catTestfisher <-
function (tab)
{
st <- if (!is.matrix(tab) || nrow(tab) < 2 | ncol(tab) <
2)
list(p.value = NA, statistic = NA, parameter = NA)
else {
rowcounts <- tab %*% rep(1, ncol(tab))
tab <- tab[rowcounts > 0, ]
if (!is.matrix(tab))
list(p.value = NA, statistic = NA, parameter = NA)
else fisher.test(tab)
}
list(P = st$p.value, stat = "", df = "",
testname = "Fisher's Exact", statname = "", latexstat = "", namefun = "",
plotmathstat = "")
}
我想使用library(Hmisc) summaryM函数，但使用Fisher的精确测试，所以我写了一个catTestfisher函数并设置catTest = catTestfisher在我自己的summaryM2函数中，除summaryM
catTest = catTestfisher完全相同
summaryM2 <-
function (formula, groups = NULL, data = NULL, subset, na.action = na.retain,
overall = FALSE, continuous = 10, na.include = FALSE, quant = c(0.025,
0.05, 0.125, 0.25, 0.375, 0.5, 0.625, 0.75, 0.875, 0.95,
0.975), nmin = 100, test = FALSE, conTest = conTestkw,
catTest = catTestfisher, ordTest = ordTestpo)
{
marg <- length(data) && ".marginal." %in% names(data)
if (marg)
formula <- update(formula, . ~ . + .marginal.)
formula <- Formula(formula)
Y <- if (!missing(subset) && length(subset))
model.frame(formula, data = data, subset = subset, na.action = na.action)
else model.frame(formula, data = data, na.action = na.action)
X <- model.part(formula, data = Y, rhs = 1)
Y <- model.part(formula, data = Y, lhs = 1)
getlab <- function(x, default) {
lab <- attr(x, "label")
if (!length(lab) || lab == "")
default
else lab
}
if (marg) {
xm <- X$.marginal.
X$.marginal. <- NULL
}
else xm <- rep("", nrow(X))
if (length(X)) {
xname <- names(X)
if (length(xname) == 1 && !length(groups))
groups <- xname
if (!length(groups) && length(xname) > 1) {
warnings("Must specify groups when > 1 right hand side variable is present.\ngroups taken as first right hand variable.")
groups <- xname[1]
}
svar <- if (length(xname) == 1)
factor(rep(".ALL.", nrow(X)))
else do.call("interaction", list(X[setdiff(xname, groups)],
sep = " "))
group <- X[[groups]]
glabel <- getlab(group, groups)
}
else {
svar <- factor(rep(".ALL.", nrow(Y)))
group <- rep("", nrow(Y))
groups <- group.freq <- NULL
glabel <- ""
}
quants <- unique(c(quant, 0.025, 0.05, 0.125, 0.25, 0.375,
0.5, 0.625, 0.75, 0.875, 0.95, 0.975))
nv <- ncol(Y)
nameY <- names(Y)
R <- list()
for (strat in levels(svar)) {
instrat <- svar == strat
n <- integer(nv)
type <- n
comp <- dat <- vector("list", nv)
names(comp) <- names(dat) <- nameY
labels <- Units <- vector("character", nv)
if (test) {
testresults <- vector("list", nv)
names(testresults) <- names(comp)
}
gr <- group[instrat]
xms <- xm[instrat]
if (all(xms != ""))
xms <- rep("", length(xms))
group.freq <- table(gr)
group.freq <- group.freq[group.freq > 0]
if (overall)
group.freq <- c(group.freq, Combined = sum(group.freq))
for (i in 1:nv) {
w <- Y[instrat, i]
if (length(attr(w, "label")))
labels[i] <- attr(w, "label")
if (length(attr(w, "units")))
Units[i] <- attr(w, "units")
if (!inherits(w, "mChoice")) {
if (!is.factor(w) && !is.logical(w) && length(unique(w[!is.na(w)])) <
continuous)
w <- as.factor(w)
s <- !is.na(w)
if (na.include && !all(s) && length(levels(w))) {
w <- na.include(w)
levels(w)[is.na(levels(w))] <- "NA"
s <- rep(TRUE, length(s))
}
n[i] <- sum(s & xms == "")
w <- w[s]
g <- gr[s, drop = TRUE]
if (is.factor(w) || is.logical(w)) {
tab <- table(w, g)
if (test) {
if (is.ordered(w))
testresults[[i]] <- ordTest(g, w)
else testresults[[i]] <- catTest(tab)
}
if (nrow(tab) == 1) {
b <- casefold(dimnames(tab)[[1]], upper = TRUE)
