[R] cannot compile R with readline
Hello, I am trying to install R-3.4.1 on a linux cluster. I always get the following error message: checking readline/history.h usability... yes checking readline/history.h presence... yes checking for readline/history.h... yes checking readline/readline.h usability... yes checking readline/readline.h presence... yes checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... no checking for main in -lncurses... no checking for main in -ltermcap... no checking for main in -ltermlib... no checking for rl_callback_read_char in -lreadline... no configure: error: --with-readline=yes (default) and headers/libs are not available As you can see, the R configure script finds the header files, but something happens with the rl_callback_read_char. Here is more info on this from the config.log: configure:22995: checking for rl_callback_read_char in -lreadline configure:23020: mpicc -g -o conftest -O2 -fPIC -I/home/giessen/ivanov/build/packages/usr/include -I/home/giessen/ivanov/build/packages/usr/include/readline -I/home/giessen/ivanov/build/packages/usr/include -I/home/giessen/ivanov/build/packages/usr/include/readline -L/home/giessen/ivanov/build/packages/usr/lib64 -L/home/giessen/ivanov/build/packages/lib64 conftest.c -lreadline >&5 /home/giessen/ivanov/build/packages/usr/lib64/libreadline.so: undefined reference to `PC' /home/giessen/ivanov/build/packages/usr/lib64/libreadline.so: undefined reference to `tgetflag' /home/giessen/ivanov/build/packages/usr/lib64/libreadline.so: undefined reference to `tgetent' /home/giessen/ivanov/build/packages/usr/lib64/libreadline.so: undefined reference to `UP' /home/giessen/ivanov/build/packages/usr/lib64/libreadline.so: undefined reference to `tputs' /home/giessen/ivanov/build/packages/usr/lib64/libreadline.so: undefined reference to `tgoto' /home/giessen/ivanov/build/packages/usr/lib64/libreadline.so: undefined reference to `tgetnum' /home/giessen/ivanov/build/packages/usr/lib64/libreadline.so: undefined reference to `BC' /home/giessen/ivanov/build/packages/usr/lib64/libreadline.so: undefined reference to `tgetstr' collect2: error: ld returned 1 exit status I have the readline-6.3 library installed. I compiled it from source, so nothing should be missing. Any suggestions will be appreciated. Best regards, Martin __ 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.
[R] setAs: does it overwrite existing coerce methods?
Dear R users,
I am working a lot with spatial objects from the package sp. I need to write my
own method for converting a SpatialGrid
to a SpatialPoints object, because the default method as("SpatialGrid",
"SpatialPoints") returns a SpatialPoints object with
decreasing latitudes. If I write my own method (that creates a SpatialPoints
object with both longitudes and latitudes increasing)
using setAs, will it overwrite the default method provided by the sp packages?
Will this result in breaking all other methods in sp
that use as()? If the sp methods always call the as() method from sp, this
should not be the case. But if they happen to call the method I
am going to define instead of the one they expect, they might get broken. So,
what is your opinion about this is? Is there a way to safely
define a coerce method with setAs that only the code written by me uses, so
that no other code coming from packages is broken?
Thank you very much!
Best regards,
Martin
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and provide commented, minimal, self-contained, reproducible code.
[R] spectral coherence non-overlapping windows: confidence intervals?
Dear R users,
The confidence intervals for the squared coherence and phase, plotted by
plot.spec.coherence() and plot.spec.phase, respectively,
use the formulae 10.14 and 10.11 from Bloomfield, P. (1976) Fourier Analysis of
Time Series: An Introduction. Wiley:
gg - 2/x$df
se - sqrt(gg/2)
z - -qnorm((1 - ci)/2)
coh - sqrt(x$coh);
(tanh(atanh(coh) + z * se))^2; # this is the 95% line for the coherence
cl - asin(pmin(0., qt(ci, 2/gg - 2) * sqrt(gg * (coh^{ -2 } - 1)/(2 * (1
- gg); # this is for the phase
Does somebody know how these formulae extend in case of calculating the
cross-spectrum via
K non-overlapping windows, i.e. via the Welch method? I would be very thankful
if you could direct
me to some literature. I tried finding something on the topic myself, but the
information is only
for the case when one smooths with spectral windows.
Best regards,
Martin
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] field of two possible types in reference classes
Dear R users, I am learning the OOP programming with R, in particular with reference classes. If I have a class, e.g. myclass - setRefClass(class=myclass, fields=list(x=numeric)); I know that if I do not want to set any class for x, I can just type fields=list(x=ANY). But what if I want to allow x to be of two possible classes, e.g. numeric or logical. They do not inherit from each other, so setting the one and passing the other class results in an error. Any suggestions will be appreciated. Best regards, Martin __ R-help@r-project.org mailing list 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.
[R] lattice question: removing strips
Dear lattice users, I am trying to produce a lattice graph with two conditioning variables. My problem is that I only want to show the strips for the levels of the second conditioning variable. I want to remove the strips for the levels of the first conditioning variable. I tried with the strip function, but if I tell it to return FALSE or NULL whenever which.given == 1, I just get empty space below the strips for the second conditioning variable. And I want to remove that space altogether. Is it somehow achievable in lattice? I also tried setting layout.heights$strip to 0 when which.given == 1, but it seems to only work globally, so either the strips for both conditioning variables vanish, or both are present. Any suggestions will be appreciated. Best regards, __ R-help@r-project.org mailing list 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.
Re: [R] lattice question: removing strips
Dear Pascal,
Thank You very much for Your reply. Here is a minimal working example:
library(lattice);
# this is with both strips plotted:
data - data.frame(x=1:5, y=6:10, f1=c(a1, a1, a1, a2, a3),
f2=c(b1, b2, b2, b1, b2));
p - xyplot(y ~ x | f1 + f2, data=data)
print(p);
# and this is my attempt to only plot the strips for the second conditioning
variable, i.e. for f2:
my.strip - function(which.given, strip.levels, ...) {
if(which.given == 1) {
return(FALSE);
}
else {
strip.default(which.given=which.given, strip.levels=c(TRUE, FALSE), ...);
}
}
p1 - xyplot(y ~ x | f1 + f2, data=data, strip=my.strip)
print(p1);
#As You can see, here I do not get the strips for f1 potted, but there is an
empty space below
the strips for f1, which I cannot get rid of. I only want to show the strips
for f2. Directly
below them I want to see the panels themselves, instead of an empty space for
the missing f1 strips.
Any suggestions?
Best regards,
Martin
Оригинално писмо
От: Pascal Oettli
Относно: Re: [R] lattice question: removing strips
До: Martin Ivanov
Изпратено на: Понеделник, 2014, Февруари 10 12:56:21 EET
Hello,
Please provide a quot;commented, minimal, self-contained, reproducible
codequot;, as requested.
Regards,
Pascal
On 10 February 2014 19:48, Martin Ivanov wrote:
Dear lattice users,
I am trying to produce a lattice graph with two conditioning variables.
My problem is that I only want to show the strips for the levels of the
second conditioning variable.
I want to remove the strips for the levels of the first conditioning
variable.
I tried with the strip function, but if I tell it to return FALSE or NULL
whenever which.given == 1, I just get empty space below the strips for the
second conditioning variable. And I want to remove that space altogether.
Is it somehow achievable in lattice?
I also tried setting layout.heights#36;strip to 0 when which.given == 1,
but it seems to only work globally, so either
the strips for both conditioning variables vanish, or both are present.
Any suggestions will be appreciated.
Best regards,
__
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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.
--
Pascal Oettli
Project Scientist
JAMSTEC
Yokohama, Japan
__
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and provide commented, minimal, self-contained, reproducible code.
