Exporting objects plotted with plot3d() - rgl package
On 4/22/2009 12:18 PM, Alejandro Gonz?lez wrote:
Dear all, Can anybody tell me how to export a 3d figure made with the plot3d function? I'm careless about whether it's still interactive or not in another format, as long I can get it out of R.
snapshot3d() gets a bitmap in .png format. rgl.postscript() creates a Postscript or other vector format file. Some features of OpenGL aren't supported, so the quality varies quite a bit. Duncan Murdoch
Thanks! Alejandro Gonz?lez Departamento de Biodiversidad y Conservaci?n Real Jard?n Bot?nico Consejo Superior de Investigaciones Cient?ficas Claudio Moyano, 1 28014 Madrid, Spain Tel +0034 914203017 r-help-request at r-project.org escribi?:
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Re: SEM package (Jim Lemon) ---------------------------------------------------------------------- Message: 1 Date: Tue, 21 Apr 2009 11:03:52 +0100 From: William Simpson <william.a.simpson at gmail.com> Subject: [R] line wrap in R console under windows To: r-help at r-project.org Message-ID: <21ce39b20904210303h34a95282q122dc554cb7ca0de at mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 I would like the R console to wrap lines at 80 cols. It does not do so, even though I have used the Rgui Configuration Editor to set the Console cols at 80 and the Pager cols at 80. Please tell me how to set it up so I have word wrap. Just to be clear: in older/other R versions, console input is wrapped at 80 cols and so you have something that looks like blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah Instead of what I see, which is blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah$ and I need to scroll sideways to see the rest of the stuff past $ I checked the archives and saw no postings on this. Thanks very much for any help. Bill ------------------------------ Message: 2 Date: Tue, 21 Apr 2009 11:10:10 +0100 From: William Simpson <william.a.simpson at gmail.com> Subject: [R] lme for between-within anova To: r-help at r-project.org Message-ID: <21ce39b20904210310i139a53berd38642cddd13038a at mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 I have the following between-within anova: aovn1 <- aov(amplitude ~ stereo*site*stimulus + Error(subject/(site*stimulus)), stereon1) This works fine. BUT I need to do Tukey HSD multiple comparisons, and the aov() approach won't work. So I am trying the method posted on r-help: lmen1 <- lme(amplitude ~ stereo*site*stimulus, random = ~1|subject/(site*stimulus), stereon1) This doesn't work: lmen1 <- lme(amplitude ~ stereo*site*stimulus, random = ~1|subject/(site*stimulus), stereon1) Error in getGroups.data.frame(dataMix, groups) : Invalid formula for groups Please tell me what to do to get the lme() fit to work. After I get lmen1, I will do: anova(lmen1) summary(lmen1) summary(glht(lmen1, linfct=mcp(V="Tukey"))) Please tell me if that sounds right. Thanks very much for any help! Bill ============= This is the example I am following (with modifications for my expt design) You want to use lme() in package nlme, then glht() in the multcomp package. This will give you multiplicity adjusted p-values and confidence intervals. ## Example require(MASS) ## for oats data set require(nlme) ## for lme() require(multcomp) ## for multiple comparison stuff Aov.mod <- aov(Y ~ N + V + Error(B/V), data = oats) Lme.mod <- lme(Y ~ N + V, random = ~1 | B/V, data = oats) summary(Aov.mod) anova(Lme.mod) summary(Lme.mod) summary(glht(Lme.mod, linfct=mcp(V="Tukey"))) ------------------------------ Message: 3 Date: Tue, 21 Apr 2009 12:12:34 +0200 From: Liviu Andronic <landronimirc at gmail.com> Subject: Re: [R] joined R-today To: Bala subramanian <bala.biophysics at gmail.com> Cc: r-help at r-project.org Message-ID: <68b1e2610904210312g651337b6v3c4d0d29d0bd41df at mail.gmail.com> Content-Type: text/plain; charset=UTF-8 On Tue, Apr 21, 2009 at 11:57 AM, Bala subramanian <bala.biophysics at gmail.com> wrote: Dear Simon, I installed the ncdf package in the way you suggested but still i got the same error i got before. I haves pasted below the installation log and errors. Does ncdf depend on netcdf [1]? If so, perhaps it is missing, or is