r - knitr + lyx：精确逻辑回归实践中的错误

Question

您可能知道，有一种技术，称为精确逻辑回归。来自 UCLA 的 idre 提供了出色的分析示例。( http://www.ats.ucla.edu/stat/r/dae/exlogit.htm ) 当我使用示例分析进行练习时，我遇到了 knitr (+ lyx) 的错误。

在网页中的语法列表中间，下面的语法会产生错误。Knitr 似乎可以很好地解释该块，但 lyx 会产生与 pdf 输出相关的错误。

<<>>=
## model with female predictor only'
m.female <- elrm(formula = admit/ntrials ~ female, interest = ~female, iter = 22000, dataset = cdat, burnIn = 2000)
@

lyx 会产生如下错误消息：

Running: pdflatex  "logistics.regression.tex" > /dev/null
11:50:28.071: Error while exporting format: pdf2../../../src/support/Systemcall.cpp(270): Systemcall: 'pdflatex  "logistics.regression.tex"' finished with exit code 1

同时，在 lyx 的错误框中，我看到以下消息：

\end{verbatim}                    
You need to provide a definition with \DeclareInputText or \DeclareInputMath before using this key

但是，块中的上述语法在 R 终端中运行良好，没有任何问题。我应该为块添加 knitr 选项吗？那这是什么？先感谢您。

钟华

require(knitr)
require(elrm)
dat <- read.table(text = " 
female  apcalc    admit       num
 0        0        0         7
 0        0        1         1
 0        1        0         3 
 0        1        1         7
 1        0        0         5
 1        0        1         1
 1        1        0         0
 1        1        1         6",
   header = TRUE)
dat
summary(dat)
dat <- dat[rep(1:nrow(dat), dat$num), -4]
summary(dat)
xtabs(~ female + apcalc, data=dat)
xtabs(~ female + admit, data=dat)
xtabs(~ apcalc + admit, data=dat)
xtabs(~ female + apcalc + admit, data=dat)
x <- xtabs(~admit + interaction(female, apcalc), data = dat) 
x  # view cross tabs
cdat <- data.frame(female = rep(1:0, 2), apcalc = rep(1:0, each = 2), admit = x[1, ], ntrials = colSums(x)) 
cdat  # view collapsed data set
## model with female predictor only
m.female <- elrm(formula = admit/ntrials ~ female, interest = ~female, iter = 22000, dataset = cdat, burnIn = 2000)
####### the last syntax causes an error in lyx (+ knitr)

Answer 1

问题来自进度条（特别是退格键\b）。两种可能的解决方案：

1. 联系作者elrm并请求参数progress = TRUE/FALSE，elrm()以便您可以使用例如elrm(..., progress = FALSE);来抑制进度条

2. 将调用移动elrm()到单独的块并隐藏进度条的输出，例如，

   <<>>=
   require(elrm)
   dat <- read.table(text = "
   female  apcalc    admit       num
    0        0        0         7
    0        0        1         1
    0        1        0         3 
    0        1        1         7
    1        0        0         5
    1        0        1         1
    1        1        0         0
    1        1        1         6",
      header = TRUE)
   dat
   summary(dat)
   dat <- dat[rep(1:nrow(dat), dat$num), -4]
   summary(dat)
   xtabs(~ female + apcalc, data=dat)
   xtabs(~ female + admit, data=dat)
   xtabs(~ apcalc + admit, data=dat)
   xtabs(~ female + apcalc + admit, data=dat)
   x <- xtabs(~admit + interaction(female, apcalc), data = dat) 
   x  # view cross tabs
   cdat <- data.frame(female = rep(1:0, 2), apcalc = rep(1:0, each = 2), admit = x[1, ], ntrials = colSums(x)) 
   cdat  # view collapsed data set
   ## model with female predictor only
   @
   
   <<results='hide'>>=
   m.female <- elrm(formula = admit/ntrials ~ female, interest = ~female, iter = 22000, dataset = cdat, burnIn = 2000)
   @
   
   <<>>=
   summary(m.female)
   @