Re: [R] Lack-of-fit test for linear mixed effects model (lme) including two fixed effects
This is really the sort of issue that should be discussed with a local statistical expert. (1) It is, a statistical, not an R programming question; (2) Would be better posed on the R-sig-mixed-moodels list anyway; (3) As lack of fit tests tend to be basically useless and scientifically meaningless, the real question is what is the context for your question -- what are the meaningful practical (not statistical) concerns that you want to address with the test? Again, the sort of thing best discussed in person with a local expert. Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. H. Gilbert Welch On Sat, May 17, 2014 at 10:22 AM, Isabella Zwiener izwie...@gmx.de wrote: Dear list members, I fitted a linear mixed effects model using the lme function from nlme package. In the model I included two fixed effects, one being continuous and one a factor having 4 categories. Furthermore, I have one random effect (id) which I want to include as a random intercept only. I used the following code: fit1 - lme(outcome ~ fixed1 + fixed2, random = ~1|id) Now I would like to perform a lack-of-fit test. In a previous post (where there was only one continuous fixed effect) I have seen the following suggestion: fit1 - lme(outcome ~ fixed1, random = ~1|id, method=ML) fit2 - lme(outcome ~ factor(fixed1, ordered=TRUE), random = ~1|id, method=ML) anova(fit1,fit2) Now my questions are: 1) How do I perform a lack-of-fit test with one continuous and one factor as fixed affects? 2) Is it necessary to set method=ML for the lack-of-fit test? 3) If I have to use method=ML for the lack-of-fit test, should I use method=ML also in my model taht I would like to interpret? In my original model I used REML, but only because this is the default in lme and I did not change it. As I have not applied a lack-of-fit test before, I would really be glad for any help! Best regards, John __ 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.
Re: [R] Lamperti trnasformation simulation.
On 17/05/14 19:10, Xuse Chuse wrote: Dear users, I am trying to simulate a Lamperti transformation of a brownian motion: W(e_t). Could anyone give some clue how to do it? Thank you beforehand. Regards, C. [[alternative HTML version deleted]] __ 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. See package sde, and Stefano Iacus' excellent book. Simon. -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au http://www.evolutionarystatistics.org Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. Statistics is the grammar of science - Karl Pearson. __ 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] How to Optimize two functions together in R
This deals with the multi-objective optimisation. Try MCO and emoa packages. http://stats.stackexchange.com/questions/77580/optimization-of-multiple-objective-functions-with-constraints On 15 May 2014 17:47, Mingxuan Han han...@purdue.edu wrote: I am trying to minimize two functions with same set of parameter(x,y). Currently I can only use optim() to minimize the each function one by one. Is there any solution I can use to optimize two functions with same set of (X,Y) together. -- View this message in context: http://r.789695.n4.nabble.com/How-to-Optimize-two-functions-together-in-R-tp4690654.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] Discrete and Continuous variables
Perhaps something involving: sapply(dataFrame, function(z) length(unique(z))) Pat On 17/05/2014 17:31, a...@dpi.inpe.br wrote: Hello everybody! I have a data frame with discrete and continuous variables something like this: 011.462707165309.0171912.57041000. 101.552373295559.0171809.01701000. 011.195954445809.0171750.1000. 220.964678766059.0171707.10681000. 101.469273923250.559.0170750. 201.652678853500.707.1068750. Discrete variables should be specified as factor as.factor() and continuos variables as numeric as.numeric(). The problem is: The users that will enter with the variables. Is it possible identify which input variable are continuous or discrete? Thank guys! __ 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. -- Patrick Burns pbu...@pburns.seanet.com twitter: @burnsstat @portfolioprobe http://www.portfolioprobe.com/blog http://www.burns-stat.com (home of: 'Impatient R' 'The R Inferno' 'Tao Te Programming') __ 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] dev-lang/R-3.1.0: biocLite(vsn) removes all files in /
As alternative, just use R itself for it: chooseBioCmirror() setRepositories() # select BioC repositories here install.packages(vsn) Which should so the trick without any additional tools not shiped with R directly. Best, Uwe Ligges On 18.05.2014 07:38, Jeff Newmiller wrote: Then you had best not do it again if you don't like that result. 1) This is not the right mailing list for issues having to do with bioconductor. Please go to the bioconductor mailing list for that. 2) Running random scripts straight from the internet as root without reviewing them is exactly the kind of thing any experienced *nix user would never do. That is why user-level accounts have limits on the things they can do. I doubt you are supposed to be running anything with your current directory set to /, ever, especially not logged in as root. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On May 17, 2014 10:16:46 PM PDT, Juergen Rose r...