Re: [R] How to access https page
On 09/03/2015 22:39, Hui Du wrote: Hi All, I am trying to parse some information from website, say, a linkedin page. The linkedin url was url = "http://www.linkedin.com/in/huidu"; I had no problem to use readLines and XML package to collect the information I need. However, that url became " https://www.linkedin.com/in/huidu"; now. url = "https://www.linkedin.com/in/huidu"; It failed readLines function. readLines(url) Error in file(con, "r") : cannot open the connection In addition: Warning message: In file(con, "r") : unsupported URL scheme Do you know any way to read-in web information if the url is https? Thanks a lot. Try R-devel, soon to become R 3.2.0. That has support for this on platforms where libcurl is installed (which should be possible almost everywhere). You did not give the 'at a minimum' information required by the posting guide. This has long been possible on Windows with --internet2. Hui [[alternative HTML version deleted]] __ 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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford 1 South Parks Road, Oxford OX1 3TG, UK __ 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.
Re: [R] Alpha not working in geom_rect
I have run into this a couple of times ... If you generate the rectangles once
per row of your data, the fill gets more and more "dense" so your alpha seems
to not work. The annotate call only paints the rectangle once so you don't have
this problem.
---
Jeff NewmillerThe . . Go Live...
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On March 9, 2015 3:24:23 PM PDT, adel daoud wrote:
>Hi Jim,
>
>Thanks for the input but that did not work. I am suing Rstudio by the
>way
>and I guess that has a better device that would support ggplot output.
>
>The annotate options works but that does not explain why the geom_area
>does
>not work:
>annotate("rect", xmin=2, xmax=10, ymin=0, ymax=1, fill="black",
>alpha=0.5)
>
>Best
>Adel
>
>
>--
>
>Adel Daoud, PhD, Researcher
>
>
>
>The New School for Social Research,
>
>Visiting Scholar in the Economics Department,
>
>6 East 16th Street New York, NY 10003,
>
>dao...@newschool.edu
>
>
>
>
>
>University of Gothenburg
>
>Department of Sociology and Work Science,
>
>Box 720
>
>405 30, Göteborg, Sweden
>
>Visiting address: Sprängkullsgatan 25, room F411
>
>Sprängkullsgatan 25, room K109
>
>+46 031-786 41 73
>
>adel.da...@sociology.gu.se
>
>On Sun, Mar 8, 2015 at 12:46 AM, Jim Lemon
>wrote:
>
>> Hi Adel,
>> Almost certainly because the device you were using doesn't support
>> transparency.Try it with a PDF device and check the resulting file in
>a PDF
>> reader:
>>
>> pdf("ad.pdf")
>> print(p)
>> dev.off()
>>
>> Jim
>>
>>
>> On Sun, Mar 8, 2015 at 4:39 AM, Adel wrote:
>>
>>> Hi
>>> I am trying to activate the alpha argument to work, but for some
>reason it
>>> does not to play with me. Anybody has an idea why?
>>>
>>>
>>> p <- ggplot(data = prediction_df, aes(x=x, y=prediction,
>fill=threshold))
>>> +
>>> geom_area(colour="black", size=.2, alpha=.4) +
>>> scale_fill_brewer(palette="Set1",
>>> breaks=rev(levels(prediction_df$threshold)))
>>> p + geom_rect(aes(xmin=2, xmax=10, ymin=(0), ymax=(1)),
>fill="black",
>>> alpha=0.5)
>>>
>>>
>>> prediction_df
>>> x prediction threshold
>>> 1 -10 0.5694161 noAF
>>> 2 -9 0.5700513 noAF
>>> 3 -8 0.5706863 noAF
>>> 4 -7 0.5713211 noAF
>>> 5 -6 0.5719556 noAF
>>> 6 -5 0.5725899 noAF
>>> 7 -4 0.5732240 noAF
>>> 8 -3 0.5738578 noAF
>>> 9 -2 0.5744914 noAF
>>> 10 -1 0.5751247 noAF
>>> 11 0 0.5757578 noAF
>>> 12 1 0.5763906 noAF
>>> 13 2 0.5770232 noAF
>>> 14 3 0.5776556 noAF
>>> 15 4 0.5782876 noAF
>>> 16 5 0.5789195 noAF
>>> 17 6 0.5795510 noAF
>>> 18 7 0.5801823 noAF
>>> 19 8 0.5808134 noAF
>>> 20 9 0.5814441 noAF
>>> 21 10 0.5820747 noAF
>>> 22 -10 0.2359140 singleAF
>>> 23 -9 0.2356847 singleAF
>>> 24 -8 0.2354550 singleAF
>>> 25 -7 0.2352249 singleAF
>>> 26 -6 0.2349943 singleAF
>>> 27 -5 0.2347634 singleAF
>>> 28 -4 0.2345321 singleAF
>>> 29 -3 0.2343003 singleAF
>>> 30 -2 0.2340682 singleAF
>>> 31 -1 0.2338356 singleAF
>>> 32 0 0.2336027 singleAF
>>> 33 1 0.2333694 singleAF
>>> 34 2 0.2331357 singleAF
>>> 35 3 0.2329016 singleAF
>>> 36 4 0.2326671 singleAF
>>> 37 5 0.2324322 singleAF
>>> 38 6 0.2321969 singleAF
>>> 39 7 0.2319613 singleAF
>>> 40 8 0.2317253 singleAF
>>> 41 9 0.2314889 singleAF
>>> 42 10 0.2312522 singleAF
>>> 43 -10 0.1946699 multipleAF
>>> 44 -9 0.1942640 multipleAF
>>> 45 -8 0.1938587 multipleAF
>>> 46 -7 0.1934540 multipleAF
>>> 47 -6 0.1930500 multipleAF
>>> 48 -5 0.1926467 multipleAF
>>> 49 -4 0.1922440 multipleAF
>>> 50 -3 0.1918419 multipleAF
>>> 51 -2 0.1914404 multipleAF
>>> 52 -1 0.1910397 multipleAF
>>> 53 0 0.1906395 multipleAF
>>> 54 1 0.1902400 multipleAF
>>> 55 2 0.1898411 multipleAF
>>> 56 3 0.1894429 multipleAF
>>> 57 4 0.1890453 multipleAF
>>> 58 5 0.1886483 multipleAF
>>> 59 6 0.1882520 multipleAF
>>> 60 7 0.1878564 multipleAF
>>> 61 8 0.1874613 multipleAF
>>> 62 9 0.1870669 multipleAF
>>> 63 10 0.1866732 multipleAF
>>>
>>>
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>>
>http://r.789695.n4.nabble.com/Alpha-not-working-in-geom-rect-tp4704291.html
>>> Sent from the R help mailing list archive at Nabble.com.
>>>
>>> __
>>> 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 g
Re: [R] Change the argument function inside R function in GPfit package
I guess I should re-frame my question with real data. > xx [,1] [1,] 0.0 [2,] 0.2 [3,] 0.4 [4,] 0.6 [5,] 0.8 > yy [,1] [1,] 0.000 [2,] 0.1652000 [3,] 0.4343223 [4,] 0.5996505 [5,] 0.7195857 > cor.mat [,1] [,2] [,3] [,4][,5] [1,] 1.0 0.64822376 0.1873066 0.02489388 0.001546431 [2,] 0.648223760 1. 0.6482238 0.18730656 0.024893894 [3,] 0.187306626 0.64822376 1.000 0.64822364 0.187306626 [4,] 0.024893881 0.18730656 0.6482236 1. 0.648223880 [5,] 0.001546431 0.02489389 0.1873066 0.64822388 1.0 or xx <- structure(c(0, 0.19994947575, 0.3998989515, 0.60028498471, 0.799797903), .Dim = c(5L, 1L)) yy <- structure(c(0, 0.165199951246566, 0.43432234091, 0.599650488376824, 0.719585664934966), .Dim = c(5L, 1L)) cor.mat <- structure(c(1, 0.648223760165366, 0.187306626057348, 0.0248938807581023, 0.00154643121052443, 0.648223760165366, 1, 0.648223760165366, 0.187306559286623, 0.0248938938021518, 0.187306626057348, 0.648223760165366, 1, 0.648223640552069, 0.187306626057348, 0.0248938807581023, 0.187306559286623, 0.648223640552069, 1, 0.64822387977866, 0.00154643121052443, 0.0248938938021518, 0.187306626057348, 0.64822387977866, 1), .Dim = c(5L, 5L)) Now if I do, > GP_fit(xx, yy, corr=cor.mat) Error in corr$type : $ operator is invalid for atomic vectors How could I fix it? Thanks! -M On Mon, Mar 9, 2015 at 2:14 PM, C W wrote: > Hi R list, > > I am using the GPfit package to fit Gaussian Process model. > > The kernel in the package is, > K(x, x') = sigma^2 * exp(x-x')^2 > > My kernel have an extra term, > K((x, z), (x', z')) = sigma^2 * exp(x-x')^2 * exp(z-z')^2 > > The function corr_matrix() is, > corr_matrix(X, beta, corr=list(type="exponential",power=1.95)) > github source: https://github.com/cran/GPfit/blob/master/R/corr_matrix.R > > I am changing the corr argument, so it looks like mine. How should I do > it? > > Also, what package do you guys recommend for GP modeling? I know GPstuff > or GPML but that's Matlab. > > Thanks very much. > > Mike > [[alternative HTML version deleted]] __ 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] How to access https page
Hi All, I am trying to parse some information from website, say, a linkedin page. The linkedin url was url = "http://www.linkedin.com/in/huidu"; I had no problem to use readLines and XML package to collect the information I need. However, that url became " https://www.linkedin.com/in/huidu"; now. url = "https://www.linkedin.com/in/huidu"; It failed readLines function. > readLines(url) Error in file(con, "r") : cannot open the connection In addition: Warning message: In file(con, "r") : unsupported URL scheme Do you know any way to read-in web information if the url is https? Thanks a lot. Hui [[alternative HTML version deleted]] __ 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.
Re: [R] APE
It's hard to tell what you did exactly. Did you do: mytree <- compute.brlen(mytree) ? That should have worked. I've cc'ed this message to r-sig-phylo, which is the more appropriate forum. Cheers, Simon. On 10/03/15 07:05, Beth Williams wrote: Dear All, I am having some trouble with R and would be extremely grateful if anyone has a way around this. I have loaded a nexus tree from PAUP into R using the command read.nexus and this loaded, it was reported as "rooted; with no branch lengths". I then used the command "compute.brlen(mytree)" to compute the branch lengths and this was reported as "rooted; includes branch lengths". I added my community data (samp) and then tried to compute the phylogenetic diversity with the command "> pd(samp, mytree, include.root=TRUE)" however it said it could not calculate the PD as there were no branch lengths. Is there a way to incorporate the branch lengths into the calculation for PD? Thanks for your time, Beth [[alternative HTML version deleted]] __ 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. -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. Senior 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. Basically, I'm not interested in doing research and I never have been. I'm interested in understanding, which is quite a different thing. - David Blackwell __ 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.
Re: [R] How to access https page
Hi Hui, I have used the source_url function in the devtools package with good results. Give it a shot! Best, Jorge.- On Tue, Mar 10, 2015 at 9:39 AM, Hui Du wrote: > Hi All, > > I am trying to parse some information from website, say, a linkedin page. > The linkedin url was > > url = "http://www.linkedin.com/in/huidu"; > > I had no problem to use readLines and XML package to collect the > information I need. However, that url became " > https://www.linkedin.com/in/huidu"; now. > > url = "https://www.linkedin.com/in/huidu"; > > It failed readLines function. > > > readLines(url) > Error in file(con, "r") : cannot open the connection > In addition: Warning message: > In file(con, "r") : unsupported URL scheme > > > Do you know any way to read-in web information if the url is https? Thanks > a lot. > > Hui > > [[alternative HTML version deleted]] > > __ > 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. > [[alternative HTML version deleted]] __ 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] svg2swf - controlling the looping of flash files
Hi
I'm using svg2swf to collate a number of svg outputs into an swf file. I've
got this working (mainly.) except that I can't control the looping behaviour
of the swf file. In other words, when it's loaded into html it loops
continuously. Is there any way to stop the animation looping, so it just
plays through once when loaded? The code I use is (broadly):
svg("testplot%d.svg",onefile = FALSE)
for(j in 1:360){
print(cloud(x~y*z, groups=tail,
data=norm_dots_chart, screen=list(z=0,x=0,y=j)))
}
dev.off()
output = svg2swf(sprintf("testplot%d.svg", 1:360), interval =
0.04)
swf2html(output)
Thank you!
[[alternative HTML version deleted]]
__
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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.
[R] R can't find tcl-tk
Hi, I've installed the latest version of R from source on Amazon Linux with the following config flags: ./configure --with-tcl-config=/opt/ActiveTcl-8.6/lib/tclConfig.sh --with-tk-config=/opt/ActiveTcl-8.6/lib/tkConfig.sh After running make and make install, I try to run R and install the 'anesrake' package, but one of the dependencies fails with this error: error: Tcl/Tk support is not available on this system How can I fix this? regards, imran [[alternative HTML version deleted]] __ 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.
