[R] Displaying p-values in latex

[Marc Schwartz]

On Thu, 2005-07-28 at 14:00 -0700, Juned Siddique wrote:
> Hi. I want to create a table in latex with regression coefficients and their
> corresponding p-values. My code is below. How do I format the p-values so
> that values less than 0.0001 are formated as <.0001 rather than just rounded
> to 0.0000? Thank you.
> 
> model<-lm(y~x1+x2)
> 
> output<-summary(model)
> output<-as.matrix(coefficients(output))
> output<-format.df(ouput,cdec=c(2,2,2,4))
> 
> latex(output,longtable=TRUE, file="C:/model.tex")

I have not used Frank's latex() function, so there may be a setting that
helps with this, but something along the lines of:

# Using one example from ?lm:

ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
group <- gl(2,10,20, labels=c("Ctl","Trt"))
weight <- c(ctl, trt)
lm.D9 <- lm(weight ~ group)

output <- (summary(lm.D9))
output <- as.matrix(coefficients(output))
output <- format.df(output, rdec = c(2, 2, 2, 4))

# Here is the line to re-format the p values
# Note that column alignment on the decimal may be problematic here 
# depending upon the specifications for column justifications. 
# If the column is right justified, it should be easier, since we 
# are forcing four decimal places.

output[, 4] <- ifelse(as.numeric(output[, 4]) < 0.0001, 
                      "$<$0.0001", sprintf("%6.4f", output[, 4]))


> output
            Estimate Std. Error t value Pr(>|t|)   
(Intercept) "5.03"   "0.22"     "22.85" "$<$0.0001"
groupTrt    "-0.37"  "0.3114"   "-1.19" "0.2490"   
attr(,"col.just")
[1] "r" "r" "r" "r"


Note the use of "$" to indicate math mode for the symbols. Presumably
Frank has a similar approach when the object passed to latex() is a
model, since the heading for the p value column should end up being
something like:

   Pr($>$$|$t$|$)

and the minus signs in the second line should similarly be surrounded:

   $-$0.37

I have cc:d Frank here for his clarifications.

HTH,

Marc Schwartz