug02
cstats <- data.frame(cstats, check.names=FALSE)
## Added row.names=lab below 10jul02 - S+ was dropping dimnames[[1]]
##attr(cstats,'row.names') <- lab 12aug02
col.just <- rep("c",length(gl))
if(dcolumn && all(prtest!='none') &&
gl[length(gl)] %in% c('P-value','Test Statistic'))
col.just[length(col.just)] <- '.'
if(prn) {
cstats <- data.frame(N=nn, cstats, check.names=FALSE)
col.just <- c("r",col.just)
}
if(!insert.bottom)
legend <- NULL
else {
legend <- paste(if(any(type==2)) {
paste("\\noindent {\\",outer.size," $a$\\
}{",bld,"$b$\\ }{\\",
outer.size," $c$\\ } represent the lower
quartile $a$, the median $b$, and the upper quartile $c$\\ for
continuous variables.",
if(prmsd) '~~$x\\pm s$ represents
$\\bar{X}\\pm 1$ SD.'
else '',
'\\\\', sep="")
} else NULL,
if(prn) '$N$\\ is the number of non--missing
values.\\\\',
if(any(type==1) && npct=='numerator')
'Numbers after percents are frequencies.\\\\',
sep="\n")
legend <- NULL
if(any(type==2)) {
legend <- paste("\\noindent {\\", outer.size, " $a$\\ }{", bld,
"$b$\\ }{\\", outer.size,
" $c$\\ } represent the lower quartile $a$, the
median $b$, and the upper quartile $c$\\ for continuous variables.",
if(prmsd) '~~$x\\pm s$ represents $\\bar{X}\\pm
1$ SD.'
else '',
'\\\\\n', sep="")
}
if(prn) {
legend <- paste(legend,
'$N$\\ is the number of non--missing values.\\\\\n',
sep='')
}
if(any(type==1) && npct=='numerator') {
legend <- paste(legend,
'Numbers after percents are frequencies.\\\\\n',
sep='')
}
if(length(testUsed))
legend <-paste(legend,
if(length(testUsed)==1)'\\noindent Test used:'
else '\\indent Tests used:',
if(length(testUsed)==1) paste(testUsed,'test')
else
paste(paste('$^{',1:length(testUsed),'}$',testUsed,
' test',sep=''),collapse='; '))
## added rowname=lab 12aug02 added '\n\n' 4mar03 for ctable=T
}
if(length(auxc)) {
if(length(auxc) != nrow(cstats))
stop(paste('length of auxCol (',length(auxCol[[1]]),
') is not equal to number or variables in table (',
nv,').', sep=''))
auxcc <- format(auxc)
auxcc[is.na(auxc)] <- ''
cstats <- cbind(auxcc, cstats)
nax <- names(auxCol)
heads <- get2rowHeads(nax)
names(cstats)[1] <- heads[[1]]
if(length(col.just)) col.just <- c('r', col.just)
if(length(extracolheads)) extracolheads <- c(heads[2], extracolheads)
}
resp <- 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,
...)
if(dotchart)
resp$style <- unique(c(resp$style, 'calc', 'epic', 'color'))
resp
}
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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