[R] avoiding eval parse with indexing
Hello, I would like to get an advice on how the notorious eval(parse()) construct could possibly be avoided in the following example. I have an array x, which can have different number of dimensions, but I am only interested in extracting, say, the first element of the first dimension. Currently I achieve this in this way: eval(parse(text=paste0(x[1, paste(rep(, , length(dim(x)) - 1), collapse=), ]))) Is it possible to avoid the eval parse here? How? Best regards, Martin __ R-help@r-project.org mailing list 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.
[R] [Fw: Re: avoiding eval parse with indexing ]
---BeginMessage--- Dear Mr Gunter, with a slight correction: z - array(1:24,dim=2:4) d - dim(z) ix - lapply(d[-1], seq_len) do.call([, c(list(z),1,ix)) [,1] [,2] [,3] [,4] [1,]17 13 19 [2,]39 15 21 [3,]5 11 17 23 your suggestion worked and is exactly what I wanted! Thank You very much indeed! I want to get rid of all eval(parse) constructs in my code, and this was the greatest obstacle I had. Now I will be able to do this. As they say, eval parse in the code is just lack on knowledge. Best regards, Martin Оригинално писмо От: Florent D. Относно: Re: [R] avoiding eval parse with indexing До: Bert Gunter Изпратено на: Неделя, 2013, Май 26 18:07:26 EEST library(abind) asub(x, 1, 1) On Sun, May 26, 2013 at 10:43 AM, Bert Gunter wrote: Martin: Well, assuming I understand, one approach would be to first get the dim attribute of the array and then create the appropriate call using that: z - array(1:24,dim=2:4) d - dim(z) ix -lapply(d[-c(1,1)],seq_len) do.call(quot;[quot;, c(list(z),1,1,ix)) [1] 1 7 13 19 Is that what you want? -- Bert On Sun, May 26, 2013 at 6:56 AM, Martin Ivanov wrote: Hello, I would like to get an advice on how the notorious eval(parse()) construct could possibly be avoided in the following example. I have an array x, which can have different number of dimensions, but I am only interested in extracting, say, the first element of the first dimension. Currently I achieve this in this way: eval(parse(text=paste0(quot;x[1quot;, paste(rep(quot;, quot;, length(dim(x)) - 1), collapse=quot;quot;), quot;]quot;))) Is it possible to avoid the eval parse here? How? Best regards, Martin __ R-help@r-project.org mailing list 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ R-help@r-project.org mailing list 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. ---End Message--- __ R-help@r-project.org mailing list 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.
Re: [R] avoiding eval parse with indexing
Dear Arun, Thank You very much, your suggestion also works and seems to also be more convenient. I think though, that Mr Gunter's suggestion should be more efficient, as it uses directly the Extract operator. Thank You all very much for Your responsiveness. R does have a wonderful community! Best regards, Martin Оригинално писмо От: arun Относно: Re: [R] avoiding eval parse with indexing До: Martin Ivanov Изпратено на: Неделя, 2013, Май 26 18:48:33 EEST Hi, You could use: library(abind) #using Berend's and Bert's example x1 - array(runif(9),dim=c(3,3)) x2 - array(runif(8),dim=c(2,2,2)) z - array(1:24,dim=2:4) #applying your code: eval(parse(text=paste0(quot;x1[1quot;,paste(rep(quot;,quot;,length(dim(x1))-1),collapse=quot;quot;),quot;]quot;))) #[1] 0.6439062 0.7139397 0.6017418 eval(parse(text=paste0(quot;x2[1quot;,paste(rep(quot;,quot;,length(dim(x2))-1),collapse=quot;quot;),quot;]quot;))) # [,1] [,2] #[1,] 0.026671344 0.2116831 #[2,] 0.003903368 0.1551140 eval(parse(text=paste0(quot;z[1quot;,paste(rep(quot;,quot;,length(dim(z))-1),collapse=quot;quot;),quot;]quot;))) # [,1] [,2] [,3] [,4] #[1,] 1 7 13 19 #[2,] 3 9 15 21 #[3,] 5 11 17 23 asub(x1,1,1,drop=TRUE) #[1] 0.6439062 0.7139397 0.6017418 asub(x2,1,1,drop=TRUE) # [,1] [,2] #[1,] 0.026671344 0.2116831 #[2,] 0.003903368 0.1551140 asub(z,1,1,drop=TRUE) # [,1] [,2] [,3] [,4] #[1,] 1 7 13 19 #[2,] 3 9 15 21 #[3,] 5 11 17 23 A.K. - Original Message - From: Martin Ivanov To: r-help@r-project.org Cc: Sent: Sunday, May 26, 2013 9:56 AM Subject: [R] avoiding eval parse with indexing Hello, I would like to get an advice on how the notorious eval(parse()) construct could possibly be avoided in the following example. I have an array x, which can have different number of dimensions, but I am only interested in extracting, say, the first element of the first dimension. Currently I achieve this in this way: eval(parse(text=paste0(quot;x[1quot;, paste(rep(quot;, quot;, length(dim(x)) - 1), collapse=quot;quot;), quot;]quot;))) Is it possible to avoid the eval parse here? How? Best regards, Martin __ R-help@r-project.org mailing list 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. __ R-help@r-project.org mailing list 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.
[R] mcmapply should be parallel, but runs serial?
Dear all,
I am running R-3.0 on Slackware64 Linux (Linux marto 2.6.38.4 #1 SMP Thu Apr 21
20:48:11 CDT 2011 x86_64 Intel(R) Core(TM) i5-2520M CPU @ 2.50GHz GenuineIntel
GNU/Linux)
Here is a minimal example:
library(parallel);
fun - function(fileName) { file.create(fileName); Sys.sleep(time=120); }
mcmapply(fileName=c(mcm1, mcm2), FUN=fun, mc.cores=2);
mclapply(X=c(mcl1, mcl2), FUN=fun, mc.cores=2);
Just compare the time stamps of the mcm* and mcl* files. You will see that
while the mcl* files have equal time stamps, i.e. they have been created
simultaneously,
the mcm files are created one after the other, with exactly 120 seconds of
difference.
This is what I see on my machine:
bash-4.1$ ls -l mcm*
-rw-r--r-- 1 marto users 0 May 11 14:25 mcm1
-rw-r--r-- 1 marto users 0 May 11 14:27 mcm2
bash-4.1$ ls -l mcl*
-rw-r--r-- 1 marto users 0 May 11 14:29 mcl1
-rw-r--r-- 1 marto users 0 May 11 14:29 mcl2
Any ideas?
Best regards,
Martin
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[R] cannot compile R on Cray XE6 HLRS HERMIT
Dear All,
I am trying to compile R-3.0 on Cray xe6 (HLRS) HERMIT, no success so far.