Re: [R] question about the geometric distribution, please
Maybe you are looking for rnbinom? JS Huang 636.536.5635 -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Erin Hodgess Sent: Monday, March 09, 2015 3:52 PM To: R help Subject: [R] question about the geometric distribution, please Hello! The function rgeom is based on the geometric distribution such that x = 0, 1, Is there a function which produces the geometric results such that x = 1, 2, ... please? Thought I'd check before I started coding. Thank you! Sincerely, Erin -- Erin Hodgess Associate Professor Department of Mathematical and Statistics University of Houston - Downtown mailto: erinm.hodg...@gmail.com [[alternative HTML version deleted]] __ 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. Confidentiality Notice: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify me immediately by replying to this message and deleting it from your computer. Thank you. __ 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.
Re: [R] Alpha not working in geom_rect
Hi Jim,
Thanks for the input but that did not work. I am suing Rstudio by the way
and I guess that has a better device that would support ggplot output.
The annotate options works but that does not explain why the geom_area does
not work:
annotate("rect", xmin=2, xmax=10, ymin=0, ymax=1, fill="black", alpha=0.5)
Best
Adel
--
Adel Daoud, PhD, Researcher
The New School for Social Research,
Visiting Scholar in the Economics Department,
6 East 16th Street New York, NY 10003,
dao...@newschool.edu
University of Gothenburg
Department of Sociology and Work Science,
Box 720
405 30, Göteborg, Sweden
Visiting address: Sprängkullsgatan 25, room F411
Sprängkullsgatan 25, room K109
+46 031-786 41 73
adel.da...@sociology.gu.se
On Sun, Mar 8, 2015 at 12:46 AM, Jim Lemon wrote:
> Hi Adel,
> Almost certainly because the device you were using doesn't support
> transparency.Try it with a PDF device and check the resulting file in a PDF
> reader:
>
> pdf("ad.pdf")
> print(p)
> dev.off()
>
> Jim
>
>
> On Sun, Mar 8, 2015 at 4:39 AM, Adel wrote:
>
>> Hi
>> I am trying to activate the alpha argument to work, but for some reason it
>> does not to play with me. Anybody has an idea why?
>>
>>
>> p <- ggplot(data = prediction_df, aes(x=x, y=prediction, fill=threshold))
>> +
>> geom_area(colour="black", size=.2, alpha=.4) +
>> scale_fill_brewer(palette="Set1",
>> breaks=rev(levels(prediction_df$threshold)))
>> p + geom_rect(aes(xmin=2, xmax=10, ymin=(0), ymax=(1)), fill="black",
>> alpha=0.5)
>>
>>
>> prediction_df
>> x prediction threshold
>> 1 -10 0.5694161 noAF
>> 2 -9 0.5700513 noAF
>> 3 -8 0.5706863 noAF
>> 4 -7 0.5713211 noAF
>> 5 -6 0.5719556 noAF
>> 6 -5 0.5725899 noAF
>> 7 -4 0.5732240 noAF
>> 8 -3 0.5738578 noAF
>> 9 -2 0.5744914 noAF
>> 10 -1 0.5751247 noAF
>> 11 0 0.5757578 noAF
>> 12 1 0.5763906 noAF
>> 13 2 0.5770232 noAF
>> 14 3 0.5776556 noAF
>> 15 4 0.5782876 noAF
>> 16 5 0.5789195 noAF
>> 17 6 0.5795510 noAF
>> 18 7 0.5801823 noAF
>> 19 8 0.5808134 noAF
>> 20 9 0.5814441 noAF
>> 21 10 0.5820747 noAF
>> 22 -10 0.2359140 singleAF
>> 23 -9 0.2356847 singleAF
>> 24 -8 0.2354550 singleAF
>> 25 -7 0.2352249 singleAF
>> 26 -6 0.2349943 singleAF
>> 27 -5 0.2347634 singleAF
>> 28 -4 0.2345321 singleAF
>> 29 -3 0.2343003 singleAF
>> 30 -2 0.2340682 singleAF
>> 31 -1 0.2338356 singleAF
>> 32 0 0.2336027 singleAF
>> 33 1 0.2333694 singleAF
>> 34 2 0.2331357 singleAF
>> 35 3 0.2329016 singleAF
>> 36 4 0.2326671 singleAF
>> 37 5 0.2324322 singleAF
>> 38 6 0.2321969 singleAF
>> 39 7 0.2319613 singleAF
>> 40 8 0.2317253 singleAF
>> 41 9 0.2314889 singleAF
>> 42 10 0.2312522 singleAF
>> 43 -10 0.1946699 multipleAF
>> 44 -9 0.1942640 multipleAF
>> 45 -8 0.1938587 multipleAF
>> 46 -7 0.1934540 multipleAF
>> 47 -6 0.1930500 multipleAF
>> 48 -5 0.1926467 multipleAF
>> 49 -4 0.1922440 multipleAF
>> 50 -3 0.1918419 multipleAF
>> 51 -2 0.1914404 multipleAF
>> 52 -1 0.1910397 multipleAF
>> 53 0 0.1906395 multipleAF
>> 54 1 0.1902400 multipleAF
>> 55 2 0.1898411 multipleAF
>> 56 3 0.1894429 multipleAF
>> 57 4 0.1890453 multipleAF
>> 58 5 0.1886483 multipleAF
>> 59 6 0.1882520 multipleAF
>> 60 7 0.1878564 multipleAF
>> 61 8 0.1874613 multipleAF
>> 62 9 0.1870669 multipleAF
>> 63 10 0.1866732 multipleAF
>>
>>
>>
>>
>>
>> --
>> View this message in context:
>> http://r.789695.n4.nabble.com/Alpha-not-working-in-geom-rect-tp4704291.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> __
>> 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.
>>
>
>
[[alternative HTML version deleted]]
__
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] APE
Dear All, I am having some trouble with R and would be extremely grateful if anyone has a way around this. I have loaded a nexus tree from PAUP into R using the command read.nexus and this loaded, it was reported as "rooted; with no branch lengths". I then used the command "compute.brlen(mytree)" to compute the branch lengths and this was reported as "rooted; includes branch lengths". I added my community data (samp) and then tried to compute the phylogenetic diversity with the command "> pd(samp, mytree, include.root=TRUE)" however it said it could not calculate the PD as there were no branch lengths. Is there a way to incorporate the branch lengths into the calculation for PD? Thanks for your time, Beth [[alternative HTML version deleted]] __ 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.
Re: [R] question about the geometric distribution, please
On Mar 9, 2015, at 1:52 PM, Erin Hodgess wrote: > Hello! > > The function rgeom is based on the geometric distribution such that x = 0, > 1, > > Is there a function which produces the geometric results such that x = 1, > 2, ... > please? > > Thought I'd check before I started coding. This seemed unclear or trivial. Cannot decide which from the description. The arguments to rgeom are "n" and "prob". If you want a geometric-like result with a "shifted" range, then just add one to the rgeom result. > > Thank you! > > Sincerely, > Erin > > > -- > Erin Hodgess > Associate Professor > Department of Mathematical and Statistics > University of Houston - Downtown > mailto: erinm.hodg...@gmail.com > > [[alternative HTML version deleted]] -- David Winsemius Alameda, CA, USA __ 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] increase max. console output lines
Hi, I have a lengthy R script, which just got a bit too long for the console output to cache all executions history, i.e. when scrolling to the top the first few commands executed are not listed any more. What is the current limit (characters? lines?) and how do I increase it? R is 2.14, Win7, 64-bit if that matters. thanks, Thomas __ 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] Revolutions blog: February roundup
For more than 6 years, Revolution Analytics staff and guests have written about R every weekday at the Revolutions blog: http://blog.revolutionanalytics.com and every month I post a summary of articles from the previous month of particular interest to readers of r-help. In case you missed them, here are some articles related to R from the month of February: The John M. Chambers Statistical Software Award announcement for 2015: http://bit.ly/1CWIfXT The new R package "distcomp" allows researchers to collaborate on data spread across multiple sites: http://bit.ly/1CWIfXU I gave an interview to theCUBE on R, data science, and Microsoft's acquisition of Revolution Analytics: http://bit.ly/1CWIfaC R is used to measure impact of climate change, and other Strata keynote presentations: http://bit.ly/1CWIfqQ Some tricks for monitoring the progress on parallel R jobs using foreach: http://bit.ly/1CWIfaD "Analytics Marketplaces" are all the rage today, but CRAN was there first: http://bit.ly/1CWIfXS A preview of some of the major R-related conferences and events of 2015: http://bit.ly/1CWIfXV The checkpoint package has been updated to make it even easier to run R scripts with fixed R package versions: http://bit.ly/1CWIfqS A tutorial to introduce R to users of Microsoft Excel: http://bit.ly/1CWIfqT R used to assess the "virality" of posts on new-media sites like Buzzfeed: http://bit.ly/1CWIfqU A review of the HP Workshop on Distributed Computing in R featuring Luke Tierney, Dirk Eddelbuettel, Martin Morgan, Simon Urbanek and other R luminaries: http://bit.ly/1CWIfXX R is the top-ranked language on GitHub, as measured by the number of forks per repository: http://bit.ly/1CWIfXW You can use the rcrunchbase package to access data on startup companies: http://bit.ly/1CWIfXY The R package "syuzhet" applies sentiment analysis to novels to infer their dramatic arc: http://bit.ly/1CWIfqX The new "quickcheck" package provides assertion-based testing with random inputs for R: http://bit.ly/1CWIfqY A theorem for calculating an upper bound for the generalization error of a machine learning classifier: http://bit.ly/1CWIfXZ Some practical advice for sharing Shiny applications with shinyapps.io: http://bit.ly/1CWIfqZ A visualization of Paris's street orientations reveals the history of the city: http://bit.ly/1CWIfY0 General interest stories (not related to R) in the past month included: how our brains trick us into seeing the wrong colors (http://bit.ly/1CWIfr0), an hilarious parody of cooking shows (http://bit.ly/1CWIfr4), a new ASA website to help journalists with Statistics (http://bit.ly/1CWIfY1), the statistical model behind the rules of cricket (http://bit.ly/1CWIfY2), and why rivers meander (http://bit.ly/1CWIfr6). Meeting times for local R user groups (http://bit.ly/eC5YQe) can be found on the updated R Community Calendar at: http://bit.ly/bb3naW If you're looking for more articles about R, you can find summaries from previous months at http://blog.revolutionanalytics.com/roundups/. You can receive daily blog posts via email using services like blogtrottr.com, or join the Revolution Analytics mailing list at http://revolutionanalytics.com/newsletter to be alerted to new articles on a monthly basis. As always, thanks for the comments and please keep sending suggestions to me at da...@revolutionanalytics.com or via Twitter (I'm @revodavid). Cheers, # David -- David M Smith Chief Community Officer, Revolution Analytics http://blog.revolutionanalytics.com Tel: +1 (650) 646-9523 (Chicago IL, USA) Twitter: @revodavid __ 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.
Re: [R] calculate value in dependence of target value
This works for your example data, but I'd recommend testing it carefully before
using it.