@rz.uni-potsdam.de wrote: I had the following files in /: root@caiman:/root(8)# ll / total 160301 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ -rw-r--r-- 1 root root 38673 May 14 14:22 boot_local-d.log lrwxrwxrwx 1 root root11 Jan 22 2011 data - data_caiman/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 data_impala - /net/impala/data_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 data_lynx2 - /net/lynx2/data_lynx2/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ -rw--- 1 root root 15687 Dec 26 13:42 grub.cfg_old lrwxrwxrwx 1 root root11 Jan 23 2011 home - home_caiman/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 home_impala - /net/impala/home_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 home_lynx2 - /net/lynx2/home_lynx2/ lrwxrwxrwx 1 root root 5 Mar 30 04:25 lib - lib64/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ -rw-r--r-- 1 root root 1797418 May 14 14:22 login.log drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 4 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 270 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ -rw-r--r-- 1 root root 162191459 Jan 13 2011 stage3-amd64-20110113.tar.bz2 dr-xr-xr-x 12 root root 0 May 14 14:21 sys/ drwxrwxrwt 16 root root 1648 May 17 17:14 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ Then I did as root: R source(http://bioconductor.org/biocLite.R;) biocLite(vsn) Save workspace image? [y/n/c]: n root@caiman:/root(15)# ll / total 93 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 2 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 272 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ dr-xr-xr-x 12 root root 0 May 17 17:38 sys/ drwxrwxrwt 19 root root 1752 May 17 18:33 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ I.e., all not directory files in / disappeared. This happens on two systems. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
Re: [R] dev-lang/R-3.1.0: biocLite(vsn) removes all files in /
This would be very bad and certainly unintended if it were the responsibility of biocLite. Can we communicate off-list about this? In particular can you report noquote(readLines(http://bioconductor.org/biocLite.R;)) ? Martin Morgan On 05/17/2014 10:16 PM, Juergen Rose wrote: I had the following files in /: root@caiman:/root(8)# ll / total 160301 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ -rw-r--r-- 1 root root 38673 May 14 14:22 boot_local-d.log lrwxrwxrwx 1 root root11 Jan 22 2011 data - data_caiman/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 data_impala - /net/impala/data_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 data_lynx2 - /net/lynx2/data_lynx2/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ -rw--- 1 root root 15687 Dec 26 13:42 grub.cfg_old lrwxrwxrwx 1 root root11 Jan 23 2011 home - home_caiman/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 home_impala - /net/impala/home_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 home_lynx2 - /net/lynx2/home_lynx2/ lrwxrwxrwx 1 root root 5 Mar 30 04:25 lib - lib64/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ -rw-r--r-- 1 root root 1797418 May 14 14:22 login.log drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 4 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 270 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ -rw-r--r-- 1 root root 162191459 Jan 13 2011 stage3-amd64-20110113.tar.bz2 dr-xr-xr-x 12 root root 0 May 14 14:21 sys/ drwxrwxrwt 16 root root 1648 May 17 17:14 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ Then I did as root: R source(http://bioconductor.org/biocLite.R;) biocLite(vsn) Save workspace image? [y/n/c]: n root@caiman:/root(15)# ll / total 93 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 2 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 272 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ dr-xr-xr-x 12 root root 0 May 17 17:38 sys/ drwxrwxrwt 19 root root 1752 May 17 18:33 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ I.e., all not directory files in / disappeared. This happens on two systems. __ 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. -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 __ 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 with xts
I have 3 xts objects: test, cond1, cond2 You can download here: https://dl.dropboxusercontent.com/u/102669/obj.rar My problem is very simple. test [ cond1 cond2] = NA THIS WORKS test [ cond1 cond2] = -test [ cond1 cond2] THIS DOESN'T WORKS Why? My objective is to substitute all values in test (when cond1 cond2) with the corresponding values of test but with negative sign __ 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] help with xts
Presumably -z is not defined for an xts class object,z ? (whereas indexing is) -- Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. H. Gilbert Welch On Sun, May 18, 2014 at 7:25 AM, Pete freeri...@gmail.com wrote: I have 3 xts objects: test, cond1, cond2 You can download here: https://dl.dropboxusercontent.com/u/102669/obj.rar My problem is very simple. test [ cond1 cond2] = NA THIS WORKS test [ cond1 cond2] = -test [ cond1 cond2] THIS DOESN'T WORKS Why? My objective is to substitute all values in test (when cond1 cond2) with the corresponding values of test but with negative sign __ 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.