Here is my experience:
I use this to configure and make R:
CC=cc \
CXX=CC \
F77=ftn \
FC=ftn \
CPPFLAGS=-I$PREFIX/include \
LDFLAGS=-L$PREFIX/lib${LIBDIRSUFFIX} \
./configure --prefix=$PREFIX \
--exec-prefix=$PREFIX \
--bindir=$PREFIX/bin \
--sbindir=$PREFIX/sbin \
--sysconfdir=$PKG/etc \
--localstatedir=$PKG/var \
--libdir=$PREFIX/lib${LIBDIRSUFFIX} \
--datarootdir=$PREFIX/share \
--datadir=$PREFIX/share \
--infodir=$PREFIX/info \
--mandir=$PREFIX/man \
--docdir=$PREFIX/doc/$PRGNAM-$VERSION \
rdocdir=$PREFIX/doc/$PRGNAM-$VERSION \
rincludedir=$PREFIX/include \
rsharedir=$PREFIX/share \
--disable-BLAS-shlib \
--with-blas \
--with-lapack \
--without-x \
|| exit 1
make || exit 1
My environment is as follows:
1) modules/3.2.6.7 13)
udreg/2.3.2-1.0401.5929.3.3.gem 25)
configuration/1.0-1.0401.35391.1.2.gem
2) xtpe-network-gemini 14) ugni/4.0-1.0401.5928.9.5.gem
26) hosts/1.0-1.0401.35364.1.115.gem
3) xtpe-interlagos 15) pmi/4.0.1-1..9421.73.3.gem
27) lbcd/2.1-1.0401.35360.1.2.gem
4) cray-mpich2/5.6.4 16)
dmapp/3.2.1-1.0401.5983.4.5.gem 28)
nodehealth/5.0-1.0401.38460.12.18.gem
5) eswrap/1.0.917)
gni-headers/2.1-1.0401.5675.4.4.gem 29) pdsh/2.26-1.0401.37449.1.1.gem
6) torque/2.5.918) xpmem/0.1-2.0401.36790.4.3.gem
30) shared-root/1.0-1.0401.37253.3.50.gem
7) moab/6.1.5.s199219)
job/1.5.5-0.1_2.0401.35380.1.10.gem 31) switch/1.0-1.0401.36779.2.72.gem
8) system/ws_tools 20)
csa/3.0.0-1_2.0401.37452.4.50.gem 32) xe-sysroot/4.1.40
9) system/hlrs-defaults21)
dvs/1.8.6_0.9.0-1.0401.1401.1.120 33) atp/1.6.2
10) xt-asyncpe/5.19 22) rca/1.0.0-2.0401.38656.2.2.gem
11) gcc/4.7.2 23)
audit/1.0.0-1.0401.37969.2.32.gem
12) xt-libsci/12.0.01 24) ccm/2.2.0-1.0401.37254.2.142
1. PrgEnv-gnu/4.1.40
checking for C libraries of cc -std=gnu99...
-L/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64
-L/opt/cray/udreg/2.3.2-1.0401.5929.3.3.gem/lib64
-L/opt/cray/ugni/4.0-1.0401.5928.9.5.gem/lib64
-L/opt/cray/pmi/4.0.1-1..9421.73.3.gem/lib64
-L/opt/cray/dmapp/3.2.1-1.0401.5983.4.5.gem/lib64
-L/opt/cray/xpmem/0.1-2.0401.36790.4.3.gem/lib64
-L/opt/cray/rca/1.0.0-2.0401.38656.2.2.gem/lib64
-L/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/lib
-L/opt/cray/libsci/12.0.01/gnu/47/interlagos/lib
-L/opt/cray/xe-sysroot/4.1.40/usr/lib64 -L/opt/cray/xe-sysroot/4.1.40/lib64
-L/opt/cray/xe-sysroot/4.1.40/usr/lib/alps -L/usr/lib/alps
-L/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2
-L/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64
-L/lib/../lib64 -L/usr/lib/../lib64
-L/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../.. -lrca
-L/opt/cray/atp/1.6.2/lib/ -lAtpSigHCommData -lAtpSigHandler -lgfortran
-lscicpp_gnu -lsci_gnu_mp -lstdc++ -lmpich_gnu_47 -lmpl -lrt
-lxpmem -ldmapp -lugni -lpmi -lalpslli -lalpsutil -ludreg -lpthread -lm -lgomp
-lgcc_eh
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no
extra underscore
checking whether ftn appends underscores to external names... yes
checking whether ftn appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether ftn and cc -std=gnu99 agree on int and double... configure:
WARNING: ftn and cc -std=gnu99 disagree on int and double
configure: error: Maybe change CFLAGS or FFLAGS?
2. PrgEnv-gnu/4.1.40 + craype-target-native
R is now configured for x86_64-unknown-linux-gnu
Source directory: .
Installation directory:/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr
C compiler:cc -std=gnu99 -g -O2
Fortran 77 compiler: gfortran -g -O2
C++ compiler: CC -g -O2
Fortran 90/95 compiler:ftn -g -O2
Obj-C compiler:
Interfaces supported:
External libraries:readline
Additional capabilities: JPEG
Options enabled: shared R library, shared BLAS, R profiling, memory
profiling, strict barrier, static HTML
Recommended packages: yes
nmath/*.o` ../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a
../extra/tre/libtre.a ../extra/xz/liblzma.a -L../../lib -lRblas -lgfortran
-lm -lquadmath -lreadline -lncurses -lrt -ldl -lm
make[4]: Entering directory
`/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/build/tmp/R-3.0.0/src/main'
mkdir -p -- /univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/build/tmp/R-3.0.0/bin/exec
make[4]: Leaving directory
`/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/build/tmp/R-3.0.0/src/main'
make[3]: Leaving
[R] lattice: ticks at the joining sides of panels?
Dear R users, I would like to produce a lattice graph that keeps the ticks at the joining sides of the panels. For example: library(lattice) library(datasets) xyplot(lat ~ long | cut(depth, 2), data = quakes, between=list(x=1)) You can see that ticks are plotted at the sides 1 (bottom), 2 (right) and 3 (top) of panel 1 and 1 (bottom), 3 (top) and 4 (right) of panel 2. Is it possible to plot ticks at side 4 (right) of panel 1 and side 2 (left) of panel 2? Thank You very much for Your attention. Best regards, Martin __ R-help@r-project.org mailing list 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.
Re: [R] non-overlapping blocks bootstrap?
Dear Rafael, Thank You very much for Your reply. I need to use non-overlapping blocks and such that each block ends with an element having an index multiple of 3 in the original series. For example if I have the numbers: 1 2 3 4 5 6 7 8 9, the samples I could take are: 123 456 789, 456 789 123, 789 123 456, 789 456 123, 456 123 789 and 123 789 456. As You see, the blocks must contain consecutive elements from the original sample. The reason why I need exactly that resampling is that my data are monthly and are stratified by season. So in effect my time series looks like this, e.g. for the summer: 1 2 34 5 6 7 8 9 10 11 12 ... : the indices in the data J J AJ J A J J A J J A : the months 19891990 1991 1992 : the years and so on. So the block size of 3 is naturally determined by the nature of my data. I assume the interannual correlations are negligible compared to the intraseasonal ones and neglect the former. Best regards, Martin Оригинално писмо От: Rafael Robledo Относно: Re: [R] non-overlapping blocks bootstrap? До: Martin Ivanov Изпратено на: Вторник, 2013, Февруари 5 23:57:52 EET If you only need to take blocks of a defined size from a time series, you may use sample function (which default behavior is to sample without replace). For example: tt - 1:24 ss - sample(tt, replace=F) bs - 3 nb - length(tt) / bs res - split(ss, rep(1:nb, each=bs)) Hope this helps, On Tue, Feb 5, 2013 at 8:28 AM, Martin Ivanov wrote: Dear R users, I need to perform a block bootstrap to a time series. The block size must be 3 and the blocks must NOT overlap. I found a number of functions for bootstrap in R (tsboot, tsbootstrap in tseries, and LocSig in SpatialVx), but neither of them seems to implement non-overlapping blocks. Is there a way to perform a bootstrap with non-overlapping fixed-size blocks in R? Best regards, Martin __ R-help@r-project.org mailing list 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. -- Rafael Robledo J. On Tue, Feb 5, 2013 at 8:28 AM, Martin Ivanov wrote: Dear R users, I need to perform a block bootstrap to a time series. The block size must be 3 and the blocks must NOT overlap. I found a number of functions for bootstrap in R (tsboot, tsbootstrap in tseries, and LocSig in SpatialVx), but neither of them seems to implement non-overlapping blocks. Is there a way to perform a bootstrap with non-overlapping fixed-size blocks in R? Best regards, Martin __ R-help@r-project.org mailing list 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. -- Rafael R. __ R-help@r-project.org mailing list 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.