> dat <- data.frame(ID=11:14, VALUE=c(1, 5, 3, 2)*1)
> HURD <- c(50, 75, 100)*1000
> PCT <- c(.02, .04, .08, .1)
> dat$CVALUE <- cumsum(dat$VALUE)
> dat$LVALUE <- dat$CVALUE - dat$VALUE
> dat
ID VALUE CVALUE LVALUE
1 11 1 1 0
2 12 5 6 1
3 13 3 9 6
4 14 2 11 9
>
> for (idx in seq_len(nrow(dat))) {
+ rng <- sort(c(HURD, unlist(dat[idx,3:4])))
+ a <- which(names(rng) == "LVALUE")
+ b <- which(names(rng) == "CVALUE")
+ diff(rng[a:b])
+ ng <- length(diff(rng[a:b]))
+ dat$MARGE[idx] <- sum(PCT[a:(a+ng-1)]* diff(rng[a:b]))
+ }
> dat
ID VALUE CVALUE LVALUE MARGE
1 11 1 1 0 200
2 12 5 6 1 1200
3 13 3 9 6 1800
4 14 2 11 9 1800
-
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352
-Original Message-
From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us]
Sent: Monday, March 9, 2015 2:22 PM
To: Matthias Weber
Cc: David L Carlson; r-help@r-project.org
Subject: Re: [R] calculate value in dependence of target value
> target <- 10
>
> breakpts <- data.frame( PctTarget=c(50,75,100,Inf), Mult=c(2,4,8,10) )
> breakpts$LastPct <- c( 0, breakpts$PctTarget[ -nrow( breakpts ) ] )
> breakpts$Range <- cut( breakpts$PctTarget, c( 0, breakpts$PctTarget ),
include.lowest=TRUE )
> breakpts$DeltaPct <- with( breakpts, diff( c( 0, PctTarget ) ) )
> breakpts$CumMARGE <- target / 1e4 * with( breakpts, cumsum( DeltaPct *
Mult ) )
> breakpts$LastCumMARGE <- c( 0, breakpts$CumMARGE[ -nrow( breakpts ) ] )
>
> dta <- data.frame( ID=11:14, VALUE=c(1,5,3,2) )
> dta$CumVALUE <- cumsum( dta$VALUE )
> dta$CumPct <- 100 * dta$CumVALUE / target
> dta$Range <- cut( dta$CumPct, c( 0, breakpts$PctTarget ),
include.lowest=TRUE )
>
> dta
ID VALUE CumVALUE CumPct Range
1 11 11 10[0,50]
2 12 56 60 (50,75]
3 13 39 90 (75,100]
4 14 2 11110 (100,Inf]
> breakpts
PctTarget Mult LastPct Range DeltaPct CumMARGE LastCumMARGE
1502 0[0,50] 50 10000
2754 50 (50,75] 25 2000 1000
3 1008 75 (75,100] 25 4000 2000
4 Inf 10 100 (100,Inf] Inf Inf 4000
>
> #dta2 <- merge( dta, breakpts, all.x=TRUE, by="Range" )
> #dta2 <- dta2[ order( dta2$ID ), ]
>
> dta2 <- cbind( dta, breakpts[ match( dta$Range, breakpts$Range ),
-which( "Range"==names( breakpts ) ) ] )
>
> dta2$CumMARGE <- with( dta2, Mult/100 * ( CumVALUE - target * LastPct /
100 ) + LastCumMARGE )
> dta2$MARGE <- with( dta2, diff( c( 0, CumMARGE ) ) )
>
> dta2
ID VALUE CumVALUE CumPct Range PctTarget Mult LastPct DeltaPct
CumMARGE LastCumMARGE MARGE
1 11 11 10[0,50]502 0 50
2000 200
2 12 56 60 (50,75]754 50 25
1400 1000 1200
3 13 39 90 (75,100] 1008 75 25
3200 2000 1800
4 14 2 11110 (100,Inf] Inf 10 100 Inf
5000 4000 1800
>
>
> target <- 10
>
> breakpts <- data.frame( PctTarget=c(50,75,100,Inf), Mult=c(2,4,8,10) )
> breakpts$LastPct <- c( 0, breakpts$PctTarget[ -nrow( breakpts ) ] )
> breakpts$Range <- cut( breakpts$PctTarget, c( 0, breakpts$PctTarget ),
include.lowest=TRUE )
> breakpts$DeltaPct <- with( breakpts, diff( c( 0, PctTarget ) ) )
> breakpts$CumMARGE <- target / 1e4 * with( breakpts, cumsum( DeltaPct *
Mult ) )
> breakpts$LastCumMARGE <- c( 0, breakpts$CumMARGE[ -nrow( breakpts ) ] )
>
> dta <- data.frame( ID=11:14, VALUE=c(1,5,3,2) )
> dta$CumVALUE <- cumsum( dta$VALUE )
> dta$CumPct <- 100 * dta$CumVALUE / target
> dta$Range <- cut( dta$CumPct, c( 0, breakpts$PctTarget ),
include.lowest=TRUE )
>
> dta
ID VALUE CumVALUE CumPct Range
1 11 11 10[0,50]
2 12 56 60 (50,75]
3 13 39 90 (75,100]
4 14 2 11110 (100,Inf]
> breakpts
PctTarget Mult LastPct Range DeltaPct CumMARGE LastCumMARGE
1502 0[0,50] 50 10000
2754 50 (50,75] 25 2000 1000
3 1008 75 (75,100] 25 4000 2000
4 Inf 10 100 (100,Inf] Inf Inf 4000
>
> #dta2 <- merge( dta, breakpts, all.x=TRUE, by="Range" )
> #dta2 <- dta2[ order( dta2$ID ), ]
>
> dta2 <- cbind( dta, breakpts[ match( dta$Range, breakpts$Range ),
-which( "Range"==names( breakpts ) ) ] )
>
> dta2$CumMARGE <- with( dta2, Mult/100 * ( CumVALUE - target * LastPct /
100 ) + LastCumMARGE )
> dta2$MARGE <- diff( c( 0, dta2$CumMARGE ) )
>
> dta2
ID VALUE CumVALUE CumPct R
[R] question about the geometric distribution, please
Hello! The function rgeom is based on the geometric distribution such that x = 0, 1, Is there a function which produces the geometric results such that x = 1, 2, ... please? Thought I'd check before I started coding. Thank you! Sincerely, Erin -- Erin Hodgess Associate Professor Department of Mathematical and Statistics University of Houston - Downtown mailto: erinm.hodg...@gmail.com [[alternative HTML version deleted]] __ 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.
Re: [R] calculate value in dependence of target value
target <- 10 breakpts <- data.frame( PctTarget=c(50,75,100,Inf), Mult=c(2,4,8,10) ) breakpts$LastPct <- c( 0, breakpts$PctTarget[ -nrow( breakpts ) ] ) breakpts$Range <- cut( breakpts$PctTarget, c( 0, breakpts$PctTarget ), include.lowest=TRUE ) breakpts$DeltaPct <- with( breakpts, diff( c( 0, PctTarget ) ) ) breakpts$CumMARGE <- target / 1e4 * with( breakpts, cumsum( DeltaPct * Mult ) ) breakpts$LastCumMARGE <- c( 0, breakpts$CumMARGE[ -nrow( breakpts ) ] ) dta <- data.frame( ID=11:14, VALUE=c(1,5,3,2) ) dta$CumVALUE <- cumsum( dta$VALUE ) dta$CumPct <- 100 * dta$CumVALUE / target dta$Range <- cut( dta$CumPct, c( 0, breakpts$PctTarget ), include.lowest=TRUE ) dta ID VALUE CumVALUE CumPct Range 1 11 11 10[0,50] 2 12 56 60 (50,75] 3 13 39 90 (75,100] 4 14 2 11110 (100,Inf] breakpts PctTarget Mult LastPct Range DeltaPct CumMARGE LastCumMARGE 1502 0[0,50] 50 10000 2754 50 (50,75] 25 2000 1000 3 1008 75 (75,100] 25 4000 2000 4 Inf 10 100 (100,Inf] Inf Inf 4000 #dta2 <- merge( dta, breakpts, all.x=TRUE, by="Range" ) #dta2 <- dta2[ order( dta2$ID ), ] dta2 <- cbind( dta, breakpts[ match( dta$Range, breakpts$Range ), -which( "Range"==names( breakpts ) ) ] ) dta2$CumMARGE <- with( dta2, Mult/100 * ( CumVALUE - target * LastPct / 100 ) + LastCumMARGE ) dta2$MARGE <- with( dta2, diff( c( 0, CumMARGE ) ) ) dta2 ID VALUE CumVALUE CumPct Range PctTarget Mult LastPct DeltaPct CumMARGE LastCumMARGE MARGE 1 11 11 10[0,50]502 0 50 2000 200 2 12 56 60 (50,75]754 50 25 1400 1000 1200 3 13 39 90 (75,100] 1008 75 25 3200 2000 1800 4 14 2 11110 (100,Inf] Inf 10 100 Inf 5000 4000 1800 target <- 10 breakpts <- data.frame( PctTarget=c(50,75,100,Inf), Mult=c(2,4,8,10) ) breakpts$LastPct <- c( 0, breakpts$PctTarget[ -nrow( breakpts ) ] ) breakpts$Range <- cut( breakpts$PctTarget, c( 0, breakpts$PctTarget ), include.lowest=TRUE ) breakpts$DeltaPct <- with( breakpts, diff( c( 0, PctTarget ) ) ) breakpts$CumMARGE <- target / 1e4 * with( breakpts, cumsum( DeltaPct * Mult ) ) breakpts$LastCumMARGE <- c( 0, breakpts$CumMARGE[ -nrow( breakpts ) ] ) dta <- data.frame( ID=11:14, VALUE=c(1,5,3,2) ) dta$CumVALUE <- cumsum( dta$VALUE ) dta$CumPct <- 100 * dta$CumVALUE / target dta$Range <- cut( dta$CumPct, c( 0, breakpts$PctTarget ), include.lowest=TRUE ) dta ID VALUE CumVALUE CumPct Range 1 11 11 10[0,50] 2 12 56 60 (50,75] 3 13 39 90 (75,100] 4 14 2 11110 (100,Inf] breakpts PctTarget Mult LastPct Range DeltaPct CumMARGE LastCumMARGE 1502 0[0,50] 50 10000 2754 50 (50,75] 25 2000 1000 3 1008 75 (75,100] 25 4000 2000 4 Inf 10 100 (100,Inf] Inf Inf 4000 #dta2 <- merge( dta, breakpts, all.x=TRUE, by="Range" ) #dta2 <- dta2[ order( dta2$ID ), ] dta2 <- cbind( dta, breakpts[ match( dta$Range, breakpts$Range ), -which( "Range"==names( breakpts ) ) ] ) dta2$CumMARGE <- with( dta2, Mult/100 * ( CumVALUE - target * LastPct / 100 ) + LastCumMARGE ) dta2$MARGE <- diff( c( 0, dta2$CumMARGE ) ) dta2 ID VALUE CumVALUE CumPct Range PctTarget Mult LastPct DeltaPct CumMARGE LastCumMARGE MARGE 1 11 11 10[0,50]502 0 50 2000 200 2 12 56 60 (50,75]754 50 25 1400 1000 1200 3 13 39 90 (75,100] 1008 75 25 3200 2000 1800 4 14 2 11110 (100,Inf] Inf 10 100 Inf 5000 4000 1800 On Mon, 9 Mar 2015, Matthias Weber wrote: Hi David, thanks for the reply. My spelling of the numbers was not correct. What I mean with 100.000 is 10.00 ! I have corrected the values in my example below me. Maybe you can understand it better now. Crucially is, that the "MARGE" rises up in dependence of the ID. The ID 11 will be count with 2% because we don't reach the 50% hurdle (5). The ID 12 will reach the 50% hurdle, so the ID 12 should be count with 1200 (result of 4 * 2% + 1 * 4%). The 1 with 4% will be credited more, because they exceed the 50% Target Value. Thanks for your help. Best regards. Mat -Urspr?ngliche Nachricht- Von: David L Carlson [mailto:dcarl...@tamu.edu] Gesendet: Montag, 9. M?rz 2015 16:08 An: Matthias Weber; r-help@r-project.org Betreff: RE: calculate value in dependence of target value It
Re: [R] SPSS command "match files" for merging one-to-many (hierarchical) equivalent in R?
> On Mar 9, 2015, at 1:53 PM, Duncan Murdoch wrote: > > On 09/03/2015 1:40 PM, Kristina Loderer wrote: >> Dear R community, >> >> to combine data sets of hierarchical, nested nature (i.e., data sets >> linked by, for example, the variable "study ID" and then also by >> "outcome_variable_1" and "outcome_variable_2") I can use the match files >> command in SPSS. What is the equivalent command / function in R? Is it >> the merge function, or the match function? The more I read, the more >> confused I become.. >> > > I don't know SPSS at all, so I can't help you. If nobody else does, you > might try putting together a tiny example in R showing what you're starting > with, and what you want to produce. From what you wrote, I'd guess merge(), > not match(), but you might really be asking for something completely > different. > > Duncan Murdoch Based upon the info here: http://www.ats.ucla.edu/stat/spss/modules/merge.htm I would go with ?merge, since the desired functionality appears to be a relational join operation. Regards, Marc Schwartz __ 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.
Re: [R] SPSS command "match files" for merging one-to-many (hierarchical) equivalent in R?
On 09/03/2015 1:40 PM, Kristina Loderer wrote: Dear R community, to combine data sets of hierarchical, nested nature (i.e., data sets linked by, for example, the variable "study ID" and then also by "outcome_variable_1" and "outcome_variable_2") I can use the match files command in SPSS. What is the equivalent command / function in R? Is it the merge function, or the match function? The more I read, the more confused I become.. I don't know SPSS at all, so I can't help you. If nobody else does, you might try putting together a tiny example in R showing what you're starting with, and what you want to produce. From what you wrote, I'd guess merge(), not match(), but you might really be asking for something completely different. Duncan Murdoch __ 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.
Re: [R] Help with optim() to maximize log-likelihood
yes Ben, this works indeed! Thanks a million!! On Mon, Mar 9, 2015 at 7:17 PM, Ben Bolker wrote: > Sophia Kyriakou gmail.com> writes: > > > > > hello, I am using the optim function to maximize the log likelihood of a > > generalized linear mixed model and I am trying to replicate glmer's > > estimated components. If I set both the sample and subject size to > q=m=100 > > I replicate glmer's results for the random intercept model with > parameters > > beta=-1 and sigma^2=1. But if I change beta to 2 glmer works and optim > > gives me the error message "function cannot be evaluated at initial > > parameters". > > > > If anyone could please help? > > Thanks > > snip to make gmane happy. > > It looks like you're getting floating-point under/overflow. If you do > all the computations on the log scale first and then exponentiate, > it seems to work, i.e.: > > piYc_ir[i,] <- lchoose(m,Y[i]) + Y[i]*(z+beta) + > (-z^2/(2*exp(psi))) - > m*(log1p(exp(z+beta))) - 0.5*(log(2*pi)+psi) > piYc_ir[i,] <- exp(piYc_ir[i,]) > > follow-ups should probably go to r-sig-mixed-mod...@r-project.org > instead ... > > Ben Bolker > > __ > 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. > [[alternative HTML version deleted]] __ 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] Fitting fevd fuction to list R
I have data for 90 climate stations. For each station, I have made 100+
simulations using a statistical model. So, in R, I have 90 dataframes, each
dataframe has 100+ simulations arranged column-wise.
