irst line
cmd_args=commandArgs()
to
cmd_args <- commandArgs(TRUE)
makes a lot of sense in most cases. I haven't read your whole script so
I don't know it it makes sense for you.
Duncan Murdoch
Please advise,
Ana
On Sat, Nov 23, 2019 at 4:16 AM Ben Tupper wrote:
Hi,
I think you wa
ke
library(utf8)
string1 <- utf8_normalize(string1)
string2 <- utf8_normalize(string2)
string1 == string2 # Should now work as expected
Duncan Murdoch
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so I think you'll have to post a
reproducible example if you want help.
Duncan Murdoch
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PLEASE do read the posting guide http://www.R-
-log10(p), or adding 3
to the reference line, as Ana requested.
Or just multiply them by 1000 and pass them to qq():
qq(dd$P*1000, main = "Q-Q plot of small GWAS p-values")
As far as I can see, there's no way to tell qqman::qq to move the
reference line.
Duncan Murdoch
J
n", stdout = TRUE, stderr = TRUE)
These are based on reading the help pages, which sometimes helps.
Duncan Murdoch
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PLEASE do read the p
On 04/11/2019 9:25 a.m., Duncan Murdoch wrote:
On 04/11/2019 8:31 a.m., Luigi Marongiu wrote:
Dear all,
I am plotting some values with lattice barchart: the y-axis is
automatically ordered alphabetically; is it possible to order the
entries by number, so that the 'larger' histograms would
rder(Normal + Tumour + Metastasis)
df$Ordered <- ordered(Family, levels = Family[o])
barchart(Ordered ~ Normal+Tumour+Metastasis, data = df, stack = TRUE,
xlim=c(1,1000),
main = "Ordered by total",
xlab = expression(bol
On 31/10/2019 5:17 a.m., Christofer Bogaso wrote:
As I said the name 'AAA31' is itself a variable. So I cant hard-code
it within the save() function
Use the list= argument to save().
Duncan Murdoch
On Thu, Oct 31, 2019 at 2:45 PM Jim Lemon wrote:
Hi Christofer,
This is a guess, but have
x assumes.
I think Witold's request is quite hard to do. The right way to handle
expressions is as hierachical objects, like those returned from
parse(text = z). Turning those into character vectors of lexical tokens
doesn't make sense.
Perhaps if Witold explained the context of what he is tryi
On 27/10/2019 7:01 p.m., Martin Møller Skarbiniks Pedersen wrote:
Hi,
I am trying to convert a small python computation to R but my R version
gets the wrong result.
You are using log10() in R, when you should be using log().
The python code:
import math import log
x = log(2)
for i in
y "merge"). Are those from dplyr and base? Showing us
str(lr), str(asign), and sessionInfo() would be helpful.
Duncan Murdoch
dim(l4)
[1] 166941635 8
dim(asign)
[1] 107371528 5
On Wed, Oct 23, 2019 at 5:32 PM Ana Marija wrote:
Hello,
I have two data frames lik
On 06/10/2019 8:23 a.m., vod vos wrote:
The problem is aa, bb and cc all in a single csv file
contains no blank line.
So what steps do you need, and which of them do you need help with?
Duncan Murdoch
The single csv file like list output.
aa(cm)
1, 2 , 3,
bb(mm)
1, 2, 3,
4, 5, 6
e rules for expanding that you'll need in your real data,
but for your example step 4 could be
aa <- rep(aa, each = 3)
Then step 5 could be
result <- data.frame(aa, bb, cc)
Duncan Murdoch
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o* options with underscores, and a dozen with embedded hyphens.
Duncan Murdoch
Best Regards,
W. Michels, Ph.D.
On Fri, Sep 27, 2019 at 9:04 AM Martin Maechler
wrote:
Martin Maechler
on Mon, 23 Sep 2019 16:14:36 +0200 writes:
Richard O'Keefe
on Sat, 21 Sep 2019 09:39:18 +1200 writes:
isn't obvious: you need to load it into
an empty location (either your global environment in a clean new
session, or one created specially for the purpose). E.g.
env <- new.env()
load("~/Baseball/RetroSheetDocumentation/ari18.test2.rda", envir = env)
ls(
uot;environment" in particular), and this could end up
confusing users who don't need the more general overview.