[R] non-overlapping blocks bootstrap?
Dear R users, I need to perform a block bootstrap to a time series. The block size must be 3 and the blocks must NOT overlap. I found a number of functions for bootstrap in R (tsboot, tsbootstrap in tseries, and LocSig in SpatialVx), but neither of them seems to implement non-overlapping blocks. Is there a way to perform a bootstrap with non-overlapping fixed-size blocks in R? Best regards, Martin __ R-help@r-project.org mailing list 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.
[R] print and cat not working with parallelised functions?
Dear R Community,
I am running R version 2.15.2 with package parallel version 2.15.2.
The problem is that cat and print do not produce any output. Also assigning
objects to the .GlobalEnv does not work. This makes it difficult for me to
debug code. This can be seen from the
following minimal working example:
library(parallel)
fun2 - function(x) {
b - x; # try to export the object to the workspace
print(x); # try to print x
}
fun1 - function(d) {
cl - makeCluster(getOption(cl.cores, detectCores()));
parSapply(cl=cl, X=seq_along(d), FUN=fun2);
stopCluster(cl=cl);
}
fun3 - function(d) sapply(X=seq_along(d), FUN=fun2);
fun1(d=1:5)
a - fun3(d=1:5)
print only works when fun3 is called, that is when there is no parallelisation.
The
same is also true for the - assignment.
I am almost sure this is not a bug, but a feature, so I would like to ask you
for some explanation and also for some ideas how to handle debugging code when
no printing or exporting objects to the workspace works.
Any suggestions will be appreciated.
Best regards,
Martin Ivanov
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Re: [R] get: problem with environments
Dear Prof. Lumley, Thank You very much for Your reply. I implemented Your idea not to directly call get from sapply, but inside a function, supplied to sapply. In this way the 3-rd parent frame is always the correct one, no matter whether I invoke testfun2() all by itself or inside another function. So my code is finally stable. It is quite tricky that when I call get() directly from sapply(), like this: sapply(X=, FUN=get, envir=parent.frame()), actually envir is an argument not to get, but to sapply, so it is evaluated in the environment of the caller, i.e. in the environment of testfun1, whose parent is the workspace, which of course does not contain the variables in the body of testfun1. In testfun2() sapply() calls get() from within a function and the envir argument to get() is supplied directly to it, i.e. it is evaluated in the environment of get(). Its first parent is the environment of the function calling get(), its second parent is the environment of sapply() and its third parent is the environment of testfun2(), which I need. That is why testfun2() works. I hope I have correctly understood this matter. Please correct me if I am wrong. Nevertheless the code is finally stable and it is thanks to Your suggestion. Best regards, Martin Ivanov Оригинално писмо От: Thomas Lumley Относно: Re: [R] get: problem with environments До: R. Michael Weylandt Изпратено на: Четвъртък, 2012, Октомври 11 01:52:14 EEST On Thu, Oct 11, 2012 at 11:18 AM, R. Michael Weylandt wrote: Thanks Prof Lumley, I'm still not sure how this gets to the call stack of 5 or 6 the OP reported or the difference between GUI amp; Terminal. Any thoughts there? I don't see how the terminal version is getting 5 and 6 rather than 1 and 2, but my testfun2() lets the OP do what he was originally trying to do. The difference between testfun() and print(testfun()) (ie, 1 vs 2, or 5 vs 6) is because of lazy evaluation: in print(testfun()), testfun() is called from inside print() when it needs the value to do method dispatch. I can't reproduce the value of 5, so I can't help much. For anyone wanting to experiment further, it would probably be simpler to use testfun-function() sys.nframe() rather than looking at whether a variable is found or not. I can't see how testfun() typed at the global command prompt can return anything other than 1, but maybe something is getting in between the console and the evaluator. For example: testfun() [1] 1 print(testfun()) [1] 2 capture.output(testfun()) [1] quot;[1] 6quot; I don't see why a pure console program should do this on Linux, though. -thomas -- Thomas Lumley Professor of Biostatistics University of Auckland __ R-help@r-project.org mailing list 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.
[R] get: problem with environments
Dear R users,
I am running R-2.15.1 in Linux Slackware64-14.0. Here is my minimal working
example:
testfun - function (x) {
a - 0;
sapply(X=a, FUN=get, envir=sys.frame(which=x));
}
Inside R, that is R called from within a Linux terminal, the following code
works:
testfun(x=5)
print(testfun(x=6))
But within rkward the above code fails and the following works:
testfun(x=1)
print(testfun(x=2))
As you can see, the number of contexts up the call stack that contain the
variable a
varies depending on the implementation. If I call testfun() from within
print(), I have to go
one context up the call stack than if I call testfun() alone by itself. This
implies
some inherent instability of my code.
Actually I need to provide get() access to the calling environment of sapply().
According to the documentation of parent.frame(), The parent frame of a
function evaluation is the environment in which the function was called. I
tried to use parent.frame() instead of sys.frame() above,
but the variable a is never found, regardless of what value I give to the
parameter n of
parent.frame().
I have basically three questions:
1. Do You have an idea how I could implement the code
more stably, so that the variable a is always visible to get, regardless of
whether testfun
is used alone by itself or called from within another function?
2. Why does the implementation with parent.frame() not work?
3. Why does the number of contexts in the call stack differ in R and in rkward?
It seems that when R is called from within the Linux terminal the call stack
contains 4 contexts more that it does when is called from rkward. This also
points to the instability of the code which I would like to solve.
Any suggestions on any on the above questions will be greatly appreciated.
Best regards,
Martin
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Re: [R] get: problem with environments
Thank You very much for Your replies.
Dear Michael,
Does this persist after a new session (perhaps running as R --vanilla) and/or
reinstall?
Yes, it does. After running R --vanilla, still there are 4 contexts more on the
call stack.
You didn't show us how you tried to use parent.frame()
I did it like this:
testfun1 - function (x1) {
a1 - 1;
sapply(X=a1, FUN=get, envir=parent.frame(x1));
}
testfun1(x1=1);
The above code never succeeds no matter what a number I give to x1.
3. Why does the number of contexts in the call stack differ in R and in
rkward?
It shouldn't. This is an issue that needs further sorting out.
Here is some more info on my setup:
sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-slackware-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
[4] LC_COLLATE=C LC_MONETARY=en_USLC_MESSAGES=en_US
[7] LC_PAPER=C LC_NAME=CLC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.15.1
Best regards,
Martin
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[R] cannot allocate a vector of size error, what explodes the the memory consumption?
Dear R users, I keep getting the message Error: cannot allocate a vector of size 543.2 Mb on my 64 bit Linux machine with 4 Gb of memory. I studied the problem and it occurs at the last lines of my code: .. a - laply(.); save(a, file= file.RData); rm(a); a is a 4-d array of size about 600 Mb. 3 minutes before R exits and displays the error message, the memory consumption of R (diagnosed with top) is 1.8 Gb. 2 minutes before the error, the memory consumption of R suddenly expands to 2.8 Gb and one minute before the error it is 3 Gb. This is why I suspect the problem is with my code. I have checked the same code with smaller data sets, it works perfectly. But with larger data sets, that is when the size of a gets bigger than, say, about 500 Mb, I get the error. Actually 99% of the time the memory consumption is up to 1.8 Gb. This is while things are going within laply. And at the end, at these 3 last lines something causes more than doubling of the R memory consumption. Have you got any idea what the culprit is? Any suggestions will be appreciated. Best regards, Martin - Гражданска отговорност – Цените на компаниите http://www.sdi.bg/onlineInsurance/?utm_source=gbgutm_medium=txtLinkutm_content=home __ R-help@r-project.org mailing list 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.