Re: [R] help with xts
Using subset assignment with an array usually doesn't work well with xts/zoo objects. Your case wouldn't even work with a matrix because you have NA in your array. In this case, you can achieve the same result using multiplication: pos.neg.1 - ((cond1 cond2)*-2+1) test - test * pos.neg.1 Best, -- Joshua Ulrich | about.me/joshuaulrich FOSS Trading | www.fosstrading.com On Sun, May 18, 2014 at 9:25 AM, Pete freeri...@gmail.com wrote: I have 3 xts objects: test, cond1, cond2 You can download here: https://dl.dropboxusercontent.com/u/102669/obj.rar My problem is very simple. test [ cond1 cond2] = NA THIS WORKS test [ cond1 cond2] = -test [ cond1 cond2] THIS DOESN'T WORKS Why? My objective is to substitute all values in test (when cond1 cond2) with the corresponding values of test but with negative sign __ 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] unable to collate and parse R files for package -- unexpected end of input
This is the error I get attempting to build and install a package I wrote.
I am using R Studio (but I did try with R CMDs as well).
The file that is blamed in the error is the last file alphabetically. If I
remove that file. I get the same error on the remaining last file
alphabetically. So my guess is that it isn't actually one of these files.
However, I have no clue how to troubleshoot this problem. I am quite new
to R.
I built a generator to create this R pkg. But it is based on a very
similar one that works okay that I built by hand.
They are available in their entirety on GitHub at:
https://github.com/mlhim/R_test_prj
The one that works is: ccdTest244AllDatatypes299a8123d9f7
The one that doesn't work is: ccdTest244AllDatatypesa5c7aca0036f
The 00install.out file isn't particularly enlightening:
-
* installing *source* package âccdTest244AllDatatypesa5c7aca0036fâ ...
** R
Error in parse(outFile) :
/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0036f.Rcheck/00_pkg_src/ccdTest244AllDatatypesa5c7aca0036f/R/meta:43:0:
unexpected end of input
41: return('
http://www.ccdgen.com/ccdlib/ccd-31598ac4-eac4-4f45-928e-a5c7aca0036f.xsd')
42: }
^
ERROR: unable to collate and parse R files for package
âccdTest244AllDatatypesa5c7aca0036fâ
* removing
â/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0036f.Rcheck/ccdTest244AllDatatypesa5c7aca0036fâ
* installing *source* package âccdTest244AllDatatypesa5c7aca0036fâ ...
** R
Error in parse(outFile) :
/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0036f.Rcheck/00_pkg_src/ccdTest244AllDatatypesa5c7aca0036f/R/meta:43:0:
unexpected end of input
41: return('
http://www.ccdgen.com/ccdlib/ccd-31598ac4-eac4-4f45-928e-a5c7aca0036f.xsd')
42: }
^
ERROR: unable to collate and parse R files for package
âccdTest244AllDatatypesa5c7aca0036fâ
* removing
â/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0036f.Rcheck/ccdTest244AllDatatypesa5c7aca0036fâ
-
Any help is greatly appreciated.
This is part of a large open source effort in healthcare interoperability
and data analysis.
Thanks In Advance,
Tim
Timothy Cook
LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
MLHIM http://www.mlhim.org
[[alternative HTML version deleted]]
__
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] filename of current device
On 14/05/2014 23:04, Andreas Leha wrote:
Hi all,
how do I find out about the filename, the currently open (let's say pdf)
device is writing to?
If I find 'dev.cur()' returning 'pdf 3' when I expect 'nulldevice 1' I
would like to know, which file that pdf device is actually targeting.
Any help for my poor organization is highly appreciated...
You cannot know this for an arbitrary device, at least not from R.
Most files in R are opened with the C call fopen() and thereafter
referred to by a file handle: the file can be renamed, unlinked ...
whilst the handle is open. Some system utilities[*] may be able to tell
you what filepaths are/were associated with file handles open in a
process, but it cannot be done portably.
However, in R-devel there is the possibility of a device recording extra
information about itself. See the NEWS item
• Graphics devices can add attributes to their description in
.Device and .Devices. Several of those included with R use a
filepath attribute.
AFAIR the pdf() device does: let's see
pdf('/tmp/foo.pdf')
dev.cur()
pdf
2
.Devices
[[1]]
[1] null device
[[2]]
[1] pdf
attr(,filepath)
[1] /tmp/foo.pdf
There is at least one exception: for historical reasons locked in by
undocumented use in package tkrplot, the win.metafile() device does
include the file path in the device 'name'.
[*] They have existed at least on Linux, Windows and OS X.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@r-project.org mailing list
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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.