I think Hadley's description in Advanced R (online here:
https://adv-r.hadley.nz/functions.html#lexical-scoping) is a pretty
clear description of how R wor
's not
really a mystery.
Duncan Murdoch
On Thu, 26 Sep 2019 at 23:56, Martin Møller Skarbiniks Pedersen
wrote:
On Wed, 25 Sep 2019 at 11:03, Francesco Ariis wrote:
Dear R users/developers,
while ploughing through "An Introduction to R" [1], I found the
expression "static scop
AM PDT, Duncan Murdoch
wrote:
On 21/09/2019 7:38 a.m., Jeff Newmiller wrote:
The dplyr::select function returns a special variety of data.frame
called a tibble.
I don't think that's always true. The docs say it returns "An object
of
the same class as .data.", and that's what I'm
c(1,1,2,2), b=1:4) %>% subset(a == 1))
'data.frame': 2 obs. of 2 variables:
$ a: num 1 1
$ b: int 1 2
But I believe there are other dplyr functions that take dataframes as
input and return tibbles, I just don't know which ones.
Duncan Murdoch
The tibble has certain features designed t
Presumably data %>% select(col1, col2) isn't giving you a dataframe.
However, you haven't given us a reproducible example, so I can't tell
you what it's doing. But that's where you should look.
Duncan Murdoch
__
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use of this my
first reaction was don't feed the trolls.
Why have a second reaction? Trolls are bullies, bullies should be ignored.
Duncan Murdoch
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sentations of them, because it's hard to do that without
introducing changes. In other words, don't use eval(parse()).
Duncan Murdoch
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PL
]]
Please don't post HTML to the list -- it's a plain text list. That's
also pretty well documented.
Duncan Murdoch
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PLEASE do read the posting
; if not, you
probably have to contact them to find out why it's showing up. The R
team can't do anything about it.
Duncan Murdoch
On 15/09/2019 10:07 p.m., Steven Yen wrote:
Hello Duncan:
Below I am sending
(1) message from installation of a .zip file;
(2) from installation of aod from CRAN;
(3
On 15/09/2019 1:44 a.m., Steven Yen wrote:
Can someone help me understand why Rtools is needed when installing a
package from CRAN, and from a zipped file? What's the point?
Please don't just repeat your post when you've been asked for additional
supporting information.
Duncan Murdoch
lly run "Install.packages", not "install.packages"? R is
case sensitive, so those are different. But in any case, that message
probably isn't coming from R, it is coming from some contributed package
or front end.
Posting the result of sessionInfo() would help us to diagnose where
operations ...
if (dev.cur() == 1 || identical(recordPlot(), blankPlot))
plot(ecdf(rnorm(100)))
else
plot(ecdf(rnorm(100)), add=TRUE, col=i)
Duncan Murdoch
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work is being done by a C routine, but it's
conceivable you could use the stringi::stri_read_raw function to do the
reading, and convince the C routine to handle the raw value instead of a
character value.
- Find a way to split up your file into smaller pieces.
Duncan Murdoch
___
l versions are in subdirectories of
https://svn.r-project.org/R/tags . Pick one of these, and then follow
links to src etc. within it.
Duncan Murdoch
On Monday, 5 August 2019, 15:32:00 CEST, Jeff Newmiller
wrote:
Seems like you are looking in the wrong place. Did you download the sourc
things in your function; quantmod does
very complicated things in getSymbols(). One of those complicated
things is breaking, it's not pdf() that's breaking.
Duncan Murdoch
R version 3.6.0 (2019-04-26) on Mac 10.14.5
# R --silent --vanilla < s2.r
library(quantmod)
options("getSym
You posted this identical question to
https://stackoverflow.com/q/57206597/2554330, and didn't fix it based on
the comment asking for a reproducible example. Please don't crosspost.
On 25/07/2019 3:15 p.m., Mark Mendel wrote:
When installing from a private repo, fails if the package depends
to distribute
copies of R and other packages come from their licenses. If you don't
follow their licenses, you may be in violation of their copyright.
Duncan Murdoch
I am sorry , it all came out in wrong way.I didn't intended to hurt anyones
sentiment.
I totally love the community and it's work so
(either by you, when you notice a bug in the contributed package and can
fix it, or by one of us, when you post the reprex and we dig in).