[R] contour line labels in trellis contourplot
Hello, In the classical function contour labels are drawn so that each contour line is broken at the place of the label, so that the label does not overlap the line. In the trellis contoourplot the labels are placed beside or over the line, controlled by the label.style parameter, but I could not find an option that would place the labels just as in the classical contour: breaking the contour line to make place for the label. Have You got any ideas how breaking the contours to make place for the labels could be achieved in a trellis contourplot? Best regards, Martin __ R-help@r-project.org mailing list 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.
[R] why does this simple example NOT work?
Hello, I want to create and save objects in a loop, but this is precluded by the following obstacle: this part of the script fails to work: assign(x=paste(a, 1, sep=), value=1); save(paste(a, 1, sep=), file=paste(paste(a, 1, sep=), .RData, sep=)) Do you know any workaround? I am already out of ideas. Best regards, Martin __ R-help@r-project.org mailing list 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.
[R] overlay contourplot with labels over spplot with color regions?
Dear R users, I have the following problem. I plot a SpatialPixelsDataFrame object with spplot and I need to add a contourplot of another spatial variable. To be more precise, I plot the SpatialPixelsDataFrame of the mean precipitation over Germany with coloured regions and I want to overlay the isolines of the 500, 1000 and 1500 m height above sea level. Of course I can plot the lines as SpatialLines using the sp.layout argument to spplot, but so I lose the labels on the lines. And I want the height above sea level to be labelled just as it is labelled in a contour plot. Is it possible to achieve that with lattice? I am still new to lattice, so I beg Your excuse in case I am asking something trivial. I googled a lot and tried a lot of things, but none worked. I tried with contour, it does work with Spatial objects, but unfortunately contour does not seem work with lattice. And the lattice equivalent contourplot does not recognise Spatial objects. I am already out of ideas. I am looking forward to Your replies. Any suggestions will be appreciated. Best regards, Martin __ R-help@r-project.org mailing list 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.
[R] contour lines with number labels in lattice?
Dear R users, I am new to lattice but am trying to get to grips with it. I need to add contour lines for the topography to a plot I created with spplot. The topography is available as a SpatialPixelsDataFrame object Z_sfc. If I plot it as spatial lines, after converting to a SpatialLines object: imageZ - as.image.SpatialGridDataFrame(x=Z_sfc); cLZ - contourLines(x=imageZ$x, y=imageZ$y, z=imageZ$z, levels = pretty(range(imageZ$z, na.rm=TRUE), 5)); sldfZ_sfc - ContourLines2SLDF(cL=cLZ, proj4string=CRS(proj4string(Z_sfc))) topography - list(sp.lines, sldfZ_sfc, first=FALSE, col=black); and then using the sp.layout=topgraphy argument to spplot, I lose the number labels on the lines. Is it possible in lattice to print the height of the isolines just as it is printed with contour? I tried with contour, it does work with SpatialPixelsDataFrame, but unfortunately contour does not seem work with lattice. And the lattice equivalent contourplot does not recognise SpatialPixelsDataFrame objects. Is it possible somehow to add a contour plot of Z_sfc to my plot? Many thanks in advance. Martin __ R-help@r-project.org mailing list 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.
[R] tck = 0 for the colorkey?
Dear R users, I am struggling with the colorkey on a levelplot lattice graphic. I want that no ticks are printed on the colorkey. That is, I want their size tck=0. Merely setting tck=0 t in the colorkey parameter does not work. Setting it in the lattice.par.set() removes the ticks from the levelplot, but not from the colorkey. Any suggestions will be appreciated. Best regards, Martin - Гражданска отговорност – Цените на компаниите http://www.sdi.bg/onlineInsurance/?utm_source=gbgutm_medium=txtLinkutm_content=home __ R-help@r-project.org mailing list 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.
[R] minor axis ticks in trellis graphics?
Dear R users, I need to add minor axis ticks to my graph. In traditional R this is easily achievable by simply adding a second axis with the minor ticks. But how to do that in trellis? I am already out of ideas. Any suggestions will be appreciated. Best regards, Martin - Гражданска отговорност – Цените на компаниите http://www.sdi.bg/onlineInsurance/?utm_source=gbgutm_medium=txtLinkutm_content=home __ R-help@r-project.org mailing list 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.
[R] trellis margin sizes in absolute units
Dear R users, I have a lot of experience with traditional R graphics, but I decided to turn to trellis as it was recommended for spatial graphs by the sp package. In traditional R graphics I always first set the size of the device region absolute units (e.g. mm) and then I firmly fix the inner margins with mai and the outer margins with oma also in absolute units. What is left from the device region is for the plot region. That is my general idea. My question is, is it possible to achieve that full control with trellis graphics? I have tried with the *.paddings parameters, but it seems to me that the margins are still larger than I have set them. Here is my example code: (mp is a SpatialPixelsDataFrame) xlim - c(.96*bbox(mp)[1, 1], 1.02*bbox(mp)[1, 2]); ylim - c(.992*bbox(mp)[2, 1], 1.005*bbox(mp)[2, 2]); b - 1; t - 2; # b, t : should be bottom and top figure margins l - 1; r - 6; # l, r : should be left and right figure margins asp - mapasp(data=mp, xlim=xlim, ylim=ylim); # I have set the width of the device region as w millimetres and here I calculate # its height, taking care of the aspect ratio h - b + t + asp*(w - (l + r)); postscript(output, onefile=FALSE, paper=special, width=w/25.4, height=h/25.4, horizontal=FALSE, fonts=c(Times), print.it=FALSE, colormodel=rgb, pointsize=12); # here I set all the possible paddings to make sure that all other margins are 0: trellis.par.set(layout.widths=list(left.padding=l, right.padding=r, key.ylab.padding = 0, ylab.axis.padding = 0, axis.key.padding = 0, units=mm), layout.heights=list(bottom.padding=b, top.padding=t, main.key.padding = 0, key.axis.padding = 0, axis.xlab.padding = 0, xlab.key.padding = 0, key.sub.padding = 0, units=mm), axis.components=list(bottom=list(pad1=.8), left=list(pad1=.8))); But still, the resulting margins are larger than I expect and to achieve the desired effect I have to set some parameters to negative numbers. So I guess there are some other graphical parameters that come into play, about which I do not know. Which margins are these *.padding parameters controlling: the outer (device) or the inner (figure) margins? Any suggestions will be appreciated. Regards, Martin - Гражданска отговорност – Цените на компаниите http://www.sdi.bg/onlineInsurance/?utm_source=gbgutm_medium=txtLinkutm_content=home __ R-help@r-project.org mailing list 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.
Re: [R] number of decimal places in a number?
Dear R users,
Thank You very much for Your responsiveness. I think the suggestion of arun's
modification of Josh's code works best and it is what I am going to implement.
Cite Ellison:
Surely the issue is not the particular numeric resolution of the numbers but
the idea that the bounding box limits should be integer multiples of the
resolution?
Is that not accomplished more straightforwardly by things like
min - resol * floor( min(lat)/resol )
max - resol * ceil( max(lat)/resol )
?
Dear Ellison,
not the bounding box limits, but the bounding box RANGE needs to be an integer
multiple of the resolution, that is max-min=ineger*resolution. The bbox limits
must just be rounded to the same number of digits as the resolution and include
all available values, of course.
Best regards.