Now, I would like to fit an extreme value distribution (EVD) to each climate
station. That is, fit an EVD each to the 100+ simulations and make an average
of the results. Repeat the same for all other climate stations.
So far, I can apply 'fevd' function to each column in a dataframe. How can I
apply this on list object?
library(extRemes)
out.df <- lapply(df, fevd,type="GEV",method = c("MLE"))# fit GEv to each column
of dataframe
#lapply(out.df,plot) # make plots for all columns
rlcis<-lapply(out.df,return.level,
do.ci=TRUE,method="normal",return.period=c(2,5,10,20,50,100))# calc return and
CIs for all columns
lst=list(df,df,df,df)
df=structure(list(Sim001 = c(120.79, 59.35, 51.14, 104.85, 51.09,
138.91, 254.94, 56.44, 68.3, 51.69, 51.31, 51.08, 37.17, 38.02,
62.13, 111.48, 118.38, 45.54, 44.87, 49.59), Sim002 = c(50.25,
31.17, 67.48, 104.56, 59.82, 38.09, 50.76, 70.25, 35.8, 59.2,
47.89, 55.21, 74.38, 51.88, 124.09, 91.86, 109.28, 65.61, 69.54,
55.89), Sim003 = c(30.22, 50.07, 57.66, 57.97, 62.73, 43.84,
103.61, 53.05, 60.71, 46.57, 65.87, 33.27, 60.24, 43.63, 115.68,
37.24, 43.27, 46.38, 122.97, 86.02), Sim004 = c(38.6, 39.02,
45.74, 201.55, 110.78, 49.91, 63.5, 48.65, 94.43, 37.01, 32.61,
46.39, 120.25, 45.38, 70.26, 94.02, 67.35, 55.62, 59.3, 33.96
), Sim005 = c(43.54, 68.42, 86.02, 78.9, 40.68, 59.97, 34.5,
48.47, 68.81, 32, 49.53, 51.23, 51.42, 61.17, 38.02, 52.96, 45.25,
39.18, 42.33, 97.15), Sim006 = c(45.96, 65.21, 94.81, 106.71,
46.95, 26.93, 39.45, 33.79, 50.36, 31.22, 128.37, 177.03, 82.07,
58.02, 32.5, 96.37, 73.77, 48.96, 143.52, 50.14), Sim007 = c(66.3,
53.99, 162.7, 100.22, 48.76, 74.06, 49.3, 62.66, 158, 82.57,
94.07, 93.01, 53.88, 160.91, 63.71, 44.93, 63.82, 56.7, 58.92,
101.52), Sim008 = c(130.62, 75.48, 126.46, 49.97, 71.69, 66.81,
89.33, 52.68, 29.19, 75.88, 89.69, 59.41, 84.16, 104.49, 65.04,
66.41, 88.5, 56.64, 62.48, 77.08), Sim009 = c(60.58, 71.85, 62.08,
57.4, 63.08, 45.38, 50.97, 59.42, 159.44, 120.94, 58.66, 54.57,
77.45, 49.63, 48.88, 91.03, 103.42, 56.9, 97.04, 69.89), Sim010 = c(48.63,
51.07, 65.13, 47.59, 94.73, 42.43, 68.77, 95.83, 42.16, 133.1,
67.2, 56.91, 138.57, 39.26, 79.75, 123.67, 64.27, 64.83, 78.88,
89.74), Sim011 = c(59.85, 53.73, 116.88, 95.06, 113.44, 87.64,
47.37, 42.42, 36.69, 39.11, 76.91, 59.85, 76.29, 118.37, 39.14,
50.76, 98.06, 40.71, 53.03, 42.93), Sim012 = c(128.35, 60.21,
60.19, 51.69, 51.47, 35.44, 101.72, 82.83, 50.72, 68.66, 80.84,
59.98, 79.84, 35.52, 128.69, 53.35, 84.77, 18.38, 28.98, 48),
Sim013 = c(52.88, 117.11, 103.3, 103.59, 119.06, 62.66, 65.64,
75.91, 81.78, 80.31, 22.83, 79.22, 51.33, 79.63, 86.26, 54.44,
42.86, 63.95, 166.87, 58.48), Sim014 = c(50.28, 123.9, 35.87,
133.52, 94.28, 62.35, 58.54, 42.08, 67.7, 101.44, 34.68,
45.98, 60.99, 60.06, 79.76, 61.93, 59.4, 42.02, 56.45, 81.41
), Sim015 = c(50.32, 39.01, 100.3, 105.38, 55.49, 36.36,
56.49, 107.52, 38.7, 73.09, 98.22, 44.19, 50.17, 56.69, 44.82,
44.09, 57.57, 52.55, 90.37, 78.62), Sim016 = c(35.2, 62.77,
35.25, 52.05, 93.51, 65.84, 43.85, 54.52, 39.17, 62.02, 47.6,
34.42, 190.57, 38.46, 94.9, 73.34, 78.5, 52.84, 103.7, 51.48
), Sim017 = c(69.03, 58.19, 130.37, 80.04, 52.96, 65.14,
65.08, 45.95, 65.35, 41.95, 78.67, 78.41, 56.51, 63.52, 52.93,
52.32, 70.14, 81.59, 70.99, 105.02), Sim018 = c(55.98, 44.37,
59.07, 36.65, 44.16, 26.62, 125.38, 75.54, 75.46, 25.62,
22.95, 65.74, 72.86, 53.5, 32.05, 58.98, 70.87, 30.95, 78.25,
54.75), Sim019 = c(147.82, 37.48, 161.91, 46.28, 95.4, 74.79,
53.51, 58.73, 50.96, 32.03, 50.08, 60.03, 76.75, 45.31, 58.29,
52.91, 42.84, 74.52, 83.19, 43.8), Sim020 = c(59.33, 218.52,
64.55, 73.07, 59.9, 39.09, 129.88, 61.53, 56.7, 38.55, 62.2,
29.25, 52.74, 57.86, 46.04, 80.03, 44.61, 88.52, 45.36, 93.97
), Sim021 = c(93.44, 41.32, 67.08, 99.15, 89.43, 31.64, 38.59,
65.08, 58.9, 52.7, 47.39, 47.91, 90.93, 54.57, 51.26, 44.59,
33.52, 38.69, 44.92, 50.46), Sim022 = c(43.37, 43.47, 63.15,
77.19, 117.13, 77.32, 65.36, 67.49, 49.18, 87.66, 70.09,
110.66, 70.85, 46.71, 55.36, 45.53, 30.55, 51.7, 46.08, 65.91
), Sim023 = c(65.76, 42.75, 50.2, 58.23, 69.27, 75.63, 46.72,
72.47, 62.53, 50.87, 58.8, 63.61, 39.99, 91.36, 66.07, 100.32,
55.34, 32.59, 59.8, 43.96), Sim024 = c(174.2, 70.17, 47.86,
71.24, 91.39, 40.5, 28.66, 64.57, 33.02, 46.27, 68.56, 56.68,
97.28, 46.24, 65.76, 72.53, 60.26, 128.26, 85.63, 107.29),
Sim025 = c(84.66, 38.95, 43.63, 41.33, 108.67, 62.94, 64.73,
57.26, 42.11, 100.24, 28, 35.95, 175.8, 61.64, 81.42, 67.55,
68.12, 35.1, 46.63, 105.43), Sim026 = c(64.17, 55.25, 59.21,
49.21, 104.75, 129.05, 76.05, 69.88, 110.19, 40.71, 103.17,
74.32, 64.18, 55.66, 105.93, 36.25, 81.08, 75.96, 81.67,
99.22), Sim027 = c(55.07, 53.32, 71.68, 37.51, 96.35, 42.25,
41.22, 41.09, 67.46, 69.64
[R] SPSS command "match files" for merging one-to-many (hierarchical) equivalent in R?
Dear R community, to combine data sets of hierarchical, nested nature (i.e., data sets linked by, for example, the variable "study ID" and then also by "outcome_variable_1" and "outcome_variable_2") I can use the match files command in SPSS. What is the equivalent command / function in R? Is it the merge function, or the match function? The more I read, the more confused I become.. Thank your for help in advance! Kristina Loderer - Kristina Loderer Ludwig-Maximilians-Universität München Department Psychologie Leopoldstr. 13 D-80802 München Telefon: +49 (89) 2180-6047 Email: kristina.lode...@psy.lmu.de - __ 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] Change the argument function inside R function in GPfit package
Hi R list, I am using the GPfit package to fit Gaussian Process model. The kernel in the package is, K(x, x') = sigma^2 * exp(x-x')^2 My kernel have an extra term, K((x, z), (x', z')) = sigma^2 * exp(x-x')^2 * exp(z-z')^2 The function corr_matrix() is, corr_matrix(X, beta, corr=list(type="exponential",power=1.95)) github source: https://github.com/cran/GPfit/blob/master/R/corr_matrix.R I am changing the corr argument, so it looks like mine. How should I do it? Also, what package do you guys recommend for GP modeling? I know GPstuff or GPML but that's Matlab. Thanks very much. Mike [[alternative HTML version deleted]] __ 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.
Re: [R] R/3.1.3 source installation
This is the wrong list: see the posting guide. As it is about compiled
code, R-help is quite inappropriate, and as it is Mac-specific, post to
R-sig-mac.
The issue appears to be that you did not follow the R-admin manual and
used the wrong Fortran compiler: gfortran-4.2.3 is documented for
Mountain Lion or earlier. But you did not say exactly what you did use
On 09/03/2015 17:47, White Sky wrote:
R 3.1.3 is available for installation via source-code.
However ./configure terminates with
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... unknown
configure: WARNING: unknown Fortran name-mangling scheme
checking whether gfortran appends underscores to external names... unknown
configure: error: cannot use Fortran
Mac OSX 10.9.5 gfortran-4.2.3 (64bit)
Underscores are appended to external names by default but this doesn't seem to
be recognised.
I have a feeling the problem might in the configure* file## DANGER! We really
needs the results of _AC_F77_NAME_MANGLING as## stored in the cache var
ac_cv_f77_mangling which is not documented
## and hence may change ...
and then
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${F77} appends underscores to external names"
>&5$as_echo_n "checking whether ${F77} appends underscores to external names... " >&6; }
if ${r_cv_prog_f77_append_underscore+:} false; then :
[[alternative HTML version deleted]]
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--
Brian D. Ripley, rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK
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[R] R/3.1.3 source installation
R 3.1.3 is available for installation via source-code.
However ./configure terminates with
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... unknown
configure: WARNING: unknown Fortran name-mangling scheme
checking whether gfortran appends underscores to external names... unknown
configure: error: cannot use Fortran
Mac OSX 10.9.5 gfortran-4.2.3 (64bit)
Underscores are appended to external names by default but this doesn't seem to
be recognised.
I have a feeling the problem might in the configure* file## DANGER! We really
needs the results of _AC_F77_NAME_MANGLING as## stored in the cache var
ac_cv_f77_mangling which is not documented
## and hence may change ...
and then
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${F77} appends
underscores to external names" >&5$as_echo_n "checking whether ${F77} appends
underscores to external names... " >&6; }
if ${r_cv_prog_f77_append_underscore+:} false; then :
[[alternative HTML version deleted]]
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Re: [R] plotting the one-dimensional density of events in time
Tom and Bill--
Thanks! Both excellent solutions.
--Chris
Christopher W. Ryan, MD, MS
cryanatbinghamtondotedu
Early success is a terrible teacher. You’re essentially being rewarded
for a lack of preparation, so when you find yourself in a situation
where you must prepare, you can’t do it. You don’t know how.
--Chris Hadfield, An Astronaut's Guide to Life on Earth
William Dunlap wrote:
> You could change the x component of density's output back into a Date object
> and let plot choose a Date axis in its usual way. E.g.,
> > den <- density(as.numeric(dd))
> > den$x <- as.Date(den$x, origin=as.Date("1970-01-01"))
> > plot(den$x, den$y)
> (You probably will also want to normalize the y component to be on a
> specific
> per time unit, say day or year, basis.)
>
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Fri, Mar 6, 2015 at 1:03 PM, Christopher W. Ryan
> mailto:cr...@binghamton.edu>> wrote:
>
> I have the dates of occurence of a repetitive event. I would like to
> plot the density of these events, as well as their specific temporal
> location. This is as far as I have gotten:
>
> # generate some sample data: dates in 2014
> random.dates <- sample(1:31, 100, replace=TRUE)
> random.months <- sample(1:12, 100, replace=TRUE)
> dd <- as.Date(as.character((paste(random.dates, random.months, "2014",
> sep="-"))), format="%d-%m-%Y")
> dd <- dd[!is.na (dd)]
>
> # plot density with a "rug".
> density(as.numeric(dd))
> plot(density(as.numeric(dd)))
> rug(as.numeric(dd))
>
> # But horizontal axis label is not very informative
> # would prefer labeling the start of each month
> plot(density(as.numeric(dd)), axes=FALSE)
> library(zoo)
> new.axis <- as.yearmon(dd)
>
> # but then what? This is where I get stuck--adding back a sensible axis
>
> Grateful for any guidance.
