that it produces output, which is computationally hard to
distinguish from truly random numbers. For this purpose, i suggest
to use the package rngSetSeed provided currently at
http://www.cs.cas.cz/~savicky/randomNumbers/
It is based on AES and Fortuna similarly as randaes, but these
components
algorithms to break it. However, if you use it for a simulation,
then the simulation will be biased only if it contains an algorithm,
which breaks MD5. The probability that this happens just by chance
is small.
Petr Savicky.
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, it is better to
use the array initialization even for a single number seed.
Petr Savicky.
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information about
that.
Package CORElearn (i am a coauthor) uses random number generation
under OpenMP in C++. This requires to have a separate copy of the
generator with its own memory for each thread.
Do you want to use it in C or C++?
Petr Savicky
On Wed, Feb 22, 2012 at 12:17:25PM -0600, Paul Johnson wrote:
[...]
In order for this to be easy for users, I need to put the init streams
and set current stream functions into a package, and then streamline
the process of creating the seed array. My opinion is that CRAN is
now overflowed
is
[,1]
seed1 124370417
seed2 205739774
FALSE TRUE
5 994
This means that if the streams x, y are generated from the two
seeds above, then y is almost exactly equal to x shifted by 1.
What is the current state of your project?
Petr Savicky
exactly.
I hope.
Saving .Random.seed should be a safe strategy.
Petr Savicky.
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is the maximum
for a single integer seed.
Petr Savicky.
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the distribution
uniquely, this is also a description of the required distribution.
The distribution is concentrated in a 2 dimensional subspace, since
the covariance matrix has rank 2.
Hope this helps.
Petr Savicky.
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out1
FALSE TRUE
94258
For a numeric matrix, the ratio of the running times is larger in
the same direction.
Petr Savicky.
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the vector to the original order of the rows.
Petr Savicky.
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... looks like a package
You may want to clean up by 'rm -rf /tmp/RtmpQ0WawT/Rd2pdf41481e1'
Is it intentional not to test the presence of pdflatex during R CMD check?
Petr Savicky.
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for breakage is higer, however.
Can you describe the error in more detail? Is it related to consistency
of converting a number to character and back?
Petr Savicky.
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] 2
nrow(unique(cbind(9*x)))
[1] 4
Petr Savicky.
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712
Petr Savicky.
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vectors and uses a transformation of the column using rank().
For example,
temp3 - as.matrix(rank(temp1, ties.method=max))
match(temp3, unique(temp3))
[1] 1 2 3 4 4 5 6 7 7 7 6 6 6 8 8 8 6 6 6 9 9 9 6 6
Can this be used in your code?
Petr Savicky
grDevices utils datasets methods base
gcc --version
gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46)
Petr Savicky.
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)
do not produce an error, if the compiled R runs in the same shell,
where make check was run. However, they produce the error, if R is
started in a new shell.
The command
find /usr -name liblzma*
has empty output.
Petr Savicky.
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,
9.995001)
for (x in example4) print(x, digits=7)
[1] 9.99
[1] 10
I appreciate comments.
Petr Savicky.
###--- R function that does the same as 'scientific' in
###--- /usr/local/R-0.50/src/main/format.c
###--- ~~~||~~
scientific1 - function(x
results on different platforms,
however, it cannot be generally guaranteed. For tree construction, even
minor differences in rounding may influence comparisons and this may
result in a different form of the tree.
Petr Savicky.
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on this.
Petr Savicky.
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are
(6 - 5.9994)/5.9994
[1] 0.00010001
(6 - 5.9994001)/5.9994001
[1] 9.999333e-05
Here, one digit output is chosen if the relative error is
less than 10^-4 and not otherwise.
Petr Savicky.
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https
of the user input.
Petr Savicky.
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of the device numbers, but sometimes,
it could be useful to open, say, device 4, even if device 3
is not needed. Is there a way, how to open a device with a
given number without opening devices with smaller numbers?
Petr Savicky.
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it. Thank you
very much for this information.
Petr Savicky.