Оригинално писмо
От: arun
Относно: Re: [R] number of decimal places in a number?
До: ted.hard...@wlandres.net
Изпратено на: Събота, 2012, Юли 7 22:50:03 EEST
Hi,
I checked the count for the cases (A) and (F) with a variant of Josh's
function:
decimalnumcount-function(x){stopifnot(class(x)==quot;characterquot;)
x-gsub(quot;(.*)(#92;#92;.)|([0]*#36;)quot;,quot;quot;,x)
nchar(x)
}
A)
x-quot;123456789.123456789quot;
decimalnumcount(x)
#[1] 9
x-quot;923456789.123456789quot;
decimalnumcount(x)
#[1] 9
B)
x-quot;0.012345quot;
decimalnumcount(x)
#[1] 10
c)
x - c(quot;3.14quot;, quot;3.142quot;, quot;3.1400quot;,
quot;123456.123456789quot;, quot;123456789.123456789quot;,pi,sqrt(2))
decimalnumcount(x)
#[1] 2 3 2 9 9 14 13
x
[1] quot;3.14quot; quot;3.142quot;
quot;3.1400quot;
[4] quot;123456.123456789quot; quot;123456789.123456789quot;
quot;3.14159265358979quot;
[7] quot;1.4142135623731quot;
D)
x - c(3.14, 3.142, 3.1400, 123456.123456789, 123456789.123456789,pi,sqrt(2))
decimalnumcount(as.character(x) )
[1] 2 3 2 9 6 14 13
#as.character(x)
#[1] quot;3.14quot; quot;3.142quot;
quot;3.14quot; quot;123456.123456789quot;
#[5] quot;123456789.123457quot; quot;3.14159265358979quot;
quot;1.4142135623731quot;
E)
print(pi,22)
#[1] 3.141592653589793115998
print(sqrt(2),22)
#[1] 1.414213562373095145475
x - c(quot;3.14quot;, quot;3.142quot;, quot;3.1400quot;,
quot;123456.123456789quot;,
quot;123456789.123456789quot;,quot;3.141592653589793115998quot;,quot;1.414213562373095145475quot;)
decimalnumcount(x)
#[1] 2 3 2 9 9 21 21
F)
formatC(pi,format=quot;fquot;,digits=22)
#[1] quot;3.1415926535897931159980quot;
formatC(sqrt(2),format=quot;fquot;,digits=22)
#[1] quot;1.4142135623730951454746quot;
x - c(quot;3.14quot;, quot;3.142quot;, quot;3.1400quot;,
quot;123456.123456789quot;,
quot;123456789.123456789quot;,formatC(pi,format=quot;fquot;,digits=22),formatC(sqrt(2),format=quot;fquot;,digits=22))
decimalnumcount(x)
#[1] 2 3 2 9 9 21 22
G)
# formatC() didn't show the limitations of print()
print(sqrt(2),22)
#[1] 1.414213562373095145475
print(sqrt(2),35)
#Error in print.default(sqrt(2), 35) : invalid 'digits' argument
formatC(sqrt(2),35)
#[1] quot;1.4142135623730951454746218587388285quot;
or,
formatC(sqrt(2),format=quot;fquot;,digits=35)
#[1] quot;1.41421356237309514547462185873882845quot;
#using 22
x - c(quot;3.14quot;, quot;3.142quot;, quot;3.1400quot;,
quot;123456.123456789quot;,
quot;123456789.123456789quot;,formatC(pi,format=quot;fquot;,digits=35),formatC(sqrt(2),format=quot;fquot;,digits=50))
decimalnumcount(x)
#[1] 2 3 2 9 9 35 50
So, I guess it will be better to deal with character strings rather than
using as.character.
A.K.
- Original Message -
From: quot;ted.hard...@wlandres.netquot;
To: r-help@r-project.org
Cc: Martin Ivanov
Sent: Saturday, July 7, 2012 8:12 AM
Subject: Re: [R] number of decimal places in a number?
I had thought of also (as well as my numerical routing) suggesting
a quot;gsub()quot; type solution like Joshua's below, but held back because
the result could depend on how the number arose (keyboard input,
file input, or from computation within R).
However, I now also realise that (again because of binary rounding
errors), the quot;gsub()quot; method has interesting differences from my
numerical method. Example:
[A] (as from my original method):
f(123456789.123456789)
# [1] 7
[B] (the quot;gsub()quot; method)
nchar(gsub(quot;(.*#92;#92;.)|([0]*#36;)quot;, quot;quot;,
as.character(123456789.123456789)))
# [1] 6
Now look at:
[C] (what as.character() does to 123456789.123456789)
as.character(123456789.123456789)
# [1] quot;123456789.123457quot;
[D] (quot;22quot; is the maximum number of decimal digits for print())
print(123456789.123456789,22)
# [1] 123456789.1234568
So as.character() has rounded it to 6 decimal places (agreeing
with [B]), while
[R] number of decimal places in a number?
Dear R users, I need a function that gets a number and returns its number of actual decimal places. For example f(3.14) should return 2, f(3.142) should return 3, f(3.1400) should also return 2 and so on. Is such function already available in R? If not, could you give me a hint how to achieve that? Many thanks in advance. - Гражданска отговорност – Цените на компаниите http://www.sdi.bg/onlineInsurance/?utm_source=gbgutm_medium=txtLinkutm_content=home __ R-help@r-project.org mailing list 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.
Re: [R] number of decimal places in a number?
Dear Mr Harding,
Thank You very much for Your responsiveness.
There would seem to be no clean general solution to this
question. An important issue would be: What use do you
want to put the result to?
I need this trick for the following task.
I am writing a function which has to determine the bounding box for a
spatial data set. The bounding box is a matrix(c(minLon minLat, maxLon,
maxLat)).
I have the longitudes (lon) and latitudes (lat), and I have a resolution (r),
for example
r = 0.004. The bounding box must have the same number of digits as resolution.
So I first have to truncate min(lon) and min(lat) to 3 decimal places,
then take the ceiling of max(lat)*10^3 and max(lon)*10^3 divided by 10^3. So I
have the
maximal interval with resolution r for each variable (lat or lon). Then I have
to determine
the number of cells in each direction, which I take as
ceiling((maxLat-minLat)/r) and
ceiling((maxLon-minLon)/r). Here is an example of my code:
# get the first n digits from a number
truncf - function(x, digits) {
# some control:
for(i in c(x, digits)) if(!(is.numeric(get(i)) length(get(i)) == 1))
stop(i, in truncatef must be a numeric scalar!);
## make sure that digits is an integer:
if(as.integer(digits) - digits) stop(Please provide an integer digits to
truncf!);
x - trunc(x*10^digits)/10^digits;
x;
}
for(i in 0:5) if(!(resolution*10^i - as.integer(resolution*10^i))) break;
lonMin - truncf(x=min(lon), digits=i); lonMax -
ceiling(x=max(lon)*10^i)/10^i;
latMin - truncf(min(lat), digits=i); latMax - ceiling(x=max(lat)*10^i)/10^i;
cells.dim - ceiling(c(lonMax - lonMin, latMax - latMin)/resolution);
I hope this sheds more light on my issue.
Best regards,
Martin
-
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[R] triangles point left, filled?
Dear R users, I want to plot not only triangles point up and triangles point down, which is easy using the pch argument to points. I want to plot left and right pointing triangles as well. They must be fillable with colour. I browsed a little in the documentation, tried rotating the up and down pointing triangles, but of no avail. Any suggestions will be appreciated. Regards, Martin Ivanov - 100 лв БОНУС. Най-високи коефициенти. Tempobet.com http://bg.tempobet.com/affiliates/3208311 __ R-help@r-project.org mailing list 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.
