2008/7/25 Frank E Harrell Jr <[EMAIL PROTECTED]>
> 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...
>
>
>> - 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.
I tryed to modify the argument digit (with digit = 3, digit = 1 and digit =
10), but there is always 4 decimals in the first line.
>
>
>
>>
>> +----------------------------+------------------------------------------+------------------------------------------+------------------------------------+
>> | |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.
Thank you, I will try it very soon.
>
>
>
>> % 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.
Thank you very much.
>
>
> 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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