not up-to-date. Also, it's a good habit to install.packages('ncdf', dep=TRUE). Regards, Liviu [1] http://www.unidata.ucar.edu/software/netcdf/ ------------------------------ Message: 4 Date: Tue, 21 Apr 2009 06:12:32 -0400 From: "John Sorkin" <jsorkin at grecc.umaryland.edu> Subject: [R] Package or packages for randomization in a clinical trial To: <r-help at r-project.org> Message-ID: <49ED63CE.91DF.00CB.0 at grecc.umaryland.edu> Content-Type: text/plain; charset=US-ASCII Can anyone recommend a package that can be used to randomize subjects? I am looking for a generalized package, or several packages that can accomplish unrestricted randomization (i.e. simple random assignment) restricted randomization including stratified randomization, blocked randomization, and adaptive randomization. Thanks, John John David Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing) Confidentiality Statement: This email message, including any attachments, is for th...{{dropped:6}} ------------------------------ Message: 5 Date: Tue, 21 Apr 2009 12:21:09 +0200 From: Bala subramanian <bala.biophysics at gmail.com> Subject: Re: [R] joined R-today To: Liviu Andronic <landronimirc at gmail.com> Cc: r-help at r-project.org Message-ID: <288df32a0904210321l64d25470yea9aef47c5859221 at mail.gmail.com> Content-Type: text/plain Hi, Yes ncdf needs netcdf, netcdf is already installed in my fedora10. I reinstalled ncdf with the following option install.packages('ncdf',dep=TRUE) library(ncdf)> library(ncdf) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/lib/R/library/ncdf/libs/ncdf.so': /usr/lib/R/library/ncdf/libs/ncdf.so: cannot restore segment prot after reloc: Permission denied Error in library(ncdf) : .First.lib failed for 'ncdf' Again the same error, Bala On Tue, Apr 21, 2009 at 12:12 PM, Liviu Andronic <landronimirc at gmail.com>wrote: On Tue, Apr 21, 2009 at 11:57 AM, Bala subramanian <bala.biophysics at gmail.com> wrote: Dear Simon, I installed the ncdf package in the way you suggested but still i got the same error i got before. I haves pasted below the installation log and errors. Does ncdf depend on netcdf [1]? If so, perhaps it is missing, or is not up-to-date. Also, it's a good habit to install.packages('ncdf', dep=TRUE). Regards, Liviu [1] http://www.unidata.ucar.edu/software/netcdf/ [[alternative HTML version deleted]] ------------------------------ Message: 6 Date: Tue, 21 Apr 2009 22:25:01 +1200 From: Seyit Ali Kayis <s_a_kayis at hotmail.com> Subject: [R] Sampling in R To: <r-help at r-project.org> Message-ID: <BAY105-W34886F283B2E531D6C5844B4770 at phx.gbl> Content-Type: text/plain Dear R users, I need to do sampling without replacement (bootstraps). I have two variables (Xvar, Yvar). I have a correlation from original data set cor(Xvar, Yvar)=0.6174221. I am doing 50000 sampling, and in each sampling calculating correlations, saving, sorting and getting 95% cutt off point (0.1351877). I am getting maximum value as 0.3507219 (much smaller than correlation of my original data). I repeated the sampling a couple of time and none of them produced a correlation coefficient higher than my original data set. However, if I sort out my Xvar and Yvar and obtain correlation it is 0.9657125 which is much higher than correlation for my original data. I am doing sampling in another program and getting at least 1% higher correlation than mine. Now I am getting confused with sampling(random data) in R. My data and codes for the scenario above are below Xvar<-c(0.1818182,0.5384615,0.5535714,0.4680851,0.4545455,0.4385965,0.5185185,0.4035088,0.4901961,0.3650794,0.462963,0.4,0.56,0.3965517,0.4909091, 0.4716981,0.4310345,0.2,0.1509434,0.2647059,0.173913,0.1914894,0.1914894,0.1489362,0.1363636,0.2244898,0.2325581,0.1333333,0.1818182,0.1702128, 0.2173913,0.2380952,0.1632653,0.5614035,0.3396226,0.4909091,0.3770492,0.5,0.5185185,0.5,0.4666667,0.4464286,0.362069,0.4285714,0.4561404, 0.4736842,0.4545455,0.4166667,0.4181818,0.4590164,0.5166667,0.5423729,0.4833333,0.5454545,0.4393939,0.5172414,0.4098361,0.4745763,0.4754098, 0.5166667,0.5,0.4603175,0.42,0.4038462,0.4897959,0.3148148,0.3673469,0.4,0.4583333,0.3877551,0.4375,0.4117647,0.4313725,0.5333333,0.3962264, 