I'm currently doing some data analysis on population data, so reporting the standard errors in the tables of parameter coefficients just doesn't really make statistical sense. I've done a fair bit of searching and can't find any way to customize the xtable output to remove it. Can anyone point me in the right direction?
Thanks a lot, I didn't post this lightly; if it's something obvious, I apologize for having wasted time!
so after my (other) whole long-winded answer... this works too:
xtable(summary(model1)$coefficients[,c(1,3,4)])
Or more generically:
sm <- summary(SomeModel)
SE.indx <- which(colnames(sm$coefficients) == "Std. Error") # find which column is Std. Error (usually 2nd)
sm$coefficients <- sm$coefficients[, -SE.indx] # Remove it
xtable(sm$coefficients) # call xtable on just the coefficients table
% latex table generated in R 2.15.1 by xtable 1.7-0 package
% Sun Dec 9 00:01:46 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{rrrr}
\hline
& Estimate & t value & Pr($>$$|$t$|$) \\
\hline
(Intercept) & 29.80 & 30.70 & 0.00 \\
crim & -0.31 & -6.91 & 0.00 \\
age & -0.09 & -6.50 & 0.00 \\
\hline
\end{tabular}
\end{center}
\end{table}
Using the first example in help(lm):
xtable(as.matrix(coef(lm.D9)))
% latex table generated in R 2.15.2 by xtable 1.7-0 package
% Sat Dec 8 19:53:09 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{rr}
\hline
& x \\
\hline
(Intercept) & 5.03 \\
groupTrt & -0.37 \\
\hline
\end{tabular}
\end{center}
\end{table}
I agreed with not using std erros if this were descriptions of a population and not just a sample. By that reasoning, however, you would not want to leave in p-values or t-statistics. That was the reason I only included the coefficients. To remove the standard error column only from the summary coefficient matrix:
xtable( coef(summary(lm.D9))[,-2] )
% latex table generated in R 2.15.2 by xtable 1.7-0 package
% Sat Dec 8 21:02:17 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{rrrr}
\hline
& Estimate & t value & Pr($>$$|$t$|$) \\
\hline
(Intercept) & 5.03 & 22.85 & 0.00 \\
groupTrt & -0.37 & -1.19 & 0.25 \\
\hline
\end{tabular}
\end{center}
\end{table}
Looking at str(summary(Model1))
we see that $coefficients
has the Std. Error
Std. Error
value we want to remove.
lesserSummary <- function(x) {
## returns same as summary(x), but with "Std. Error" remove from coefficients.
## and class of object is "modifiedSummary"
# grab the summary
sm <- summary(x)
# find which column is std error
SE.indx <- which(colnames(sm$coefficients) == "Std. Error")
# remove it
sm$coefficients <- sm$coefficients[, -SE.indx]
# give it some class
class(sm) <- "modifiedSummary"
# return it
sm
}
xtable.modifiedSummary <-
function (x, caption = NULL, label = NULL, align = NULL, digits = NULL, display = NULL, ...) {
# x is a modifiedSummary object
# This function is a modification of xtable:::xtable.summary.lm
# Key Difference is simply the number of columns that x$coef is expected to have
# (Here 3. Originally 4)
x <- data.frame(x$coef, check.names = FALSE)
class(x) <- c("xtable", "data.frame")
caption(x) <- caption
label(x) <- label
align(x) <- switch(1 + is.null(align), align, c("r", "r", "r", "r"))
digits(x) <- switch(1 + is.null(digits), digits, c(0, 4, 2, 4))
display(x) <- switch(1 + is.null(display), display, c("s", "f", "f", "f"))
return(x)
}
xtable_mod <- function(x) {
# Wrapper function to xtable.modified summary, calling first lesserSummary on x
xtable(lesserSummary(x))
}
xtable_mod(model1)
% latex table generated in R 2.15.1 by xtable 1.7-0 package
% Sat Dec 8 23:44:54 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{rrrr}
\hline
& Estimate & t value & Pr($>$$|$t$|$) \\
\hline
(Intercept) & 29.8007 & 30.70 & 0.0000 \\
crim & -0.3118 & -6.91 & 0.0000 \\
age & -0.0896 & -6.50 & 0.0000 \\
\hline
\end{tabular}
\end{center}
\end{table}
You can likely modify the call to xtable, but you first need to follow it down a bit: start by looking at the source for xtable:
xtable
# function (x, caption = NULL, label = NULL, align = NULL, digits = NULL,
# display = NULL, ...)
# {
# UseMethod("xtable")
# }
# <environment: namespace:xtable>
We see that it simply has a call to UseMethod()
. So lets see which methods are available:
methods(xtable)
# [1] xtable.anova* xtable.aov* xtable.aovlist*
# [4] xtable.coxph* xtable.data.frame* xtable.glm*
# [7] xtable.lm* xtable.matrix* xtable.prcomp*
# [10] xtable.summary.aov* xtable.summary.aovlist* xtable.summary.glm*
# [13] xtable.summary.lm* xtable.summary.prcomp* xtable.table*
# [16] xtable.ts* xtable.zoo*
There are several. Note that the ones with an asterisk *
are non-visible.
The method called is determined by the class of the object we are calling xtable
on.
Let's say our output is Model1
We take a look at its class: '
class(Model1)
# [1] "lm"
So the source we want to look at is xtable.lm
.
xtable.lm
# Error: object 'xtable.lm' not found
Error? That's right, it is non-visible. So we use the package name with triple-colons. Note: please be sure to read the notice in the help file ?":::"
xtable:::xtable.lm
# function (x, caption = NULL, label = NULL, align = NULL, digits = NULL,
# display = NULL, ...)
# {
# return(xtable.summary.lm(summary(x), caption = caption, label = label,
# align = align, digits = digits, display = display))
# }
# <environment: namespace:xtable>
We notice that xtable.lm
calls xtable.summary.lm
and passes as its first argument a summary(x)
, where x is our model.
So that leads us to two place to investigate: summary
and xtable.summary.lm
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