Duncan Murdoch
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s
readRDS. If that's not just a typo above, then the loadRDS function
you're using doesn't work. Use the base package functions instead.
- There's a bug in R.
In any case, we can't do much to help you without a reproducible example.
Duncan Murdoch
_
a more faithful representation of discrete data using
something like
plot(table(x))
Duncan Murdoch
On 2019/7/12 下午 05:10, Steven wrote:
# Can someone help with this simple frequency histogram problem (n = 15)?
# I use four class limits: [90,95], [95,100], [100,105], [105,110
ot;else stmt.2" is not a valid statement.
I'm sure that's just a typo, but I can't think of a variation on it that
is different from the one before.
Duncan Murdoch
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is generated based on time of day and
process number, so is almost certainly different in every session.
(Sometimes you want a repeated seed for reproducibility, but it's always
bad when you're surprised by one.)
Duncan Murdoch
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everse order to what you want, e.g.
within(df, {c <- a; b<-a*2; c<-b*3})
but to me that is a lot less clear than Eric's solution.
Duncan Murdoch
On July 3, 2019 8:25:32 AM PDT, Eric Berger wrote:
Nice suggestion, Richard.
On Wed, Jul 3, 2019 at 4:28 PM Richard O'Keefe
w
On 01/07/2019 8:28 p.m., Duncan Murdoch wrote:
On 01/07/2019 5:41 a.m., Marvin Kiene wrote:
Additionally, the 'help.search()' always just gives the result: "No results
found", for all of my students.
Those students are probably using RStudio. This appears to be an
incom
This will cause lots of things to appear in an external browser instead
of in the RStudio display, so it's not the nicest workaround, but at
least it's fairly easy.
Duncan Murdoch
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obably roughly proportional to the object.size() results.
Duncan Murdoch
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PLEASE do read the posting guide http://www.R-project.org/posting-guid
get different results if I set
M[13, 17] <- TRUE
or leave it FALSE.
Hopefully people found the transitivity discussion interesting, even if
I won't use it for this problem.
Duncan Murdoch
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o also become TRUE *after* M[i,k] changes. This
seems to imply that an iterative solution is necessary.
Right, that's a good point.
Duncan Murdoch
One such procedure, via repeated matrix multiplication to check for and
impose transitivity, appears to be suggested by this discussion:
https://math
ges together into a single
PNG, and use texture coordinates to choose which image is used for each
vertex. It's probably a lot more trouble than just plotting the
surfaces separately.
I am thankful for the rare previlige of directly getting help from the
developer of the rgl package on this foru
& M[j,k] both
being TRUE implies M[i,k] is TRUE?
The operation should only change FALSE or NA values to TRUE values; TRUE
values should never be changed.
Duncan Murdoch
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On 17/06/2019 1:19 p.m., Duncan Murdoch wrote:
Suppose I have a square logical matrix M which I'm thinking of as a
relation between the row/column numbers.
I can make it into a symmetric relation (i.e. M[i,j] being TRUE implies
M[j,i] is TRUE) by the calculation
M <- M |
nto the shade3d() call in the same
way, or the material argument to qmesh3d.
Duncan Murdoch
Once again, I would like to thank you for your fantastic help.
Thanking you,
Ravi
On Thursday, 13 June 2019, 22:52:07 CEST, Duncan Murdoch
wrote:
On 13/06/2019 4:32 p.m., Duncan Murdoch wrote:
On 13/06/2019 4:32 p.m., Duncan Murdoch wrote:
On 13/06/2019 12:47 p.m., ravi via R-help wrote:
Hi,I want to plot a surface joining a circle on a plane with another circle (a
little offset w.r.t. the first one) on a parallel plane. This is a very
simplified version of my problem.
I
quads3d(quads, col = "green")
There are more efficient ways to do this (the for loop would be slow if
you had bigger vectors), but this should give you the idea.
Duncan Murdoch
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(confirmed by my.package-manual.log,
my.package-manual.tex, Rdlatex.log):
You have \describe with no \item. That leads to illegal LaTeX.
Instead of
\describe{
bar
\tabular{ll}{
...
you should have
\describe{
\item{bar}{
\tabular{ll}{
...
}
Duncan Murdoch
Rd:
\format
you start R, it will be fine on Linux, as far as I
can see.