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at the
R level is, actually
formatC(1204.245, digits=20) # [1] 1204.24498909
See
http://rwiki.sciviews.org/doku.php?id=misc:r_accuracy
or FAQ 7.31 for more examples.
Petr Savicky.
Is there a way to pass the arguments differently?
I'm using Windows and Visual Studio C++ 2005
of a double x to character type, which preserves the number exactly, may
be obtained, for example, using
formatC(x, digits=17, width=-1)
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On Tue, Feb 02, 2010 at 01:37:46PM +0100, Petr Savicky wrote:
I would like to add some more information concerning the patch C
to the function choose() proposed in the email
https://stat.ethz.ch/pipermail/r-devel/2009-December/056177.html
The patch uses transformations of choose(n, k
at https://svn.r-project.org/R/trunk/,
so the problem could be just temporary.
Petr Savicky.
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on it.
This suggests that we should get double in both cases, since all three
arguments from, to, and by are specified. I do not know, whether
having an integer result in seq() in the above case is intended or not.
Petr Savicky.
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obtained sometimes
from the original implementation and which is more accurate in all ranges of
the output.
For testing patch C a simpler script is sufficient, since we need not to take
care of the warnings. Namely
http://www.cs.cas.cz/~savicky/R-devel/test_choose_1.R
which produces the output
for both patches A
and B
in the tests, which i did.
Patch B is significantly more accurate in cases, when the result is more than 1.
In order to verify these two claims, i used the test script at
http://www.cs.cas.cz/~savicky/R-devel/test_choose_0.R
Its outputs with A and B are presented below
.
The test was run both with Intel extended and SSE arithmetic.
Petr Savicky.
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When you type in the example codes:
sprintf(%s is %f feet tall\n, Sven, 7.1)
and R returns:
[1] Sven is 7.10 feet tall\n
this is very different from the 'sprintf' function in C/C++, for in C/C++,
the format string \n usually represents a new line, but here, just
the plain text
or their modifications can be accepted.
Petr Savicky.
--- R-devel_2009-12-16/src/nmath/choose.c 2008-03-17 17:52:35.0
+0100
+++ R-devel_less_conservative/src/nmath/choose.c2009-12-17
22:43:54.0 +0100
@@ -107,19 +107,20 @@
#endif
if (fabs(k - k0) 1e-7
[9,] 0.010910034 -4.5180723 -4.5180723
[10,] -0.009273529NaN -4.6805913
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(CentOS and openSUSE).
On the other hand, for the package
http://www.cs.cas.cz/~savicky/R-devel/something_0.0.0.tar.gz
which demonstrates the problem, the modified R detected the code/doc mismatch.
The diff of the two outputs of R CMD check was
[savi...@uivtx test]$ diff original modified
. It is designed
primarily for printing vectors, where the rules are more complicated
to achieve a good unified format for all numbers. May be, someone else
can say more about it. The above analysis may be obtained by inspecting
the R source code.
Petr Savicky
. It is designed
primarily for printing vectors, where the rules are more complicated
to achieve a good unified format for all numbers. May be, someone else
can say more about it. The above analysis may be obtained by inspecting
the R source code.
Petr Savicky
For the package at
http://www.cs.cas.cz/~savicky/R-devel/something_0.0.0.tar.gz
which is a minor part of some other package only to demonstrate the
problem, i get (under R version 2.11.0 Under development 2009-12-12 r50714
and also under R-2.9.2, openSUSE 11.1 (x86_64) and CentOS release 5.2
On Mon, Nov 30, 2009 at 04:00:12AM +0100, dsim...@gmail.com wrote:
a - c(1:10)
b - c(1:10)
cor.test(a, b, method = spearman, alternative = greater, exact = TRUE)
Spearman's rank correlation rho
data: a and b
S = 0, p-value 2.2e-16
alternative hypothesis: true rho is
] 0.5999778
See
http://wiki.r-project.org/rwiki/doku.php?id=misc:r_accuracy
for more examples and explanations.
Petr Savicky.