pres <- c("1", "Y", "YES", "PRESENT")
abse <- c("0", "N", "NO", "ABSENT")
jj <- match(b, pres, nomatch = 0)
if (jj > 0)
bc <- abse[jj]
else {
jj <- match(b, abse, nomatch = 0)
if (jj > 0)
bc <- pres[jj]
}
if (jj) {
tab <- rbind(tab, rep(0, ncol(tab)))
dimnames(tab)[[1]][2] <- bc
}
}
if (overall)
tab <- cbind(tab, Combined = apply(tab, 1,
sum))
comp[[i]] <- tab
type[i] <- 1
}
else {
sfn <- function(x, quant) {
o <- options(digits = 10)
on.exit(options(o))
c(quantile(x, quant), Mean = mean(x), SD = sqrt(var(x)),
N = sum(!is.na(x)))
}
qu <- tapply(w, g, sfn, simplify = TRUE, quants)
if (test)
testresults[[i]] <- conTest(g, w)
if (overall)
qu$Combined <- sfn(w, quants)
comp[[i]] <- matrix(unlist(qu), ncol = length(quants) +
3, byrow = TRUE, dimnames = list(names(qu),
c(format(quants), "Mean", "SD", "N")))
if (any(group.freq <= nmin))
dat[[i]] <- lapply(split(w, g), nmin = nmin,
function(x, nmin) if (length(x) <= nmin)
x
else NULL)
type[i] <- 2
}
}
else {
w <- as.numeric(w) == 1
n[i] <- sum(!is.na(apply(w, 1, sum)) & xms ==
"")
g <- as.factor(gr)
ncat <- ncol(w)
tab <- matrix(NA, nrow = ncat, ncol = length(levels(g)),
dimnames = list(dimnames(w)[[2]], levels(g)))
if (test) {
pval <- numeric(ncat)
names(pval) <- dimnames(w)[[2]]
d.f. <- stat <- pval
}
for (j in 1:ncat) {
tab[j, ] <- tapply(w[, j], g, sum, simplify = TRUE,
na.rm = TRUE)
if (test) {
tabj <- rbind(table(g) - tab[j, ], tab[j,
])
st <- catTest(tabj)
pval[j] <- st$P
stat[j] <- st$stat
d.f.[j] <- st$df
}
}
if (test)
testresults[[i]] <- list(P = pval, stat = stat,
df = d.f., testname = st$testname, statname = st$statname,
latexstat = st$latexstat, plotmathstat = st$plotmathstat)
if (overall)
tab <- cbind(tab, Combined = apply(tab, 1,
sum))
comp[[i]] <- tab
type[i] <- 3
}
}
labels <- ifelse(nchar(labels), labels, names(comp))
R[[strat]] <- list(stats = comp, type = type, group.freq = group.freq,
labels = labels, units = Units, quant = quant, data = dat,
N = sum(!is.na(gr) & xms == ""), n = n, testresults = if (test) testresults)
}
structure(list(results = R, group.name = groups, group.label = glabel,
call = call, formula = formula), class = "summaryM")
}
在尝试对以下数据进行测试后，我收到警告并显示错误：
library(Hmisc)
set.seed(173)
sex <- factor(sample(c("m","f"), 500, rep=TRUE))
treatment <- factor(sample(c("Drug","Placebo"), 500, rep=TRUE))
> summaryM2(sex ~ treatment, test=TRUE, overall = TRUE)
Error in round(teststat, 2) :
non-numeric argument to mathematical function
我尝试逐行逐步执行summaryM2功能，但无法弄清楚导致问题的原因。
答案 0 :(得分：0)
在catTestfisher函数中，输出变量stat（测试统计量）和df（自由度）应该是数字变量，而不是空字符串。在编程中，stat被掩盖到teststat以便在输出之前进行四舍五入（因此round("", 2)的错误消息是non-numeric argument to mathematical function）。参见summary.formula code）中的第1718至1721行。
您可以设置df = NULL，但是stat需要一个值（不是NA或NULL），否则不返回任何输出。您可以通过设置stat = 0（或其他任何数字）来解决该问题，然后仅使用prtest = "P"显示p值。
catTestfisher2 <- function (tab)
{
st <- fisher.test(tab)
list(P = st$p.value, stat = 0, df = NULL,
testname = st$method, statname = "", latexstat = "", namefun = "",
plotmathstat = "")
}
output <- summaryM(sex ~ treatment, test=TRUE, overall = TRUE, catTest = catTestfisher2)
print(output, prtest = "P")
Descriptive Statistics (N=500)
+-------+-----------+-----------+-----------+-------+
| |Drug |Placebo |Combined |P-value|
| |(N=257) |(N=243) |(N=500) | |
+-------+-----------+-----------+-----------+-------+
|sex : m|0.52 (133)|0.52 (126)|0.52 (259)| 1 |
+-------+-----------+-----------+-----------+-------+
请注意，无需定义您自己的summaryM2函数。只需使用catTest =即可传递函数。