Re: [R] dev-lang/R-3.1.0: biocLite(vsn) removes all files in /
On 18 May 2014, at 07:38 , Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Then you had best not do it again if you don't like that result. 1) This is not the right mailing list for issues having to do with bioconductor. Please go to the bioconductor mailing list for that. Hmm, this is one case where I'd really rather not scare people off R-help. Non-BioC users do use BioC packages from time to time and what Juergen did is what the BioConductor web pages tells new users to do (probably minus the as-root bit). A warn-off on R-help seems entirely warranted. Good to see that Martin Morgan is taking the issue very seriously in his post below. 2) Running random scripts straight from the internet as root without reviewing them is exactly the kind of thing any experienced *nix user would never do. That is why user-level accounts have limits on the things they can do. I doubt you are supposed to be running anything with your current directory set to /, ever, especially not logged in as root. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On May 17, 2014 10:16:46 PM PDT, Juergen Rose r...@rz.uni-potsdam.de wrote: I had the following files in /: root@caiman:/root(8)# ll / total 160301 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ -rw-r--r-- 1 root root 38673 May 14 14:22 boot_local-d.log lrwxrwxrwx 1 root root11 Jan 22 2011 data - data_caiman/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 data_impala - /net/impala/data_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 data_lynx2 - /net/lynx2/data_lynx2/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ -rw--- 1 root root 15687 Dec 26 13:42 grub.cfg_old lrwxrwxrwx 1 root root11 Jan 23 2011 home - home_caiman/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 home_impala - /net/impala/home_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 home_lynx2 - /net/lynx2/home_lynx2/ lrwxrwxrwx 1 root root 5 Mar 30 04:25 lib - lib64/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ -rw-r--r-- 1 root root 1797418 May 14 14:22 login.log drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 4 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 270 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ -rw-r--r-- 1 root root 162191459 Jan 13 2011 stage3-amd64-20110113.tar.bz2 dr-xr-xr-x 12 root root 0 May 14 14:21 sys/ drwxrwxrwt 16 root root 1648 May 17 17:14 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ Then I did as root: R source(http://bioconductor.org/biocLite.R;) biocLite(vsn) Save workspace image? [y/n/c]: n root@caiman:/root(15)# ll / total 93 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 2 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 272 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ dr-xr-xr-x 12 root root 0 May 17 17:38 sys/ drwxrwxrwt 19 root root 1752 May 17 18:33 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ I.e., all not
Re: [R] unable to collate and parse R files for package -- unexpected end of input
On 18/05/2014, 12:54 PM, Timothy W. Cook wrote:
This is the error I get attempting to build and install a package I wrote.
I am using R Studio (but I did try with R CMDs as well).
The file that is blamed in the error is the last file alphabetically. If I
remove that file. I get the same error on the remaining last file
alphabetically. So my guess is that it isn't actually one of these files.
However, I have no clue how to troubleshoot this problem. I am quite new
to R.
This indicates that you open a block using { (or perhaps [ or (),
but never close it. Unfortunately the parser doesn't tell you where the
opening brace was.
A quick way to locate which file is to parse your source files one at a
time; e.g.
for (f in list.files(somedir/R, full.names=TRUE)) parse(f)
This will get an error on the first file with unmatched braces. It
won't tell you where to look in that file, but it's usually not too hard
to find that by looking. There are ways to find the spot automatically,
but they're not trivial: see the discussion of partial parse results in
?parse, and fill in a bunch of blanks. Here without much explanation is
an example.
f - some file with unbalanced braces
text - readLines(f)
src - srcfile(text)
parse(text=text, srcfile=src) # Generates error
d - getParseData(src)
d[d$token == '{' d$parent == 0,]
This will print something like
line1 col1 line2 col2 id parent token terminal text
217373373 217 0 '{' TRUE{
telling you that the brace on line 37 was never matched. If you don't
find anything, try other kinds of parens or brackets, though they are
less likely.
Duncan Murdoch
I built a generator to create this R pkg. But it is based on a very
similar one that works okay that I built by hand.
They are available in their entirety on GitHub at:
https://github.com/mlhim/R_test_prj
The one that works is: ccdTest244AllDatatypes299a8123d9f7
The one that doesn't work is: ccdTest244AllDatatypesa5c7aca0036f
The 00install.out file isn't particularly enlightening:
-
* installing *source* package ‘ccdTest244AllDatatypesa5c7aca0036f’ ...
** R
Error in parse(outFile) :
/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0036f.Rcheck/00_pkg_src/ccdTest244AllDatatypesa5c7aca0036f/R/meta:43:0:
unexpected end of input
41: return('
http://www.ccdgen.com/ccdlib/ccd-31598ac4-eac4-4f45-928e-a5c7aca0036f.xsd')
42: }
^
ERROR: unable to collate and parse R files for package
‘ccdTest244AllDatatypesa5c7aca0036f’
* removing
‘/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0036f.Rcheck/ccdTest244AllDatatypesa5c7aca0036f’
* installing *source* package ‘ccdTest244AllDatatypesa5c7aca0036f’ ...