V[8]
# [1] 0.7
V[8]==0.7
# [1] FALSE
# Rounding!?
V[9]
# [1] 0.8
V[9]==0.8
# [1] TRUE
# Back to normal
# The generated sequence is fine for all values except
On Sat, Aug 22, 2009 at 12:00:44AM +0200, Martin Maechler wrote:
I have taken up the issue now,
and after thinking, studying the source, trying to define a
'method = string' argument, came to the conclusion that both
the implementation and documentation (and source code self-explanation)
are
replying to).
Petr Savicky.
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On Wed, Aug 12, 2009 at 04:02:28PM +0200, Martin Maechler wrote:
PS == Petr Savicky savi...@cs.cas.cz
on Wed, 12 Aug 2009 13:50:46 +0200 writes:
PS Let me add the following to the discussion of identical(0, -0).
PS I would like to suggest to replace the paragraph
PS
On Tue, Aug 11, 2009 at 10:04:20AM +0200, Martin Maechler wrote:
DM == Duncan Murdoch murd...@stats.uwo.ca
on Mon, 10 Aug 2009 11:51:53 -0400 writes:
DM For people who want to play with these, here are some functions that
let
DM you get or set the payload value in a NaN.
On Sat, Aug 08, 2009 at 10:39:04AM -0400, Prof. John C Nash wrote:
I'll save space and not include previous messages.
My 2 cents: At the very least the documentation needs a fix. If it is
easy to do, then Ted Harding's suggestion of a switch (default OFF) to
check for sign difference would
On Mon, Aug 10, 2009 at 05:47:57AM -0400, Duncan Murdoch wrote:
I wouldn't mind a strict option. It would compare bit patterns, so
would distinguish +0 from -0, and different NaN values.
I think that a logical option strict in the above meaning could be
useful for debugging. The default may
On Tue, Aug 04, 2009 at 04:25:09PM +0200, lueth...@student.ethz.ch wrote:
Hi
I created the following vectors:
p_1=c(0.2,0.2,0.2,0.2,0.1,0.25,0.4,0.1,0.25,0.4,0.1,0.25,0.4,0.1,0.25,0.4,0.2,0.5,0.8,0.2,0.5,0.8,0.2,0.5,0.8,0.2,0.5,0.8)
I get an incorrect result for
(41/10-1/10)%%1
[1] 1
Note that due to rounding errors, 41/10-1/10 is
formatC(41/10-1/10, digits=20) # [1] 3.9995559
Besides FAQ 7.31, related information may be found also at
http://wiki.r-project.org/rwiki/doku.php?id=misc:r_accuracy
Petr.
On Fri, Jul 03, 2009 at 07:57:49AM -0700, Martin Morgan wrote:
[...]
sort.list is always called but used only to determine the order of
levels, so unnecessary when levels are provided.
I think, this is correct. Replacing
ind - sort.list(x)
by
if (missing(levels))
ind - sort.list(x)
On Sun, Jun 14, 2009 at 02:56:01PM -0400, Gabor Grothendieck wrote:
If read.csv's colClasses= argument is NOT used then read.csv accepts
double quoted numerics:
1: read.csv(stdin())
0: A,B
1: 1,1
2: 2,2
3:
A B
1 1 1
2 2 2
However, if colClasses is used then it seems that it does
I am sorry for not including the attachment mentioned in my
previous email. Attached now. Petr.
--- R-devel/src/library/utils/R/readtable.R 2009-05-18 17:53:08.0
+0200
+++ R-devel-readtable/src/library/utils/R/readtable.R 2009-06-25
10:20:06.0 +0200
@@ -143,9 +143,6 @@
On Sun, Jun 14, 2009 at 09:21:24PM +0100, Ted Harding wrote:
On 14-Jun-09 18:56:01, Gabor Grothendieck wrote:
If read.csv's colClasses= argument is NOT used then read.csv accepts
double quoted numerics:
1: read.csv(stdin())
0: A,B
1: 1,1
2: 2,2
3:
A B
1 1 1
2 2 2
On Sat, May 30, 2009 at 07:32:52PM +0200, Martin Maechler wrote:
vQ == Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no
on Sat, 30 May 2009 11:16:43 +0200 writes:
[...]