I wouldn't choose that as the default way to run R (it's pretty
irritating not to have readline support), but it is a workaround for
this bug.
Duncan Murdoch
Hence, if you have a Windows machine that can look at the file syst
ution for the statistic when calculating that probability.
Duncan Murdoch
am I completely out of track?
sorry but I'm here missing the point somewhere, somehow...
thank you for the feedback
[[alternative HTML version deleted]]
__
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These look like very fragile suggestions. Allow x^2 to be an argument
(named expr, for example) to plotFx, don't force a user to write a
function in a very particular way. Then use deparse(substitute(expr))
in the title.
Duncan Murdoch
On 06/06/2019 4:33 p.m., Bert Gunter wrote:
Well
On 06/06/2019 5:04 p.m., Richard O'Keefe wrote:
How can expanding tildes anywhere but the beginning of a file name NOT be
considered a bug?
It looks like a bug in R, but not necessarily a bug in libreadline: we
may just be using tilde_expand improperly.
Duncan Murdoch
On Thu, 6 Jun
in R exts or R intro manual. Maybe
it would be worth considering to add something about it to debug help page.
It's in the ?browser help page, which is linked from ?debug.
Duncan Murdoch
Best regards
Petr
-Original Message-----
From: Duncan Murdoch
Sent: Thursday, June 6, 2019 11:11 AM
Enter without
choosing one, it will do the same as the previous time, so you've
probably used "s" sometime in the past.
Duncan Murdoch
Best regards
Petr
sessionInfo()
R Under development (unstable) (2018-03-07 r74369)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows
ULL) {
if (!is.null(prob) && max(prob) == min(prob))
prob <- NULL
sample(x = x, size = size, replace = replace, prob = prob)
}
You might want a looser tolerance on the vector of probabilities
depending on your context.
Duncan Murdoch
__
R-help
,2,"
1,2,5
1,2,"6"
I see
> count.fields("~/temp/test.txt",sep=",")
[1] 3 3 NA NA NA 3
indicating that there are problems on lines 3-5 (a missing closing quote
on line 3).
Duncan Murdoch
__
R-help@r-project.org ma
h
at the end, which was added by R CMD build. If you don't have a line
like that, you'll get the note you saw.
Duncan Murdoch
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P
.
The X11() message is suspicious.
I'm wondering what type of object you're trying to copy...?
I think Ed was running the Cygwin build of R. Cygwin can run the
Windows build of R, and it sounds as though that's what you did (and
what Ed should do.)
Duncan Murdoch
unable to contact X11 display
Is this supported in any way? Thanks
Cygwin is not supported in any way by the R project, as far as I know.
There's a native Windows build that is supported, and I'd strongly
recommend you use it instead.
Duncan Murdoch
_
On 14/05/2019 2:42 p.m., Rui Barradas wrote:
Hello,
There is a mailing list dedicated to package development. See
https://stat.ethz.ch/mailman/listinfo/r-package-devel
There are also instructions to follow at
https://cran.r-project.org/web/packages/policies.html
Duncan Murdoch
Hope
version of LogisticDx is 0.2 from 2015, and it doesn't
export those functions. Source for version 0.1 from 2014 is available,
and it does contain those functions, but I wouldn't touch them with a
ten foot pole unless I first heard from the author why he left them out
of the next release.
Duncan
have to follow this rule, but it
causes lots of confusion when they don't.
Duncan Murdoch
Best,
Jens
[Disclaimer: This is my first post here, following advice of how to
proceed with possible bugs from here: https://www.r-project.org/bugs.html]
SUMMARY
While `lm` alone accepts formula
On 29/04/2019 9:44 p.m., Rolf Turner wrote:
On 30/04/19 1:31 PM, Duncan Murdoch wrote:
On 29/04/2019 9:25 p.m., Duncan Murdoch wrote:
On 29/04/2019 8:43 p.m., Rolf Turner wrote:
On 30/04/19 12:19 PM, Jeff Newmiller wrote:
Since you now have this indirect dependency, you should make sure
On 29/04/2019 9:25 p.m., Duncan Murdoch wrote:
On 29/04/2019 8:43 p.m., Rolf Turner wrote:
On 30/04/19 12:19 PM, Jeff Newmiller wrote:
Since you now have this indirect dependency, you should make sure you
have updated this gaggle of packages. I have found that the
dependencies do
.quosures rlang
is due to issues with ggplot2 or rlang. Have you tried updating both of
those?