** R
Error in parse(outFile) :
/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0036f.Rcheck/00_pkg_src/ccdTest244AllDatatypesa5c7aca0036f/R/meta:43:0:
unexpected end of input
41: return('
http://www.ccdgen.com/ccdlib/ccd-31598ac4-eac4-4f45-928e-a5c7aca0036f.xsd')
42: }
^
ERROR: unable to collate and parse R files for package
‘ccdTest244AllDatatypesa5c7aca0036f’
* removing
‘/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0036f.Rcheck/ccdTest244AllDatatypesa5c7aca0036f’
-
Any help is greatly appreciated.
This is part of a large open source effort in healthcare interoperability
and data analysis.
Thanks In Advance,
Tim
Timothy Cook
LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
MLHIM http://www.mlhim.org
[[alternative HTML version deleted]]
__
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.
Re: [R] unable to collate and parse R files for package -- unexpected end of input
Thanks Duncan. Exactly what I needed. A push in the right direction to
finding it.
I've already found the file and I am sure to find the problem child soon.
Cheers,
Tim
On Sun, May 18, 2014 at 5:24 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote:
On 18/05/2014, 12:54 PM, Timothy W. Cook wrote:
This is the error I get attempting to build and install a package I wrote.
I am using R Studio (but I did try with R CMDs as well).
The file that is blamed in the error is the last file alphabetically. If
I
remove that file. I get the same error on the remaining last file
alphabetically. So my guess is that it isn't actually one of these files.
However, I have no clue how to troubleshoot this problem. I am quite
new
to R.
This indicates that you open a block using { (or perhaps [ or (),
but never close it. Unfortunately the parser doesn't tell you where the
opening brace was.
A quick way to locate which file is to parse your source files one at a
time; e.g.
for (f in list.files(somedir/R, full.names=TRUE)) parse(f)
This will get an error on the first file with unmatched braces. It won't
tell you where to look in that file, but it's usually not too hard to find
that by looking. There are ways to find the spot automatically, but
they're not trivial: see the discussion of partial parse results in
?parse, and fill in a bunch of blanks. Here without much explanation is an
example.
f - some file with unbalanced braces
text - readLines(f)
src - srcfile(text)
parse(text=text, srcfile=src) # Generates error
d - getParseData(src)
d[d$token == '{' d$parent == 0,]
This will print something like
line1 col1 line2 col2 id parent token terminal text
217373373 217 0 '{' TRUE{
telling you that the brace on line 37 was never matched. If you don't
find anything, try other kinds of parens or brackets, though they are less
likely.
Duncan Murdoch
I built a generator to create this R pkg. But it is based on a very
similar one that works okay that I built by hand.
They are available in their entirety on GitHub at:
https://github.com/mlhim/R_test_prj
The one that works is: ccdTest244AllDatatypes299a8123d9f7
The one that doesn't work is: ccdTest244AllDatatypesa5c7aca0036f
The 00install.out file isn't particularly enlightening:
-
* installing *source* package
ââ¬ËccdTest244AllDatatypesa5c7aca0036fââ¬â¢
...
** R
Error in parse(outFile) :
/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0
036f.Rcheck/00_pkg_src/ccdTest244AllDatatypesa5c7aca0036f/R/meta :43:0:
unexpected end of input
41: return('
http://www.ccdgen.com/ccdlib/ccd-31598ac4-eac4-4f45-928e-a5c7aca0036f.xsd
')
42: }
^
ERROR: unable to collate and parse R files for package
ââ¬ËccdTest244AllDatatypesa5c7aca0036fââ¬â¢
* removing
ââ¬Ë/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0
036f.Rcheck/ccdTest244AllDatatypesa5c7aca0036fââ¬â¢
* installing *source* package
ââ¬ËccdTest244AllDatatypesa5c7aca0036fââ¬â¢
...
** R
Error in parse(outFile) :
/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0
036f.Rcheck/00_pkg_src/ccdTest244AllDatatypesa5c7aca0036f/R/meta :43:0:
unexpected end of input
41: return('
http://www.ccdgen.com/ccdlib/ccd-31598ac4-eac4-4f45-928e-a5c7aca0036f.xsd
')
42: }
^
ERROR: unable to collate and parse R files for package
ââ¬ËccdTest244AllDatatypesa5c7aca0036fââ¬â¢
* removing
ââ¬Ë/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0
036f.Rcheck/ccdTest244AllDatatypesa5c7aca0036fââ¬â¢
-
Any help is greatly appreciated.