vQ one simple way to improve the code is as follows; instead of
(simplified)
vQ const char*
On Fri, May 29, 2009 at 03:53:02PM +0200, Martin Maechler wrote:
my version of *using* the function was
1 SEXP attribute_hidden StringFromReal(double x, int *warn)
2 {
3 int w, d, e;
4 formatReal(x, 1, w, d, e, 0);
5 if (ISNA(x)) return NA_STRING;
6 else return
On Wed, May 27, 2009 at 10:51:38PM +0200, Martin Maechler wrote:
I have very slightly modified the changes (to get rid of -Wall
warnings) and also exported the function as Rf_dropTrailing0(),
and tested the result with 'make check-all' .
Thank you very much for considering the patch. -Wall
In the almost current development version (2009-05-22 r48594) and also in
https://svn.r-project.org/R/trunk/src/library/base/man/factor.Rd
?factor contains (compare the formulations marked by ^^)
\section{Warning}{
The interpretation of a factor depends on both the codes and the
On Mon, May 25, 2009 at 03:58:06PM +0800, Berwin A Turlach wrote:
Well, the first statement is a remark on comparison in general while
the second statement is specific to comparison operators and generic
methods. There are other ways of comparing objects; note:
R f1 - factor(c(a, b, c, c,
Function factor() in the current development version (2009-05-22)
guarantees that levels are different character strings. However, they
may represent the same decimal number. The following example is derived
from a posting by Stavros Macrakis in thread Match .3 in a sequence
in March
nums - 0.3
On Wed, May 20, 2009 at 11:10:11PM +0200, wolfgang.re...@gmail.com wrote:
...
Strange behavior of qbinom:
qbinom(0.01, 5016279, 1e-07)
[1] 0
qbinom(0.01, 5016279, 2e-07)
[1] 16
qbinom(0.01, 5016279, 3e-07)
[1] 16
qbinom(0.01, 5016279, 4e-07)
[1] 16
qbinom(0.01, 5016279, 5e-07)
Bug report Spearman's rank correlation test (PR#13574) was moved
to trashcan with empty Notes field. I would like to learn, what was wrong
with this bug report. Can i ask the developers to add a note to it?
Thank you in advance.
Petr.
__
On Wed, May 13, 2009 at 02:35:12PM +0200, gos...@igmm.cnrs.fr wrote:
I cannot explain why R seems to have problems adding two big numbers.
sprintf(%f,10^4+10^19) gives 10010240.00
instead of 1001.00
problems seems to arrive when i'm
On Mon, May 11, 2009 at 05:06:38PM +0200, Martin Maechler wrote:
The version I have committed a few hours ago is indeed a much
re-simplified version, using as.character(.) explicitly
The current development version (2009-05-11 r48528) contains
in ?factor a description of levels parametr
On Mon, May 11, 2009 at 05:06:38PM +0200, Martin Maechler wrote:
[...]
The version I have committed a few hours ago is indeed a much
re-simplified version, using as.character(.) explicitly
and consequently no longer providing the extra optional
arguments that we have had for a couple of days.
On Sat, May 09, 2009 at 10:55:17PM +0200, Martin Maechler wrote:
[...]
If'd revert to such a solution,
we'd have to get back to Peter's point about the issue that
he'd think table(.) should be more tolerant than as.character()
about almost equality.
For compatibility reasons, we could also
On Wed, May 06, 2009 at 10:41:58AM +0200, Martin Maechler wrote:
PD I think that the real issue is that we actually do want almost-equal
PD numbers to be folded together.
yes, this now (revision 48469) will happen by default, using signif(x, 15)
where '15' is the default for the
On Fri, May 08, 2009 at 03:18:01PM +0200, Martin Maechler wrote:
As long as we don't want to allow factor(numeric) to fail --rarely --
I think (and that actually has been a recurring daunting thought
for quite a few days) that we probably need an
extra step of checking for duplicate levels,
On Fri, May 08, 2009 at 05:14:48PM +0200, Petr Savicky wrote:
Let me suggest to consider the following modification, where match() is done
on the strings, not on the original values.
levels - unique(as.character(sort(unique(x
x - as.character(x)
f - match(x, levels)
An alternative
On Fri, May 08, 2009 at 06:48:40PM +0200, Martin Maechler wrote:
PS == Petr Savicky savi...@cs.cas.cz
on Fri, 8 May 2009 18:10:56 +0200 writes:
[...]