[R] alphahull: is low level plotting possible?
Dear R users, I am using package alphahull version 0.2-0 with R-2.13.0. Here is my problem. I have produced a 2-D plot of points and need to draw convex hulls around some subsets of these points. So I just need to add the convex hulls to the already existing plot. That is why I cannot use the plot.hull function. So, is there a way to just add the convex hulls to the already existing plot, just as the low level functions lines and points add lines and points to an already existing plot? I suspect the solution is in the arc function, but I am not sure. Any suggestions will be appreciated. Regards, Martin __ R-help@r-project.org mailing list 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.
[R] return NA instead zero when summing over an empty range?
Dear R users, the colSums function from the base package returns zero if there are no values in a range to be summed over (after removing missing values with na.rm = TRUE). Is there some way to make it return NA in that case just like colMeans does? Or any other function or some good way to achieve that? Any ideas are be welcome. Regards, Martin Ivanov - Вижте последните новини във Vesti.bg! http://www.vesti.bg/ __ R-help@r-project.org mailing list 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.
[R] 3d plot layout?
Hello! I would like to ask if R can solve the following problem. I need to produce two 3d plots on a single page, that is to arrange them one above the other. Also, I need to visualize points by means of spheres, pyramids and cubes in the 3d space. Also, I would like to fill these symbols with colours. Is this possible to be done with R? In the two dimensional case the R plots are of excellent quality, I use the layout function to arrange the plots and the symbols from 20 to 25 that can be filled. So my question is can I produce an analogous 3d plot with R? Thank you in advance. Regards, Martin __ R-help@r-project.org mailing list 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.
[R] problem with abline and lines
Dear R users, I need to plot to perpendicular straight lines. However, although I set the coefficients so that the lines are perpendicular, they do not look to be so in the plot. Here is a minimal working example: plot(x=c(-1, 1), y=c(-1, 1)); abline(a=0, b=1/sqrt(2)); abline(a=0, b=-1/sqrt(2)) Please tell me if the same problem is valid by you. I am running R-2.10.1 on Linux. Is there a way out of this? Regards, Martin __ R-help@r-project.org mailing list 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.
[R] Is this a bug? (layout and par)
Dear R users, I think I have spotted a bug in R, but as I am not sure, I first post it to you. Here is a minimal working example: default - par(no.readonly=TRUE); par(font=1, adj=0.5, cex=1, cex.lab=1, cex.axis=0.5, font.axis=2, lend=2, family=Times, omi=c(0, 0, 0, 0)) layout(mat=matrix(data=1, nrow=1), widths=lcm(7.8), heights=lcm(.8), respect=FALSE); par(mai=c(1, 9 + 20, 0, 1)/25.4); plot(x=.5, y=.5, , xaxs=i, yaxs=i, type=n, xaxt=n, yaxt=n, asp=NA) par(default); As you can see there is a number 0.5 written in the left figure region, although all writing is explicitly suppressed. Moreover, if I modify the last but one command like this: plot(x=.5, y=c(.5) , xaxs=i, yaxs=i, type=n, xaxt=n, yaxt=n, asp=NA) the output in the left margin is c(0.5. Does anyone have an explanation? Is this a bug? Can this problem be solved? Regards, Martin Ivanov __ R-help@r-project.org mailing list 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.
[R] coefs from summary.lm of an aov object
Dear R users, This is probably a very stupid question, nevertheless I obviously am not qualified enough to cope with it. I do not understand what the coefficients are that are output by running summary.lm on an aov object. I thought they should be the differential effects for the levels of the factor and the overall mean, but they are obviously not, as illustrated by the following simple example: x - c(1:15); y - factor(c(rep(a, 5), rep(b, 10))) tapply(X=x, INDEX=y, FUN=mean) ab 3.0 10.5 mean(x) [1] 8 a - aov(x ~ y) summary.lm(a)$coef Estimate Std. Error t value Pr(|t|) (Intercept) 3.0 1.192928 2.514821 0.0258555905 yb 7.5 1.461032 5.133357 0.0001921826 model.tables(a) Tables of effects y ab -5 2.5 rep 5 10.0 Besides, I fit a factor with two levels, a and b, but there is only the yb coefficient for the b level, no ya coefficient for the a factor level. I read a lot of materials on anova with R, but I could not find what are these coefficients. I would be grateful if someone gives me some clue. And what is the intercept term? I though it should be the overall mean, but it is obviously not. Regards and best wishes, Martin Ivanov __ R-help@r-project.org mailing list 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.
[R] biplot from stats: 0.8 ?
Dear forum, I need to create biplot graphic. I took a look at the code of the biplot.default function from the stats package and I found that the arrows for the variables are multiplied by a coefficient of 0.8 before plotting: ... if (var.axes) arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[2L], length = arrow.len) ... I have no idea why this is done. Could somebody clarify? Thank you in advance. Regards, Martin __ R-help@r-project.org mailing list 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.
[R] factor graphics with pca in R?
Dear R users, I need to know whether the factor graphics with principal component analysis are implemented in R. I mean the graphs where the variables are represented in a correlation circle, as described in more detail in this document: http://www.unesco.org/webworld/idams/advguide/Chapt6_4_3.htm It is not a pain to program it myself, nevertheless it would be a waste of time if it is already implemented in R. Regards, Martin __ R-help@r-project.org mailing list 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.
[R] utf8 postscript cyrillic
Dear R users, I am running R version 2.10.0 (2009-10-26). I need to prepare an eps graphic with a legend with cyrillic words. I tried setting the encoding parameter of the postscript command, but in vain, nothing seems to work. I tried with CP1251, KOI8-R, UTF-8 and Cyrillic (UTF-8 turned out to not be available under /usr/lib/R/library/grDevices/enc). All I get is in the final inscription. Has someone been successful in producing postscript legends with cyrillic words and how? Is the encoding the only thing to be tweaked? I would be glad if you share your experience. Regards, Martin __ R-help@r-project.org mailing list 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.
[R] A question on type=h plot lines
Dear R users, I need a produce a plot with a single panel and a few lines on it. Each line represents a different data set. The line types must be h, i.e. ‘histogram’ like (or ‘high-density’) vertical lines. The problem is that the vertical lines comprising a plot line of type=h are drawn from the y=0 line to the (x, y) locations. What I need is vertical lines drawn from the line y=value that I specify to the (x, y) locations. Is there a way for me to achieve that? Thank you very much for your responsiveness and attention. Regards, Martin __ R-help@r-project.org mailing list 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.