>
> Thanks.
>
> --Chris
> --
> Christopher W. Ryan, MD, MS
> cryanatbinghamtondotedu
>
> Early success is a terrible teacher. You’re essentially being rewarded
> for a lack of preparation, so when you find yourself in a situation
> where you must prepare, you can’t do it. You don’t know how.
> --Chris Hadfield, An Astronaut's Guide to Life on Earth
>
>
> ---
>
> __
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> To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
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> and provide commented, minimal, self-contained, reproducible code.
>
>
---
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Re: [R] Help with optim() to maximize log-likelihood
Sophia Kyriakou gmail.com> writes: > > hello, I am using the optim function to maximize the log likelihood of a > generalized linear mixed model and I am trying to replicate glmer's > estimated components. If I set both the sample and subject size to q=m=100 > I replicate glmer's results for the random intercept model with parameters > beta=-1 and sigma^2=1. But if I change beta to 2 glmer works and optim > gives me the error message "function cannot be evaluated at initial > parameters". > > If anyone could please help? > Thanks snip to make gmane happy. It looks like you're getting floating-point under/overflow. If you do all the computations on the log scale first and then exponentiate, it seems to work, i.e.: piYc_ir[i,] <- lchoose(m,Y[i]) + Y[i]*(z+beta) + (-z^2/(2*exp(psi))) - m*(log1p(exp(z+beta))) - 0.5*(log(2*pi)+psi) piYc_ir[i,] <- exp(piYc_ir[i,]) follow-ups should probably go to r-sig-mixed-mod...@r-project.org instead ... Ben Bolker __ 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] Book: Beginner's Guide to Data Exploration and Visualisation with R.
We are please to announce the following book: Title: Beginner's Guide to Data Exploration and Visualisation with R. Authors: Ieno & Zuur Book website: http://www.highstat.com/BGDEV.htm Paperback or EBook can be order (exclusively) from: http://www.highstat.com/bookorder.htm TOC: http://www.highstat.com/BGS/DV/TOC_Online.pdf Price: 29 GBP Outline: In 2010 we published a paper in the journal Methods in Ecology and Evolution entitled ‘A protocol for data exploration to avoid common statistical problems’. Little did we know at the time that this paper would become one of the journal’s all-time top papers, both top downloaded and top cited papers, with 22,472 downloads between 2010 and 2014. Based on this success we decided to extend the material in the paper into a book. It is part of our 'Beginner’s Guide to ...' book series. We tried to write this book in such a way that the statistical knowledge level is as low as possible. A knowledge of linear regression is all that you need. Keywords: Outliers, normality, homogeneity, collinearity, relationships, confounding. Case studies Kind regards, Alain Zuur -- Dr. Alain F. Zuur First author of: 1. Beginner's Guide to GAMM with R (2014). 2. Beginner's Guide to GLM and GLMM with R (2013). 3. Beginner's Guide to GAM with R (2012). 4. Zero Inflated Models and GLMM with R (2012). 5. A Beginner's Guide to R (2009). 6. Mixed effects models and extensions in ecology with R (2009). 7. Analysing Ecological Data (2007). Highland Statistics Ltd. 9 St Clair Wynd UK - AB41 6DZ Newburgh Tel: 0044 1358 788177 Email: highs...@highstat.com URL: www.highstat.com __ 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.
Re: [R] calculate value in dependence of target value
It is very hard to figure out what you are trying to do.
1. All of the VALUEs are greater than the target of 100
2. Your description of what you want does not match your example.
Perhaps VALUE should be divided by 1000 (e.g. not 1, but 10)?
Perhaps your targets do not apply to VALUE, but to cumulative VALUE?
-
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Matthias Weber
Sent: Monday, March 9, 2015 7:46 AM
To: r-help@r-project.org
Subject: [R] calculate value in dependence of target value
Hello together,
i have a litte problem. Maybe anyone can help me.
I have to calculate a new column in dependence of a target value.
As a example: My target value is 100.000
At the moment I have a data.frame with the following values.
IDVALUE
1 111
2 125
3 133
4 142
The new column ("MARGE") should be calculated with the following graduation:
Until the VALUE reach 50% of the target value (50.000) = 2%
Until the VALUE reach 75% of the target value (75.000) = 4%
Until the VALUE reach 100% of the target value (<100.000) = 8%
If the VALUE goes above 100% of the value (>100.000) = 10%
The result looks like this one:
IDVALUE MARGE
1 111 200 (result of 10.000 * 2%)
2 125 1200 (result of 40.000 * 2% + 10.000 * 4%)
3 133 1800 (result of 15.000 * 4% + 15.000 * 8%)
4 142 1800 (result of 10.000 * 8% + 10.000 * 10%)
Is there anyway to calculate the column "MARGE" automatically in R?
Thanks a lot for your help.
Best regards.
Mat
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Re: [R] Add sum line to plot of multiple x values
PIKAL Petr writes:
> Hi
>
> Not extremely clear what do you want to plot. Do you want to add a
> line which marks total number of files each day regardless of user? Or
> a total number of files regardless of date coloured by user?
Sorry, I was unclear. I meant that I would like to plot the following:
1. For each user: the number of files for each date (my code does this)
2. The sum of files of all users for each date (this is what I still
need)
> In each case you shall search functions geom_hline or geom_abline
>
> http://stackoverflow.com/questions/13254441/add-a-horizontal-line-to-plot-and-legend-in-ggplot2
So I don't want a straight line
> ggplot is rather complicated but very flexible
I don't mind ggplot being complicated, but I find the documentation a
little impenetrable.
Cheers,
Loris
>> -Original Message-
>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Loris
>> Bennett
>> Sent: Monday, March 09, 2015 2:56 PM
>> To: r-h...@stat.math.ethz.ch
>> Subject: [R] Add sum line to plot of multiple x values
>>
>> Hi,
>>
>> Here are my data:
>>
>> > d
>>user files date
>> 1 alice18 2013-09-15
>> 2 bob 5 2013-09-15
>> 3 carol21 2013-09-15
>> 4 alice22 2013-09-08
>> 5 bob 9 2013-09-08
>> 6 carol14 2013-09-08
>> 7 alice26 2013-09-01
>> 8 bob 3 2013-09-01
>> 9 carol22 2013-09-01
>>
>> I would like to plot the number of files against date for all users, so
>> I have:
>>
>> library(ggplot2)
>>
>> people <- c("alice","bob","carol")
>> user <- c(rep(people,3))
>> files <- c(18,5,21,22,9,14,26,3,22)
>> date <- c(rep("2013-09-15",3),rep("2013-09-08",3),rep("2013-09-
>> 01",3))
>> d <- data.frame(user=user,files=files,date=date)
>>
>> p <- ggplot()
>> p <- p + geom_line(data=d,aes(x=date,y=files,group=user,colour=user))
>>
>> I would now like to add a line to show the total number of files as a
>> function of date. I tried
>>
>> p <- p +
>> geom_line(data=d,aes(x=date,y=sum(files),group=date),colour='black')
>>
>> I don't get a black line, but the plot is scaled such that I can see
>> that sum(file) for all values of 'file', rather than those for each
>> date, is being used.
>>
>> I would like to know how to do this correctly, but I would rather be
>> able to work it out for myself. However, if I decide, say, that I
>> don't
>> know exactly what the 'group' argument does, how do I find it out?
>>
>> ?geom_line doesn't have it, although the examples there use it. ?ggplot
>> doesn't mention it. ?group gives me stuff about formatting text
>> arguments. ??group only leads me to ?ggplot2::add_group, which also
>> does
>> not seem to help.
>>
>> Am I at fault for trying to learn R in an ad hoc manner, to which the
>> documentation of R does not lend itself, or am I missing something?
>>
>> Cheers,
>>
>> Loris
>>
>> --
>> This signature is currently under construction.
>>
>> __
>> 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.
>
>
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Re: [R] calculate value in dependence of target value
Hi David,
thanks for the reply. My spelling of the numbers was not correct. What I mean
with 100.000 is 10.00 !
I have corrected the values in my example below me.
Maybe you can understand it better now.
Crucially is, that the "MARGE" rises up in dependence of the ID. The ID 11 will
be count with 2% because we don't reach the 50% hurdle (5). The ID 12 will
reach the 50% hurdle, so the ID 12 should be count with 1200 (result of 4 *
2% + 1 * 4%). The 1 with 4% will be credited more, because they exceed
the 50% Target Value.
Thanks for your help.
Best regards.
Mat
-Ursprüngliche Nachricht-
Von: David L Carlson [mailto:dcarl...@tamu.edu]
Gesendet: Montag, 9. März 2015 16:08
An: Matthias Weber; r-help@r-project.org
Betreff: RE: calculate value in dependence of target value
It is very hard to figure out what you are trying to do.
1. All of the VALUEs are greater than the target of 100 2. Your description of
what you want does not match your example.
Perhaps VALUE should be divided by 1000 (e.g. not 1, but 10)?
Perhaps your targets do not apply to VALUE, but to cumulative VALUE?
-
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Matthias Weber
Sent: Monday, March 9, 2015 7:46 AM
To: r-help@r-project.org
Subject: [R] calculate value in dependence of target value
Hello together,
i have a litte problem. Maybe anyone can help me.
I have to calculate a new column in dependence of a target value.
As a example: My target value is 10. At the moment I have a data.frame with
the following values.
IDVALUE
1 111
2 125
3 133
4 142
The new column ("MARGE") should be calculated with the following graduation:
Until the VALUE reach 50% of the target value (5) = 2%
Until the VALUE reach 75% of the target value (75000) = 4%
Until the VALUE reach 100% of the target value (<10) = 8%
If the VALUE goes above 100% of the value (>10) = 10%
The result looks like this one:
IDVALUE MARGE
1 111 200 (result of 1 * 2%)
2 125 1200 (result of 4 * 2% + 1 * 4%)
3 133 1800 (result of 15000 * 4% + 15000 * 8%)
4 142 1800 (result of 1 * 8% + 1 * 10%)
Is there anyway to calculate the column "MARGE" automatically in R?
Thanks a lot for your help.
Best regards.
Mat
This e-mail may contain trade secrets, privileged, undisclosed or otherwise
confidential information. If you have received this e-mail in error, you are
hereby notified that any review, copying or distribution of it is strictly
prohibited. Please inform us immediately and destroy the original transmittal.
Thank you for your cooperation.
Diese E-Mail kann Betriebs- oder Geschaeftsgeheimnisse oder sonstige
vertrauliche Informationen enthalten. Sollten Sie diese E-Mail irrtuemlich
erhalten haben, ist Ihnen eine Kenntnisnahme des Inhalts, eine
Vervielfaeltigung oder Weitergabe der E-Mail ausdruecklich untersagt. Bitte
benachrichtigen Sie uns und vernichten Sie die empfangene E-Mail. Vielen Dank.
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[R] Help with optim() to maximize log-likelihood
hello, I am using the optim function to maximize the log likelihood of a
generalized linear mixed model and I am trying to replicate glmer's
estimated components. If I set both the sample and subject size to q=m=100
I replicate glmer's results for the random intercept model with parameters
beta=-1 and sigma^2=1. But if I change beta to 2 glmer works and optim
gives me the error message "function cannot be evaluated at initial
parameters".
If anyone could please help?
Thanks
# likelihood function
ll <- function(x,Y,m){
beta <- x[1]
psi <- x[2]
q <- length(Y)
p <- 20
rule20 <- gaussHermiteData(p)
wStar <- exp(rule20$x * rule20$x + log(rule20$w))
# Integrate over(-Inf, +Inf) using adaptive Gauss-Hermite quadrature
g <- function(alpha, beta, psi, y, m) {-y+m*exp(alpha + beta)/(1 +
exp(alpha + beta)) + alpha/exp(psi)}
DDfLik <- deriv(expression(-y+m*exp(alpha + beta)/(1 + exp(alpha + beta))
+ alpha/exp(psi)),
namevec = "alpha", func = TRUE,function.arg = c("alpha", "beta", "psi",
"y", "m"))
int0 <- rep(NA,q)
piYc_ir <- matrix(NA,q,p)
for (i in 1:q){
muHat <- uniroot(g, c(-10, 10),extendInt ="yes", beta = beta, psi = psi, y
= Y[i], m = m)$root
jHat <- attr(DDfLik(alpha = muHat, beta, psi, Y[i], m), "gradient")
sigmaHat <- 1/sqrt(jHat)
z <- muHat + sqrt(2) * sigmaHat * rule20$x
piYc_ir[i,] <-
choose(m,Y[i])*exp(Y[i]*(z+beta))*exp(-z^2/(2*exp(psi)))/((1+exp(z+beta))^m*sqrt(2*pi*exp(psi)))
int0[i] <- sqrt(2)*sigmaHat*sum(wStar*piYc_ir[i,])
}
ll <- -sum(log(int0))
ll
}
beta <- 2
sigma2 <- 1
m <- 100
q <- 100
cl <- seq.int(q)
tot <- rep(m,q)
set.seed(123)
alpha <- rnorm(q, 0, sqrt(sigma2))
Y <- rbinom(q,m,plogis(alpha+beta))
dat <- data.frame(y = Y, tot = tot, cl = cl)
f1 <- glmer(cbind(y, tot - y) ~ 1 + (1 | cl), data = dat,family =
binomial(),nAGQ = 20)
betaH <- summary(f1)$coefficients[1]
sigma2H <- as.numeric(summary(f1)$varcor)
thetaglmer <- c(betaH,sigma2H)
logL <- function(x) ll(x,Y,m)
thetaMLb <- optim(c(plogis(sum(Y/m)),log(sigma2H)),fn=logL)$par
Error in optim(c(plogis(sum(Y/m)), log(sigma2H)), fn = logL) : function
cannot be evaluated at initial parameters
thetaglmer
[1] 2.1128529 0.8311484
(thetaML <- c(thetaMLb[1],exp(thetaMLb[2])))
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Re: [R] Extract year from date
You need to solve step 1 (converting to Date class) before you can solve
step 2 (getting the year as a number).