PS ... I have
PS strong objections against the existing implementation of
as.character(),
{(because it is not *accurate
On Wed, May 06, 2009 at 10:41:58AM +0200, Martin Maechler wrote:
PD I think that the real issue is that we actually do want almost-equal
PD numbers to be folded together.
yes, this now (revision 48469) will happen by default, using signif(x, 15)
where '15' is the default for the
On Mon, May 04, 2009 at 07:28:06PM +0200, Peter Dalgaard wrote:
Petr Savicky wrote:
For this, we get
convert(0.3)
[1] 0.3
convert(1/3)
[1] 0. # 16 digits suffice
convert(0.12345)
[1] 0.12345
convert(0.12345678901234567)
[1
On Tue, May 05, 2009 at 11:27:36AM +0200, Peter Dalgaard wrote:
I know. The point was rather that if you are not careful with rounding,
you get the some of the bars wrong (you get 2 or 3 small bars very close
to each other instead of one longer one). Computed p values from
permutation tests
On Mon, May 04, 2009 at 05:39:52PM +0200, Martin Maechler wrote:
[snip]
Let me quickly expand the tasks we have wanted to address, when
I started changing factor() for R-devel.
1) R-core had unanimously decided that R 2.10.0 should not allow
duplicated levels in factors anymore.
When
On Wed, Apr 22, 2009 at 04:30:36PM -0400, Stavros Macrakis wrote:
[snip]
Now consider 1e40, which has the property
that floor(x)==x==ceiling(x), which you might think characterizes an
integer; but it also has the property that x+1 == x. Similarly for
1/3 * 1e40.
[snip]
The number 1/3 * 1e40
On Thu, Apr 23, 2009 at 11:37:37AM +0200, Martin Maechler wrote:
[snip]
TP To test whether a value is an integer value, you can so something
like this:
is.wholenumber - function(x, tolerance = .Machine$double.eps^0.5)
TP return(abs(x - round(x)) tolerance)
On Tue, Mar 24, 2009 at 07:41:31AM -0700, Ulrike Grömping wrote:
Probably, k is needed also later. Assumig that 2^k works correctly,
the following could be sufficient
if (!is.null(nruns)){
k - round(log2(nruns))
if (!2^k==nruns) stop(nruns must be a power of 2.)}
On Tue, Mar 24, 2009 at 02:45:57PM +0100, Uwe Ligges wrote:
gives the custom error message nruns must be a power of 2., which is
generated in the first check within function FrF2:
if (!is.null(nruns)){
k - floor(log2(nruns))
if (!2^k==nruns) stop(nruns must be a power of
On Mon, Mar 16, 2009 at 07:39:23PM -0400, Stavros Macrakis wrote:
...
Let's look at the extraordinarily poor behavior I was mentioning. Consider:
nums - (.3 + 2e-16 * c(-2,-1,1,2)); nums
[1] 0.3 0.3 0.3 0.3
Though they all print as .3 with the default precision (which is
normal and
On Tue, Mar 17, 2009 at 10:15:39AM +0100, Wacek Kusnierczyk wrote:
...
there's one more curiosity about factors, in particular, ordered factors:
ord - as.ordered(nums); ord
# [1] 0.300 0.3 0.3
0.300
# Levels: 0.300
On Tue, Mar 17, 2009 at 10:04:39AM -0400, Stavros Macrakis wrote:
...
1) Factor allows repeated levels, e.g. factor(c(1),c(1,1,1)), with no
warning or error.
Yes, this is a confusing behavior, since repeated levels are never meaningful.