This is part of a large open source effort in healthcare interoperability
and data analysis.
Thanks In Advance,
Tim
Timothy Cook
LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
MLHIM http://www.mlhim.org
[[alternative HTML version deleted]]
__
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.
--
Timothy Cook
LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
MLHIM http://www.mlhim.org
[[alternative HTML version deleted]]
__
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] unable to collate and parse R files for package -- unexpected end of input
Yep, found it. I was missing a carriage return in the generator so the
closing '}' was ending up on the line above with a comment.
Thanks again.
On Sun, May 18, 2014 at 5:40 PM, Timothy W. Cook t...@mlhim.org wrote:
Thanks Duncan. Exactly what I needed. A push in the right direction to
finding it.
I've already found the file and I am sure to find the problem child soon.
Cheers,
Tim
On Sun, May 18, 2014 at 5:24 PM, Duncan Murdoch
murdoch.dun...@gmail.comwrote:
On 18/05/2014, 12:54 PM, Timothy W. Cook wrote:
This is the error I get attempting to build and install a package I
wrote.
I am using R Studio (but I did try with R CMDs as well).
The file that is blamed in the error is the last file alphabetically.
If I
remove that file. I get the same error on the remaining last file
alphabetically. So my guess is that it isn't actually one of these
files.
However, I have no clue how to troubleshoot this problem. I am quite
new
to R.
This indicates that you open a block using { (or perhaps [ or (),
but never close it. Unfortunately the parser doesn't tell you where the
opening brace was.
A quick way to locate which file is to parse your source files one at a
time; e.g.
for (f in list.files(somedir/R, full.names=TRUE)) parse(f)
This will get an error on the first file with unmatched braces. It won't
tell you where to look in that file, but it's usually not too hard to find
that by looking. There are ways to find the spot automatically, but
they're not trivial: see the discussion of partial parse results in
?parse, and fill in a bunch of blanks. Here without much explanation is an
example.
f - some file with unbalanced braces
text - readLines(f)
src - srcfile(text)
parse(text=text, srcfile=src) # Generates error
d - getParseData(src)
d[d$token == '{' d$parent == 0,]
This will print something like
line1 col1 line2 col2 id parent token terminal text
217373373 217 0 '{' TRUE{
telling you that the brace on line 37 was never matched. If you don't
find anything, try other kinds of parens or brackets, though they are less
likely.
Duncan Murdoch
I built a generator to create this R pkg. But it is based on a very
similar one that works okay that I built by hand.
They are available in their entirety on GitHub at:
https://github.com/mlhim/R_test_prj
The one that works is: ccdTest244AllDatatypes299a8123d9f7
The one that doesn't work is: ccdTest244AllDatatypesa5c7aca0036f
The 00install.out file isn't particularly enlightening:
-
* installing *source* package
ââ¬ËccdTest244AllDatatypesa5c7aca0036fââ¬â¢
...
** R
Error in parse(outFile) :
/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0
036f.Rcheck/00_pkg_src/ccdTest244AllDatatypesa5c7aca0036f/R/meta :43:0:
unexpected end of input
41: return('
http://www.ccdgen.com/ccdlib/ccd-31598ac4-eac4-4f45-928e-
a5c7aca0036f.xsd')
42: }
^
ERROR: unable to collate and parse R files for package
ââ¬ËccdTest244AllDatatypesa5c7aca0036fââ¬â¢
* removing
ââ¬Ë/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0
036f.Rcheck/ccdTest244AllDatatypesa5c7aca0036fââ¬â¢
* installing *source* package
ââ¬ËccdTest244AllDatatypesa5c7aca0036fââ¬â¢
...
** R
Error in parse(outFile) :
/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0
036f.Rcheck/00_pkg_src/ccdTest244AllDatatypesa5c7aca0036f/R/meta :43:0:
unexpected end of input
41: return('
http://www.ccdgen.com/ccdlib/ccd-31598ac4-eac4-4f45-928e-
a5c7aca0036f.xsd')
42: }
^
ERROR: unable to collate and parse R files for package
ââ¬ËccdTest244AllDatatypesa5c7aca0036fââ¬â¢
* removing
ââ¬Ë/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0
036f.Rcheck/ccdTest244AllDatatypesa5c7aca0036fââ¬â¢
-
Any help is greatly appreciated.
This is part of a large open source effort in healthcare interoperability
and data analysis.
Thanks In Advance,
Tim
Timothy Cook
LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
MLHIM http://www.mlhim.org
[[alternative HTML version deleted]]
__
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.