0.3548387,0.5272727,0.4137931,0.3928571,0.4666667,0.4210526,0.4363636,0.4545455,0.4310345,0.4237288,0.4814815,0.4912281,0.4333333,0.4,0.4285714, 0.4516129,0.5090909,0.4464286,0.4642857,0.4166667,0.4098361,0.4909091,0.3809524,0.5272727,0.4814815,0.5254237,0.627451,0.5,0.5471698,0.5454545, 0.5925926,0.5769231,0.5818182,0.4444444,0.4915254,0.4727273,0.4107143,0.4285714,0.4310345,0.4237288,0.4285714,0.440678,0.4237288,0.4807692, 0.4150943,0.4615385,0.4107143,0.4814815,0.4074074,0.4210526,0.5263158,0.440678,0.4576271,0.5344828,0.5,0.5636364,0.4677419,0.5,0.5192308, 0.4642857,0.5090909,0.58,0.4482759,0.5098039,0.4035088,0.4210526,0.5098039,0.4385965,0.5283019,0.5471698,0.625,0.4310345,0.4912281,0.5283019, 0.4576271,0.5471698,0.4745763,0.4821429) Yvar<-c(0.2553191,0.4107143,0.5660377,0.3888889,0.3606557,0.2898551,0.3818182,0.4,0.4,0.3278689,0.2903226,0.4074074,0.4181818,0.3,0.2238806,0.3728814, 0.3709677,0.2307692,0.2830189,0.2244898,0.2142857,0.2131148,0.22,0.2258065,0.2321429,0.2,0.2264151,0.22,0.2115385,0.2459016,0.1166667,0.1785714, 0.2068966,0.6,0.4285714,0.3134328,0.4461538,0.3965517,0.4769231,0.6181818,0.4827586,0.3709677,0.3965517,0.4821429,0.4545455,0.359375,0.4576271, 0.4516129,0.5272727,0.4603175,0.4,0.4912281,0.5384615,0.5,0.4516129,0.4126984,0.4655172,0.5263158,0.4925373,0.358209,0.4285714,0.4920635, 0.4482759,0.3235294,0.4,0.4375,0.440678,0.3898305,0.35,0.4528302,0.58,0.4153846,0.3174603,0.5185185,0.3870968,0.2894737,0.3709677,0.369863, 0.3676471,0.3636364,0.3088235,0.328125,0.4032258,0.4084507,0.3188406,0.3636364,0.3823529,0.2816901,0.4722222,0.5,0.3521127,0.4393939,0.3787879, 0.453125,0.4324324,0.4057971,0.4545455,0.4492754,0.5,0.4098361,0.4067797,0.3666667,0.3928571,0.4285714,0.5,0.2923077,0.4561404,0.45,0.5538462, 0.4626866,0.4057971,0.3676471,0.5322581,0.5428571,0.375,0.4411765,0.4571429,0.4,0.3846154,0.3870968,0.4915254,0.530303,0.4375,0.4918033,0.4179104, 0.4032258,0.3606557,0.5178571,0.4848485,0.390625,0.375,0.4375,0.3666667,0.4,0.4477612,0.2571429,0.4032258,0.3382353,0.4814815,0.4090909,0.3548387, 0.4821429,0.5,0.557377,0.4333333,0.5454545,0.4590164,0.3943662,0.5076923,0.5,0.3283582,0.3676471,0.559322) my.cor<-cor(Xvar, Yvar) print(my.cor) nperm<-49999 Perm.Cor<-NULL for (iperm in 1:nperm) { XvarNew<-sample(Xvar, size=length(Xvar), replace=FALSE) YvarNew<-sample(Yvar, size=length(Yvar), replace=FALSE) perm.cor<-cor(XvarNew, YvarNew) Perm.Cor<-c(Perm.Cor, perm.cor) } print(max(Perm.Cor)) XvarSorted<-sort(Xvar, decreasing=TRUE) YvarSorted<-sort(Yvar, decreasing=TRUE) max.cor<-cor(XvarSorted, YvarSorted) print(max.cor) if(mat.cor>0) Perm.Cor.Sorted<-sort(Perm.Cor, decreasing=TRUE) if(mat.cor<0) Perm.Cor.Sorted<-sort(Perm.Cor, decreasing=FALSE) T95<-Perm.Cor.Sorted[(nperm+1)*0.05] # 95% treshold value T99<-Perm.Cor.Sorted[(nperm+1)*0.01] # 99% treshold value I want to understand where I am making a mistake. Any comment is deeply appreciated. Kind Regards Seyit Ali ------------------------------------------------------------------------------------------------------------------ Dr. Seyit Ali KAYIS Selcuk University Faculty of Agriculture Kampus, Konya, TURKEY s_a_kayis at yahoo.com, s_a_kayis at hotmail.com Tell: +90 332 223 2830 Mobile: +90 535 587 1139 Fax: +90 332 241 0108 Greetings from Konya, TURKEY http://www.ziraat.selcuk.edu.tr/skayis/ ---------------------------------------------------------------------------------------------------------------------- _________________________________________________________________ Earning enough? Find out with SEEK Salary Survey %2Eco%2Enz%2F%3Ftracking%3Dsk%3Atl%3Asknzsal%3Amsnnz%3A0%3Ahottag%3Aearn%5Fenough&_t=757263783&_r=Seek_NZ_tagline&_m=EXT [[alternative HTML version deleted]] ------------------------------ Message: 7 Date: Tue, 21 Apr 2009 03:52:57 -0700 (PDT) From: onyourmark <william108 at gmail.com> Subject: [R] search through a matrix To: r-help at r-project.org Message-ID: <23153538.post at talk.nabble.com> Content-Type: text/plain; charset=us-ascii Hi. I have a 925 by 925 correlation matrix corM. I want to identify all variables that have correlation greater than 0.9. Can anyone suggest an "R way" of doing this? Thank you.
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