2) Even from distinct inputs, factor of a numeric vector
On Mon, Mar 16, 2009 at 06:36:53AM -0700, Daniel Murphy wrote:
Hello:I am trying to match the value 0.3 in the sequence seq(.2,.3). I get
0.3 %in% seq(from=.2,to=.3)
[1] FALSE
As others already pointed out, you should use seq(from=0.2,to=0.3,by=0.1)
to get 0.3 in the sequence. In order to get
Full_Name: Petr Savicky
Version: 2.7.2, 2.8.1, 2.9.0
OS: Linux
Submission from: (NULL) (147.231.6.9)
The p-value of Spearman's rank correlation test is calculated in
cor.test(x, y, method=spearman)
using algorithm AS 89. However, the way how AS 89 is used incures error,
which may be an order
seq(0,1,0.1)==0.4
[1] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
seq(0,1,0.1)==0.6
[1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
seq(0,1,0.1)==0.8
[1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
What is wrong with
Hi All:
help(cor.test) claims
For Spearman's test, p-values are computed using algorithm AS 89.
Algorithm AS 89 was introduced by the paper
D. J. Best D. E. Roberts (1975), Algorithm AS 89: The Upper Tail
Probabilities of Spearman's rho. Applied Statistics, Vol. 24, No. 3, 377-379.
Table
Hi All:
The p-value of Spearman's rank correlation test is calculated using algorithm
AS 89. However, the way how AS 89 is used incures error, which may be an order
of magnitude larger than the error of the original algorithm.
In case of no ties AS 89 expects an even value of the statistic
S =
Dear R developers:
There is a possible bug in calculating the p-value
for Spearman's rank correlation.
Line 155 in file
R-patched/src/library/stats/R/cor.test.R
is
as.double(round(q) + lower.tail),
I think, it should be
as.double(round(q) + 2*lower.tail),
The reason is that round(q)
Full_Name: Petr Savicky
Version: all versions starting from 1.7.0
OS: observed on Linux, but is platform independent
Submission from: (NULL) (62.24.91.47)
The function runif(n) contains a protection against the zero state of
Mersenne Twister stored in .Random.seed. If the state is zero
could be considered.
Petr Savicky.
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= 2; j = 624; j++)
if(RNG_Table[RNG_kind].i_seed[j] != 0) {
notallzero = 1;
break;
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2147483646 2147483646
[4,] 2147483646.5 2147483646 2147483646
[5,] 2147483647.0 2147483647 2147483647
[6,] 2147483647.5 2147483647 2147483647
[7,] 2147483648.0 NA NA
Petr Savicky.
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by a different function, not the default gc() itself.
Petr Savicky.
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or not.
Structures, for which this succeeds are then removed. Am I right?
If yes, is it possible during gc() to determine also cases,
when NAMED may be dropped from 2 to 1? How much would this increase
the complexity of gc()?
Thank you in advance for your kind reply.
Petr Savicky
- matrix(as.integer(1),nrow=5,ncol=3) + as.integer(0)
.Call(getnamed,u) # 1 (OK)
ncol(u)
.Call(getnamed,u) # 2 (so, ncol does the same)
Is this a bug?
Petr Savicky.
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, the object duplicates, but nothing more.
The main part of my previous email (question concerning
a possible bug in the behavior of nrow(a) and ncol(a))
remains open.
Petr Savicky.
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:6)
dim(a,a) # Error: 2 arguments passed to 'dim' which requires 1
May be, also other solutions exist.
Petr Savicky.
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is not 0.
I appreciate, if anybody could give me advice on the above things.
Petr Savicky.
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the initial scrambling in user_unif_init, use
seed = 3602842457U * (seed - 2358491998U);
Petr Savicky.
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Savicky.
If it may be usefull, I have written to small function (Unique and isEqual)
which can deal with this problem of the double numbers.
I also add some other conditions for the same problem.
0.3 == 0.15 + 0.15
0.3 == 0.1 + 0.2
1 - 0.7 == 0.3
0.1 == 1 - 0.9
0.2
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