Duncan Murdoch
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PLEASE do read the posting gui
. If they are a set
of irregular points, there aren't so many. One possibility is to use
persp3d(z ~ x + y) (see ?persp3d.formula for help.) Use rglwidget() to
write it in a form you can view in a web browser.
Duncan Murdoch
Thanks
Bernard McGarvey
Director, Fort Myers Beach Lions Foundation, Inc
if you want a particular recommendation, such as what form
your data is in, what you want the plot to look like, what medium do you
want to display it on, etc.
Duncan Murdoch
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https
nt in Rd
files, and perhaps also in roxygen.
Doing the search through the source code also turned up @evalRd and
@evalNamespace, which might be worth exploring.
Duncan Murdoch
Thanks Jeff,
Boris
On 2019-04-22, at 02:25, Jeff Newmiller wrote:
What tag are you creating with the eval? Your e
interested in finding how dependencies would be recursively
updated to newer versions.
Set the `lib` parameter of `install.packages` to an empty directory, and
see what gets installed there.
Duncan Murdoch
__
R-help@r-project.org mailing list
g more sensible
to do with NA values. You may also have character strings that cannot
be converted into numbers, which will also generate NA values.
I think that's the only way that message will appear.
Duncan Murdoch
Maybe a
little example will help us to understand:
charstr<-c("5
s = FALSE)
})
tmp2 <- tmp1 %>% bind_rows(.id = "id")
tmp3 <- tmp2 %>% select(id, User, Rule)
tbl <- tmp3 %>% distinct()
(You don't need pipes here, but it will make it easier to put the giant
expression back together at the end.)
M2 and HM3 are predictors.
The problem is I get the same error even when I use nlsLM(in the minpack.lm
package):
nonlin_modDH5 <- nlsLM(formulaDH5, start = list(a = 0.43143, b = 2,A = 0.09,w =
0.8,a = 0.01,C = 0.94))
You have "a" twice in your start list. That's bound to cause tro
On 18/03/2019 1:00 p.m., Jeff Newmiller wrote:
Try
?grid::`grid-package`
The "-" is not a legal character in a bare symbol.
Or
package?grid::grid
which makes use of the rarely used "type" argument to "?".
Duncan Murdoch
On March 18, 2019 9:35:17 AM PDT, Wi
counter best implemented?
Use the Rdsm package. See ?Rdsm::Rdsm for help.
Duncan Murdoch
Here is a basic sketch of what I tried:
library(parallel)
library(flock)
## begin of code in package
tmp <- tempfile()
.localstuff <- new.env()
.localstuff$N <- 0
.localstuff$tmp <- temp
tal message. But, is there a way to do a cleaner
installation without getting such message? Thanks.
Have you tried specifying the library? Then R wouldn't tell you its guess.
Duncan Murdoch
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So far I haven't been patient enough to
know what
x <- (-90:90)/5
would take. This doesn't really make sense: with
x <- (-n:n)/5
it will need to sort (2n + 1)^2 objects, but that should take something
proportional to n^2 log(n) time, and the time seems to be growing faster
than that.
bout 5 milliseconds when the difference comes last, but 0.006
milliseconds when it comes first. Of course, all(x == y) and
identical(x, y) do slightly different tests: read the docs!
Duncan Murdoch
Thanks again!
DLG
On Sat, Mar 9, 2019 at 9:07 PM Jeff Newmiller
wrote:
Regarding the
a dataset of restaurant sales.
Not a native English speaker here; what exactly do you mean by "odd" in
this case?
"Odd" numbers have a remainder of 1 when divided by 2; "even" numbers
are multiples of 2.
Duncan Murdoch
If I ignore the "subject" field, it look
but you'll need to do more work yourself to get an array of
plots like lattice gives.
Duncan Murdoch
Thank you
df = data.frame(Name = c("A", "B", "C", "D", "E"),
x_axis = c(-0.591, 0.384, -0.384, -0.032, 0.754),
can get to it using
profvis:::parse_rprof, but the maintainer (who is cc'd) might want to
fix this.