In the data you are starting with, the first value in the Date column is
41163. You don't say whether that column is numeric or character, so let's
try it both ways:
> as.Date('41163','%m/%d/%Y')
[1] NA
> as.Date(41163,'%m/%d/%Y')
Error in charToDate(x) :
character string is not in a standard unambiguous format
Whatever it is, it is not formatted "%m/%d/%Y", so step 1 fails.
On the other hand, if you start with something that is in fact formatted
as a date:
> tmp <- as.Date('3/2/2015','%m/%d/%Y')
> format(tmp,'%Y')
[1] "2015"
> as.numeric(format(tmp,'%Y'))
[1] 2015
you get the year as a number, using the method you tried.
So, what do 41163 and all the rest of the numbers in your Date column
actually represent???
Mark Sharp is probably correct in expecting that they represent the number
of days since some base date, and an easy way to see that would be to try
the core of step 1:
> as.Date(41163)
Error in as.Date.numeric(41163) : 'origin' must be supplied
It would be up to you, of course, to find out what the origin is. If
1/1/1900 is correct, then
> as.numeric( format( as.Date( 41163, origin='1900-1-1'), '%Y'))
[1] 2012
(I personally prefer to use base R as much as possible)
-Don
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
On 3/7/15, 11:50 PM, "Steve Archambault" wrote:
>Hi all,
>
>I am trying in vain to create a new object "Year" in my data frame from
>existing Date data. I have tried many different approaches, but can't seem
>to get it to work. Here is an example of some code I tried.
>
>date1<- as.Date(wells$Date,"%m/%d/%Y")
>wells$year<-as.numeric(format(date1, "%Y"))
>
>I am starting with data that looks like this.
>
>ID Date DepthtoWater_bgs test test2
>1 BC-0004 41163 260.603 1
>2 BC-0004 41255 261.654 2
>3 BC-0003 41345 166.585 3
>4 BC-0002 41351 317.856 4
>5 BC-0004 41355 262.157 5
>6 BC-0003 41438 167.558 6
>7 BC-0004 41438 265.459 7
>8 BC-0002 41443 317.25 10 8
>9 BC-0002 41521 321.25 11 9
>10 BC-0003 41522 168.65 1210
>11 BC-0004 41522 266.15 1311
>12 BC-0003 41627 168.95 1412
>13 BC-0004 41627 265.25 1513
>14 BC-0002 41634 312.31 1614
>15 BC-0003 41703 169.25 1715
>16 BC-0004 41703 265.05 1816
>17 BC-0002 41710 313.01 1917
>18 BC-0003 41795 168.85 2018
>19 BC-0004 41795 266.95 2119
>20 BC-0002 41801 330.41 2220
>21 BC-0003 41905 169.75 2321
>22 BC-0004 41905 267.75 2422
>23 BC-0002 41906 321.01 2523
>
>Any help would be greatly appreciated!
>
>-Steve
>Sent from my iPhone
>
>__
>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.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Add sum line to plot of multiple x values
Hi
Not extremely clear what do you want to plot. Do you want to add a line which
marks total number of files each day regardless of user? Or a total number of
files regardless of date coloured by user?
In each case you shall search functions geom_hline or geom_abline
http://stackoverflow.com/questions/13254441/add-a-horizontal-line-to-plot-and-legend-in-ggplot2
ggplot is rather complicated but very flexible
Petr
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Loris
> Bennett
> Sent: Monday, March 09, 2015 2:56 PM
> To: r-h...@stat.math.ethz.ch
> Subject: [R] Add sum line to plot of multiple x values
>
> Hi,
>
> Here are my data:
>
> > d
>user files date
> 1 alice18 2013-09-15
> 2 bob 5 2013-09-15
> 3 carol21 2013-09-15
> 4 alice22 2013-09-08
> 5 bob 9 2013-09-08
> 6 carol14 2013-09-08
> 7 alice26 2013-09-01
> 8 bob 3 2013-09-01
> 9 carol22 2013-09-01
>
> I would like to plot the number of files against date for all users, so
> I have:
>
> library(ggplot2)
>
> people <- c("alice","bob","carol")
> user <- c(rep(people,3))
> files <- c(18,5,21,22,9,14,26,3,22)
> date <- c(rep("2013-09-15",3),rep("2013-09-08",3),rep("2013-09-
> 01",3))
> d <- data.frame(user=user,files=files,date=date)
>
> p <- ggplot()
> p <- p + geom_line(data=d,aes(x=date,y=files,group=user,colour=user))
>
> I would now like to add a line to show the total number of files as a
> function of date. I tried
>
> p <- p +
> geom_line(data=d,aes(x=date,y=sum(files),group=date),colour='black')
>
> I don't get a black line, but the plot is scaled such that I can see
> that sum(file) for all values of 'file', rather than those for each
> date, is being used.
>
> I would like to know how to do this correctly, but I would rather be
> able to work it out for myself. However, if I decide, say, that I
> don't
> know exactly what the 'group' argument does, how do I find it out?
>
> ?geom_line doesn't have it, although the examples there use it. ?ggplot
> doesn't mention it. ?group gives me stuff about formatting text
> arguments. ??group only leads me to ?ggplot2::add_group, which also
> does
> not seem to help.
>
> Am I at fault for trying to learn R in an ad hoc manner, to which the
> documentation of R does not lend itself, or am I missing something?
>
> Cheers,
>
> Loris
>
> --
> This signature is currently under construction.
>
> __
> 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.
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[R] Add sum line to plot of multiple x values
Hi,
Here are my data:
> d
user files date
1 alice18 2013-09-15
2 bob 5 2013-09-15
3 carol21 2013-09-15
4 alice22 2013-09-08
5 bob 9 2013-09-08
6 carol14 2013-09-08
7 alice26 2013-09-01
8 bob 3 2013-09-01
9 carol22 2013-09-01
I would like to plot the number of files against date for all users, so
I have:
library(ggplot2)
people <- c("alice","bob","carol")
user <- c(rep(people,3))
files <- c(18,5,21,22,9,14,26,3,22)
date <- c(rep("2013-09-15",3),rep("2013-09-08",3),rep("2013-09-01",3))
d <- data.frame(user=user,files=files,date=date)
p <- ggplot()
p <- p + geom_line(data=d,aes(x=date,y=files,group=user,colour=user))
I would now like to add a line to show the total number of files as a
function of date. I tried
p <- p + geom_line(data=d,aes(x=date,y=sum(files),group=date),colour='black')
I don't get a black line, but the plot is scaled such that I can see
that sum(file) for all values of 'file', rather than those for each
date, is being used.
I would like to know how to do this correctly, but I would rather be
able to work it out for myself. However, if I decide, say, that I don't
know exactly what the 'group' argument does, how do I find it out?
?geom_line doesn't have it, although the examples there use it. ?ggplot
doesn't mention it. ?group gives me stuff about formatting text
arguments. ??group only leads me to ?ggplot2::add_group, which also does
not seem to help.
Am I at fault for trying to learn R in an ad hoc manner, to which the
documentation of R does not lend itself, or am I missing something?
Cheers,
Loris
--
This signature is currently under construction.
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[R] calculate value in dependence of target value
Hello together,
i have a litte problem. Maybe anyone can help me.
I have to calculate a new column in dependence of a target value.
As a example: My target value is 100.000
At the moment I have a data.frame with the following values.
IDVALUE
1 111
2 125
3 133
4 142
The new column ("MARGE") should be calculated with the following graduation:
Until the VALUE reach 50% of the target value (50.000) = 2%
Until the VALUE reach 75% of the target value (75.000) = 4%
Until the VALUE reach 100% of the target value (<100.000) = 8%
If the VALUE goes above 100% of the value (>100.000) = 10%
The result looks like this one:
IDVALUE MARGE
1 111 200 (result of 10.000 * 2%)
2 125 1200 (result of 40.000 * 2% + 10.000 * 4%)
3 133 1800 (result of 15.000 * 4% + 15.000 * 8%)
4 142 1800 (result of 10.000 * 8% + 10.000 * 10%)
Is there anyway to calculate the column "MARGE" automatically in R?
Thanks a lot for your help.
Best regards.
Mat
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Re: [R] R: Reverse Complementary Base Problem
Use reverseComplement() in the Biostrings package.
B.
On Mar 8, 2015, at 10:08 PM, saran wai wrote:
> Hi I'm new to R programming and trying to write program for Reverse and
> Complementary Base. the objective is to Design A DNA primer. So I have a DNA
> sequence with base A T C G and A complement to T; T=A;C=G;G=C. I just figure
> out How to Reverse It Already. but for the Complement i can only make it
> answer for just 1 base but cant be all of the sequence. and i dont know how
> to combine reverse and complement function. here is my code and im totallt
> confuse with it. Cn someone help me with this problem? You will be my life
> savior! thank you! strReverse <- function(x) sapply(lapply(strsplit(x,
> NULL), rev), paste, collapse="") strReverse(c("ATCGGTCAATCGA"))
> complement.base = function(base){ if(base == 'A' | base == 'a')
> print("T") if(base == 'T' | base == 't') print("A") if(base == 'G' | base
> == 'g') print("C") if(base == 'C' | base == 'c') print("G")}
> complement.base(base="A")
> [[alternative HTML version deleted]]
>
> __
> 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.
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Re: [R] Rstudio R-devel libR.so
Please read the Posting Guide. Unreleased versions of R are off-topic in this
mailing list (see the R-devel mailing list). RStudio-specific questions are
also off-topic here (should be about R, not IDEs).
---
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Sent from my phone. Please excuse my brevity.
On March 9, 2015 4:48:11 AM PDT, Karim Mezhoud wrote:
>Thanks Pascal. Not yet resolved.
>Here is an example of symbolic link between libR.so
>https://support.rstudio.com/hc/communities/public/questions/200661703-R-shared-library-usr-local-lib-R-lib-libR-so-not-found-UBUNTU-11-
>
>When I get a symbolic link with:
>
> sudo ln -s /usr/lib/R/lib/libR.so /usr/local/R-devel//lib/libR.so
>
>
>The R session had a fatal error.
>
>
>ERROR r error 4 (R code execution error) [errormsg=Error in
>.Internal(getOption(x)) :
>
>there is no .Internal function 'getOption'
>
>]; OCCURRED AT: core::Error r::exec::evaluateString(const std::string&,
>SEXPREC**, r::sexp::Protect*) /home/ubuntu/rstudio/src/cpp/r/RExec.cpp:
>
>
>
>On Mon, Mar 9, 2015 at 10:53 AM, Pascal Oettli
>wrote:
>
>> Hello,
>>
>> There is a dedicated support to RStudio here:
>https://support.rstudio.com
>>
>> Regards,
>> Pascal
>>
>> On Mon, Mar 9, 2015 at 7:41 PM, Karim Mezhoud
>wrote:
>> > Dear All,
>> > I am actually on R-devel using shell consol. When I run RStudio, it
>can't
>> > find libR.so in the new /lib folder where is libRblas.so
>libRlapack.so.
>> > At first step I configure R-devel to share library with ./configure
>> > --enable-R-shlib.
>> >
>> > when I copied libR.so from /usr/lib/R/lib/libR.so (stable version
>R 3.1)
>> > to /usr/local/R-devel/lib/libR.so (R-devel version), That doesn't
>work.
>> >
>> > please find the detail at below.
