[R] printCoefmat() and zap.ind
Martin Maechler
m@ech|er @end|ng |rom @t@t@m@th@ethz@ch
Fri Jul 7 18:12:24 CEST 2023
>>>>> Shu Fai Cheung
>>>>> on Thu, 6 Jul 2023 17:14:27 +0800 writes:
> Hi All,
> I would like to ask two questions about printCoefmat().
Good... this function, originally named print.coefmat(),
is 25 years old (in R) now:
--------------------------------------------------------------------
r1902 | maechler | 1998-08-14 19:19:05 +0200 (Fri, 14 Aug 1998) |
Changed paths:
M R-0-62-patches/CHANGES
M R-0-62-patches/src/library/base/R/anova.R
M R-0-62-patches/src/library/base/R/glm.R
M R-0-62-patches/src/library/base/R/lm.R
M R-0-62-patches/src/library/base/R/print.R
print.coefmat(.) about ok
--------------------------------------------------------------------
(yes, at the time, the 'stats' package did not exist yet ..)
so it may be a good time to look at it.
> First, I found a behavior of printCoefmat() that looks strange to me,
> but I am not sure whether this is an intended behavior:
> ``` r
> set.seed(5689417)
> n <- 10000
> x1 <- rnorm(n)
> x2 <- rnorm(n)
> y <- .5 * x1 + .6 * x2 + rnorm(n, -0.0002366, .2)
> dat <- data.frame(x1, x2, y)
> out <- lm(y ~ x1 + x2, dat)
> out_summary <- summary(out)
> printCoefmat(out_summary$coefficients)
> #> Estimate Std. Error t value Pr(>|t|)
> #> (Intercept) 1.7228e-08 1.9908e-03 0.00 1
> #> x1 5.0212e-01 1.9715e-03 254.70 <2e-16 ***
> #> x2 6.0016e-01 1.9924e-03 301.23 <2e-16 ***
> #> ---
> #> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> printCoefmat(out_summary$coefficients,
> zap.ind = 1,
> digits = 4)
> #> Estimate Std. Error t value Pr(>|t|)
> #> (Intercept) 0.000000 0.001991 0.0 1
> #> x1 0.502100 0.001971 254.7 <2e-16 ***
> #> x2 0.600200 0.001992 301.2 <2e-16 ***
> #> ---
> #> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> ```
> With zap.ind = 1, the values in "Estimate" were correctly
> zapped using digits = 4. However, by default, "Estimate"
> and "Std. Error" are formatted together. Because the
> standard errors are small, with digits = 4, zero's were added
> to values in "Estimate", resulting in "0.502100" and
> "0.600200", which are misleading because, if rounded to
> the 6th decimal place, the values to be displayed should
> be "0.502122" and "0.600162".
> Is this behavior of printCoefmat() intended/normal?
Yes, this is "normal" in the sense that zapsmall() is used.
I'm not even sure anymore if I was always aware 1998 what exactly the
simple zapsmall() function is doing.
It does not do what you want here (and actually *typically* want
for formatting numbers for display, plotting, etc):
You "really want" here and in such situations
zapOnlysmall <- function(x, dig) {
x[abs(x) <= 10^-dig] <- 0
x
}
and I think I'd replace the use of zapsmall() inside
printCoefmat() with something like zapOnlysmall() above.
This will indeed nicely solve your problem.
> Second, how can I use zap without this behavior?
> In cases like the one above, I need to use zap such that
> the intercept will not be displayed in scientific notation.
> Disabling scientific notation cannot achieve the desired
> goal.
> I tried adding cs.ind = 1:
well, from the help page ?printCoefmat
cs.ind is really about the [ind]ices of [c]oefficient + [s]cale or [s]td.err
So, for lm() you should not have to set cs.ind but rather keep
it at it's smart default of cs.ind = 1:2 .
> ```r
> printCoefmat(out_summary$coefficients,
> zap.ind = 1,
> digits = 4,
> cs.ind = 1)
> #> Estimate Std. Error t value Pr(>|t|)
> #> (Intercept) 0.0000 0.001991 0.0 1
> #> x1 0.5021 0.001971 254.7 <2e-16 ***
> #> x2 0.6002 0.001992 301.2 <2e-16 ***
> #> ---
> #> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> ```
> However, this solution is not ideal because the numbers
> of decimal places of "Estimate" and "Std. Error" are
> different. How can I get the output like this one?
> ```r
> #> Estimate Std. Error t value Pr(>|t|)
> #> (Intercept) 0.0000 0.0020 0.0 1
> #> x1 0.5021 0.0020 254.7 <2e-16 ***
> #> x2 0.6002 0.0020 301.2 <2e-16 ***
> ```
> Thanks for your attention.
> Regards,
> Shu Fai Cheung
Thank you, Shu Fai,
for your careful and thoughtful report!
Best regards,
Martin
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