Re: [R] printCoefmat() and zap.ind
(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 <- 1
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$coefficients)
#> Estimate Std. Error t value Pr(>|t|)
#> (Intercept) 0. 0.00200.001
#> x10.5021 0.0020 254.70 <2e-16 ***
#> x20.6002 0.0020 301.23 <2e-16 ***
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
```
I have to round the two columns first before calling
printCoefmat(). Not nice but works for now.
Regards,
Shu Fai Cheung
在 2023年7月8日週六 00:41，Martin Maechler 寫道：
> > Martin Maechler
> > on Fri, 7 Jul 2023 18:12:24 +0200 writes:
>
> > Shu Fai Cheung
> > on Thu, 6 Jul 2023 17:14:27 +0800 writes:
>
> >> Hi All,
>
> >> I would like to ask two questions about printCoefmat().
>
> > Good... this function, originally named print.coefmat(),
> > is 25 years old (in R) now:
>
> >
> > r1902 | maechler | 1998-08-14 19:19:05 +0200 (Fri, 14 Aug 1998) |
> > Changed paths:
> > M R-0-62-patches/CHANGES
> > M R-0-62-patches/src/library/base/R/anova.R
> > M R-0-62-patches/src/library/base/R/glm.R
> > M R-0-62-patches/src/library/base/R/lm.R
> > M R-0-62-patches/src/library/base/R/print.R
>
> > print.coefmat(.) about ok
> >
>
> > (yes, at the time, the 'stats' package did not exist yet ..)
>
> > so it may be a good time to look at it.
>
>
> >> First, I found a behavior of printCoefmat() that looks strange to
> me,
> >> but I am not sure whether this is an intended behavior:
>
> >> ``` r
> >> set.seed(5689417)
> >> n <- 1
> >> x1 <- rnorm(n)
> >> x2 <- rnorm(n)
> >> y <- .5 * x1 + .6 * x2 + rnorm(n, -0.0002366, .2)
> >> dat <- data.frame(x1, x2, y)
> >> out <- lm(y ~ x1 + x2, dat)
> >> out_summary <- summary(out)
> >> printCoefmat(out_summary$coefficients)
> >> #> Estimate Std. Error t value Pr(>|t|)
> >> #> (Intercept) 1.7228e-08 1.9908e-030.001
> >> #> 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) 0.00 0.001991 0.01
> >> #> 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
Re: [R] printCoefmat() and zap.ind
> 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 <- 1
>> 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-030.001
>> #> 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) 0.00 0.001991 0.01
>> #> 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. 0.001991 0.01
>> #> x10.5021 0.001971 254.7 <2e-16 ***
>> #> x20.6002 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|)
>>
Re: [R] printCoefmat() and zap.ind
> 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 <- 1
> 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$coefficients)
> #> Estimate Std. Error t value Pr(>|t|)
> #> (Intercept) 1.7228e-08 1.9908e-030.001
> #> x1 5.0212e-01 1.9715e-03 254.70 <2e-16 ***
> #> x2 6.0016e-01 1.9924e-03 301.23 <2e-16 ***
> #> ---
> #> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> printCoefmat(out_summary$coefficients,
> zap.ind = 1,
> digits = 4)
> #> Estimate Std. Error t value Pr(>|t|)
> #> (Intercept) 0.00 0.001991 0.01
> #> 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$coefficients,
> zap.ind = 1,
> digits = 4,
> cs.ind = 1)
> #> Estimate Std. Error t value Pr(>|t|)
> #> (Intercept) 0. 0.001991 0.01
> #> x10.5021 0.001971 254.7 <2e-16 ***
> #> x20.6002 0.001992 301.2 <2e-16 ***
> #> ---
> #> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> ```
> However, this solution is not ideal because the numbers
> of decimal places of "Estimate" and "Std. Error" are
> different. How can I get the output like this one?
> ```r
> #> Estimate Std. Error t value Pr(>|t|)
> #> (Intercept) 0. 0.0020 0.01
> #> x10.5021 0.0020 254.7 <2e-16 ***
> #> x20.6002 0.0020 301.2 <2e-16 ***
> ```
> Thanks for your attention.
> Regards,
> Shu Fai Cheung
Thank you, Shu Fai,
for your careful and thoughtful report!
Best regards,
Martin
__
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[R] printCoefmat() and zap.ind
Hi All, I would like to ask two questions about printCoefmat(). First, I found a behavior of printCoefmat() that looks strange to me, but I am not sure whether this is an intended behavior: ``` r set.seed(5689417) n <- 1 x1 <- rnorm(n) x2 <- rnorm(n) y <- .5 * x1 + .6 * x2 + rnorm(n, -0.0002366, .2) dat <- data.frame(x1, x2, y) out <- lm(y ~ x1 + x2, dat) out_summary <- summary(out) printCoefmat(out_summary$coefficients) #> Estimate Std. Error t value Pr(>|t|) #> (Intercept) 1.7228e-08 1.9908e-030.001 #> 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$coefficients, zap.ind = 1, digits = 4) #> Estimate Std. Error t value Pr(>|t|) #> (Intercept) 0.00 0.001991 0.01 #> x1 0.502100 0.001971 254.7 <2e-16 *** #> x2 0.600200 0.001992 301.2 <2e-16 *** #> --- #> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 ``` With zap.ind = 1, the values in "Estimate" were correctly zapped using digits = 4. However, by default, "Estimate" and "Std. Error" are formatted together. Because the standard errors are small, with digits = 4, zero's were added to values in "Estimate", resulting in "0.502100" and "0.600200", which are misleading because, if rounded to the 6th decimal place, the values to be displayed should be "0.502122" and "0.600162". Is this behavior of printCoefmat() intended/normal? Second, how can I use zap without this behavior? In cases like the one above, I need to use zap such that the intercept will not be displayed in scientific notation. Disabling scientific notation cannot achieve the desired goal. I tried adding cs.ind = 1: ```r printCoefmat(out_summary$coefficients, zap.ind = 1, digits = 4, cs.ind = 1) #> Estimate Std. Error t value Pr(>|t|) #> (Intercept) 0. 0.001991 0.01 #> x10.5021 0.001971 254.7 <2e-16 *** #> x20.6002 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. 0.0020 0.01 #> x10.5021 0.0020 254.7 <2e-16 *** #> x20.6002 0.0020 301.2 <2e-16 *** ``` Thanks for your attention. Regards, Shu Fai Cheung __ R-help@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.