Duncan Murdoch
Documentation for package ‘profvis’ version 0.3.5
DESCRIPTION file.
Help Pages
parse_rprof Parse Rprof output file for use with profvis
pause Pause an R process
print.profvis
unction(y)
})
if (inherits(value, "try-error")) {
cat ("something went wrong. There's information in value about
what happened.")
} else {
cat ("value is fine, there was no error.")
}
Duncan Murdoch
_
!
There are at least two packages (zoo and imputeTS) which have na.locf
functions. The one in zoo does what you want:
> zoo::na.locf(c(NA,NA,1,4,NA,2), na.rm=FALSE)
[1] NA NA 1 4 4 2
Duncan Murdoch
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g
options(warn=2)
before your script, and then the script will die at the first warning.
Duncan Murdoch
On 25/02/2019 3:45 p.m., jlu...@ria.buffalo.edu wrote:
The script is complete. When I start, the environment is empty.
The warnings are issued for these "ghost" variables well bef
ably thousands of them.
Duncan Murdoch
Personally I haven't got a clue what you are asking.
Also, please note that r-help is a world wide "community" with hundreds
of thousands of members. (I am but one of this large and unruly mob.)
It is not a single entity or "site&qu
;16:00" "16:46" "16:51" "17:35" "17:59" "18:17" "19:07" "19:08"
[18] "19:31" "21:21" "06:00" "06:20" "06:37" "06:40" "06:46" "07:20"
"07:4
. Perhaps the mirror you used
doesn't have it? I'd recommend using the cloud.r-project.org mirror
rather than a local one in almost any case.
In any case, Neal's advice to update R is likely to make your life a lot
easier.
Duncan Murdoch
> install.packages("car")
Installing
ch the packages, you haven't told R to look in the
alternate location.
Duncan Murdoch
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PLEASE do read the posting guide http://www.R-project.or
ause even though secret is defined in the caller of g()
and is therefore in the call stack, that's irrelevant: it's not in g's
evaluation frame (which has no variables) or its parent (which is the
global environment if those definitions were evaluated there).
Duncan Murdoch
Generally, u
ultInsideFn <- function() print(secret)
secret <- 'secret'
inside()
}
which is essentially equivalent, other than having a shorter header on
the outside() function.
Duncan Murdoch
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ing) installation of package
‘/tmp/Rtmp4hnMMO/file7fb929638ed8/gGnome_0.1.tar.gz’ had non-zero exit
status
That message indicates that options("warn") is 2 or higher when the
warning occurs. What is its setting before you start the install?
Duncan Murdoch
___
) describes the major R
packages for GUI programming: RGtk2, qtbase, Tcl/Tk, and gWidgets.
That book was published in 2012, and things have moved on since then.
Eric's suggestion of Shiny is newer, and is a really well-designed
system. A fairly steep learning curve, but worth it.
Duncan
::Rdiff should get what you want
even in that version. But as you note, it isn't a general purpose diff
for character vectors, it is targeted at comparing R output files.
Duncan Murdoch
- Original Message -
From: "Jeff Newmiller"
To: r-help@r-project.org, "Se
ow Thierry's advice, and don't use which() unless you really need a
vector of indices, and are prepared for an empty one.
Duncan Murdoch
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PL
always produced by subsetting the deck.
If a user does something like
topCard <- data.frame(face = "queen", suit = "spades", value = 12)
then the rownames won't match, and removing topCard will remove the
wrong one.
Duncan Murdoch
Benoit
Jeff Newmiller a écrit
rd$face & deck$suit == card$suit & deck$value =
card$value)
}
removeCard <- function(deck, card) {
deck[-whichCard(deck, card), ]
}
deck <- removeCard(deck, topCard)
Duncan Murdoch
Benoit
Jeff Newmiller a écrit :
In my programmer's head, something similar to this should "w
.
It is possible to have dynamic content in help pages. Web pages (e.g.
generated using R-markdown or Shiny) are even more flexible for content,
but maybe not meeting your requirement for displaying in an ESS buffer
or Linux terminal window.
Duncan Murdoch
El mié., 2 ene. 2019 a las 14:31, Jeff
.
Duncan Murdoch
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained
to
display help. You might be able to adapt it to your own needs, though
it won't be trivial.
Duncan Murdoch
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PLEASE do read the posting guide
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