[R] printCoefmat() and zap.ind
Shu Fai Cheung
@hu|@|@cheung @end|ng |rom gm@||@com
Sun Jul 9 03:25:03 CEST 2023
(Sorry for sending it twice. I forgot to reply
to the mailing list.)
Many many thanks for the comments and examples!
I could write my own function to achieve what
I want to do. However, I would like to find a method that
uses built-in functions only and prints the output in a format
identical to that of the default output of print.summary.lm(),
which uses printCoefmat() internally.
It seems that this cannot be done easily for now. This
is a workaround.
```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)
out_summary$coefficients[, "Estimate"] <-
round(out_summary$coefficients[, "Estimate"], 4)
out_summary$coefficients[, "Std. Error"] <-
round(out_summary$coefficients[, "Std. Error"], 4)
printCoefmat(out_summary$coefficients)
#> Estimate Std. Error t value Pr(>|t|)
#> (Intercept) 0.0000 0.0020 0.00 1
#> x1 0.5021 0.0020 254.70 <2e-16 ***
#> x2 0.6002 0.0020 301.23 <2e-16 ***
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
```
I have to round the two columns first before calling
printCoefmat(). Not nice but works for now.
Regards,
Shu Fai Cheung
在 2023年7月8日週六 00:41，Martin Maechler <maechler using stat.math.ethz.ch> 寫道：
> >>>>> Martin Maechler
> >>>>> on Fri, 7 Jul 2023 18:12:24 +0200 writes:
>
> >>>>> Shu Fai Cheung
> >>>>> on Thu, 6 Jul 2023 17:14:27 +0800 writes:
>
> >> Hi All,
>
> >> I would like to ask two questions about printCoefmat().
>
> > Good... this function, originally named print.coefmat(),
> > is 25 years old (in R) now:
>
> > --------------------------------------------------------------------
> > r1902 | maechler | 1998-08-14 19:19:05 +0200 (Fri, 14 Aug 1998) |
> > Changed paths:
> > M R-0-62-patches/CHANGES
> > M R-0-62-patches/src/library/base/R/anova.R
> > M R-0-62-patches/src/library/base/R/glm.R
> > M R-0-62-patches/src/library/base/R/lm.R
> > M R-0-62-patches/src/library/base/R/print.R
>
> > print.coefmat(.) about ok
> > --------------------------------------------------------------------
>
> > (yes, at the time, the 'stats' package did not exist yet ..)
>
> > so it may be a good time to look at it.
>
>
> >> First, I found a behavior of printCoefmat() that looks strange to
> me,
> >> but I am not sure whether this is an intended behavior:
>
> >> ``` r
> >> set.seed(5689417)
> >> n <- 10000
> >> x1 <- rnorm(n)
> >> x2 <- rnorm(n)
> >> y <- .5 * x1 + .6 * x2 + rnorm(n, -0.0002366, .2)
> >> dat <- data.frame(x1, x2, y)
> >> out <- lm(y ~ x1 + x2, dat)
> >> out_summary <- summary(out)
> >> printCoefmat(out_summary$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.
>
> well..., now that I tried to change it "globally" in
> printCoefmat() and I see how many of the lm() summary or anova()
> outputs .. outputs that get slightly changed, and sometimes
> quite unfavourably,
>
> I think that the "hard" replacement of zapsmall() by
> zapOnlysmall() {above} is too drastic, ... even though it helps
> in your case.
>
> ... back to the "drawing board" ...
>
> Martin
>
>
> >> 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
>
> > ______________________________________________
> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
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