>> > Karim mezhoud
>> >
>> >
>> >
>> >
>> > $which R
>> > /usr/bin/R
>> > $R
>> >> R.Version()[13]
>> > $version.string
>> > [1] "R version 3.1.2 (2014-10-31)
>> >
>> >> Sys.getenv("R_HOME")
>> > [1] "/usr/lib/R"
>> >
>> >> .Library
>> > [1] "/usr/lib/R/library"
>> >> .libPaths()
>> > [1] "/home/mezhoud/R/x86_64-pc-linux-gnu-library/3.1"
>> > [2] "/usr/local/lib/R/site-library"
>> > [3] "/usr/lib/R/site-library"
>> > [4] "/usr/lib/R/library"
>> > "
>> >
>> >
>> > $sudo apt-get build-dep r-base
>> > $sudo apt-get install subversion ccache
>> > $mkdir ~/svn/
>> > $cd ~/svn/
>> > $svn co https://svn.r-project.org/R/trunk r-devel/R
>> >
>> > $cd /svn/r-devel/R
>> > $./configure --enable-R-shlib
>> > $make
>> > $make check
>> > $sudo make install rhome=/usr/local/R-devel
>> >
>> > $which R
>> > /usr/local/bin/R
>> >
>> > $cd /usr/local/bin
>> > $R
>> >
>> >>R.Version()[13]
>> > $version.string
>> > [1] "R Under development (unstable) (2015-03-07 r67951)"
>> >
>> >> .libPaths()
>> > [1] "/usr/local/R-devel/library"
>> >> .Library
>> > [1] "/usr/local/R-devel/library"
>> >
>> >> Sys.getenv("R_HOME")
>> > [1] "/usr/local/R-devel"
>> >
>> > $rstudio
>> > R shared library (/usr/local/R-devel/lib/libR.so) not found.
>> > If this is a custom build of R, was it built with the
>--enable-R-shlib
>> > option?
>> >
>> > $export RSTUDIO_WHICH_R=/usr/local/bin/R
>> > $rstudio
>> > R shared library (/usr/local/R-devel/lib/libR.so) not found.
>> > If this is a custom build of R, was it built with the
>--enable-R-shlib
>> > option?
>> >
>> > $export RSTUDIO_WHICH_R=/usr/local/R-devel/bin/R
>> > $rstudio
>> > R shared library (/usr/local/R-devel/lib/libR.so) not found.
>> > If this is a custom build of R, was it built with the
>--enable-R-shlib
>> > option?
>> >
>> > $sudo locate libR.so
>> > /usr/lib/libR.so
>> > /usr/lib/R/lib/libR.so
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > __
>> > 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.
>>
>>
>>
>> --
>> Pascal Oettli
>> Project Scientist
>> JAMSTEC
>> Yokohama, Japan
>>
>
> [[alternative HTML version deleted]]
>
>__
>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.
__
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https://stat.ethz.ch/mail
[R] R: Reverse Complementary Base Problem
Hi I'm new to R programming and trying to write program for Reverse and
Complementary Base. the objective is to Design A DNA primer. So I have a DNA
sequence with base A T C G and A complement to T; T=A;C=G;G=C. I just figure
out How to Reverse It Already. but for the Complement i can only make it answer
for just 1 base but cant be all of the sequence. and i dont know how to
combine reverse and complement function. here is my code and im totallt confuse
with it. Cn someone help me with this problem? You will be my life savior!
thank you! strReverse <- function(x) sapply(lapply(strsplit(x, NULL), rev),
paste, collapse="") strReverse(c("ATCGGTCAATCGA")) complement.base =
function(base){ if(base == 'A' | base == 'a') print("T") if(base == 'T'
| base == 't') print("A") if(base == 'G' | base == 'g') print("C") if(base
== 'C' | base == 'c') print("G")} complement.base(base="A")
[[alternative HTML version deleted]]
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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] Show all elements
Hi, Look to the following code: set.seed(1) dados = data.frame(valor=rnorm(100),var=sample(LETTERS[c(1,2,3,5)],100,replace=T),peso=rpois(100,2)) dados[1:10,] dados$var <- factor(dados$var,levels=LETTERS[1:5]) table(dados$var) A B C D E 31 31 19 0 19 When I try to use summarize, Hmisc package it shows me the result without D category. g1 <- function(y) wtd.mean(y[,1],y[,2]) summarize(dados[,c(1,3)], llist(var=dados$var), g1,stat.name = 'med') var med 1 A 0.02589377 2 B 0.37123239 3 C -0.57820359 4 E 0.39584514 How do I get med = NA or something else with summarize? I realy need to the function to return all factors in the var even it they are an empty set. thanks in advance. leandro [[alternative HTML version deleted]] __ 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.
Re: [R] "survMisc" package
The package maintainer may be able to give help. However, I don't get the same output as you (3.1.2). Perhaps you can update and solve your problem. > require(survMisc) Loading required package: survMisc Loading required package: survival Loading required package: splines Loading required package: ggplot2 Attaching package: ‘survMisc’ The following object is masked from ‘package:ggplot2’: autoplot The following objects are masked from ‘package:stats’: AIC, BIC, median, quantile > data(kidney,package="KMsurv") > s1 <- survfit(Surv(time=time, event=delta) ~ type, data=kidney ) > comp(s1) $tne t n e n_type=1 e_type=1 n_type=2 e_type=2 1: 0.5 119 6 766 430 2: 1.5 103 1 600 431 3: 2.5 98 2 562 420 4: 3.5 89 2 491 401 5: 4.5 79 2 430 362 6: 5.5 73 1 400 331 7: 6.5 66 1 351 310 8: 8.5 55 2 300 252 9: 9.5 49 1 270 221 10: 10.5 45 1 250 201 11: 11.5 40 1 220 181 12: 15.5 25 2 141 111 13: 16.5 23 1 130 101 14: 18.5 20 1 11091 15: 23.5 9 15041 16: 26.5 5 13021 $tests $tests$lrTests ChiSq df p Log-rank 2.529506318 1 0.11174 Gehan-Breslow (mod~ Wilcoxon) 0.002084309 1 0.96359 Tarone-Ware 0.402738202 1 0.52568 Peto-Peto 1.399160019 1 0.23686 Mod~ Peto-Peto (Andersen) 1.275908836 1 0.25866 Flem~-Harr~ with p=1, q=1 9.834062861 1 0.00171 $tests$supTests Q p Log-rank1.590442 0.22347 Gehan-Breslow (mod~ Wilcoxon) 1.430499 0.30511 Tarone-Ware 1.260498 0.41467 Peto-Peto 1.166979 0.48551 Mod~ Peto-Peto (Andersen) 1.185549 0.47085 Renyi Flem~-Harr~ with p=1, q=1 7.460348 0.0 -Original Message- From: Endy BlackEndy [mailto:pert...@gmail.com] Sent: Sunday, March 08, 2015 12:44 PM To: r-help Subject: [R] "survMisc" package Hi R users. I have some problems with the package “survMisc”. When I am loading it I am getting the following > library(survMisc) Loading required package: survival Loading required package: splines Loading required package: km.ci Loading required package: ggplot2 Loading required package: data.table data.table 1.9.4 For help type: ?data.table *** NB: by=.EACHI is now explicit. See README to restore previous behaviour. Loading required package: gridExtra Loading required package: grid Loading required package: rpart Attaching package: ‘survMisc’ The following objects are masked from ‘package:stats’: AIC, BIC, median, quantile In the above output I noticed the line with the three stars (*). In order to restore the data.table in its previous behavior I tried to locate the README file but I couldn’t. I ignored that NB in the previous output and I continue to run the example given in the above mentioned package for the routine comp(). The commands and the output are given below. > ### 2 curves > data(kidney,package="KMsurv") > s1 <- survfit(Surv(time=time, event=delta) ~ type, data=kidney ) > comp(s1) $tne t n e n_type=1 e_type=1 n_type=2 e_type=2 1: 1.586 2 431 431 2: 3.580 2 401 401 3: 4.572 4 362 362 4: 5.566 2 331 331 5: 8.560 4 302 30 2 6: 9.554 2 271 271 7: 10.5 50 2 251 251 8: 11.544 2 22 1 221 9: 15.528 4 14 2 142 10: 16.5 26 2 13 1 131 11: 18.5 22 2 11 1 111 12: 23.5 8 24 1 41 13: 26.5 6 23 1 31 $tests $tests$lrTests ChiSq df p Log-rank0 1 1 Gehan-Breslow (mod~ Wilcoxon) 0 1 1 Tarone-Ware 0 1 1 Peto-Peto 0 1 1 Mod~ Peto-Peto (Andersen)0 1 1 Flem~-Harr~ with p=1, q=1
Re: [R] Rstudio R-devel libR.so
Thanks Pascal. Not yet resolved.
Here is an example of symbolic link between libR.so
https://support.rstudio.com/hc/communities/public/questions/200661703-R-shared-library-usr-local-lib-R-lib-libR-so-not-found-UBUNTU-11-
When I get a symbolic link with:
sudo ln -s /usr/lib/R/lib/libR.so /usr/local/R-devel//lib/libR.so
The R session had a fatal error.
ERROR r error 4 (R code execution error) [errormsg=Error in
.Internal(getOption(x)) :
there is no .Internal function 'getOption'
]; OCCURRED AT: core::Error r::exec::evaluateString(const std::string&,
SEXPREC**, r::sexp::Protect*) /home/ubuntu/rstudio/src/cpp/r/RExec.cpp:
On Mon, Mar 9, 2015 at 10:53 AM, Pascal Oettli wrote:
> Hello,
>
> There is a dedicated support to RStudio here: https://support.rstudio.com
>
> Regards,
> Pascal
>
> On Mon, Mar 9, 2015 at 7:41 PM, Karim Mezhoud wrote:
> > Dear All,
> > I am actually on R-devel using shell consol. When I run RStudio, it can't
> > find libR.so in the new /lib folder where is libRblas.so libRlapack.so.
> > At first step I configure R-devel to share library with ./configure
> > --enable-R-shlib.
> >
> > when I copied libR.so from /usr/lib/R/lib/libR.so (stable version R 3.1)
> > to /usr/local/R-devel/lib/libR.so (R-devel version), That doesn't work.
> >
> > please find the detail at below.
> > Karim mezhoud
> >
> >
> >
> >
> > $which R
> > /usr/bin/R
> > $R
> >> R.Version()[13]
> > $version.string
> > [1] "R version 3.1.2 (2014-10-31)
> >
> >> Sys.getenv("R_HOME")
> > [1] "/usr/lib/R"
> >
> >> .Library
> > [1] "/usr/lib/R/library"
> >> .libPaths()
> > [1] "/home/mezhoud/R/x86_64-pc-linux-gnu-library/3.1"
> > [2] "/usr/local/lib/R/site-library"
> > [3] "/usr/lib/R/site-library"
> > [4] "/usr/lib/R/library"
> > "
> >
> >
> > $sudo apt-get build-dep r-base
> > $sudo apt-get install subversion ccache
> > $mkdir ~/svn/
> > $cd ~/svn/
> > $svn co https://svn.r-project.org/R/trunk r-devel/R
> >
> > $cd /svn/r-devel/R
> > $./configure --enable-R-shlib
> > $make
> > $make check
> > $sudo make install rhome=/usr/local/R-devel
> >
> > $which R
> > /usr/local/bin/R
> >
> > $cd /usr/local/bin
> > $R
> >
> >>R.Version()[13]
> > $version.string
> > [1] "R Under development (unstable) (2015-03-07 r67951)"
> >
> >> .libPaths()
> > [1] "/usr/local/R-devel/library"
> >> .Library
> > [1] "/usr/local/R-devel/library"
> >
> >> Sys.getenv("R_HOME")
> > [1] "/usr/local/R-devel"
> >
> > $rstudio
> > R shared library (/usr/local/R-devel/lib/libR.so) not found.
> > If this is a custom build of R, was it built with the --enable-R-shlib
> > option?
> >
> > $export RSTUDIO_WHICH_R=/usr/local/bin/R
> > $rstudio
> > R shared library (/usr/local/R-devel/lib/libR.so) not found.
> > If this is a custom build of R, was it built with the --enable-R-shlib
> > option?
> >
> > $export RSTUDIO_WHICH_R=/usr/local/R-devel/bin/R
> > $rstudio
> > R shared library (/usr/local/R-devel/lib/libR.so) not found.
> > If this is a custom build of R, was it built with the --enable-R-shlib
> > option?
> >
> > $sudo locate libR.so
> > /usr/lib/libR.so
> > /usr/lib/R/lib/libR.so
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > 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.
>
>
>
> --
> Pascal Oettli
> Project Scientist
> JAMSTEC
> Yokohama, Japan
>
[[alternative HTML version deleted]]
__
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.
Re: [R] Rstudio R-devel libR.so
Hello,
There is a dedicated support to RStudio here: https://support.rstudio.com
Regards,
Pascal
On Mon, Mar 9, 2015 at 7:41 PM, Karim Mezhoud wrote:
> Dear All,
> I am actually on R-devel using shell consol. When I run RStudio, it can't
> find libR.so in the new /lib folder where is libRblas.so libRlapack.so.
> At first step I configure R-devel to share library with ./configure
> --enable-R-shlib.
>
> when I copied libR.so from /usr/lib/R/lib/libR.so (stable version R 3.1)
> to /usr/local/R-devel/lib/libR.so (R-devel version), That doesn't work.
>
> please find the detail at below.