--
Timothy Cook
LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
MLHIM http://www.mlhim.org
--
Timothy Cook
LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
MLHIM http://www.mlhim.org
[[alternative HTML version
[R] Is there an easier way than this to list all functions in the global environment?
After an unsuccessful search thru several books plus online documentation, I
was unable to find a simple way to do this, so I wrote my own function (see
below) to do it. I'm relatively new to R however, so I'm guessing that there
must be an easier way to do it.
I want to list all functions and only the functions (not other objects also) in
the global environment.
I'm working with several old R workspaces that contain a very large number of
objects -- functions, data structures, etc. and I would to be able to easily
find out which objects are functions.
The function below (listfunc()) works fine. I'm just asking this for future
reference.
+++
listfunc - function() {
# lists names of all function objects in the global environment
obj - objects(.GlobalEnv)
funclist - character(length = 0)
for (i in 1:length(obj)) {
if (mode(get(obj[i])) == function) funclist - c(funclist,obj[i])
}
return(funclist)
}
+++
__
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] Is there an easier way than this to list all functions in the global environment?
Tena koe Byron
Many years ago, I came across the following function by Simon Fear:
function (splitby = mode, pos = 1, ...)
{
lsout - ls(pos = pos, ...)
tapply(lsout, sapply(lsout, function(x) {
splitby(get(x))
}), invisible)
}
from which one can deduce that, given your obj, the following line could
replace your loop:
obj[sapply(obj, function(x) mode(get(x))=='function')]
For future reference, it can be slow in R to continually append to an object:
test - character(0)
system.time(for (i in 1:10^5) test - c(test, as.character(i)))
# user system elapsed
# 47.860.02 47.89
test - character(10^5)
system.time(for (i in 1:10^5) test[i] - as.character(i))
# user system elapsed
# 0.250.000.25
HTH
Peter Alspach
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Byron Dom
Sent: Monday, 19 May 2014 10:50 a.m.
To: r-help@r-project.org
Subject: [R] Is there an easier way than this to list all functions in the
global environment?
After an unsuccessful search thru several books plus online documentation, I
was unable to find a simple way to do this, so I wrote my own function (see
below) to do it. I'm relatively new to R however, so I'm guessing that there
must be an easier way to do it.
I want to list all functions and only the functions (not other objects also) in
the global environment.
I'm working with several old R workspaces that contain a very large number of
objects -- functions, data structures, etc. and I would to be able to easily
find out which objects are functions.
The function below (listfunc()) works fine. I'm just asking this for future
reference.
+++
listfunc - function() {
# lists names of all function objects in the global environment obj -
objects(.GlobalEnv) funclist - character(length = 0) for (i in 1:length(obj)) {
if (mode(get(obj[i])) == function) funclist - c(funclist,obj[i])
}
return(funclist)
}
+++
__
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.
The contents of this e-mail are confidential and may be ...{{dropped:14}}
__
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] Saving the ouput data
Or you can try help(sink). JWDougherty __ 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] Is there an easier way than this to list all functions in the global environment?
Hi,
You may also check ?lsf.str()
c(lsf.str())
A.K.
On Sunday, May 18, 2014 7:27 PM, Peter Alspach
peter.alsp...@plantandfood.co.nz wrote:
Tena koe Byron
Many years ago, I came across the following function by Simon Fear:
function (splitby = mode, pos = 1, ...)
{
lsout - ls(pos = pos, ...)
tapply(lsout, sapply(lsout, function(x) {
splitby(get(x))
}), invisible)
}
from which one can deduce that, given your obj, the following line could
replace your loop:
obj[sapply(obj, function(x) mode(get(x))=='function')]
For future reference, it can be slow in R to continually append to an object:
test - character(0)
system.time(for (i in 1:10^5) test - c(test, as.character(i)))
# user system elapsed
# 47.86 0.02 47.89
test - character(10^5)
system.time(for (i in 1:10^5) test[i] - as.character(i))
# user system elapsed
# 0.25 0.00 0.25
HTH
Peter Alspach
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Byron Dom
Sent: Monday, 19 May 2014 10:50 a.m.
To: r-help@r-project.org
Subject: [R] Is there an easier way than this to list all functions in the
global environment?
After an unsuccessful search thru several books plus online documentation, I
was unable to find a simple way to do this, so I wrote my own function (see
below) to do it. I'm relatively new to R however, so I'm guessing that there
must be an easier way to do it.
I want to list all functions and only the functions (not other objects also) in
the global environment.
I'm working with several old R workspaces that contain a very large number of
objects -- functions, data structures, etc. and I would to be able to easily
find out which objects are functions.
The function below (listfunc()) works fine. I'm just asking this for future
reference.