[R] cannot reproduce matlab wavelet results with R
Dear R users, I want to get the D1 details reconstructed to the level of my time series. My original time series is NH$annual[,] and it has 118 elements. This is the code I use and the results: library(wavelets) NHj - extend.series(X=NH$annual[,], method=reflection, length=powerof2, j=7); detach(package:wavelets) attributes(mra(X=NHj, filter=d4, n.levels=7, boundary=reflection, fast=TRUE, method=dwt))$D[[1]][1:20] [1] -0.0363166651 0.0793856487 0.0229855716 -0.0863862067 0.0586129763 [6] -0.0552697096 0.0049741291 0.0327406169 0.0006990289 -0.0150729128 [11] -0.0203610433 0.0424490289 -0.0103379856 -0.0072504717 -0.0310480084 [16] 0.0543716287 0.0491613932 -0.1187032803 0.0317373320 0.0132924682 detach(package:wavelets) library(waveslim) mra(x=NHj, wf = d4, J = 7, method = dwt, boundary = reflection)$D1[1:20] [1] -0.0363166651 0.0793856487 0.0229855716 -0.0863862067 0.0586129763 [6] -0.0552697096 0.0049741291 0.0327406169 0.0006990289 -0.0150729128 [11] -0.0203610433 0.0424490289 -0.0103379856 -0.0072504717 -0.0310480084 [16] 0.0543716287 0.0491613932 -0.1187032803 0.0317373320 0.0132924682 detach(package:waveslim) library(wmtsa) wavMRDSum(x=NHj, wavelet=d4,levels=1, xform=dwt, reflect=FALSE, keep.smooth=FALSE, keep.details=TRUE)[1:20] t=0 t=1 t=2 t=3 t=4 -0.1449234169 0.0166815113 0.0229855716 -0.0863862067 0.0586129763 t=5 t=6 t=7 t=8 t=9 -0.0552697096 0.0049741291 0.0327406169 0.0006990289 -0.0150729128 t=10 t=11 t=12 t=13 t=14 -0.0203610433 0.0424490289 -0.0103379856 -0.0072504717 -0.0310480084 t=15 t=16 t=17 t=18 t=19 0.0543716287 0.0491613932 -0.1187032803 0.0317373320 0.0132924682 detach(package:wmtsa) library(wavethresh) NHwd.obj - wd(data=NHj, filter.number=4, family=DaubExPhase, type=wavelet, bc=symmetric, verbose=TRUE); NHwd.objA0 - putC(wd=NHwd.obj, level=6, v=rep(0,2^6), boundary=FALSE, index=FALSE); D1 - accessC(wd=wr(wd=NHwd.objA0, start.level = 6, return.object = TRUE, verbose = TRUE),level=7,boundary=FALSE); D1[1:20] [1] -0.25283845 0.06657357 0.03389600 -0.04797488 0.05665413 -0.09317851 [7] 0.06466827 0.06839502 -0.07792329 -0.06458924 0.07678030 0.04101479 [13] -0.08070069 0.06491276 -0.02459910 -0.05140745 0.07088627 -0.03537575 [19] 0.01366095 -0.01599816 As you can see, with wavethresh the results are quite different. Have I messed something up? Is this the correct way of getting the D1 details? I am a former matlab user, and the results I get with it are only reproducible in R with the other 3 packages and the d2 or haar wavelets. With any other wavelet, e.g. d4 I get different results.I would be very thankful to you if you give me some clue. I really apologize for taking some of your precious time. I wish you fruitful work. Regards, Martin 27.03.2009 __ R-help@r-project.org mailing list 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.
[R] wavethresh start.level problem
Dear R users, I am running R-2.8.1 with wavethresh-2.2-11 I have a problem with the function wr, used for reconstructing wd objects. The problem is that I cannot set start.level to any integer value greater than 1. Whenever I set it to any value greater than 1, I get: Building level: 1 reflect: access error (-1,3) Error in mywr(wd = sw.db2A0, start.level = 5, verbose = TRUE, return.object = TRUE) : convolveC: error exit (6) My series is 2^7 long, so I should be able to start the reconstruction from higher levels. Does any one know how to get round this problem? I need to start the reconstruction from higher levels, because I need the approximations and details series reconstructed for each level at the resolution of the highest level. For this reason I need to set the respective approximations coefficients to 0. If I start reconstruction from the lowest level, during reconstruction the coefficients are recalculated and they are no longer 0. I would be grateful also if someone suggests some alternative way of calculating the reconstructions I need, for example using different packages. I selected wavethresh to work with because it is last updated and seems well supported. Regards, Martin Ivanov __ R-help@r-project.org mailing list 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.
[R] arima additive vs multiplicative seasonality
Hello! I would like to ask whether the seasonality implemented in arima() is additive or multiplicative? I searched a lot, but I could not find an answer to that question, although it has been asked other times too. Thank you very much for your attention. Regards, Martin __ R-help@r-project.org mailing list 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.
[R] arima additive seasonality
Hello! I asked in this forum about what kind of seasonality the function arima() from stats implements. Now that I have been answered that it implements the Box-Jenkins multiplicative seasonality, I would like to ask whether there is in R possibility to model ARIMA with additive seasonality. I mean whether there is a function or package that implements additive seasonality. In case there is no such function, I would be thankful if someone suggests some code for the purpose. Thank you very much for your attention. Regards, Martin __ R-help@r-project.org mailing list 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.
[R] univariate impulse responses
Dear R users, I need to calculate the univariate impulse response function for a series of data. Unfortunately the vars package does not support univariate analysis. If I try to evaluate a single series like this: VAR(y=xres,p=1,type=none,ic=AIC) the result is Error in VAR(y = xres, p = 1, type = none, ic = AIC) : The matrix 'y' should contain at least two variables. For univariate analysis consider ar() and arima() in package stats. However, the irf function does not work with objects output by ar or arima. Any ideas what I could do? Regards, Martin - Крайна цел - Да оцелееш! www.survivor.btv.bg __ R-help@r-project.org mailing list 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.
[R] a question on impulse responses
Dear R users, I am using the vars package to calculate the impulse response functions and the forecast error variance decomposition of a VAR model. Unfortunately I do not know whether these functions assume unit or one standard deviation shocks. I tried to look into the code of these functions, but in vain: neither irf, nor vars::irf, nor vars:::irf output the code of the functions. Does someone know whether irf and fevd assume one standard deviation or a unit shock? How can I see the code of these functions? Regards, Martin Ivanov - Крайна цел - Да оцелееш! www.survivor.btv.bg __ R-help@r-project.org mailing list 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.
[R] vars shocks assumption
Dear R users, I am using the vars package to calculate the impulse response functions and the forecast error variance decomposition of a VAR model. Unfortunately I do not know whether these functions assume unit or one standard deviation shocks. I tried to look into the code of these functions, but in vain: neither irf, nor vars::irf, nor vars:::irf output the code of the functions. Does someone know whether irf and fevd assume one standard deviation or a unit shock? How can I see the code of these functions? Regards, Martin Ivanov - Крайна цел - Да оцелееш! www.survivor.btv.bg __ R-help@r-project.org mailing list 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.
[R] impulse responses: standard deviation or unit shocks?
Dear R users, I am using the vars package to calculate the impulse response functions and the forecast error variance decomposition of a VAR model. Unfortunately I do not know whether these functions assume unit or one standard deviation shocks. I tried to look into the code of these functions, but in vain: neither irf, nor vars::irf, nor vars:::irf output the code of the functions. Does someone know whether irf and fevd assume one standard deviation or a unit shock? How can I see the code of these functions? - Крайна цел - Да оцелееш! www.survivor.btv.bg __ R-help@r-project.org mailing list 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.
[R] irfs from a no intercept VAR
Dear R users, I need perform structural analysis on a no intercept VAR model. Unfortunately the functions irf.VAR and dfev that come with the MSBVAR package only work with objects output by the reduced.form.var function, which seems to only evaluate VAR models with intercept. Is there a way to suppress the estimation of intercept term in reduced.form.var? Do I need to modify the code, and if I do, how? Is there a way to apply irf and dfev to objects of type systemfit? Regards, Martin Ivanov - Крайна цел - Да оцелееш! www.survivor.btv.bg __ R-help@r-project.org mailing list 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.
[R] rearrange data columns
Dear R users, I need to to the the following. Let a= 1 2 3 4 5 6 and b= -1 -2 -3 be (2x3) matrices. -4 -5 -6 I need to combine the two matrices into a new (2x6) matrix like this: ab = ( 1 -1 2 -2 3 -3 ) 4 -4 5 -5 6 -6 How can this be done in R? - Крайна цел - Да оцелееш! www.survivor.btv.bg __ R-help@r-project.org mailing list 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.