> Karim mezhoud
>
>
>
>
> $which R
> /usr/bin/R
> $R
>> R.Version()[13]
> $version.string
> [1] "R version 3.1.2 (2014-10-31)
>
>> Sys.getenv("R_HOME")
> [1] "/usr/lib/R"
>
>> .Library
> [1] "/usr/lib/R/library"
>> .libPaths()
> [1] "/home/mezhoud/R/x86_64-pc-linux-gnu-library/3.1"
> [2] "/usr/local/lib/R/site-library"
> [3] "/usr/lib/R/site-library"
> [4] "/usr/lib/R/library"
> "
>
>
> $sudo apt-get build-dep r-base
> $sudo apt-get install subversion ccache
> $mkdir ~/svn/
> $cd ~/svn/
> $svn co https://svn.r-project.org/R/trunk r-devel/R
>
> $cd /svn/r-devel/R
> $./configure --enable-R-shlib
> $make
> $make check
> $sudo make install rhome=/usr/local/R-devel
>
> $which R
> /usr/local/bin/R
>
> $cd /usr/local/bin
> $R
>
>>R.Version()[13]
> $version.string
> [1] "R Under development (unstable) (2015-03-07 r67951)"
>
>> .libPaths()
> [1] "/usr/local/R-devel/library"
>> .Library
> [1] "/usr/local/R-devel/library"
>
>> Sys.getenv("R_HOME")
> [1] "/usr/local/R-devel"
>
> $rstudio
> R shared library (/usr/local/R-devel/lib/libR.so) not found.
> If this is a custom build of R, was it built with the --enable-R-shlib
> option?
>
> $export RSTUDIO_WHICH_R=/usr/local/bin/R
> $rstudio
> R shared library (/usr/local/R-devel/lib/libR.so) not found.
> If this is a custom build of R, was it built with the --enable-R-shlib
> option?
>
> $export RSTUDIO_WHICH_R=/usr/local/R-devel/bin/R
> $rstudio
> R shared library (/usr/local/R-devel/lib/libR.so) not found.
> If this is a custom build of R, was it built with the --enable-R-shlib
> option?
>
> $sudo locate libR.so
> /usr/lib/libR.so
> /usr/lib/R/lib/libR.so
>
> [[alternative HTML version deleted]]
>
> __
> 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.
--
Pascal Oettli
Project Scientist
JAMSTEC
Yokohama, Japan
__
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] Rstudio R-devel libR.so
Dear All,
I am actually on R-devel using shell consol. When I run RStudio, it can't
find libR.so in the new /lib folder where is libRblas.so libRlapack.so.
At first step I configure R-devel to share library with ./configure
--enable-R-shlib.
when I copied libR.so from /usr/lib/R/lib/libR.so (stable version R 3.1)
to /usr/local/R-devel/lib/libR.so (R-devel version), That doesn't work.
please find the detail at below.
Karim mezhoud
$which R
/usr/bin/R
$R
> R.Version()[13]
$version.string
[1] "R version 3.1.2 (2014-10-31)
> Sys.getenv("R_HOME")
[1] "/usr/lib/R"
> .Library
[1] "/usr/lib/R/library"
> .libPaths()
[1] "/home/mezhoud/R/x86_64-pc-linux-gnu-library/3.1"
[2] "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"
[4] "/usr/lib/R/library"
"
$sudo apt-get build-dep r-base
$sudo apt-get install subversion ccache
$mkdir ~/svn/
$cd ~/svn/
$svn co https://svn.r-project.org/R/trunk r-devel/R
$cd /svn/r-devel/R
$./configure --enable-R-shlib
$make
$make check
$sudo make install rhome=/usr/local/R-devel
$which R
/usr/local/bin/R
$cd /usr/local/bin
$R
>R.Version()[13]
$version.string
[1] "R Under development (unstable) (2015-03-07 r67951)"
> .libPaths()
[1] "/usr/local/R-devel/library"
> .Library
[1] "/usr/local/R-devel/library"
> Sys.getenv("R_HOME")
[1] "/usr/local/R-devel"
$rstudio
R shared library (/usr/local/R-devel/lib/libR.so) not found.
If this is a custom build of R, was it built with the --enable-R-shlib
option?
$export RSTUDIO_WHICH_R=/usr/local/bin/R
$rstudio
R shared library (/usr/local/R-devel/lib/libR.so) not found.
If this is a custom build of R, was it built with the --enable-R-shlib
option?
$export RSTUDIO_WHICH_R=/usr/local/R-devel/bin/R
$rstudio
R shared library (/usr/local/R-devel/lib/libR.so) not found.
If this is a custom build of R, was it built with the --enable-R-shlib
option?
$sudo locate libR.so
/usr/lib/libR.so
/usr/lib/R/lib/libR.so
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem with function that adds rows to dataframe based on conditional statement
Hi
As you do not accept solution with adding so many NA rows for those you do not
have repetitions I think that merge together with some preparation is the way
to go.
First of all do not use cbind when constructing data frame
comAn=data.frame(animals,animalYears,animalMass)
# indicator variable how many repetitions in each combination animal year have
comAn$ind<-ave(comAn$animalYears, paste(comAn$animals, comAn$animalYears),
FUN=table)
# expected levels (depends on how many years and repetitions for each year do
you have)
lev<-expand.grid(levels(comAn$animals), 1:2, 2)
# to correct names
names(lev)[1:2]<-names(comAn)[1:2]
names(lev)[3]<-"ind"
merge(lev, comAn, all=T)
leads to put NA to the row in which required combination is missing.
You can then propagate this NA to any column you wish.
Cheers
Petr
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Curtis
> Burkhalter
> Sent: Friday, March 06, 2015 10:01 PM
> To: Tom Wright
> Cc: r-help@r-project.org
> Subject: Re: [R] problem with function that adds rows to dataframe
> based on conditional statement
>
> Hey Tom,
>
> This solution works great, but if I try to then insert it in my
> function that I've displayed above and apply it to my split dataframe I
> get the error message:
>
> Error in `[.default`(xj, i) : invalid subscript type 'list'
>
> The reason why I need to try and get this to work within the function
> is that I'm trying to apply it to a much larger dataframe
> (nrow=12000,ncol=14). The actual data I'm working with consists of a
> sampling year, a site, and a bunch of response variables. For each
> sampling year by site combination I have 3 within year sampling
> occasions. For the sampling year by site combinations that don't have 3
> sampling events I need to fill in the missing occasions with the NAs.
>
> Can you see why I might be getting this error message?
>
> Thanks
>
>
>
> On Fri, Mar 6, 2015 at 1:48 PM, Tom Wright wrote:
>
> > If all you want is to add a row of na's could you just do something
> > like:
> >
> > nExpectedRows<-length(unique(animals)) * length(unique(animalYears))
> *
> > 2
> >
> > newDf<-data.frame(animals=rep(NA,nExpectedRows-nrow(comAn)),
> > animalYears=rep(NA,nExpectedRows-nrow(comAn)),
> > animalMass=rep(NA,nExpectedRows-nrow(comAn)))
> >
> > comAn = rbind(comAn,newDf)
> >
> >
> >
> > On Thu, 2015-03-05 at 13:41 -0700, Curtis Burkhalter wrote:
> > > Hello everyone,
> > >
> > > I'm having a problem with a function that I wrote that is supposed
> > > to
> > add a
> > > row to dataframe based upon a conditional statement. To explain
> I've
> > > used an example below:
> > >
> > > #create data frame
> > > animals=c("bird","dog","cat")
> > > animals=rep(animals,each=4)
> > > animals=animals[1:11]
> > > animalYears=c(1,1,2,2,1,1,2,2,1,1,2)
> > > animalMass=round(runif(11,min=10,max=50),0)
> > >
> > > comAn=as.data.frame(cbind(animals,animalYears,animalMass))
> > > comAn
> > >
> > > * animals* *animalYears* *animalMass*
> > > 1 bird 1 30
> > > 2 bird 1 32
> > > 3 bird 2 27
> > > 4 bird 2 16
> > > 5 dog 1 22
> > > 6 dog 1 25
> > > 7 dog 2 41
> > > 8 dog 2 22
> > > 9 cat 1 30
> > > 10 cat 1 37
> > > 11 cat 2 49
> > >
> > > We can see here that for every type of animal I have two years of
> > > mass measurements, except for the cat in year 2. What I want to do
> > > is add an additional row to the end of the dataframe that consists
> > > strictly of NAs and then I can substitute those out later.
> > >
> > > So what I first did was split the 'comAn' dataframe into the
> > > different Animal by Year combos.
> > >
> > > #This line splits 'com_An' into a list ordered by the Animal by
> Year
> > combos
> > > comAn_split=split(comAn, paste(comAn$animals,comAn$animalYear))
> > >
> > > Then I wrote the function that identifies whether a particular
> > > Animal by Year combo is less than two rows in length and if so it
> > > should add
> > another
> > > row that consists only of NAs using the vector 'NAs':
> > >
> > > #This function identifies the length of each Animal by Year combo
> > > and
> > then
> > > #uses the rbind function built in R to add a row #to each animal by
> > > year combo if they have less than 2 samples
> > >
> > > addNA <- function(comAn) {
> > > NAs=c(NA,NA,NA)
> > > ind <- seq_len(nrow(comAn))
> > > comAn[ifelse(length(ind)<2,rbind(NAs),length(ind)),]
> > > }
> > >
> > > #This applies the function addNs to the animals data organized in
> > > list format addedNAcomAn <- do.call(rbind, lapply(comAn_split,
> > > addNA)) addedNAcomAn
> > >
> > > When I apply the function to the list of the different Animal by
> > > Year combos this is what I get:
> > >
[R] R 3.1.3 is released
The build system rolled up R-3.1.3.tar.gz (codename "Smooth Sidewalk") this
morning.
The list below details the changes in this release.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.1.3.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = cebbdd1eb8cd620bf2a6ac84c9e731c2
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = a699fa0eeef280b78134f0abe0b1c1b0
MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac
MD5 (NEWS) = 8790db3a8000910f0bf00fb1ee039634
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 8e2f4d1d5228663ae598a09bf1e2bc6b
MD5 (R-latest.tar.gz) = 53a85b884925aa6b5811dfc361d73fc4
MD5 (R.css) = 444535b9cb76ddff1bab1e1865a3fb14
MD5 (README) = aece1dfbd18c1760128c3787f5456af6
MD5 (RESOURCES) = a59076c1ac7e9bab0f0a38b3f57a3914
MD5 (THANKS) = 1989ce89fb3891420c9964dc418ab71c
MD5 (R-3/R-3.1.3.tar.gz) = 53a85b884925aa6b5811dfc361d73fc4
This is the relevant part of the NEWS file
CHANGES IN R 3.1.3:
NEW FEATURES:
* The internal method of download.file() can now handle files
larger than 2GB on 32-bit builds which support such files (tested
on 32-bit R running on 64-bit Windows).
* kruskal.test() warns on more types of suspicious input.
* The as.dendrogram() method for "hclust" objects gains a check
argument protecting against memory explosion for invalid inputs.
* capabilities() has a new item long.double which indicates if the
build uses a long double type which is longer than double.
* nlm() no longer modifies the callback argument in place (a new
vector is allocated for each invocation, which mimics the
implicit duplication that occurred in R < 3.1.0); note that this
is a change from the previously documented behavior. (PR#15958)
* icuSetCollate() now accepts locale = "ASCII" which uses the basic
C function strcmp and so collates strings byte-by-byte in
numerical order.
* sessionInfo() tries to report the OS version in use (not just
that compiled under, and including details of Linux
distributions).
* model.frame() (used by lm() and many other modelling functions)
now warns when it drops contrasts from factors. (Wish of
PR#16119)
* install.packages() and friends now accept the value type =
"binary" as a synonym for the native binary type on the platform
(if it has one).
* Single source or binary files can be supplied for
install.packages(type = "both") and the appropriate type and
repos = NULL will be inferred.
* New function pcre_config() to report on some of the configuration
options of the version of PCRE in use. In particular, this
reports if regular expressions using \p{xx} are supported.
* (Windows.) download.file(cacheOK = FALSE) is now supported when
internet2.dll is used.
* browseURL() has been updated to work with Firefox 36.0 which has
dropped support for the -remote interface.
INSTALLATION and INCLUDED SOFTWARE:
* The included version of PCRE has been updated to 8.36.
* configure accepts MAKEINFO=texi2any as another way to ensure
texinfo 5.x is used when both 5.x and 4.x are installed.
UTILITIES:
* R CMD check now checks the packages used in \donttest sections of
the examples are specified in the DESCRIPTION file. (These are
needed to run the examples interactively.)
* R CMD check checks for the undeclared use of GNU extensions in
Makefiles, and for Makefiles with a missing final linefeed.
R CMD build will correct line endings in all Makefiles, not just
those in the src directory.
* R CMD check notes uses of library() and require() in package
code: see the section 'Suggested packages' of 'Writing R
Extensions' for good practice.
DEPRECATED AND DEFUNCT:
* The configure option --with-valgrind-instrumentation=3 is
deprecated and will be removed in R 3.2.0.
BUG FIXES:
* (Windows.) Rscript.exe was missing a manifest specifying the
modern style for common controls (e.g., the download progress
bar).
* If a package had extra documentation files but no vignette, the
HTML help system produced an empty index page.
* The parser now gives an error if a null character is included in
a string using Unicode escapes. (PR#16046)
* qr.Q() failed on complex arguments due to pre-3.0(!) typo.
(PR#16054)
* abs() failed with named arguments when the argument was complex.
(PR#16047)
* "noquote" objects may now be used as columns in dataframes.
(PR#15997)
* Some value