+++
listfunc - function() {
# lists names of all function objects in the global environment obj -
objects(.GlobalEnv) funclist - character(length = 0) for (i in 1:length(obj)) {
if (mode(get(obj[i])) == function) funclist - c(funclist,obj[i])
}
return(funclist)
}
+++
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Re: [R] dev-lang/R-3.1.0: biocLite(vsn) removes all files in /
On Sun, 18 May 2014 07:16:46 +0200 Juergen Rose r...@rz.uni-potsdam.de wrote: What disappeared are links and three files. The links are recreatable, although they would be better placed in user space rather than under /. Of the three files, the *bz2 appears to be part of a Gentoo release, the second a grub configuration backup - not needed, and the last a log file. While the locaton of these files and links might be an idiosyncrasy of the Linux distribution you are using, most distributions are inherently more careful in configuration. You should get into the habit of creating a user with more limited scope than root and learn to use su and sudo if you need super-user rights. Working from root could seriously imperil your system and your work's integrity. JWDougherty __ 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] Testing parallel regression assumption
Dear Rose : I saw your questions about the R function that performs brant test. Have you worked out ? Please give some advice. I need to do the brant test in R . Thank you very much! sincerely! Anna __ 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] Second axis on bottom of graph
Sorry, I'm enclosing incomplete not-runnable code. axis(1,tick=TRUE,at=horTicLocs,labels=rep(,length(horLabels)),padj=0) staxlab(1,at=horTicLocs,labels=horLabels,srt=90,adj=c(1,0)) nFrqTicInvls=9; frqTicLocs - vector(length=nFrqTicInvls+1); frqLabels - vector(length=nFrqTicInvls+1); frqInvl=(horAxisLims[2]-horAxisLims[1])/nFrqTicInvls for(i in 1:(nFrqTicInvls+1))frqTicLocs[i]=horAxisLims[1]+(i-1)*frqInvl for(i in 1:(nFrqTicInvls+1))frqLabels[i]=.jcall(OuWid,S,sR,frqTicLocs[i],as.integer(4)) for(i in 1:(nFrqTicInvls+1))print(frqLabels[i]) axis(1,tick=TRUE,line=3.5,at=frqTicLocs,labels=rep(,length(frqLabels)),padj=0) staxlab(1,at=frqTicLocs,labels=frqLabels,srt=90,adj=c(1,0)) The first axis and first staxlab works. The second axis is OK below the first axis. The print(frqLabels[i]) is OK. But the second staxlab puts the frqLabels[i] on the first (upper) axis. I must have to add something to the second staxlab to select second axis? Hurr -- View this message in context: http://r.789695.n4.nabble.com/Second-axis-on-bottom-of-graph-tp4690696p4690803.html Sent from the R help mailing list archive at Nabble.com. __ 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] Second axis on bottom of graph
On Sun, 18 May 2014 09:56:03 PM Hurr wrote: Sorry, I'm enclosing incomplete not-runnable code. axis(1,tick=TRUE,at=horTicLocs,labels=rep(,length(horLabels)),padj=0) staxlab(1,at=horTicLocs,labels=horLabels,srt=90,adj=c(1,0)) nFrqTicInvls=9; frqTicLocs - vector(length=nFrqTicInvls+1); frqLabels - vector(length=nFrqTicInvls+1); frqInvl=(horAxisLims[2]-horAxisLims[1])/nFrqTicInvls for(i in 1:(nFrqTicInvls+1))frqTicLocs[i]=horAxisLims[1]+(i-1)*frqInvl for(i in 1: (nFrqTicInvls+1))frqLabels[i]=.jcall(OuWid,S,sR,frqTicLocs[i],as.integ er(4)) for(i in 1:(nFrqTicInvls+1))print(frqLabels[i]) axis(1,tick=TRUE,line=3.5,at=frqTicLocs,labels=rep(,length(frqLabels)),pad j=0) staxlab(1,at=frqTicLocs,labels=frqLabels,srt=90,adj=c(1,0)) The first axis and first staxlab works. The second axis is OK below the first axis. The print(frqLabels[i]) is OK. But the second staxlab puts the frqLabels[i] on the first (upper) axis. I must have to add something to the second staxlab to select second axis? Try looking at the help page, in particular the top.line argument. Jim __ 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-es] Utilizar scripts de PHP en R
Hola a todos, Estoy interesado en usar un Script de PHP desde R y me gustarÃa saber si eso es posible y como se hace. Muchas gracias de antemano por las respuestas. [[alternative HTML version deleted]] ___ R-help-es mailing list R-help-es@r-project.org https://stat.ethz.ch/mailman/listinfo/r-help-es
